diff --git a/imports/bfo_import.obo b/imports/bfo_import.obo index 3a3dcb0..c13d079 100644 --- a/imports/bfo_import.obo +++ b/imports/bfo_import.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/imports/bfo_import/pco/releases/2020-02-13/bfo_import.owl/pco/imports/bfo_import.obo +data-version: pco/releases/2020-08-26/imports/bfo_import.obo ontology: pco/imports/bfo_import.obo [Term] diff --git a/imports/bfo_import.owl b/imports/bfo_import.owl index d0e3934..aabae7a 100644 --- a/imports/bfo_import.owl +++ b/imports/bfo_import.owl @@ -8,7 +8,7 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - + diff --git a/imports/ecocore_import.obo b/imports/ecocore_import.obo new file mode 100644 index 0000000..63b4899 --- /dev/null +++ b/imports/ecocore_import.obo @@ -0,0 +1,31 @@ +format-version: 1.2 +data-version: pco/releases/2020-08-26/imports/ecocore_import.obo +ontology: pco/imports/ecocore_import.obo + +[Term] +id: ECOCORE:00000045 +name: symbiotroph +def: "heterotroph that acquires nutrition from a symbiont" [] +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string + +[Term] +id: ECOCORE:00000146 +name: parasite +def: "A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host" [] +xref: https://www.wikidata.org/entity/Q10253316 +is_a: ECOCORE:00000045 ! symbiotroph +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string + +[Typedef] +id: editor_note +name: editor note +namespace: uberon +def: "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." [] +xref: IAO:0000116 +property_value: IAO:0000111 "editor note" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + diff --git a/imports/ecocore_import.owl b/imports/ecocore_import.owl new file mode 100644 index 0000000..9f4601a --- /dev/null +++ b/imports/ecocore_import.owl @@ -0,0 +1,246 @@ + + + + + + + + + + + + + + + + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + 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 label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + has curation status + + + + + + + + definition + definition + textual definition + + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 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.obfoundry.org/obo/obi> + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + 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 + term editor + + + + + + + + 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 + definition source + + + + + + + + + database_cross_reference + + + + + + + + + has_obo_namespace + + + + + + + + + + + + + + + + + + + + + + shorthand + + + + + + + + + + + + + + label + + label + + + + + + + + + + + + + heterotroph that acquires nutrition from a symbiont + http://orcid.org/0000-0002-2908-3327 + symbiotroph + + + + + + + + + A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host + http://orcid.org/0000-0002-2908-3327 + https://www.wikidata.org/entity/Q10253316 + parasite + + + + + + + diff --git a/imports/envo_import.obo b/imports/envo_import.obo index afdec1c..55e2eb5 100644 --- a/imports/envo_import.obo +++ b/imports/envo_import.obo @@ -1,63 +1,20 @@ format-version: 1.2 -data-version: pco/imports/envo_import/pco/releases/2020-02-13/envo_import.owl/pco/imports/envo_import.obo -default-namespace: ENVO -remark: ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. \n\nNew terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ \n\n\nPlease see www.environmentontology.org for more information and citations. -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 186 Logical Axioms: 30] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 114 Logical Axioms: 19] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 132 Logical Axioms: 23] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 40 Logical Axioms: 6] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 21 Logical Axioms: 2] -ontology: pco/imports/envo_import.obo -property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-4366-3088 xsd:string -property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-6601-2165 xsd:string -property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8343-612X xsd:string -property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0003-1604-1512 xsd:string -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0002-6962-2807 xsd:string +data-version: pco/releases/2020-08-26/imports/envo_import.owl +ontology: pco/imports/envo_import [Term] -id: ENVO:00000070 -name: construction -def: "A feature that has been constructed by deliberate human effort." [MA:ma] -synonym: "constructed feature" EXACT [] -is_a: BFO:0000040 -is_a: ENVO:00002297 ! environmental feature -is_a: ENVO:01000813 ! astronomical body part -property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string - -[Term] -id: ENVO:00002297 -name: environmental feature -def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] -comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. -is_a: BFO:0000040 - -[Term] -id: ENVO:01000254 -name: environmental system -def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] -comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. -synonym: "environment" EXACT [] -xref: EcoLexicon:environment -is_a: BFO:0000040 -creation_date: 2013-09-23T16:04:08Z +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] [Term] id: ENVO:01000744 name: human dwelling def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] -is_a: ENVO:00000070 ! construction +is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string -[Term] -id: ENVO:01000813 -name: astronomical body part -def: "A material part of an astronomical body." [] -subset: envoAstro -subset: envoPolar -is_a: BFO:0000040 -is_a: ENVO:00002297 ! environmental feature - [Term] id: ENVO:01001369 name: tidal mangrove shrubland @@ -67,6 +24,6 @@ comment: This class aligns to the Coastal and Marine Ecological Classification S subset: envoCmecs subset: envoMarine xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ENVO:01000254 ! environmental system +is_a: BFO:0000040 ! material entity created_by: http://orcid.org/0000-0002-4366-3088 diff --git a/imports/envo_import.owl b/imports/envo_import.owl index 69bb002..fda39c8 100644 --- a/imports/envo_import.owl +++ b/imports/envo_import.owl @@ -7,27 +7,13 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:doap="http://usefulinc.com/ns/doap#" + xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - http://orcid.org/0000-0002-4366-3088 - http://orcid.org/0000-0002-6601-2165 - http://orcid.org/0000-0002-8343-612X - http://orcid.org/0000-0003-1604-1512 - https://orcid.org/0000-0002-6962-2807 - ENVO - ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. - -New terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ - - -Please see www.environmentontology.org for more information and citations. - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 186 Logical Axioms: 30] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 114 Logical Axioms: 19] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 132 Logical Axioms: 23] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>) VersionIRI(<null>))) [Axioms: 40 Logical Axioms: 6] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>) VersionIRI(<null>))) [Axioms: 21 Logical Axioms: 2] + + @@ -59,27 +45,43 @@ Please see www.environmentontology.org for more information and citations. + + + term editor + + + + + + + + definition source + + + + - + - + - + - + - + - + @@ -105,14 +107,6 @@ Please see www.environmentontology.org for more information and citations. - - - has_obo_namespace - - - - @@ -121,12 +115,6 @@ Please see www.environmentontology.org for more information and citations. - - - - - @@ -160,75 +148,17 @@ Please see www.environmentontology.org for more information and citations. - - - - - - - - - - - A feature that has been constructed by deliberate human effort. - "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference - constructed feature - construction - - - - - A feature that has been constructed by deliberate human effort. - MA:ma - - - - - - - - - A material entity which determines an environmental system. - ENVO - ENVO:00002297 - A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. - environmental feature - - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - - - - - - - - A system which has the disposition to environ one or more material entities. - 2013-09-23T16:04:08Z - EcoLexicon:environment - environment - In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. - environmental system + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. Subclasses will be added by inference. @@ -243,25 +173,12 @@ Please see www.environmentontology.org for more information and citations. - - - - - A material part of an astronomical body. - envoAstro - envoPolar - astronomical body part - - - - - + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. - http://orcid.org/0000-0002-4366-3088 + CMECS:577 https://cmecscatalog.org/cmecs/classification/unit/577.html envoCmecs diff --git a/imports/go_import.obo b/imports/go_import.obo index b44e307..dbf879d 100644 --- a/imports/go_import.obo +++ b/imports/go_import.obo @@ -1,12 +1,14 @@ format-version: 1.2 -data-version: pco/releases/2020-02-13/go_import.obo +data-version: pco/releases/2020-08-26/imports/go_import.obo ontology: pco/imports/go_import.obo [Term] id: GO:0007610 name: behavior namespace: biological_process +alt_id: GO:0023032 alt_id: GO:0044708 +alt_id: GO:0044709 def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). subset: gocheck_do_not_manually_annotate @@ -19,7 +21,7 @@ synonym: "single-organism behavior" RELATED [] xref: Wikipedia:Behavior is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-20T14:06:08Z [Term] @@ -30,7 +32,7 @@ alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] -comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl @@ -46,7 +48,7 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] @@ -58,8 +60,8 @@ comment: Behavior such as predation which involves members of different species synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior +is_a: GO:0007610 ! behavior is_a: GO:0051703 ! intraspecies interaction between organisms -is_a: GO:0051705 ! multi-organism behavior property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -72,8 +74,9 @@ subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 @@ -82,7 +85,7 @@ namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] subset: goslim_pir synonym: "intraspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -99,21 +102,3 @@ synonym: "physiological interaction with other organism" EXACT [] is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -[Term] -id: GO:0051705 -name: multi-organism behavior -namespace: biological_process -alt_id: GO:0023032 -alt_id: GO:0044709 -def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] -subset: goslim_pir -synonym: "behavioral interaction between organisms" EXACT [] -synonym: "behavioral interaction with other organism" EXACT [] -synonym: "behavioral signaling" NARROW [] -synonym: "behavioral signalling" NARROW [GOC:mah] -synonym: "behavioural interaction between organisms" EXACT [] -synonym: "behavioural interaction with other organism" EXACT [] -is_a: GO:0007610 ! behavior -is_a: GO:0051704 ! multi-organism process -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - diff --git a/imports/go_import.owl b/imports/go_import.owl index 3644886..a1444ff 100644 --- a/imports/go_import.owl +++ b/imports/go_import.owl @@ -9,7 +9,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -33,6 +33,14 @@ + + + + + + + + @@ -73,14 +81,6 @@ - - - - - - - - @@ -164,9 +164,11 @@ The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. - janelomax + jl 2012-09-20T14:06:08Z + GO:0023032 GO:0044708 + GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour @@ -198,7 +200,7 @@ A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - janelomax + jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 @@ -219,7 +221,7 @@ - Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process @@ -235,8 +237,8 @@ + - Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour @@ -261,8 +263,9 @@ - + Any process in which an organism has an effect on an organism of a different species. + interaction with another species interspecies interaction interspecies interaction with other organisms @@ -285,7 +288,7 @@ - + Any process in which an organism has an effect on an organism of the same species. intraspecies interaction with other organisms biological_process @@ -325,41 +328,6 @@ A biological process which involves another organism of the same or different species. GOC:jl - - - - - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GO:0023032 - GO:0044709 - behavioral interaction between organisms - behavioral interaction with other organism - behavioural interaction between organisms - behavioural interaction with other organism - behavioral signaling - behavioral signalling - biological_process - GO:0051705 - - - multi-organism behavior - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GOC:ai - - - - - behavioral signalling - GOC:mah - diff --git a/imports/iao_import.obo b/imports/iao_import.obo new file mode 100644 index 0000000..2c544ea --- /dev/null +++ b/imports/iao_import.obo @@ -0,0 +1,14 @@ +format-version: 1.2 +data-version: pco/releases/2020-08-26/imports/iao_import.obo +ontology: pco/imports/iao_import.obo + +[Typedef] +id: IAO:0000136 +name: is about +def: "A (currently) primitive relation that relates an information artifact to an entity." [] +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string + diff --git a/imports/iao_import.owl b/imports/iao_import.owl new file mode 100644 index 0000000..949800b --- /dev/null +++ b/imports/iao_import.owl @@ -0,0 +1,191 @@ + + + + + + + + + + + + + + + + + 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 + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + has curation status + + + + + + + + definition + + 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 + + + + + + + + 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 + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + This document is about information artifacts and their representations + + A (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + diff --git a/imports/ncbitaxon_import.obo b/imports/ncbitaxon_import.obo index 39455ea..cf87fb0 100644 --- a/imports/ncbitaxon_import.obo +++ b/imports/ncbitaxon_import.obo @@ -1,90 +1,138 @@ format-version: 1.2 -data-version: pco/releases/2020-02-13/ncbitaxon_import.obo +data-version: pco/releases/2020-08-26/imports/ncbitaxon_import.obo ontology: pco/imports/ncbitaxon_import.obo -[Term] -id: NCBITaxon:1 -name: root -synonym: "all" RELATED synonym [] - [Term] id: NCBITaxon:10239 name: Viruses +namespace: ncbi_taxonomy synonym: "Vira" RELATED synonym [] synonym: "Viridae" RELATED synonym [] synonym: "viruses" RELATED blast_name [] -is_a: NCBITaxon:1 ! root +xref: GC_ID:1 +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:117570 name: Teleostomi -is_a: NCBITaxon:7776 ! Gnathostomata +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:7776 ! Gnathostomata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:117571 name: Euteleostomi +namespace: ncbi_taxonomy +alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] +xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi - -[Term] -id: NCBITaxon:12884 -name: Viroids -synonym: "Viroid" RELATED synonym [] -synonym: "viroids" RELATED blast_name [] -is_a: NCBITaxon:1 ! root +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:131221 name: Streptophytina +namespace: ncbi_taxonomy synonym: "Charophyta/Embryophyta group" RELATED synonym [] -synonym: "charophyte/embryophyte group" RELATED synonym [] +synonym: "charophyte/embryophyte group" EXACT equivalent_name [] +xref: GC_ID:1 is_a: NCBITaxon:35493 ! Streptophyta +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:131567 name: cellular organisms +namespace: ncbi_taxonomy synonym: "biota" RELATED synonym [] -is_a: NCBITaxon:1 ! root +xref: GC_ID:1 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:1338369 name: Dipnotetrapodomorpha +namespace: ncbi_taxonomy +xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:1437010 name: Boreoeutheria +namespace: ncbi_taxonomy synonym: "Boreotheria" RELATED synonym [] +xref: GC_ID:1 +xref: PMID:11743200 +xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:1437180 name: Acrogymnospermae +namespace: ncbi_taxonomy +xref: GC_ID:1 is_a: NCBITaxon:58024 ! Spermatophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:2 name: Bacteria +namespace: ncbi_taxonomy synonym: "bacteria" RELATED blast_name [] synonym: "eubacteria" EXACT genbank_common_name [] synonym: "Monera" RELATED in_part [] -synonym: "not Bacteria Haeckel 1894" RELATED synonym [] synonym: "Procaryotae" RELATED in_part [] synonym: "Prokaryota" RELATED in_part [] synonym: "Prokaryotae" RELATED in_part [] synonym: "prokaryote" RELATED in_part [] synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11542017 +xref: PMID:11542087 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:270744 +xref: PMID:7520741 +xref: PMID:8123559 +xref: PMID:8186100 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:207598 name: Homininae +namespace: ncbi_taxonomy synonym: "Homo/Pan/Gorilla group" RELATED synonym [] +xref: GC_ID:1 is_a: NCBITaxon:9604 ! Hominidae +property_value: has_rank NCBITaxon:subfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:2157 name: Archaea +namespace: ncbi_taxonomy synonym: "archaea" RELATED blast_name [] synonym: "Archaebacteria" RELATED synonym [] synonym: "Mendosicutes" RELATED synonym [] @@ -95,11 +143,40 @@ synonym: "Prokaryota" RELATED in_part [] synonym: "Prokaryotae" RELATED in_part [] synonym: "prokaryote" RELATED in_part [] synonym: "prokaryotes" RELATED in_part [] +xref: GC_ID:11 +xref: PMID:10425795 +xref: PMID:10425796 +xref: PMID:10425797 +xref: PMID:10490293 +xref: PMID:10843050 +xref: PMID:10939651 +xref: PMID:10939673 +xref: PMID:10939677 +xref: PMID:11211268 +xref: PMID:11321083 +xref: PMID:11321113 +xref: PMID:11411719 +xref: PMID:11540071 +xref: PMID:11541975 +xref: PMID:11542064 +xref: PMID:11542149 +xref: PMID:11760965 +xref: PMID:12054223 +xref: PMID:2112744 +xref: PMID:25527841 +xref: PMID:270744 +xref: PMID:8123559 +xref: PMID:8590690 +xref: PMID:9103655 +xref: PMID:9336922 is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:2759 name: Eukaryota +namespace: ncbi_taxonomy synonym: "Eucarya" RELATED synonym [] synonym: "Eucaryotae" RELATED synonym [] synonym: "eucaryotes" EXACT genbank_common_name [] @@ -107,224 +184,367 @@ synonym: "Eukarya" RELATED synonym [] synonym: "Eukaryotae" RELATED synonym [] synonym: "eukaryotes" EXACT common_name [] synonym: "eukaryotes" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 +xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms +property_value: has_rank NCBITaxon:superkingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:3041 name: Chlorophyta +namespace: ncbi_taxonomy synonym: "algae" RELATED in_part [] synonym: "Chlorophycota" RELATED synonym [] synonym: "Chlorophyta sensu Bremer 1985" RELATED synonym [] synonym: "green algae" EXACT genbank_common_name [] synonym: "green algae" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:23020233 is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:314146 name: Euarchontoglires +namespace: ncbi_taxonomy +xref: GC_ID:1 +xref: PMID:11214319 +xref: PMID:12082125 +xref: PMID:12878460 +xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria +property_value: has_rank NCBITaxon:superorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:314293 name: Simiiformes +namespace: ncbi_taxonomy synonym: "Anthropoidea" RELATED synonym [] +xref: GC_ID:1 is_a: NCBITaxon:376913 ! Haplorrhini +property_value: has_rank NCBITaxon:infraorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:314295 name: Hominoidea +namespace: ncbi_taxonomy synonym: "ape" EXACT common_name [] synonym: "apes" EXACT genbank_common_name [] +xref: GC_ID:1 is_a: NCBITaxon:9526 ! Catarrhini +property_value: has_rank NCBITaxon:superfamily +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:3193 name: Embryophyta +namespace: ncbi_taxonomy synonym: "higher plants" EXACT common_name [] synonym: "land plants" EXACT common_name [] synonym: "land plants" RELATED blast_name [] synonym: "plants" EXACT common_name [] +xref: GC_ID:1 is_a: NCBITaxon:131221 ! Streptophytina +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32523 name: Tetrapoda +namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] +xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32524 name: Amniota +namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] +xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32525 -name: Theria +name: Theria +namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] +xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:33090 name: Viridiplantae +namespace: ncbi_taxonomy synonym: "Chlorobionta" RELATED synonym [] -synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] -synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name [] +synonym: "chlorophyte/embryophyte group" EXACT equivalent_name [] +synonym: "Chloroplastida" RELATED synonym [] synonym: "green plants" EXACT common_name [] synonym: "green plants" RELATED blast_name [] +xref: GC_ID:1 +xref: PMID:16248873 +xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:33154 name: Opisthokonta +namespace: ncbi_taxonomy synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] +xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:33208 name: Metazoa +namespace: ncbi_taxonomy synonym: "Animalia" RELATED synonym [] synonym: "animals" RELATED blast_name [] synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT common_name [] +xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:33213 name: Bilateria +namespace: ncbi_taxonomy +xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:33511 name: Deuterostomia +namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT common_name [] +xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:3398 -name: Magnoliophyta +name: Magnoliopsida +namespace: ncbi_taxonomy synonym: "Angiospermae" RELATED synonym [] synonym: "angiosperms" EXACT common_name [] synonym: "flowering plants" EXACT genbank_common_name [] synonym: "flowering plants" RELATED blast_name [] +synonym: "Magnoliophyta" RELATED synonym [] +xref: GC_ID:1 +xref: PMID:25249442 is_a: NCBITaxon:58024 ! Spermatophyta +property_value: has_rank NCBITaxon:class +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:35493 name: Streptophyta +namespace: ncbi_taxonomy +xref: GC_ID:1 is_a: NCBITaxon:33090 ! Viridiplantae +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:376913 name: Haplorrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 is_a: NCBITaxon:9443 ! Primates +property_value: has_rank NCBITaxon:suborder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:40674 name: Mammalia +namespace: ncbi_taxonomy synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] +xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota +property_value: has_rank NCBITaxon:class +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + +[Term] +id: NCBITaxon:4751 +name: Fungi +namespace: ncbi_taxonomy +synonym: "fungi" RELATED in_part [] +synonym: "fungi" RELATED blast_name [] +synonym: "Mycota" RELATED genbank_synonym [] +xref: GC_ID:1 +xref: PMID:11062127 +xref: PMID:12684019 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:58023 name: Tracheophyta +namespace: ncbi_taxonomy synonym: "vascular plants" EXACT common_name [] synonym: "vascular plants" RELATED blast_name [] +xref: GC_ID:1 is_a: NCBITaxon:3193 ! Embryophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:58024 name: Spermatophyta +namespace: ncbi_taxonomy synonym: "seed plants" EXACT common_name [] synonym: "seed plants" RELATED blast_name [] +xref: GC_ID:1 is_a: NCBITaxon:78536 ! Euphyllophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:6072 name: Eumetazoa +namespace: ncbi_taxonomy +xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7711 name: Chordata +namespace: ncbi_taxonomy synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] +xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia +property_value: has_rank NCBITaxon:phylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7742 -name: Vertebrata +name: Vertebrata +namespace: ncbi_taxonomy synonym: "Vertebrata" EXACT scientific_name [] synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] -is_a: NCBITaxon:89593 ! Craniata +xref: GC_ID:1 +is_a: NCBITaxon:89593 ! Craniata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7776 -name: Gnathostomata +name: Gnathostomata +namespace: ncbi_taxonomy synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] -is_a: NCBITaxon:7742 ! Vertebrata +xref: GC_ID:1 +is_a: NCBITaxon:7742 ! Vertebrata +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:78536 name: Euphyllophyta -synonym: "euphyllophytes" RELATED synonym [] +namespace: ncbi_taxonomy +synonym: "euphyllophytes" EXACT equivalent_name [] +xref: GC_ID:1 is_a: NCBITaxon:58023 ! Tracheophyta +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:8287 name: Sarcopterygii +namespace: ncbi_taxonomy +xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi +property_value: has_rank NCBITaxon:superclass +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:89593 -name: Craniata +name: Craniata +namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] +xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata +property_value: has_rank NCBITaxon:subphylum +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:9347 name: Eutheria +namespace: ncbi_taxonomy synonym: "eutherian mammals" EXACT common_name [] synonym: "placental mammals" EXACT common_name [] synonym: "Placentalia" RELATED synonym [] synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] -is_a: NCBITaxon:32525 ! Theria +xref: GC_ID:1 +is_a: NCBITaxon:32525 ! Theria +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:9443 name: Primates +namespace: ncbi_taxonomy synonym: "Primata" RELATED synonym [] synonym: "primate" EXACT equivalent_name [] synonym: "primates" RELATED blast_name [] +xref: GC_ID:1 is_a: NCBITaxon:314146 ! Euarchontoglires +property_value: has_rank NCBITaxon:order +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:9526 name: Catarrhini +namespace: ncbi_taxonomy +xref: GC_ID:1 is_a: NCBITaxon:314293 ! Simiiformes +property_value: has_rank NCBITaxon:parvorder +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:9604 name: Hominidae +namespace: ncbi_taxonomy synonym: "great apes" EXACT genbank_common_name [] synonym: "Pongidae" RELATED synonym [] +xref: GC_ID:1 is_a: NCBITaxon:314295 ! Hominoidea +property_value: has_rank NCBITaxon:family +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:9605 name: Homo +namespace: ncbi_taxonomy synonym: "humans" EXACT common_name [] +xref: GC_ID:1 is_a: NCBITaxon:207598 ! Homininae +property_value: has_rank NCBITaxon:genus +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:9606 name: Homo sapiens +namespace: ncbi_taxonomy synonym: "human" EXACT genbank_common_name [] synonym: "man" EXACT common_name [] +xref: GC_ID:1 is_a: NCBITaxon:9605 ! Homo +property_value: has_rank NCBITaxon:species +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl diff --git a/imports/ncbitaxon_import.owl b/imports/ncbitaxon_import.owl index 3211368..33371dd 100644 --- a/imports/ncbitaxon_import.owl +++ b/imports/ncbitaxon_import.owl @@ -6,9 +6,10 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + @@ -24,28 +25,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + - + + + - + + + + + + + + + + + @@ -53,28 +100,35 @@ - + + + + + + + + + - - all - root - - - - - all - - - + + GC_ID:1 + ncbi_taxonomy Vira Viridae viruses + Viruses @@ -102,6 +156,9 @@ + GC_ID:1 + ncbi_taxonomy + Teleostomi @@ -111,7 +168,11 @@ + NCBITaxon:40673 + GC_ID:1 bony vertebrates + ncbi_taxonomy + Euteleostomi @@ -123,47 +184,28 @@ - - - - - Viroid - viroids - Viroids - - - - - Viroid - - - - - - viroids - - - - - + + GC_ID:1 + charophyte/embryophyte group + ncbi_taxonomy Charophyta/Embryophyta group - charophyte/embryophyte group + Streptophytina - - Charophyta/Embryophyta group - + + charophyte/embryophyte group + - charophyte/embryophyte group + Charophyta/Embryophyta group @@ -172,8 +214,10 @@ - + GC_ID:1 + ncbi_taxonomy biota + cellular organisms @@ -189,6 +233,9 @@ + GC_ID:1 + ncbi_taxonomy + Dipnotetrapodomorpha @@ -198,7 +245,12 @@ + GC_ID:1 + PMID:11743200 + PMID:11791233 + ncbi_taxonomy Boreotheria + Boreoeutheria @@ -214,6 +266,9 @@ + GC_ID:1 + ncbi_taxonomy + Acrogymnospermae @@ -223,23 +278,45 @@ + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11542017 + PMID:11542087 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:270744 + PMID:7520741 + PMID:8123559 + PMID:8186100 + PMID:8590690 + PMID:9103655 + PMID:9336922 eubacteria + ncbi_taxonomy Monera Procaryotae Prokaryota Prokaryotae bacteria - not Bacteria Haeckel 1894 prokaryote prokaryotes + Bacteria - - - - eubacteria - - @@ -270,12 +347,6 @@ bacteria - - - - not Bacteria Haeckel 1894 - - @@ -288,6 +359,12 @@ prokaryotes + + + + eubacteria + + @@ -295,7 +372,11 @@ + + GC_ID:1 + ncbi_taxonomy Homo/Pan/Gorilla group + Homininae @@ -311,6 +392,34 @@ + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11541975 + PMID:11542064 + PMID:11542149 + PMID:11760965 + PMID:12054223 + PMID:2112744 + PMID:25527841 + PMID:270744 + PMID:8123559 + PMID:8590690 + PMID:9103655 + PMID:9336922 + ncbi_taxonomy Archaebacteria Mendosicutes Metabacteria @@ -321,6 +430,7 @@ archaea prokaryote prokaryotes + Archaea @@ -390,13 +500,19 @@ + + GC_ID:1 + PMID:23020233 + PMID:30257078 eucaryotes eukaryotes + ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes + Eukaryota @@ -448,11 +564,16 @@ + + GC_ID:1 + PMID:23020233 green algae + ncbi_taxonomy Chlorophycota Chlorophyta sensu Bremer 1985 algae green algae + Chlorophyta @@ -492,6 +613,14 @@ + + GC_ID:1 + PMID:11214319 + PMID:12082125 + PMID:12878460 + PMID:15522813 + ncbi_taxonomy + Euarchontoglires @@ -501,7 +630,11 @@ + + GC_ID:1 + ncbi_taxonomy Anthropoidea + Simiiformes @@ -517,8 +650,12 @@ + + GC_ID:1 ape apes + ncbi_taxonomy + Hominoidea @@ -540,10 +677,13 @@ + GC_ID:1 higher plants land plants plants + ncbi_taxonomy land plants + Embryophyta @@ -577,7 +717,10 @@ + GC_ID:1 tetrapods + ncbi_taxonomy + Tetrapoda @@ -593,7 +736,10 @@ + GC_ID:1 amniotes + ncbi_taxonomy + Amniota @@ -609,8 +755,11 @@ + GC_ID:1 Theria - Theria <Mammalia> + ncbi_taxonomy + + Theria <mammals> @@ -625,35 +774,48 @@ + + GC_ID:1 + PMID:16248873 + PMID:30257078 + Chlorophyta/Embryophyta group + chlorophyte/embryophyte group green plants + ncbi_taxonomy Chlorobionta - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group + Chloroplastida green plants + Viridiplantae - green plants - + Chlorophyta/Embryophyta group + - - Chlorobionta - + + chlorophyte/embryophyte group + + + + + + green plants + - Chlorophyta/Embryophyta group + Chlorobionta - chlorophyte/embryophyte group + Chloroplastida @@ -669,8 +831,11 @@ + GC_ID:1 + ncbi_taxonomy Fungi/Metazoa group opisthokonts + Opisthokonta @@ -692,10 +857,14 @@ + + GC_ID:1 metazoans multicellular animals + ncbi_taxonomy Animalia animals + Metazoa @@ -729,6 +898,9 @@ + GC_ID:1 + ncbi_taxonomy + Bilateria @@ -738,7 +910,10 @@ + GC_ID:1 deuterostomes + ncbi_taxonomy + Deuterostomia @@ -754,11 +929,17 @@ + + GC_ID:1 + PMID:25249442 angiosperms flowering plants + ncbi_taxonomy Angiospermae + Magnoliophyta flowering plants - Magnoliophyta + + Magnoliopsida @@ -778,6 +959,12 @@ Angiospermae + + + + Magnoliophyta + + @@ -791,6 +978,10 @@ + + GC_ID:1 + ncbi_taxonomy + Streptophyta @@ -800,6 +991,10 @@ + + GC_ID:1 + ncbi_taxonomy + Haplorrhini @@ -809,8 +1004,12 @@ + + GC_ID:1 mammals + ncbi_taxonomy mammals + Mammalia @@ -828,12 +1027,50 @@ + + + + + + GC_ID:1 + PMID:11062127 + PMID:12684019 + ncbi_taxonomy + Mycota + fungi + + Fungi + + + + + Mycota + + + + + + fungi + + + + + + fungi + + + + + + GC_ID:1 vascular plants + ncbi_taxonomy vascular plants + Tracheophyta @@ -855,8 +1092,11 @@ + GC_ID:1 seed plants + ncbi_taxonomy seed plants + Spermatophyta @@ -878,6 +1118,9 @@ + GC_ID:1 + ncbi_taxonomy + Eumetazoa @@ -887,8 +1130,12 @@ + + GC_ID:1 chordates + ncbi_taxonomy chordates + Chordata @@ -910,10 +1157,13 @@ + GC_ID:1 Vertebrata vertebrates + ncbi_taxonomy vertebrates - Vertebrata <Metazoa> + + Vertebrata <vertebrates> @@ -940,9 +1190,12 @@ + GC_ID:1 Gnathostomata jawed vertebrates - Gnathostomata <vertebrate> + ncbi_taxonomy + + Gnathostomata <vertebrates> @@ -963,14 +1216,17 @@ - euphyllophytes + GC_ID:1 + euphyllophytes + ncbi_taxonomy + Euphyllophyta - + euphyllophytes - + @@ -979,6 +1235,10 @@ + + GC_ID:1 + ncbi_taxonomy + Sarcopterygii @@ -988,8 +1248,12 @@ + + GC_ID:1 Craniata - Craniata <chordata> + ncbi_taxonomy + + Craniata <chordates> @@ -1004,11 +1268,14 @@ + GC_ID:1 eutherian mammals placental mammals placentals + ncbi_taxonomy Placentalia placentals + Eutheria @@ -1048,9 +1315,13 @@ + + GC_ID:1 primate + ncbi_taxonomy Primata primates + Primates @@ -1078,6 +1349,10 @@ + + GC_ID:1 + ncbi_taxonomy + Catarrhini @@ -1087,8 +1362,12 @@ + + GC_ID:1 great apes + ncbi_taxonomy Pongidae + Hominidae @@ -1110,7 +1389,11 @@ + + GC_ID:1 humans + ncbi_taxonomy + Homo @@ -1126,8 +1409,12 @@ + + GC_ID:1 human man + ncbi_taxonomy + Homo sapiens diff --git a/imports/pato_import.obo b/imports/pato_import.obo index 0ad1915..c0ad17f 100644 --- a/imports/pato_import.obo +++ b/imports/pato_import.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-02-13/pato_import.obo +data-version: pco/releases/2020-08-26/imports/pato_import.obo ontology: pco/imports/pato_import.obo [Term] diff --git a/imports/pato_import.owl b/imports/pato_import.owl index a6894b8..510070d 100644 --- a/imports/pato_import.owl +++ b/imports/pato_import.owl @@ -1,15 +1,21 @@ - + @@ -25,6 +31,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -33,6 +63,170 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + is a defining property chain axiom + + + + + + + + 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. + + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -89,6 +283,14 @@ + + + + + + + + @@ -105,89 +307,2380 @@ + + + + + + + + - + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + + + + + + + + BFO:0000050 + external + quality + part_of + part_of + + part of + part of + part_of + + + http://www.obofoundry.org/ro/#OBO_REL: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) + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + BFO:0000051 + external + quality + has_part + has_part + We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. + + has part + has part + has_part + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + PATOC:CJM + + + + + + + + + + + + + + + + + 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 + http://www.obofoundry.org/ro/#OBO_REL: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. + + + precedes + + + + + + + + + + + + + + + + + + + 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 + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs 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 + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + + + + 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 + + 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 + http://www.obofoundry.org/ro/#OBO_REL:has_participant + + has participant + + + + + + + + + + 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. + dos + 2017-05-24T09:30:46Z + + has regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + + has negative regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + + has component activity + + + + + + + + + + + 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. + dos + 2017-05-24T09:49:21Z + + has component process + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:38Z + + directly negatively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:47Z + + directly positively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + + 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. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + + has 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. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + + immediately preceded by + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + + immediately precedes + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + overlaps + + + + + + + + + true + + + + + + + + + + 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. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + + has component + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + + positively regulates + + + + + + + + + + + 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. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + + capable of + + + + + + + + + + + + + + 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. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + + capable of part of + + + + + + + + + + true + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + + temporally related to + + + + + + + + + + + + + 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. + Chris Mungall + consumes + + + has input + + + + + + + + + + + + + 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. + + acts upstream of + + + + + + + + + + + + + + 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 + + acts upstream of or within + + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + causally upstream of, negative effect + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + 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 + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + + involved in + + + + + + + + + + + inverse of enables + Chris Mungall + + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + + positively regulated by + + + + + + + + + + inverse of has input + Chris Mungall + + + + input of + + + + + + + + + + + + inverse of upstream of + Chris Mungall + + causally downstream of + + + + + + + + + + + + Chris Mungall + + immediately causally downstream of + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + 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. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + + involved in negative regulation of + + + + + + + + + + + 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 + Chris Mungall + involved in or reguates + + involved in or involved in regulation of + + + + + + + + + + + + + + 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. + Chris Mungall + executes activity in + enables activity in + + + is active in + + + + + + + + + true + + + + + 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. + GOC:cjm + GOC:dos + + + + + + + + + + + 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. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + 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. + Chris Mungall + binds + molecularly binds with + + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + + phosphorylates + + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + molecularly controls + + directly regulates activity of + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + directly inhibits + molecularly decreases activity of + + directly negatively regulates 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. + Chris Mungall + Vasundra Touré + directly activates + molecularly increases activity of + + directly positively regulates activity of + + + + + + + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + + helper property (not for use in curation) + + + + + + + + + + + + + + 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. + Chris Mungall + + + has part that occurs in + + + + + + + + + true + + + + + + + + + Chris Mungall + + is kinase activity + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + + causal agent in 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between processes + + + + + + + + + + + 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 + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between entities + + + + + + + + + + Chris Mungall + + causally influenced by (entity-centric) + + causally influenced by + + + + + + + + + Chris Mungall + + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + + molecular interaction relation helper property + + + + + + + + + + + + + + + + + + + + + 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). + Chris Mungall + Vasundra Touré + + causally influences (entity-centric) + + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + + directly regulates + + + + + + + + + + + + + + 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 + Chris Mungall + + has part structure that is capable of + + + + + + + + + + + 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. + Chris Mungall + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + + capable of negatively regulating + + + + + + + + + + + + + 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. + + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + + process has causal agent + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + + directly negatively regulates + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + + causally upstream of or within, positive effect + + + + + + + + + + + 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. + Vasundra Touré + + regulates activity of + + + + + + + + + + + + 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. + quality + decreased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + + decreased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + 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. + quality + different_in_magnitude_relative_to + + different_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + + + 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. + quality + increased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + + increased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + 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. + quality + reciprocal_of + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + + reciprocal_of + + + + + 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. + PATOC:CJM + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + continuant + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + + occurrent + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + + process + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + + specifically dependent continuant + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + + material entity + + + + + + + + + molecular process + + molecular_function + + + + + + + + + + catalytic activity + + + + + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + jl + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + + biological_process + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + + + + true + + + + kinase activity + + + + + + + + + + transferase activity + + + + + + + + + + transferase activity, transferring phosphorus-containing groups + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality (PATO) + PATO:0000072 + quality + PATO:0000001 + + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + + quality + PATO:0000068 + TODO: define this or obsolete it and move children somewhere else. + + qualitative + + + + + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + quality + PATO:0000069 + + + deviation (from_normal) + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + PATOC:GVG + + + + + + + + + + + + + + + The number of entities of this type that are part of the whole organism. + PATO:0000053 + PATO:0000071 + PATO:0001169 + PATO:0001226 + presence or absence in organism + quantitative + quality + count in organism + number + presence + PATO:0000070 + + This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. + + amount + + + + + The number of entities of this type that are part of the whole organism. + PATOC:GVG + + + + + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + + rate + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + PATOC:melissa + + + + + + + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + + quality + average + PATO:0000461 + + + + + normal + + + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + PATOC:GVG + + + + + - - - + + + A quality inhering in a bearer by virtue of the bearer's existence. + + quality + present in organism + PATO:0000467 + + + + present + + + + + A quality inhering in a bearer by virtue of the bearer's existence. + PATOC:GVG + - + + + + + + + + + + + + + + + + An amount which is relatively high. + + PATO:0000420 + PATO:0000650 + increased number + present in greater numbers in organism + supernumerary + quality + accessory + increased + PATO:0000470 + + + increased amount + + + + + An amount which is relatively high. + PATOC:GVG + - + - - - + + + + + + + + + + + + + + + A rate which is relatively low. + + slow rate + quality + PATO:0000911 + + + + decreased rate + + + + + A rate which is relatively low. + PATO:GVG + - + + + + + + + + + + + + + + + + A rate which is relatively high. + + fast rate + high rate + quality + PATO:0000912 + + + + increased rate + + + + + A rate which is relatively high. + PATO:GVG + - + - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 - trait + + + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + PATO:0002079 + Wikipedia:Physical_property + relational physical quality quality - PATO:0000001 + PATO:0001018 + - quality + physical quality - + - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG - + - - - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + + + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality - PATO:0000161 + density + PATO:0001019 - rate + mass density - + - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. - PATOC:melissa + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. + WordNet:WordNet + + + + + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + quality + PATO:0001164 + + + + dense + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + PATOC:GVG @@ -196,6 +2689,7 @@ + A quality which inheres in an process. PATO:0001239 PATO:0001240 @@ -291,6 +2785,148 @@ + + + + + + + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + OBO_REL:has_part + extra or missing physical or functional parts + has or lacks parts of type + mereological quality + number of + quality + cardinality + number + PATO:0001555 + + + + has number of + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + PATOC:CJM + + + + + + + + + + + + + + + + + + + + + A density which is higher relative to the normal or average. + + high density + quality + PATO:0001788 + + + increased mass density + + + + + A density which is higher relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A density which is lower relative to the normal or average. + + low density + quality + PATO:0001790 + + + decreased mass density + + + + + A density which is lower relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + An amount which is relatively low. + + PATO:0000419 + PATO:0000468 + decreased number + present in fewer numbers in organism + quality + decreased + reduced + subnumerary + PATO:0001997 + + + decreased amount + + + + + An amount which is relatively low. + PATOC:GVG + + + + @@ -323,6 +2959,1181 @@ physical quality of a process + + + + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:39:43Z + quality + PATO:0002300 + + increased quality + + + + + A quality that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:40:15Z + quality + PATO:0002301 + + decreased quality + + + + + A quality that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:50:59Z + quality + PATO:0002302 + + decreased process quality + + + + + A quality of a process that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:51:54Z + quality + PATO:0002303 + + decreased object quality + + + + + A quality of an object that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:53:08Z + quality + PATO:0002304 + + increased process quality + + + + + A quality of a process that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:54:01Z + quality + PATO:0002305 + + increased object quality + + + + + A quality of an object that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/imports/ro_import.obo b/imports/ro_import.obo index 339d156..aa9b7f2 100644 --- a/imports/ro_import.obo +++ b/imports/ro_import.obo @@ -1,697 +1,6 @@ format-version: 1.2 -data-version: pco/releases/2020-02-13/ro_import.owl -ontology: pco/imports/ro_import -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: ()\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) - -[Term] -id: BFO:0000002 -name: continuant -def: "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." [] -disjoint_from: BFO:0000003 ! occurrent -relationship: BFO:0000050 BFO:0000002 ! part of continuant -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000003 -name: occurrent -def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: BFO:0000050 BFO:0000003 ! part of occurrent -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000004 -name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] -is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000004 ! part of independent continuant -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000006 -name: spatial region -is_a: BFO:0000141 ! immaterial entity -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000015 -name: process -def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] -is_a: BFO:0000003 ! occurrent -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000019 -name: quality -is_a: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000019 ! part of quality -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000020 -name: specifically dependent continuant -def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -is_a: BFO:0000002 ! continuant -relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000040 -name: material entity -def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] -is_a: BFO:0000004 ! independent continuant -disjoint_from: BFO:0000141 ! immaterial entity -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000141 -name: immaterial entity -is_a: BFO:0000004 ! independent continuant -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: GO:0003674 -name: molecular_function -is_a: BFO:0000015 ! process -property_value: IAO:0000589 "molecular process" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0003824 -name: catalytic activity -is_a: GO:0003674 ! molecular_function -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0008150 -name: biological_process -is_a: BFO:0000015 ! process -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0016301 -name: kinase activity -is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0016740 -name: transferase activity -is_a: GO:0003824 ! catalytic activity -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0016772 -name: transferase activity, transferring phosphorus-containing groups -is_a: GO:0016740 ! transferase activity -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Typedef] -id: BFO:0000050 -name: part of -def: "a core relation that holds between a part and its whole" [] -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf -property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string -is_transitive: true -is_a: RO:0002131 ! overlaps -inverse_of: BFO:0000051 ! has part - -[Typedef] -id: BFO:0000051 -name: has part -def: "a core relation that holds between a whole and its part" [] -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: RO:0002131 ! overlaps - -[Typedef] -id: BFO:0000062 -name: preceded by -def: "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." [] -subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000062 -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - -[Typedef] -id: BFO:0000063 -name: precedes -def: "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." [] -subset: ro-eco -property_value: IAO:0000111 "precedes" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000063 -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: BFO:0000066 -name: occurs in -def: "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" [] -comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000050 BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[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" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: RO:0000052 -name: inheres in -def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string -property_value: IAO:0000112 "this red color inheres in this apple" xsd:string -property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -is_a: RO:0002314 ! inheres in part of -inverse_of: RO:0000053 ! bearer of - -[Typedef] -id: RO:0000053 -name: bearer of -def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant - -[Typedef] -id: RO:0000056 -name: participates in -def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000002 ! continuant -range: BFO:0000003 ! occurrent -inverse_of: RO:0000057 ! has participant - -[Typedef] -id: RO:0000057 -name: has participant -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: BFO:0000051 RO:0000057 - -[Typedef] -id: RO:0000080 -name: quality of -def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000052 ! inheres in -inverse_of: RO:0000086 ! has quality - -[Typedef] -id: RO:0000086 -name: has quality -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -range: BFO:0000019 ! quality -is_a: RO:0000053 ! bearer of - -[Typedef] -id: RO:0001015 -name: location of -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: RO:0001025 ! located in - -[Typedef] -id: RO:0001018 -name: contained in -subset: ro-eco -property_value: IAO:0000111 "contained in" xsd:string -property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string -property_value: IAO:0000116 "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):" xsd:string -property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string -property_value: IAO:0000118 "contained_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000004 ! independent continuant -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains - -[Typedef] -id: RO:0001019 -name: contains -subset: ro-eco -property_value: IAO:0000111 "contains" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 - -[Typedef] -id: RO:0001025 -name: located in -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true - -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "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." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: dos -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "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." [] -comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "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." [] -comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002018 ! has component process -created_by: dos -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "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." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: dos -creation_date: 2017-05-24T09:49:21Z - -[Typedef] -id: RO:0002019 -name: has ligand -def: "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." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002233 ! has input -created_by: dos -creation_date: 2017-07-19T17:30:36Z - -[Typedef] -id: RO:0002022 -name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002334 ! regulated by -inverse_of: RO:0002578 ! directly regulates -created_by: dos -creation_date: 2017-09-17T13:52:24Z - -[Typedef] -id: RO:0002023 -name: directly negatively regulated by -def: "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." [GOC:dos] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos -creation_date: 2017-09-17T13:52:38Z - -[Typedef] -id: RO:0002024 -name: directly positively regulated by -def: "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." [GOC:dos] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002629 ! directly positively regulates -created_by: dos -creation_date: 2017-09-17T13:52:47Z - -[Typedef] -id: RO:0002025 -name: has effector activity -def: "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." [GOC:dos] -comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_functional: true -is_a: RO:0002017 ! has component activity -is_a: RO:0002211 ! regulates -created_by: dos -creation_date: 2017-09-22T14:14:36Z - -[Typedef] -id: RO:0002086 -name: ends after -comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) -subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002087 -name: immediately preceded by -comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: BFO:0000062 ! preceded by -inverse_of: RO:0002090 ! immediately precedes - -[Typedef] -id: RO:0002090 -name: immediately precedes -comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) -subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0002575 BFO:0000063 -is_a: BFO:0000063 ! precedes - -[Typedef] -id: RO:0002131 -name: overlaps -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: ro-eco -property_value: IAO:0000114 IAO:0000125 -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: BFO:0000051 RO:0002131 -is_a: RO:0002323 ! mereotopologically related to -transitive_over: BFO:0000050 ! part of -expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] - -[Typedef] -id: RO:0002180 -name: has component -def: "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." [] -subset: ro-eco -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002211 -name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -holds_over_chain: RO:0002578 RO:0002578 -is_transitive: true -is_a: RO:0002411 ! causally upstream of -inverse_of: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002212 -name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002211 -is_a: RO:0002211 ! regulates -is_a: RO:0002305 ! causally upstream of, negative effect -inverse_of: RO:0002335 ! negatively regulated by - -[Typedef] -id: RO:0002213 -name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002211 -holds_over_chain: RO:0002212 RO:0002212 -is_transitive: true -is_a: RO:0002211 ! regulates -is_a: RO:0002304 ! causally upstream of, positive effect -inverse_of: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002215 -name: capable of -def: "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. " [] -subset: ro-eco -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: RO:0002216 ! capable of part of -expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] - -[Typedef] -id: RO:0002216 -name: capable of part of -def: "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." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "has function in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso "defining-property-chains-involving-reflexivity" -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process -expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] - -[Typedef] -id: RO:0002217 -name: actively participates in -def: "x actively participates in y if and only if x participates in y and x realizes some active role" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "agent in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000056 ! participates in -inverse_of: RO:0002218 ! obsolete has active participant - -[Typedef] -id: RO:0002218 -name: obsolete has active participant -def: "x has participant y if and only if x realizes some active role that inheres in y" [] -subset: ro-eco -property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "has agent" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000057 ! has participant -is_obsolete: true - -[Typedef] -id: RO:0002222 -name: temporally related to -comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. -subset: ro-eco -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent - -[Typedef] -id: RO:0002233 -name: has input -def: "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." [] -subset: ro-eco -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "consumes" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000040 ! material entity -is_a: RO:0000057 ! has participant -inverse_of: RO:0002352 ! input of - -[Typedef] -id: RO:0002263 -name: acts upstream of -def: "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." [] -property_value: IAO:0000112 "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." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of -holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0002264 -name: acts upstream of or within -def: "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." [] -synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within -holds_over_chain: RO:0002327 RO:0002418 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002304 -name: causally upstream of, positive effect -comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002411 -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004047 ! causally upstream of or within, positive effect - -[Typedef] -id: RO:0002305 -name: causally upstream of, negative effect -comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002411 -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004046 ! causally upstream of or within, negative effect - -[Typedef] -id: RO:0002314 -name: inheres in part of -def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "defining-property-chains-involving-reflexivity" -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002502 ! depends on -transitive_over: BFO:0000050 ! part of +data-version: pco/releases/2020-08-26/imports/ro_import.obo +ontology: pco/imports/ro_import.obo [Typedef] id: RO:0002321 @@ -701,621 +10,4 @@ subset: ro-eco property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl - -[Typedef] -id: RO:0002323 -name: mereotopologically related to -def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 - -[Typedef] -id: RO:0002327 -name: enables -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string -property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002215 ! capable of -inverse_of: RO:0002333 ! enabled by -transitive_over: BFO:0000051 ! has part -transitive_over: RO:0002017 ! has component activity - -[Typedef] -id: RO:0002328 -name: functionally related to -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl - -[Typedef] -id: RO:0002329 -name: part of structure that is capable of -def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "false" xsd:boolean -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002331 -name: involved in -def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso Involved:in -holds_over_chain: RO:0002327 BFO:0000050 -is_a: RO:0002217 ! actively participates in -is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002333 -name: enabled by -def: "inverse of enables" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000057 ! has participant -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002334 -name: regulated by -def: "inverse of regulates" [] -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000589 "regulated by (processual)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_transitive: true -is_a: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002335 -name: negatively regulated by -def: "inverse of negatively regulates" [] -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002336 -name: positively regulated by -def: "inverse of positively regulates" [] -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002350 -name: member of -def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -is_a: BFO:0000050 ! part of -inverse_of: RO:0002351 ! has member - -[Typedef] -id: RO:0002351 -name: has member -def: "has member is a mereological relation between a collection and an item." [] -property_value: IAO:0000119 "SIO" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002352 -name: input of -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000056 ! participates in -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002379 -name: spatially coextensive with -def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002404 -name: causally downstream of -def: "inverse of upstream of" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: BFO:0000062 ! preceded by -is_a: RO:0002427 ! causally downstream of or within -inverse_of: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002405 -name: immediately causally downstream of -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002087 ! immediately preceded by -is_a: RO:0002404 ! causally downstream of -inverse_of: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002410 -name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "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.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl - -[Typedef] -id: RO:0002411 -name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_transitive: true -is_a: BFO:0000063 ! precedes -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002412 -name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0002575 RO:0002411 -is_a: RO:0002090 ! immediately precedes -is_a: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002418 -name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] -synonym: "affects" RELATED [] -property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "influences (processual)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_transitive: true -is_a: RO:0002501 ! causal relation between processes -inverse_of: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002427 -name: causally downstream of or within -def: "inverse of causally upstream of or within" [] -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_transitive: true -is_a: RO:0002501 ! causal relation between processes - -[Typedef] -id: RO:0002428 -name: involved in regulation of -def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 RO:0002211 -holds_over_chain: RO:0002331 RO:0002211 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0002431 ! involved in or involved in regulation of - -[Typedef] -id: RO:0002429 -name: involved in positive regulation of -def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002428 -holds_over_chain: RO:0002327 RO:0002213 -holds_over_chain: RO:0002331 RO:0002213 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002430 -name: involved in negative regulation of -def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002428 -holds_over_chain: RO:0002327 RO:0002212 -holds_over_chain: RO:0002331 RO:0002212 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002431 -name: involved in or involved in regulation of -def: "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" [] -property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "involved in or reguates" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002264 ! acts upstream of or within -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002432 -name: is active in -def: "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." [GOC:cjm, GOC:dos] -synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "executes activity in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002131 ! overlaps -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002434 -name: interacts with -def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] -subset: ro-eco -synonym: "in pairwise interaction with" EXACT [] -property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI -property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_symmetric: true - -[Typedef] -id: RO:0002436 -name: molecularly interacts with -def: "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." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso ECO:0000353 -property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -is_symmetric: true -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002447 -name: phosphorylates -property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002448 -name: activity directly regulates activity of -def: "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B." [] -synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002436 ! molecularly interacts with -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002449 -name: activity directly negatively regulates activity of -def: "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] -synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "inhibits" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002448 ! activity directly regulates activity of - -[Typedef] -id: RO:0002450 -name: activity directly positively regulates activity of -def: "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] -synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "activates" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002448 ! activity directly regulates activity of - -[Typedef] -id: RO:0002464 -name: helper property (not for use in curation) -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl - -[Typedef] -id: RO:0002479 -name: has part that occurs in -def: "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." [] -subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} - -[Typedef] -id: RO:0002481 -name: is kinase activity -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0002500 -name: causal agent in process -def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002595 ! causal relation between material entity and a process -inverse_of: RO:0002608 ! process has causal agent - -[Typedef] -id: RO:0002501 -name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002502 -name: depends on -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso BFO:0000169 - -[Typedef] -id: RO:0002506 -name: causal relation between material entities -property_value: IAO:0000116 "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" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002559 -name: causally influenced by -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (material entity to material entity)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002506 ! causal relation between material entities -inverse_of: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002563 -name: interaction relation helper property -property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -is_a: RO:0002464 ! helper property (not for use in curation) - -[Typedef] -id: RO:0002564 -name: molecular interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002563 ! interaction relation helper property - -[Typedef] -id: RO:0002566 -name: causally influences -def: "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (material entity to material entity)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002506 ! causal relation between material entities - -[Typedef] -id: RO:0002578 -name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0002575 RO:0002211 -is_a: RO:0002211 ! regulates -is_a: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002584 -name: has part structure that is capable of -def: "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" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: BFO:0000051 RO:0002215 -is_a: RO:0002328 ! functionally related to -is_a: RO:0002595 ! causal relation between material entity and a process - -[Typedef] -id: RO:0002595 -name: causal relation between material entity and a process -def: "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." [] -property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000040 ! material entity -range: BFO:0000015 ! process -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002596 -name: capable of regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002215 RO:0002211 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002597 -name: capable of negatively regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002215 RO:0002212 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002598 -name: capable of positively regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002215 RO:0002213 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002608 -name: process has causal agent -def: "Inverse of 'causal agent in process'" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002629 -name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002578 -is_a: RO:0002213 ! positively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002630 -name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002578 -is_a: RO:0002212 ! negatively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0004031 -name: enables subfunction -def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 BFO:0000051 -is_a: RO:0002328 ! functionally related to -created_by: cjm -creation_date: 2018-01-25T23:20:13Z - -[Typedef] -id: RO:0004032 -name: acts upstream of or within, positive effect -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect -holds_over_chain: RO:0002327 RO:0004047 -is_a: RO:0002264 ! acts upstream of or within -created_by: cjm -creation_date: 2018-01-26T23:49:30Z - -[Typedef] -id: RO:0004033 -name: acts upstream of or within, negative effect -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002264 -holds_over_chain: RO:0002327 RO:0004046 -is_a: RO:0002264 ! acts upstream of or within -created_by: cjm -creation_date: 2018-01-26T23:49:51Z - -[Typedef] -id: RO:0004034 -name: acts upstream of, positive effect -def: "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" [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect -holds_over_chain: RO:0002327 RO:0002304 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: cjm -creation_date: 2018-01-26T23:53:14Z - -[Typedef] -id: RO:0004035 -name: acts upstream of, negative effect -def: "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" [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect -holds_over_chain: RO:0002327 RO:0002305 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: cjm -creation_date: 2018-01-26T23:53:22Z - -[Typedef] -id: RO:0004046 -name: causally upstream of or within, negative effect -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002418 -is_a: RO:0002418 ! causally upstream of or within -created_by: cjm -creation_date: 2018-03-13T23:55:05Z - -[Typedef] -id: RO:0004047 -name: causally upstream of or within, positive effect -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002418 -is_a: RO:0002418 ! causally upstream of or within -created_by: cjm -creation_date: 2018-03-13T23:55:19Z diff --git a/imports/ro_import.owl b/imports/ro_import.owl index df06d81..c49c1d8 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -9,13 +9,10 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - + + @@ -31,340 +28,41 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - editor note - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - is a defining property chain axiom - - - - - - - - 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. - - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - + in_subset - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -379,3230 +77,16 @@ - - - - - - - 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 https://code.google.com/p/obo-relations/wiki/ROAndTime - 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 - - - - - - - - - - part of - - - http://www.obofoundry.org/ro/#OBO_REL: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 https://code.google.com/p/obo-relations/wiki/ROAndTime - 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 - - - has part - - - - - - - - - - - - - - - - - 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 - http://www.obofoundry.org/ro/#OBO_REL: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. - - - precedes - - - - - - - - - - - - - - - - - - - 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 - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs 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 - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - 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 - - - bearer of - - - - - - - - - - - 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 - - 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 - http://www.obofoundry.org/ro/#OBO_REL:has_participant - - has participant - - - - - - - - - - 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 - - quality of - - - - - - - - - - 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 - - - - - - - - - - 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 https://code.google.com/p/obo-relations/wiki/ROAndTime - location_of - - - location of - - - - - + - - - - - - - - - contained in - Containment is location not involving parthood, and arises only where some immaterial continuant is involved. - 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): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - - contained_in - + + 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 + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions - - contained in + ecologically related to - - - - - - - contains - - - - contains - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - - located in - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - - 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. - dos - 2017-05-24T09:30:46Z - - has regulatory component activity - - - - - - - - - - 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. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - - has negative regulatory component activity - - - - - - - - - - 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. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - - has positive regulatory component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - - has component activity - - - - - - - - - - - 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. - dos - 2017-05-24T09:49:21Z - - has component process - - - - - - - - - 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. - dos - 2017-07-19T17:30:36Z - - has ligand - - - - - - - - - - dos - 2017-09-17T13:52:24Z - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - - directly regulated by - - - - - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos - - - - - - - - - - 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. - dos - 2017-09-17T13:52:38Z - - directly negatively regulated by - - - - - 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. - GOC:dos - - - - - - - - - - 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. - dos - 2017-09-17T13:52:47Z - - directly positively regulated by - - - - - 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. - GOC:dos - - - - - - - - - - - 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. - dos - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - - has 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. - GOC:dos - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - - ends after - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - - immediately preceded by - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - - immediately precedes - - - - - - - - - - - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - - - - overlaps - - - - - - - - - true - - - - - - - - - - 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. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - - has component - - - - - - - - - - - - - - - - - - - process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit - Chris Mungall - David Hill - Tanya Berardini - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - - regulates - - - - - - - - - - - Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. - Chris Mungall - - negatively regulates (process to process) - - - negatively regulates - - - - - - - - - - - - - - - - Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. - Chris Mungall - - positively regulates (process to process) - - - positively regulates - - - - - - - - - - - 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. - Chris Mungall - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) - - - capable of - - - - - - - - - - - - - - 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. - Chris Mungall - has function in - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) - - capable of part of - - - - - - - - - - true - - - - - - - - - - x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall - agent in - - actively participates in - - - - - - - - - 'heart development' has active participant some Shh protein - - x has participant y if and only if x realizes some active role that inheres in y - This may be obsoleted and replaced by the original 'has agent' relation - Chris Mungall - has agent - - - obsolete has active participant - true - - - - - - - - - - - Chris Mungall - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - - temporally related to - - - - - - - - - - - - - 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. - Chris Mungall - consumes - - - has input - - - - - - - - - - - - - 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. - - acts upstream of - - - - - - - - - - - - - - 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 - - acts upstream of or within - - - - - - - - - - - - cjm - holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y - - causally upstream of, positive effect - - - - - - - - - - - cjm - holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y - - causally upstream of, negative effect - - - - - - - - - - - - - - - - - q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. - Because part_of is transitive, inheres in is a sub-relation of inheres in part of - Chris Mungall - - - - inheres in part of - - - - - - - - - - true - - - - - - - - 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 - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions - - - ecologically related to - - - - - - - - A mereological relationship or a topological relationship - Chris Mungall - 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 - - - - - - - - - - - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity - Chris Mungall - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. - - enables - - - - - - - - A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall - This is a grouping relation that collects relations used for the purpose of connecting structure and function - - functionally related to - - - - - - - - - - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall - false - - part of structure that is capable of - - - - - - - - - true - - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall - actively involved in - enables part of - - involved in - - - - - - - - - - - inverse of enables - Chris Mungall - - enabled by - - - - - - - - - - - - inverse of regulates - Chris Mungall - regulated by (processual) - - - regulated by - - - - - - - - - inverse of negatively regulates - Chris Mungall - - - negatively regulated by - - - - - - - - - inverse of positively regulates - Chris Mungall - - - positively regulated by - - - - - - - - - - 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 - - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - - has member - - - - - - - - - - inverse of has input - Chris Mungall - - - - input of - - - - - - - - - - - - - - - A lump of clay and a statue - x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios - - spatially coextensive with - - - - - - - - - - - - inverse of upstream of - Chris Mungall - - causally downstream of - - - - - - - - - - - - Chris Mungall - - immediately causally downstream of - - - - - - - - - This relation groups causal relations between material entities and causal relations between processes - 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. - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causally related to - - - - - - - - - - - - p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain - Chris Mungall - - causally upstream of - - - - - - - - - - - p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. - Chris Mungall - - - immediately causally upstream of - - - - - - - - - - - p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. - We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall - influences (processual) - affects - - causally upstream of or within - - - - - - - - - - inverse of causally upstream of or within - Chris Mungall - - - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall - - involved in regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall - - - involved in positive regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall - - - involved in negative regulation of - - - - - - - - - - - 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 - Chris Mungall - involved in or reguates - - involved in or involved in regulation of - - - - - - - - - - - - - - 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. - Chris Mungall - executes activity in - enables activity in - - - is active in - - - - - - - - - true - - - - - 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. - GOC:cjm - GOC:dos - - - - - - - - - - - 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. - Chris Mungall - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. - in pairwise interaction with - - - interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - - 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. - Chris Mungall - binds - molecularly binds with - - molecularly interacts with - - http://purl.obolibrary.org/obo/MI_0915 - - - - - - - - - Axiomatization to GO to be added later - Chris Mungall - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. - - phosphorylates - - - - - - - - - - - - - - - Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - Chris Mungall - molecularly controls - - activity directly regulates activity of - - - - - - - - - - - - - - Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - inhibits - molecularly decreases activity of - - activity directly negatively regulates activity of - - - - - - - - - - - - - - Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - activates - molecularly increases activity of - - activity directly positively regulates activity of - - - - - - - - Chris Mungall - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - - helper property (not for use in curation) - - - - - - - - - - - - - - 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. - Chris Mungall - - - has part that occurs in - - - - - - - - - true - - - - - - - - - Chris Mungall - - is kinase activity - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - - - causal agent in 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between processes - - - - - - - - Chris Mungall - - depends on - - - - - - - - - - - - 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 - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between material entities - - - - - - - - - - Chris Mungall - - causally influenced by (material entity to material entity) - - causally influenced by - - - - - - - - - Chris Mungall - - interaction relation helper property - - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - Chris Mungall - - molecular interaction relation helper property - - - - - - - - - - - - - - - - - - - Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b - Chris Mungall - - causally influences (material entity to material entity) - - causally influences - - - - - - - - - - Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - Chris Mungall - - directly regulates (processual) - - - directly regulates - - - - - - - - - - - - - - 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 - Chris Mungall - - has part structure that is capable of - - - - - - - - - - - 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. - Chris Mungall - - - causal relation between material entity and a process - - - - - - - - - - - - - pyrethroid -> growth - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - - - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - - - capable of negatively regulating - - - - - - - - - - - - - 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. - - - capable of positively regulating - - - - - - - - - Inverse of 'causal agent in process' - - - process has causal agent - - - - - - - - - - Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. - - directly positively regulates (process to process) - - - directly positively regulates - - - - - - - - - - Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. - - directly negatively regulates (process to process) - - - directly negatively regulates - - - - - - - - - - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm - 2018-01-25T23:20:13Z - - enables subfunction - - - - - - - - - - - - - - cjm - 2018-01-26T23:49:30Z - - acts upstream of or within, positive effect - - - - - - - - - - - - - - - cjm - 2018-01-26T23:49:51Z - - acts upstream of or within, negative effect - - - - - - - - - - - - - - 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 - - cjm - 2018-01-26T23:53:14Z - - acts upstream of, positive effect - - - - - - - - - - - - - - - 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 - - cjm - 2018-01-26T23:53:22Z - - acts upstream of, negative effect - - - - - - - - - - - cjm - 2018-03-13T23:55:05Z - - causally upstream of or within, negative effect - - - - - - - - - - cjm - 2018-03-13T23:55:19Z - - causally upstream of or within, positive effect - - - - - - - - - - - - - - - - - - - - - - - - - - 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. - - continuant - - - - - - - - - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. - - occurrent - - - - - - - - - - - - - - - - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - - independent continuant - - - - - - - - - - spatial region - - - - - - - - - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - - process - - - - - - - - - - - - - - - - quality - - - - - - - - - - - - - - - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - - specifically dependent continuant - - - - - - - - - - - - - - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - - material entity - - - - - - - - - - - - - - - - immaterial entity - - - - - - - - - molecular process - - molecular_function - - - - - - - - - - catalytic activity - - - - - - - - - - biological_process - - - - - - - - - - - - true - - - - kinase activity - - - - - - - - - - transferase activity - - - - - - - - - - transferase activity, transferring phosphorus-containing groups - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/imports/stato_import.obo b/imports/stato_import.obo new file mode 100644 index 0000000..c6dcab1 --- /dev/null +++ b/imports/stato_import.obo @@ -0,0 +1,49 @@ +format-version: 1.2 +data-version: pco/releases/2020-08-26/imports/stato_import.obo +ontology: pco/imports/stato_import.obo + +[Term] +id: IAO:0000027 +name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string +property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string +property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + +[Term] +id: IAO:0000109 +name: measurement datum +def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "measurement datum" xsd:string +property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:string +property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000119 group:OBI xsd:string +property_value: IAO:0000119 "OBI_0000305" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + +[Term] +id: STATO:0000047 +name: count +def: "a count is a data item denoted by an integer and represented the number of instances or occurences of an entity" [] +is_a: IAO:0000109 ! measurement datum +property_value: IAO:0000112 "a count of 4 resulting from counting limbs in humans" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string +property_value: IAO:0000117 "Orlaith Burke" xsd:string +property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string +property_value: IAO:0000119 "STATO" xsd:string +property_value: STATO:0000032 "" xsd:string + diff --git a/imports/stato_import.owl b/imports/stato_import.owl new file mode 100644 index 0000000..3000f3d --- /dev/null +++ b/imports/stato_import.owl @@ -0,0 +1,371 @@ + + + + + Camille Maumet (http://orcid.org/0000-0002-6290-553X) + Chris Mungall (http://orcid.org/0000-0002-6601-2165) + Hanna Cwiek (https://orcid.org/0000-0001-9113-567X) + Nolan Nichols (http://orcid.org/0000-0003-1099-3328) + Thomas Nichols (http://orcid.org/0000-0002-4516-5103) + Alejandra Gonzalez-Beltran (http://orcid.org/0000-0003-3499-8262) + Orlaith Burke + Philippe Rocca-Serra (http://orcid.org/0000-0001-9853-5668) + STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. + This Ontology is distributed under a Creative Commons Attribution License + Statistical Method, Design of Experiment, Plots, Statistical Model + STATO: the statistical methods ontology + http://creativecommons.org/licenses/by/3.0/ + https://github.com/ISA-tools/stato/issues + http://stato-ontology.org/ + stat-ontology@googlegroups.com + RC1.4 + + + + + + + + + + + + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + 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 label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + + + + + + + example + + 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 + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + definition + textual definition + + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 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.obfoundry.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 term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + + + + + + + + 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 + + + + + + + + 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> + + imported from + + + + + + + + an alternative term used for STATO statistical ontology and ISA team + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO alternative term + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + label + label + + + + + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + + data item + + + + + + + + + measurement datum + Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + + measurement datum + + + + + + + + + a count of 4 resulting from counting limbs in humans + + a count is a data item denoted by an integer and represented the number of instances or occurences of an entity + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO + + count + + + + + + + diff --git a/pco-base.obo b/pco-base.obo index 1c082c0..89d34f8 100644 --- a/pco-base.obo +++ b/pco-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-02-13/pco-base.owl +data-version: pco/releases/2020-08-26/pco-base.owl remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco/pco-base property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -8,8 +8,21 @@ property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string -property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string +property_value: http://purl.org/dc/elements/1.1/description "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Population and Community Ontology" xsd:string property_value: http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 xsd:string +property_value: http://purl.org/dc/terms/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string + +[Term] +id: CARO:0000012 +name: multicellular organism +def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] +comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. +comment: MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. +is_a: CARO:0010004 ! organism +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "multicellular organism" xsd:string [Term] id: CARO:0001010 @@ -24,12 +37,16 @@ property_value: IAO:0000589 "organism or virus" xsd:string id: CARO:0010004 name: organism def: "An individual member of a clade." [] -comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. is_a: CARO:0001010 ! organism or virus or viroid property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string property_value: IAO:0000589 "organism" xsd:string +[Term] +id: ECOCORE:00000045 +is_a: CARO:0001010 ! organism or virus or viroid + [Term] id: GO:0051704 is_a: BFO:0000015 @@ -46,6 +63,7 @@ comment: May be of the same or different species. is_a: BFO:0000027 intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "group of organism" xsd:string @@ -67,18 +85,20 @@ id: PCO:0000002 name: ecological community def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +is_a: PCO:0000029 ! multi-species collection of organisms property_value: IAO:0000118 "multispecies community" xsd:string property_value: IAO:0000119 ISBN:0865423504 xsd:string [Term] id: PCO:0000003 name: quality of a population -def: "A quality that inheres in a biological population." [] +def: "A quality that inheres in a population of organisms." [] comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. intersection_of: PATO:0002003 intersection_of: RO:0000052 PCO:0000001 ! population of organisms property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string +property_value: IAO:0000116 "This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community." xsd:string [Term] id: PCO:0000004 @@ -93,8 +113,8 @@ property_value: IAO:0000116 "These may not belong under BFO:quality. May be bett [Term] id: PCO:0000005 name: population process -def: "A process that has as primary participant a population. " [] -comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +def: "A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction." [] +comment: The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. is_a: BFO:0000015 relationship: RO:0000057 PCO:0000001 ! population of organisms property_value: IAO:0000114 IAO:0000123 @@ -102,21 +122,23 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000006 name: population birth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of birth of a population of organisms." [] +is_a: PATO:0000161 property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000007 name: population death rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of death of a population of organsisms." [] +is_a: PATO:0000161 property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000008 name: population growth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of growth of a population." [] +is_a: PATO:0000161 property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string [Term] id: PCO:0000009 @@ -160,28 +182,37 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 -name: predator role -is_a: BFO:0000023 -property_value: IAO:0000114 IAO:0000124 +name: obsolete predator role +is_a: ObsoleteClass +property_value: IAO:0000116 "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 -name: prey role -is_a: BFO:0000023 -property_value: IAO:0000114 IAO:0000124 +name: obsolete prey role +is_a: ObsoleteClass +property_value: IAO:0000116 "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 -name: symbiont role -is_a: BFO:0000023 -property_value: IAO:0000114 IAO:0000124 +name: obsolete symbiont role +is_a: ObsoleteClass +property_value: IAO:0000116 "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000017 name: species as a collection of organisms -def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as members every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as parts every organism of a species and no organisms of any other species." [] comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +synonym: "taxonomic group" EXACT [] +xref: GENO:0000113 +xref: Species +xref: TAXRANK:0000006 is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000059 ! taxon as collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string @@ -190,6 +221,9 @@ id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms +intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -230,7 +264,7 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000023 name: community species evenness -def: "A quality of a community that reflects how close in abundance all species in a community are." [] +def: "A quality of an ecological community that reflects how close in abundance all species in a community are." [] is_a: PCO:0000004 ! quality of an ecological community property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -244,12 +278,12 @@ is_a: PCO:0000031 ! organismal entity relationship: RO:0002321 ENVO:01000744 relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string [Term] id: PCO:0000025 -name: red population +name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 @@ -257,7 +291,7 @@ is_obsolete: true [Term] id: PCO:0000026 -name: red organism +name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 @@ -277,7 +311,7 @@ property_value: IAO:0000118 "human population" xsd:string [Term] id: PCO:0000028 -name: community +name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). is_a: ObsoleteClass @@ -290,6 +324,7 @@ id: PCO:0000029 name: multi-species collection of organisms def: "A collection of organisms that consists of two or more organisms from at least two species." [] is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 PCO:0000001 {minCardinality="2"} ! population of organisms property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string @@ -352,9 +387,9 @@ property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000037 name: potluck +def: "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." [] is_a: PCO:0000033 ! human social gathering activity property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string -property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -375,6 +410,72 @@ property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000040 +name: obsolete tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000041 +name: obsolete invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000042 +name: obsolete microbe +synonym: "microbial organism" EXACT [] +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000043 +name: obsolete collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000044 +name: obsolete multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000045 +name: obsolete single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000046 +name: obsolete microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000047 name: tidal mangrove shrubland community def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] synonym: "mangrove community" RELATED [] @@ -385,62 +486,150 @@ relationship: BFO:0000050 ENVO:01001369 property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] -id: PCO:0000041 +id: PCO:0000048 name: invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO is_a: PATO:0001241 [Term] -id: PCO:0000042 +id: PCO:0000049 name: microbe synonym: "microbial organism" EXACT [] is_a: CARO:0001010 ! organism or virus or viroid -relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye [Term] -id: PCO:0000043 +id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe -intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe +intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! microbe +intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000044 +id: PCO:0000051 name: multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] is_a: PCO:0000029 ! multi-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000045 +id: PCO:0000052 name: single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000046 +id: PCO:0000053 name: microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] is_a: PCO:0000001 ! population of organisms -relationship: RO:0002351 PCO:0000042 ! microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +[Term] +id: PCO:0000054 +name: number of generations of multicellular organism +def: "A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism." [] {comment="NCIT:C88214", comment="EFO:0000507"} +synonym: "number of generations" BROAD [] +is_a: STATO:0000047 +relationship: IAO:0000136 CARO:0000012 ! multicellular organism +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 + +[Term] +id: PCO:0000057 +name: overcrowded population +def: "An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels." [] +synonym: "increased density of population" EXACT [] +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000058 +name: overcrowded human population +def: "A quality of a human population such that the density humans in an area is increased beyond sustainable levels." [] +is_a: PCO:0000057 ! overcrowded population +intersection_of: PCO:0000057 ! overcrowded population +intersection_of: RO:0000052 PCO:0000027 ! collection of humans +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000059 +name: taxon as collection of organisms +def: "A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations." [] +comment: This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. +xref: data:1868 +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000060 +name: microbial parasite +def: "An organism or virus or viroid that is a microbe and a parasite." [] +is_a: ECOCORE:00000146 +is_a: PCO:0000049 ! microbe +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000061 +name: parasite isolate population +def: "A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations." [] +is_a: PCO:0000053 ! microbial population +relationship: RO:0002351 PCO:0000060 ! microbial parasite +property_value: IAO:0000112 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811772/ +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "VEuPathDB" xsd:string + +[Term] +id: PCO:0000062 +name: Shannon diversity index +def: "A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi)." [] +synonym: "Shannon entropy" EXACT [] +synonym: "Shannon's diversity index" EXACT [] +synonym: "Shannon-Wiener index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html +property_value: IAO:0000119 "Shannon_index" + +[Term] +id: PCO:0000063 +name: Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi)." [] +synonym: "Simpson index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Simpson_index" + +[Term] +id: PCO:0000064 +name: inverse Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi)." [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Inverse_Simpson_index" + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: BFO:0000040 relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid [Term] id: PCO:0001001 name: pair of interacting organisms of the same species +def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0001000 ! pair of interacting organisms +relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms [Term] id: PCO:1000000 @@ -485,9 +674,14 @@ def: "An ecological community which is composed of co-existing populations of mi comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. synonym: "microbiota" BROAD [] is_a: PCO:0000002 ! ecological community -is_a: PCO:0000044 ! multi-species collection of microbes +is_a: PCO:0000051 ! multi-species collection of microbes property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string +[Typedef] +id: PCO:0000055 +name: has member of +domain: PCO:0000000 ! collection of organisms + diff --git a/pco-base.owl b/pco-base.owl index 37a491e..d554572 100644 --- a/pco-base.owl +++ b/pco-base.owl @@ -8,17 +8,20 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg Ramona Walls - http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. + Population and Community Ontology http://purl.obolibrary.org/obo/IAO_8000001 + http://creativecommons.org/publicdomain/zero/1.0/ The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. @@ -172,6 +175,24 @@ + + + + + + + + + + + + + + has member of + + + + @@ -267,6 +288,21 @@ + + + + + Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. + multicellular organism + Melissa Haendel + 9/18/11 + MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. + multicellular organism + + + + @@ -288,12 +324,26 @@ organism mah 7.16.2011 - A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. organism + + + + + + + + + + + + + + @@ -334,12 +384,24 @@ + + + + + + + + + + + + @@ -365,6 +427,12 @@ + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. @@ -396,18 +464,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - 2 - - - - - + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 @@ -432,8 +489,9 @@ Classes for population already exist in IDO ('organism population', I - A quality that inheres in a biological population. + A quality that inheres in a population of organisms. See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community. Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. quality of a population @@ -474,8 +532,8 @@ Classes for population already exist in IDO ('organism population', I - A process that has as primary participant a population. - Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. + The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. population process @@ -484,8 +542,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of birth of a population of organisms. population birth rate @@ -494,8 +553,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of death of a population of organsisms. population death rate @@ -504,9 +564,9 @@ Classes for population already exist in IDO ('organism population', I - + - Is a rate a quality? Population growth rate may be better classified as a process profile. + The rate of growth of a population. population growth rate @@ -575,30 +635,51 @@ Classes for population already exist in IDO ('organism population', I - - - predator role + + Interactions are now covered in EcoCore ontology. + obsolete predator role + true + + + + true + + - - - prey role + + Interactions are now covered in EcoCore ontology. + obsolete prey role + true + + + + true + + - - - symbiont role + + Interactions are now covered in EcoCore ontology. + obsolete symbiont role + true + + + + true + + @@ -606,9 +687,15 @@ Classes for population already exist in IDO ('organism population', I + - A collection of organisms that has as parts every organism of given species and no organisms of any other species. + A collection of organisms that has as members every organism of given species and no organisms of any other species. + A collection of organisms that has as parts every organism of a species and no organisms of any other species. At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + + + + taxonomic group This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. species as a collection of organisms @@ -625,21 +712,16 @@ Classes for population already exist in IDO ('organism population', I - - - - - - 1 - - - - 2 + + + 1 + + @@ -708,7 +790,7 @@ Classes for population already exist in IDO ('organism population', I If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. - A quality of a community that reflects how close in abundance all species in a community are. + A quality of an ecological community that reflects how close in abundance all species in a community are. adapted from http://en.wikipedia.org/wiki/Species_evenness community species evenness @@ -742,7 +824,7 @@ Classes for population already exist in IDO ('organism population', I An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. - Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household household @@ -755,7 +837,7 @@ Classes for population already exist in IDO ('organism population', I This is an example population added to demonstrate the modeling pattern for collections of organisms. - red population + obsolete red population true @@ -767,7 +849,7 @@ Classes for population already exist in IDO ('organism population', I An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. - red organism + obsolete red organism true @@ -810,7 +892,7 @@ Classes for population already exist in IDO ('organism population', I Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). - community + obsolete community true @@ -820,6 +902,13 @@ Classes for population already exist in IDO ('organism population', I + + + + 2 + + + A collection of organisms that consists of two or more organisms from at least two species. Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". @@ -918,8 +1007,8 @@ Classes for population already exist in IDO ('organism population', I + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 - A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. GenEpio curators potluck @@ -950,36 +1039,93 @@ Classes for population already exist in IDO ('organism population', I - + - - - - - - - - + + - - 2 - + + - A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. - pair of interacting organisms + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community - + - + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + microbial organism + microbe + + + + + + + - + + + + + + + 2 + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + @@ -990,10 +1136,225 @@ Classes for population already exist in IDO ('organism population', I + + + 2 + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + + + + + + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + number of generations + number of generations of multicellular organism + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + + + + + + + + + + + + + + + + + + + + + + An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels. + + increased density of population + overcrowded population + + + + + + + + + + + + + + + + + + + + + A quality of a human population such that the density humans in an area is increased beyond sustainable levels. + + overcrowded human population + + + + + + + + + + A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations. + + + This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. + taxon as collection of organisms + + + + + + + + + + + An organism or virus or viroid that is a microbe and a parasite. + + microbial parasite + + + + + + + + + + + + + + + + + A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations. + + VEuPathDB + parasite isolate population + + + + + + + + + + A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi). + + + Shannon entropy + Shannon's diversity index + Shannon-Wiener index + Shannon diversity index + + + + + + + + + + A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi). + + + Simpson index + Simpson diversity index + + + + + + + + + + A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi). + + + inverse Simpson diversity index + + + + + + + + + + + + 2 + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + 1 + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. pair of interacting organisms of the same species @@ -1070,7 +1431,7 @@ Classes for population already exist in IDO ('organism population', I - + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 @@ -1083,6 +1444,12 @@ Classes for population already exist in IDO ('organism population', I + + + + + + @@ -1105,19 +1472,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 https://cmecscatalog.org/cmecs/classification/unit/577.html mangrove community tidal shrubland community - tidal mangrove shrubland community + obsolete tidal mangrove shrubland community + true @@ -1125,10 +1488,12 @@ Classes for population already exist in IDO ('organism population', I - + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO - invisible to unaided eye + obsolete invisible to unaided eye + true @@ -1136,15 +1501,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + + microbial organism - microbe + obsolete microbe + true @@ -1152,24 +1513,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 - collection of microbial organisms + obsolete collection of microbial organisms + true @@ -1177,11 +1526,12 @@ Classes for population already exist in IDO ('organism population', I - - + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 - multi-species collection of microbes + obsolete multi-species collection of microbes + true @@ -1189,34 +1539,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - 1 - - - - - - - 2 - - - - - + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 - single species collection of microbes + obsolete single species collection of microbes + true @@ -1224,18 +1552,28 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 microbiota - microbial population + obsolete microbial population + true + + + + + + + https://orcid.org/0000-0001-8815-0078 + diff --git a/pco-full.obo b/pco-full.obo index 84df48c..08e5f17 100644 --- a/pco-full.obo +++ b/pco-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-02-13/pco-full.owl +data-version: pco/releases/2020-08-26/pco-full.owl remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco/pco-full property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -8,31 +8,35 @@ property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string -property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string +property_value: http://purl.org/dc/elements/1.1/description "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Population and Community Ontology" xsd:string +property_value: http://purl.org/dc/terms/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string +property_value: editor_note "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: editor_note "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000112 "Julius Caesar" xsd:string property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000002 name: continuant +def: "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." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent +relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string -property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: editor_note "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} @@ -46,13 +50,15 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000003 name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity +relationship: part_of BFO:0000003 ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string -property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} -property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: editor_note "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: editor_note "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: editor_note "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} @@ -63,10 +69,12 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string @@ -86,13 +94,27 @@ property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000005 +name: obsolete dependent continuant +def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true + +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity + [Term] id: BFO:0000015 name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string +property_value: editor_note "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string property_value: IAO:0000112 "a process of meiosis" xsd:string property_value: IAO:0000112 "a process of sleeping" xsd:string @@ -100,14 +122,21 @@ property_value: IAO:0000112 "the course of a disease" xsd:string property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + [Term] id: BFO:0000017 name: realizable entity +def: "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_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality property_value: BFO:0000179 "realizable" xsd:string property_value: BFO:0000180 "RealizableEntity" xsd:string property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string @@ -115,20 +144,29 @@ property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:str property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant + [Term] id: BFO:0000020 name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: part_of BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string @@ -140,16 +178,17 @@ property_value: IAO:0000112 "the pink color of a medium rare piece of grilled fi property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role +def: "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." [] is_a: BFO:0000017 ! realizable entity property_value: BFO:0000179 "role" xsd:string property_value: BFO:0000180 "Role" xsd:string +property_value: editor_note "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string property_value: IAO:0000112 "the priest role" xsd:string property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string @@ -157,7 +196,6 @@ property_value: IAO:0000112 "the role of a building in serving as a military tar property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl @@ -168,6 +206,9 @@ name: object aggregate is_a: BFO:0000040 ! material entity property_value: BFO:0000179 "object-aggregate" xsd:string property_value: BFO:0000180 "ObjectAggregate" xsd:string +property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: editor_note "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string property_value: IAO:0000112 "a symphony orchestra" xsd:string @@ -181,9 +222,6 @@ property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:stri property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} -property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} @@ -217,6 +255,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant property_value: BFO:0000179 "gdc" xsd:string @@ -227,13 +266,22 @@ property_value: IAO:0000112 "the sequence of this protein molecule; the sequence property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + [Term] id: BFO:0000040 name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "material" xsd:string property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: editor_note "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: editor_note "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: editor_note "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: IAO:0000112 "a flame" xsd:string property_value: IAO:0000112 "a forest fire" xsd:string property_value: IAO:0000112 "a human being" xsd:string @@ -246,9 +294,6 @@ property_value: IAO:0000112 "an aggregate of human beings." xsd:string property_value: IAO:0000112 "an energy wave" xsd:string property_value: IAO:0000112 "an epidemic" xsd:string property_value: IAO:0000112 "the undetached arm of a human being" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} @@ -263,9 +308,20 @@ name: immaterial entity is_a: BFO:0000004 ! independent continuant property_value: BFO:0000179 "immaterial" xsd:string property_value: BFO:0000180 "ImmaterialEntity" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string +property_value: editor_note "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: CARO:0000012 +name: multicellular organism +def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] +comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. +comment: MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. +is_a: CARO:0010004 ! organism +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "multicellular organism" xsd:string + [Term] id: CARO:0001010 name: organism or virus or viroid @@ -279,61 +335,34 @@ property_value: IAO:0000589 "organism or virus" xsd:string id: CARO:0010004 name: organism def: "An individual member of a clade." [] -comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. is_a: CARO:0001010 ! organism or virus or viroid property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string property_value: IAO:0000589 "organism" xsd:string [Term] -id: DbXref -is_a: IAO:0000102 ! data about an ontology part - -[Term] -id: Definition -is_a: IAO:0000102 ! data about an ontology part - -[Term] -id: ENVO:00000070 -name: construction -def: "A feature that has been constructed by deliberate human effort." [MA:ma] -synonym: "constructed feature" EXACT [] -is_a: ENVO:01000813 ! astronomical body part -property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string - -[Term] -id: ENVO:00002297 -name: environmental feature -namespace: ENVO -def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] -comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. -is_a: BFO:0000040 ! material entity +id: ECOCORE:00000045 +name: symbiotroph +def: "heterotroph that acquires nutrition from a symbiont" [] +is_a: CARO:0001010 ! organism or virus or viroid +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string [Term] -id: ENVO:01000254 -name: environmental system -def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] -comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. -synonym: "environment" EXACT [] -xref: EcoLexicon:environment -is_a: BFO:0000040 ! material entity -creation_date: 2013-09-23T16:04:08Z +id: ECOCORE:00000146 +name: parasite +def: "A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host" [] +xref: https://www.wikidata.org/entity/Q10253316 +is_a: ECOCORE:00000045 ! symbiotroph +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string [Term] id: ENVO:01000744 name: human dwelling def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] -is_a: ENVO:00000070 ! construction -property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string -property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string - -[Term] -id: ENVO:01000813 -name: astronomical body part -def: "A material part of an astronomical body." [] -subset: envoAstro -subset: envoPolar -is_a: ENVO:00002297 ! environmental feature +is_a: BFO:0000040 ! material entity +property_value: editor_note "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: editor_note "Subclasses will be added by inference." xsd:string [Term] id: ENVO:01001369 @@ -344,14 +373,29 @@ comment: This class aligns to the Coastal and Marine Ecological Classification S subset: envoCmecs subset: envoMarine xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ENVO:01000254 ! environmental system +is_a: BFO:0000040 ! material entity created_by: http://orcid.org/0000-0002-4366-3088 +[Term] +id: GO:0003674 +name: molecular_function +is_a: BFO:0000015 ! process +property_value: IAO:0000589 "molecular process" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0003824 +name: catalytic activity +is_a: GO:0003674 ! molecular_function +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0007610 name: behavior namespace: biological_process +alt_id: GO:0023032 alt_id: GO:0044708 +alt_id: GO:0044709 def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). subset: gocheck_do_not_manually_annotate @@ -364,7 +408,7 @@ synonym: "single-organism behavior" RELATED [] xref: Wikipedia:Behavior is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-20T14:06:08Z [Term] @@ -375,7 +419,7 @@ alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] -comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl @@ -390,10 +434,29 @@ synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-19T15:05:24Z +[Term] +id: GO:0016301 +name: kinase activity +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016740 +name: transferase activity +is_a: GO:0003824 ! catalytic activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +is_a: GO:0016740 ! transferase activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0035176 name: social behavior @@ -403,8 +466,8 @@ comment: Behavior such as predation which involves members of different species synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior +is_a: GO:0007610 ! behavior is_a: GO:0051703 ! intraspecies interaction between organisms -is_a: GO:0051705 ! multi-organism behavior property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -417,8 +480,9 @@ subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 @@ -427,7 +491,7 @@ namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] subset: goslim_pir synonym: "intraspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -441,46 +505,42 @@ subset: goslim_pir synonym: "interaction between organisms" EXACT [] synonym: "physiological interaction between organisms" EXACT [] synonym: "physiological interaction with other organism" EXACT [] -is_a: BFO:0000015 ! process is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -[Term] -id: GO:0051705 -name: multi-organism behavior -namespace: biological_process -alt_id: GO:0023032 -alt_id: GO:0044709 -def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] -subset: goslim_pir -synonym: "behavioral interaction between organisms" EXACT [] -synonym: "behavioral interaction with other organism" EXACT [] -synonym: "behavioral signaling" NARROW [] -synonym: "behavioral signalling" NARROW [GOC:mah] -synonym: "behavioural interaction between organisms" EXACT [] -synonym: "behavioural interaction with other organism" EXACT [] -is_a: GO:0007610 ! behavior -is_a: GO:0051704 ! multi-organism process -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - [Term] id: IAO:0000027 name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity +property_value: editor_note "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string +property_value: editor_note "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string +property_value: editor_note "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: editor_note "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: editor_note "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: IAO:0000030 name: information content entity is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000111 "information content entity" xsd:string [Term] id: IAO:0000078 name: curation status specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part +property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000111 "curation status specification" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 GROUP:OBI: xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string @@ -488,18 +548,33 @@ property_value: IAO:0000119 "OBI_0000266" xsd:string [Term] id: IAO:0000102 name: data about an ontology part -def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "data about an ontology part" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string +[Term] +id: IAO:0000109 +name: measurement datum +def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] +is_a: IAO:0000027 ! data item +property_value: editor_note "2/2/2009 is_specified_output of some assay?" xsd:string +property_value: IAO:0000111 "measurement datum" xsd:string +property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000119 group:OBI xsd:string +property_value: IAO:0000119 "OBI_0000305" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + [Term] id: IAO:0000225 name: obsolescence reason specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part +property_value: editor_note "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000111 "obsolescence reason specification" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string @@ -508,6 +583,7 @@ id: IAO:0000409 name: denotator type def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "denotator type" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string @@ -516,189 +592,168 @@ property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string id: IAO:8000000 name: ontology module is_a: IAO:0000102 ! data about an ontology part -property_value: IAO:0000116 "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." xsd:string +property_value: editor_note "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000111 "ontology module" xsd:string property_value: IAO:0000118 "ontology file" xsd:string property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string -created_by: cjm -creation_date: 2018-05-20T20:55:03Z [Term] id: IAO:8000001 name: base ontology module def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "base ontology module" xsd:string property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 -created_by: cjm -creation_date: 2018-05-20T20:55:30Z [Term] id: IAO:8000002 name: editors ontology module def: "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." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "editors ontology module" xsd:string property_value: IAO:0000118 "source ontology module" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:55:47Z [Term] id: IAO:8000003 name: main release ontology module def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] is_a: IAO:8000000 ! ontology module -property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:56:13Z +property_value: editor_note "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +property_value: IAO:0000111 "main release ontology module" xsd:string [Term] id: IAO:8000004 name: bridge ontology module def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "bridge ontology module" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies -created_by: cjm -creation_date: 2018-05-20T20:56:23Z [Term] id: IAO:8000005 name: import ontology module def: "A subset ontology module that is intended to be imported from another ontology." [] is_a: IAO:8000006 ! subset ontology module -property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: editor_note "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000111 "import ontology module" xsd:string property_value: IAO:0000118 "import file" xsd:string property_value: seeAlso http://robot.obolibrary.org/extract -created_by: cjm -creation_date: 2018-05-20T20:56:47Z [Term] id: IAO:8000006 name: subset ontology module def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "subset ontology module" xsd:string property_value: IAO:0000118 "ontology slim" xsd:string property_value: IAO:0000118 "subset ontology" xsd:string property_value: seeAlso http://robot.obolibrary.org/filter property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide -created_by: cjm -creation_date: 2018-05-20T20:58:11Z [Term] id: IAO:8000007 name: curation subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-20T20:58:38Z +property_value: IAO:0000111 "curation subset ontology module" xsd:string [Term] id: IAO:8000008 name: analysis subset ontology module def: "An ontology module that is intended for usage in analysis or discovery applications." [] is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-20T20:58:49Z +property_value: IAO:0000111 "analysis ontology module" xsd:string [Term] id: IAO:8000009 name: single layer subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "single layer ontology module" xsd:string property_value: IAO:0000118 "ribbon subset" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:59:19Z [Term] id: IAO:8000010 name: exclusion subset ontology module def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "exclusion subset ontology module" xsd:string property_value: IAO:0000118 "antislim" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:59:57Z [Term] id: IAO:8000011 name: external import ontology module def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000111 "external import ontology module" xsd:string property_value: IAO:0000118 "external import" xsd:string -created_by: cjm -creation_date: 2018-05-20T21:00:14Z [Term] id: IAO:8000012 name: species subset ontology module def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "species subset ontology module" xsd:string property_value: IAO:0000118 "taxon subset" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -created_by: cjm -creation_date: 2018-05-20T21:14:16Z [Term] id: IAO:8000013 name: reasoned ontology module def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "reasoned ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/reason -created_by: cjm -creation_date: 2018-05-20T21:20:33Z [Term] id: IAO:8000014 name: generated ontology module def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] is_a: IAO:8000000 ! ontology module -property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string -created_by: cjm -creation_date: 2018-05-20T21:21:12Z +property_value: editor_note "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +property_value: IAO:0000111 "generated ontology module" xsd:string [Term] id: IAO:8000015 name: template generated ontology module def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] is_a: IAO:8000014 ! generated ontology module +property_value: IAO:0000111 "template generated ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/template property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ -created_by: cjm -creation_date: 2018-05-20T21:21:21Z [Term] id: IAO:8000016 name: taxonomic bridge ontology module is_a: IAO:8000004 ! bridge ontology module -created_by: cjm -creation_date: 2018-05-20T21:28:15Z +property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string [Term] id: IAO:8000017 name: ontology module subsetted by expressivity is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-22T04:15:54Z +property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string [Term] id: IAO:8000018 name: obo basic subset ontology module def: "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "obo basic subset ontology module" xsd:string property_value: seeAlso "6.2" -created_by: cjm -creation_date: 2018-05-22T04:16:10Z [Term] id: IAO:8000019 name: ontology module subsetted by OWL profile is_a: IAO:8000017 ! ontology module subsetted by expressivity -created_by: cjm -creation_date: 2018-05-22T04:16:28Z +property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string [Term] id: IAO:8000020 name: EL++ ontology module is_a: IAO:8000019 ! ontology module subsetted by OWL profile -created_by: cjm -creation_date: 2018-05-22T04:16:48Z +property_value: IAO:0000111 "EL++ ontology module" xsd:string [Term] id: NCBITaxon:10239 @@ -716,7 +771,7 @@ id: NCBITaxon:117570 name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 -is_a: NCBITaxon:7776 ! Gnathostomata +is_a: NCBITaxon:7776 ! Gnathostomata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -729,22 +784,12 @@ xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl -[Term] -id: NCBITaxon:12884 -name: Viroids -namespace: ncbi_taxonomy -synonym: "Viroid" RELATED synonym [] -synonym: "viroids" RELATED blast_name [] -xref: GC_ID:1 -property_value: has_rank NCBITaxon:superkingdom -property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl - [Term] id: NCBITaxon:131221 name: Streptophytina namespace: ncbi_taxonomy synonym: "Charophyta/Embryophyta group" RELATED synonym [] -synonym: "charophyte/embryophyte group" RELATED synonym [] +synonym: "charophyte/embryophyte group" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:35493 ! Streptophyta property_value: has_rank NCBITaxon:subphylum @@ -817,7 +862,9 @@ xref: PMID:11760965 xref: PMID:12054223 xref: PMID:2112744 xref: PMID:270744 +xref: PMID:7520741 xref: PMID:8123559 +xref: PMID:8186100 xref: PMID:8590690 xref: PMID:9103655 xref: PMID:9336922 @@ -892,6 +939,7 @@ synonym: "eukaryotes" EXACT common_name [] synonym: "eukaryotes" RELATED blast_name [] xref: GC_ID:1 xref: PMID:23020233 +xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms property_value: has_rank NCBITaxon:superkingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -977,7 +1025,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32525 -name: Theria +name: Theria namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 @@ -989,11 +1037,14 @@ id: NCBITaxon:33090 name: Viridiplantae namespace: ncbi_taxonomy synonym: "Chlorobionta" RELATED synonym [] -synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] -synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name [] +synonym: "chlorophyte/embryophyte group" EXACT equivalent_name [] +synonym: "Chloroplastida" RELATED synonym [] synonym: "green plants" EXACT common_name [] synonym: "green plants" RELATED blast_name [] xref: GC_ID:1 +xref: PMID:16248873 +xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:kingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -1040,15 +1091,17 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:3398 -name: Magnoliophyta +name: Magnoliopsida namespace: ncbi_taxonomy synonym: "Angiospermae" RELATED synonym [] synonym: "angiosperms" EXACT common_name [] synonym: "flowering plants" EXACT genbank_common_name [] synonym: "flowering plants" RELATED blast_name [] +synonym: "Magnoliophyta" RELATED synonym [] xref: GC_ID:1 xref: PMID:25249442 is_a: NCBITaxon:58024 ! Spermatophyta +property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -1080,6 +1133,20 @@ is_a: NCBITaxon:32524 ! Amniota property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl +[Term] +id: NCBITaxon:4751 +name: Fungi +namespace: ncbi_taxonomy +synonym: "fungi" RELATED in_part [] +synonym: "fungi" RELATED blast_name [] +synonym: "Mycota" RELATED genbank_synonym [] +xref: GC_ID:1 +xref: PMID:11062127 +xref: PMID:12684019 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + [Term] id: NCBITaxon:58023 name: Tracheophyta @@ -1121,30 +1188,30 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7742 -name: Vertebrata +name: Vertebrata namespace: ncbi_taxonomy synonym: "Vertebrata" EXACT scientific_name [] synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:89593 ! Craniata +is_a: NCBITaxon:89593 ! Craniata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7776 -name: Gnathostomata +name: Gnathostomata namespace: ncbi_taxonomy synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 -is_a: NCBITaxon:7742 ! Vertebrata +is_a: NCBITaxon:7742 ! Vertebrata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:78536 name: Euphyllophyta namespace: ncbi_taxonomy -synonym: "euphyllophytes" RELATED synonym [] +synonym: "euphyllophytes" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:58023 ! Tracheophyta property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -1160,7 +1227,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:89593 -name: Craniata +name: Craniata namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 @@ -1178,7 +1245,7 @@ synonym: "Placentalia" RELATED synonym [] synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:32525 ! Theria +is_a: NCBITaxon:32525 ! Theria property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -1227,33 +1294,62 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl id: NCBITaxon:9606 name: Homo sapiens namespace: ncbi_taxonomy -synonym: "Home sapiens" RELATED misspelling [] -synonym: "Homo sampiens" RELATED misspelling [] -synonym: "Homo sapeins" RELATED misspelling [] -synonym: "Homo sapian" RELATED misspelling [] -synonym: "Homo sapians" RELATED misspelling [] -synonym: "Homo sapien" RELATED misspelling [] -synonym: "Homo sapience" RELATED misspelling [] -synonym: "Homo sapiense" RELATED misspelling [] -synonym: "Homo sapients" RELATED misspelling [] -synonym: "Homo sapines" RELATED misspelling [] -synonym: "Homo spaiens" RELATED misspelling [] -synonym: "Homo spiens" RELATED misspelling [] synonym: "human" EXACT genbank_common_name [] -synonym: "Humo sapiens" RELATED misspelling [] synonym: "man" EXACT common_name [] xref: GC_ID:1 is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl +[Term] +id: ObsoleteClass +name: Obsolete Class + [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -synonym: "trait" EXACT [] +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000068 +name: qualitative +namespace: quality +comment: TODO: define this or obsolete it and move children somewhere else. +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000069 +name: deviation (from_normal) +namespace: quality +def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000070 +name: amount +namespace: quality +alt_id: PATO:0000053 +alt_id: PATO:0000071 +alt_id: PATO:0001169 +alt_id: PATO:0001226 +def: "The number of entities of this type that are part of the whole organism." [PATOC:GVG] +comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. +subset: attribute_slim +synonym: "count in organism" RELATED [] +synonym: "number" RELATED [] +synonym: "presence" RELATED [] +synonym: "presence or absence in organism" EXACT [] +synonym: "quantitative" EXACT [] +is_a: PATO:0000068 ! qualitative +relationship: reciprocal_of PATO:0001555 ! has number of property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -1266,6 +1362,115 @@ subset: scalar_slim is_a: PATO:0002062 ! physical quality of a process property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0000461 +name: normal +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average." [PATOC:GVG] +subset: abnormal_slim +subset: mpath_slim +subset: value_slim +synonym: "average" RELATED [] +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000460 + +[Term] +id: PATO:0000467 +name: present +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's existence." [PATOC:GVG] +subset: absent_slim +subset: value_slim +synonym: "present in organism" RELATED [] +is_a: PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000462 + +[Term] +id: PATO:0000470 +name: increased amount +namespace: quality +alt_id: PATO:0000420 +alt_id: PATO:0000650 +def: "An amount which is relatively high." [PATOC:GVG] +subset: value_slim +synonym: "accessory" RELATED [] +synonym: "increased" RELATED [] +synonym: "increased number" EXACT [] +synonym: "present in greater numbers in organism" EXACT [] +synonym: "supernumerary" EXACT [] +is_a: PATO:0000467 ! present +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0000070 ! amount +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001997 + +[Term] +id: PATO:0000911 +name: decreased rate +namespace: quality +def: "A rate which is relatively low." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "slow rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002302 ! decreased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000912 + +[Term] +id: PATO:0000912 +name: increased rate +namespace: quality +def: "A rate which is relatively high." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "fast rate" EXACT [] +synonym: "high rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002304 ! increased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000911 + +[Term] +id: PATO:0001018 +name: physical quality +namespace: quality +alt_id: PATO:0002079 +def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] +subset: attribute_slim +synonym: "relational physical quality" EXACT [] +xref: Wikipedia:Physical_property +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001019 +name: mass density +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size." [WordNet:WordNet] +subset: attribute_slim +subset: scalar_slim +synonym: "density" RELATED [] +is_a: PATO:0001018 ! physical quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001164 +name: dense +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density." [PATOC:GVG] +subset: mpath_slim +subset: value_slim +is_a: PATO:0001019 ! mass density +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + [Term] id: PATO:0001236 name: process quality @@ -1279,6 +1484,7 @@ synonym: "quality of occurrent" EXACT [] synonym: "quality of process" EXACT [] synonym: "relational quality of occurrent" EXACT [] is_a: PATO:0000001 ! quality +disjoint_from: PATO:0001241 ! physical object quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -1321,6 +1527,72 @@ subset: scalar_slim is_a: PATO:0002003 ! population quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0001555 +name: has number of +namespace: quality +def: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts." [PATOC:CJM] +subset: attribute_slim +subset: relational_slim +synonym: "cardinality" RELATED [] +synonym: "extra or missing physical or functional parts" EXACT [] +synonym: "has or lacks parts of type" EXACT [] +synonym: "mereological quality" EXACT [] +synonym: "number" RELATED [] +synonym: "number of" EXACT [] +xref: OBO_REL:has_part +is_a: PATO:0001241 ! physical object quality +relationship: reciprocal_of PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001788 +name: increased mass density +namespace: quality +def: "A density which is higher relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "high density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002305 ! increased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001790 + +[Term] +id: PATO:0001790 +name: decreased mass density +namespace: quality +def: "A density which is lower relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "low density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002303 ! decreased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001788 + +[Term] +id: PATO:0001997 +name: decreased amount +namespace: quality +alt_id: PATO:0000419 +alt_id: PATO:0000468 +def: "An amount which is relatively low." [PATOC:GVG] +subset: value_slim +synonym: "decreased" RELATED [] +synonym: "decreased number" EXACT [] +synonym: "present in fewer numbers in organism" EXACT [] +synonym: "reduced" RELATED [] +synonym: "subnumerary" RELATED [] +is_a: PATO:0000467 ! present +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0000070 ! amount +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000470 + [Term] id: PATO:0002003 name: population quality @@ -1340,6 +1612,90 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl created_by: george creation_date: 2009-06-05T09:16:46Z +[Term] +id: PATO:0002300 +name: increased quality +namespace: quality +def: "A quality that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002301 +created_by: George Gkoutos +creation_date: 2011-06-16T06:39:43Z + +[Term] +id: PATO:0002301 +name: decreased quality +namespace: quality +def: "A quality that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002300 +created_by: George Gkoutos +creation_date: 2011-06-16T06:40:15Z + +[Term] +id: PATO:0002302 +name: decreased process quality +namespace: quality +def: "A quality of a process that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002304 +created_by: George Gkoutos +creation_date: 2011-06-16T06:50:59Z + +[Term] +id: PATO:0002303 +name: decreased object quality +namespace: quality +def: "A quality of an object that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002305 +created_by: George Gkoutos +creation_date: 2011-06-16T06:51:54Z + +[Term] +id: PATO:0002304 +name: increased process quality +namespace: quality +def: "A quality of a process that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002302 +created_by: George Gkoutos +creation_date: 2011-06-16T06:53:08Z + +[Term] +id: PATO:0002305 +name: increased object quality +namespace: quality +def: "A quality of an object that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002303 +created_by: George Gkoutos +creation_date: 2011-06-16T06:54:01Z + [Term] id: PCO:0000000 name: collection of organisms @@ -1347,9 +1703,10 @@ def: "A material entity that consists of two or more organisms, viruses, or viro comment: May be of the same or different species. is_a: BFO:0000027 ! object aggregate is_a: PCO:0000031 ! organismal entity -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "group of organism" xsd:string @@ -1371,20 +1728,22 @@ id: PCO:0000002 name: ecological community def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +is_a: PCO:0000029 ! multi-species collection of organisms property_value: IAO:0000118 "multispecies community" xsd:string property_value: IAO:0000119 ISBN:0865423504 xsd:string [Term] id: PCO:0000003 name: quality of a population -def: "A quality that inheres in a biological population." [] +def: "A quality that inheres in a population of organisms." [] comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. is_a: PATO:0002003 ! population quality intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000001 ! population of organisms -relationship: RO:0000052 PCO:0000001 ! population of organisms +intersection_of: RO:0000052 PCO:0000001 ! inheres in population of organisms +relationship: RO:0000052 PCO:0000001 ! inheres in population of organisms +property_value: editor_note "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string +property_value: editor_note "This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string [Term] id: PCO:0000004 @@ -1393,45 +1752,47 @@ def: "A quality that inheres in a community." [] comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. is_a: PATO:0002003 ! population quality intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000002 ! ecological community -relationship: RO:0000052 PCO:0000002 ! ecological community +intersection_of: RO:0000052 PCO:0000002 ! inheres in ecological community +relationship: RO:0000052 PCO:0000002 ! inheres in ecological community +property_value: editor_note "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string [Term] id: PCO:0000005 name: population process -def: "A process that has as primary participant a population. " [] -comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +def: "A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction." [] +comment: The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. is_a: BFO:0000015 ! process -relationship: RO:0000057 PCO:0000001 ! population of organisms +relationship: RO:0000057 PCO:0000001 ! has participant population of organisms property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000006 name: population birth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of birth of a population of organisms." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000007 name: population death rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of death of a population of organsisms." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000008 name: population growth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of growth of a population." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string [Term] id: PCO:0000009 name: obsolete carrying capacity def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] -is_a: ObsoleteClass -property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string property_value: IAO:0000119 ISBN:0878932739 xsd:string property_value: IAO:0000231 IAO:0000423 is_obsolete: true @@ -1441,8 +1802,8 @@ id: PCO:0000010 name: community species richness def: "The number of different species represented in an ecological community." [] is_a: PCO:0000004 ! quality of an ecological community +property_value: editor_note "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string [Term] @@ -1468,36 +1829,49 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 -name: predator role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete predator role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 -name: prey role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete prey role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 -name: symbiont role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete symbiont role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000017 name: species as a collection of organisms -def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as members every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as parts every organism of a species and no organisms of any other species." [] comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +synonym: "taxonomic group" EXACT [] +xref: GENO:0000113 +xref: Species +xref: TAXRANK:0000006 is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000059 ! taxon as collection of organisms +property_value: editor_note "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string [Term] id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms +intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid +relationship: PCO:0000055 PCO:0000017 ! has member of species as a collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -1507,8 +1881,8 @@ name: community species diversity def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. is_a: PCO:0000004 ! quality of an ecological community +property_value: editor_note "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string [Term] @@ -1517,8 +1891,8 @@ name: family def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. is_a: PCO:0000018 ! single-species collection of organisms +property_value: editor_note "Needs axioms for family relationships." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string [Term] @@ -1538,7 +1912,7 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000023 name: community species evenness -def: "A quality of a community that reflects how close in abundance all species in a community are." [] +def: "A quality of an ecological community that reflects how close in abundance all species in a community are." [] is_a: PCO:0000004 ! quality of an ecological community property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -1548,26 +1922,26 @@ property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_e id: PCO:0000024 name: household def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] -is_a: PCO:0000031 ! organismal entity -relationship: RO:0002321 ENVO:01000744 ! human dwelling -relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! Homo sapiens +is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002321 ENVO:01000744 ! ecologically related to human dwelling +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! has member Homo sapiens property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string [Term] id: PCO:0000025 -name: red population +name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000002 is_obsolete: true [Term] id: PCO:0000026 -name: red organism +name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1577,20 +1951,20 @@ name: collection of humans def: "A collection of organisms of the same species that has as members only humans." [] is_a: PCO:0000018 ! single-species collection of organisms intersection_of: PCO:0000018 ! single-species collection of organisms -intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! Homo sapiens -intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! Homo sapiens -relationship: RO:0002351 NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! has member Homo sapiens +relationship: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "human community" xsd:string property_value: IAO:0000118 "human population" xsd:string [Term] id: PCO:0000028 -name: community +name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). -is_a: ObsoleteClass -property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -1599,8 +1973,9 @@ id: PCO:0000029 name: multi-species collection of organisms def: "A collection of organisms that consists of two or more organisms from at least two species." [] is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 PCO:0000001 {minCardinality="2"} ! has member population of organisms +property_value: editor_note "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string [Term] id: PCO:0000030 @@ -1608,10 +1983,10 @@ name: agricultural household name: obsolete organismal entity def: "A household in which the majority of the income of its members is derived from agricultural activities." [] def: "A material entity that is one or more organisms, viruses or viroids." [] -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class is_a: PCO:0000024 ! household +property_value: editor_note "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000231 "wrong IRI form" xsd:string is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 @@ -1638,8 +2013,8 @@ id: PCO:0000033 name: human social gathering activity def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] is_a: GO:0035176 ! social behavior -relationship: RO:0000057 PCO:0000027 ! collection of humans -property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +relationship: RO:0000057 PCO:0000027 ! has participant collection of humans +property_value: editor_note "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] @@ -1647,7 +2022,7 @@ id: PCO:0000034 name: human community event def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1655,15 +2030,15 @@ id: PCO:0000035 name: party def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000037 name: potluck +def: "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string -property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1671,7 +2046,7 @@ id: PCO:0000038 name: wedding def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1679,90 +2054,244 @@ id: PCO:0000039 name: baby shower def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000040 +name: obsolete tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000041 +name: obsolete invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: ObsoleteClass ! Obsolete Class +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000042 +name: obsolete microbe +synonym: "microbial organism" EXACT [] +is_a: ObsoleteClass ! Obsolete Class +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000043 +name: obsolete collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000044 +name: obsolete multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000045 +name: obsolete single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000046 +name: obsolete microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000047 name: tidal mangrove shrubland community def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html is_a: PCO:0000002 ! ecological community -relationship: BFO:0000050 ENVO:01001369 ! tidal mangrove shrubland +relationship: part_of ENVO:01001369 ! tidal mangrove shrubland property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] -id: PCO:0000041 +id: PCO:0000048 name: invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO is_a: PATO:0001241 ! physical object quality [Term] -id: PCO:0000042 +id: PCO:0000049 name: microbe synonym: "microbial organism" EXACT [] is_a: CARO:0001010 ! organism or virus or viroid -relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye [Term] -id: PCO:0000043 +id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe -intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe -relationship: RO:0002351 PCO:0000042 ! microbe +intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! has member microbe +intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! has member microbe +relationship: RO:0002351 PCO:0000049 ! has member microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000044 +id: PCO:0000051 name: multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] is_a: PCO:0000029 ! multi-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000045 +id: PCO:0000052 name: single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] -is_a: PCO:0000018 ! single-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms +is_a: PCO:0000050 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000046 +id: PCO:0000053 name: microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] is_a: PCO:0000001 ! population of organisms -is_a: PCO:0000045 ! single species collection of microbes -relationship: RO:0002351 PCO:0000042 ! microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +[Term] +id: PCO:0000054 +name: number of generations of multicellular organism +def: "A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism." [] {comment="NCIT:C88214", comment="EFO:0000507"} +synonym: "number of generations" BROAD [] +is_a: STATO:0000047 ! count +relationship: IAO:0000136 CARO:0000012 ! is about multicellular organism +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 + +[Term] +id: PCO:0000057 +name: overcrowded population +def: "An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels." [] +synonym: "increased density of population" EXACT [] +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000058 +name: overcrowded human population +def: "A quality of a human population such that the density humans in an area is increased beyond sustainable levels." [] +is_a: PCO:0000057 ! overcrowded population +intersection_of: PCO:0000057 ! overcrowded population +intersection_of: RO:0000052 PCO:0000027 ! inheres in collection of humans +relationship: RO:0000052 PCO:0000027 ! inheres in collection of humans +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000059 +name: taxon as collection of organisms +def: "A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations." [] +comment: This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. +xref: data:1868 +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000060 +name: microbial parasite +def: "An organism or virus or viroid that is a microbe and a parasite." [] +is_a: ECOCORE:00000146 ! parasite +is_a: PCO:0000049 ! microbe +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000061 +name: parasite isolate population +def: "A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations." [] +is_a: PCO:0000050 ! collection of microbial organisms +is_a: PCO:0000053 ! microbial population +relationship: RO:0002351 PCO:0000060 ! has member microbial parasite +property_value: IAO:0000112 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811772/ +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "VEuPathDB" xsd:string + +[Term] +id: PCO:0000062 +name: Shannon diversity index +def: "A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi)." [] +synonym: "Shannon entropy" EXACT [] +synonym: "Shannon's diversity index" EXACT [] +synonym: "Shannon-Wiener index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html +property_value: IAO:0000119 "Shannon_index" + +[Term] +id: PCO:0000063 +name: Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi)." [] +synonym: "Simpson index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Simpson_index" + +[Term] +id: PCO:0000064 +name: inverse Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi)." [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Inverse_Simpson_index" + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: PCO:0000000 ! collection of organisms -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid [Term] id: PCO:0001001 name: pair of interacting organisms of the same species +def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms +relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms [Term] id: PCO:1000000 name: migratory population def: "A population which is participating in a migration process." [] is_a: PCO:0000001 ! population of organisms -relationship: RO:0000056 PCO:1000001 ! population migration +relationship: RO:0000056 PCO:1000001 ! participates in population migration property_value: IAO:0000114 IAO:0000123 [Term] @@ -1780,7 +2309,7 @@ name: human population migration def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration is_a: PCO:1000001 ! population migration -relationship: RO:0000057 PCO:0000027 ! collection of humans +relationship: RO:0000057 PCO:0000027 ! has participant collection of humans property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string @@ -1789,7 +2318,7 @@ id: PCO:1000003 name: human migratory population def: "A migratory population of humans, travelling with the intention of settling in a new area." [] is_a: PCO:0000027 ! collection of humans -relationship: RO:0000056 PCO:1000002 ! human population migration +relationship: RO:0000056 PCO:1000002 ! participates in human population migration property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string @@ -1800,21 +2329,1394 @@ def: "An ecological community which is composed of co-existing populations of mi comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. synonym: "microbiota" BROAD [] is_a: PCO:0000002 ! ecological community -is_a: PCO:0000044 ! multi-species collection of microbes +is_a: PCO:0000051 ! multi-species collection of microbes +property_value: editor_note "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string [Term] -id: Subset -is_a: IAO:0000102 ! data about an ontology part +id: STATO:0000047 +name: count +def: "a count is a data item denoted by an integer and represented the number of instances or occurences of an entity" [] +is_a: IAO:0000109 ! measurement datum +property_value: IAO:0000112 "a count of 4 resulting from counting limbs in humans" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string +property_value: IAO:0000117 "Orlaith Burke" xsd:string +property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string +property_value: IAO:0000119 "STATO" xsd:string +property_value: STATO:0000032 "" xsd:string + +[Typedef] +id: BFO:0000054 +name: realized in +comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realized in" xsd:string +property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string +property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string +property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string +property_value: IAO:0000118 "is realized by" xsd:string +property_value: IAO:0000118 "realized_in" xsd:string +property_value: IAO:0000600 "[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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +inverse_of: BFO:0000055 ! realizes + +[Typedef] +id: BFO:0000055 +name: realizes +comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realizes" xsd:string +property_value: IAO:0000112 "this disease course realizes this disease" xsd:string +property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string +property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string +property_value: IAO:0000600 "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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +domain: BFO:0000015 ! process +range: BFO:0000017 ! realizable entity + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "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." [] +subset: ro-eco +property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "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." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "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" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: part_of BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part_of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[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" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Term] -id: Synonym -is_a: IAO:0000102 ! data about an ontology part +[Typedef] +id: IAO:0000136 +name: is about +def: "A (currently) primitive relation that relates an information artifact to an entity." [] +property_value: editor_note "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string + +[Typedef] +id: PCO:0000055 +name: has member of +domain: PCO:0000000 ! collection of organisms + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: editor_note "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000079 +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 ! function +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000085 ! has function + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000085 +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000034 ! function +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +is_a: RO:0000052 ! inheres in + +[Typedef] +id: RO:0001000 +name: derives from +def: "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" [] +property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "derives_from" xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "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" [] +property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000111 "is location of" xsd:string +property_value: IAO:0000112 "my head is the location of my brain" xsd:string +property_value: IAO:0000112 "this cage is the location of this rat" xsd:string +property_value: IAO:0000118 "location_of" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string +property_value: IAO:0000111 "located in" xsd:string +property_value: IAO:0000112 "my brain is located in my head" xsd:string +property_value: IAO:0000112 "this rat is located in this cage" xsd:string +property_value: IAO:0000118 "located_in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true + +[Typedef] +id: RO:0002000 +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] +property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity + +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "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." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "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." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "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." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "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." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "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." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "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." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "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." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_functional: true +is_a: RO:0002017 ! has component activity +is_a: RO:0002211 ! regulates +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: has_part RO:0002131 +holds_over_chain: part_of part_of +is_a: RO:0002323 ! mereotopologically related to +transitive_over: part_of ! part_of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002180 +name: has component +def: "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." [] +subset: ro-eco +property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: has_part ! has part + +[Typedef] +id: RO:0002211 +name: regulates +def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string +property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002215 +name: capable of +def: "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. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of +expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process +expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002233 +name: has input +def: "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." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "consumes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "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." [] +property_value: IAO:0000112 "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." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "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." [] +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002321 +name: ecologically related to +def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] +subset: ro-eco +property_value: editor_note "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002327 +name: enables +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: has_part ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 part_of +is_a: RO:0000056 ! participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "regulated by (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part_of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +synonym: "affects" RELATED [] +property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "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" [] +property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "involved in or reguates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "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." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "executes activity in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso ECO:0000353 +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: editor_note "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: directly regulates activity of +def: "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0011002 ! regulates activity of + +[Typedef] +id: RO:0002449 +name: directly negatively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly inhibits" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002450 +name: directly positively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly activates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002464 +name: helper property (not for use in curation) +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "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." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} + +[Typedef] +id: RO:0002481 +name: is kinase activity +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002506 +name: causal relation between entities +property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002506 ! causal relation between entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002563 +name: interaction relation helper property +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +is_a: RO:0002464 ! helper property (not for use in curation) + +[Typedef] +id: RO:0002564 +name: molecular interaction relation helper property +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002566 +name: causally influences +def: "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)." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002506 ! causal relation between entities + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "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" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: has_part RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "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." [] +property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 has_part +is_a: RO:0002328 ! functionally related to +created_by: cjm +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "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" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: cjm +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "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" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: cjm +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0011002 +name: regulates activity of +def: "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." [] +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002566 ! causally influences + +[Typedef] +id: decreased_in_magnitude_relative_to +name: decreased_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: different_in_magnitude_relative_to +name: different_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality + +[Typedef] +id: editor_note +name: editor note +namespace: uberon +def: "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." [] +xref: IAO:0000116 +property_value: IAO:0000111 "editor note" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + +[Typedef] +id: has_part +name: has part +name: has_part +namespace: external +namespace: quality +def: "a core relation that holds between a whole and its part" [] +def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] +comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. +xref: BFO:0000051 +property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA 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'." xsd:string +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps -[Term] -id: SynonymType -is_a: IAO:0000102 ! data about an ontology part +[Typedef] +id: increased_in_magnitude_relative_to +name: increased_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: part_of +name: part of +name: part_of +namespace: external +namespace: quality +def: "a core relation that holds between a part and its whole" [] +xref: BFO:0000050 +property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA 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'." xsd:string +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: has_part ! has part + +[Typedef] +id: reciprocal_of +name: reciprocal_of +namespace: quality +def: "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." [PATOC:CJM] +comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl diff --git a/pco-full.owl b/pco-full.owl index c95c12c..b73706e 100644 --- a/pco-full.owl +++ b/pco-full.owl @@ -7,20 +7,26 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:swrl="http://www.w3.org/2003/11/swrl#" + xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" + xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg Ramona Walls - http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. + Population and Community Ontology + http://creativecommons.org/publicdomain/zero/1.0/ The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. @@ -62,12 +68,21 @@ + editor preferred label + editor preferred label + editor preferred term editor preferred term + editor preferred term~editor preferred label 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 label + editor preferred label + editor preferred term editor preferred term + editor preferred term~editor preferred label @@ -76,6 +91,7 @@ example + 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 @@ -106,6 +122,8 @@ PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 + + has curation status has curation status @@ -115,7 +133,10 @@ definition + definition + textual definition + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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 @@ -142,6 +163,7 @@ We also have the outstanding issue of how to aim different definitions to differ definition definition + textual definition @@ -154,6 +176,12 @@ We also have the outstanding issue of how to aim different definitions to differ 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.obfoundry.org/obo/obi> + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + IAO:0000116 + uberon + editor_note + true + editor_note editor note editor note @@ -170,6 +198,8 @@ We also have the outstanding issue of how to aim different definitions to differ 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 term editor @@ -183,6 +213,7 @@ We also have the outstanding issue of how to aim different definitions to differ An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + alternative term @@ -193,11 +224,14 @@ We also have the outstanding issue of how to aim different definitions to differ 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 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 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source definition source @@ -222,6 +256,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg + curator note @@ -230,13 +265,13 @@ We also have the outstanding issue of how to aim different definitions to differ - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + 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. + 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 @@ -245,10 +280,11 @@ We also have the outstanding issue of how to aim different definitions to differ + 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 + 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 The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester @@ -259,10 +295,10 @@ We also have the outstanding issue of how to aim different definitions to differ 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 - 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 + is denotator type @@ -276,6 +312,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from @@ -290,7 +327,8 @@ 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 + Chris Mungall + expand expression to @@ -326,7 +364,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. antisymmetric property part_of antisymmetric property xsd:true - use boolean value xsd:true to indicate that the property is an antisymmetric property + Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property @@ -339,12 +377,13 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. 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 . + 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/> + OBO foundry unique label @@ -353,14 +392,15 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 + 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 digit count @@ -369,12 +409,13 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Datatype: idrange:1 + 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 + 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 range allocated to @@ -383,15 +424,16 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 policy for + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for @@ -399,14 +441,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 + 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 ID prefix @@ -455,23 +498,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] is allocated id range - Add as annotation triples in the granting ontology 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 + Add as annotation triples in the granting ontology is allocated id range + + + + 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 + has ontology root term + + + + - 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 - #40 - VFB - 2018-09-21T16:43:39Z - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + 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 + #40 + VFB + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to @@ -480,6 +534,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + 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 https://github.com/geneontology/go-ontology/issues/15532 @@ -509,10 +564,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] term replaced by - Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by @@ -530,6 +585,94 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + is a defining property chain axiom + + + + + + + + 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. + + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + an alternative term used for STATO statistical ontology and ISA team + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO alternative term + + + + @@ -612,7 +755,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + + @@ -634,12 +779,36 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + @@ -675,6 +844,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + database_cross_reference @@ -700,7 +870,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - has_obo_namespace + has_obo_namespace @@ -739,6 +909,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + shorthand + + + + @@ -749,16 +934,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + - + + label + label @@ -771,6 +958,14 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -811,139 +1030,2218 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + + + + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + + + + + + + + BFO:0000050 + external + quality + part_of + part_of + + part of + part of + part_of + + + http://www.obofoundry.org/ro/#OBO_REL: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) + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + BFO:0000051 + external + quality + has_part + has_part + We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. + + has part + has part + has_part + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + PATOC:CJM + + + + + + + + + + + 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]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + + + 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]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + + + + + + + + + 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 + http://www.obofoundry.org/ro/#OBO_REL: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. + + + precedes + + + + + + + + + + + + + + + + + + + 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 + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs 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 + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + This document is about information artifacts and their representations + + A (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + + + + has member of + - + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + 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 + + bearer of + - + + + + + 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 + + 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 + http://www.obofoundry.org/ro/#OBO_REL:has_participant + + 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. + is concretized as + + + + + + + + + + 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. + concretizes + + + + + + + + + + + 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 + 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 + 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 + 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 + - + - + + + disposition of + - + - + + + 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 + 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 + derives into + - + - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - + + + + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + location_of + + location of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + located in + - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - + - - - - continuant - Continuant - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + 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 + + 2D boundary of + + + + + + + + + + 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 + + has 2D boundary + + + + + + + + + + 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. + dos + 2017-05-24T09:30:46Z + + has regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + + has negative regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + + has component activity + + + + + + + + + + + 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. + dos + 2017-05-24T09:49:21Z + + has component process + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:38Z + + directly negatively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:47Z + + directly positively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + + 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. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + + has 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. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + + immediately preceded by + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + + immediately precedes + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + overlaps + + + + + + + + + true + + + + + + + + + + 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. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + + has component + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + + positively regulates + + + + + + + + + + + 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. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + + capable of + + + + + + + + + + + + + + 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. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + + capable of part of + + + + + + + + + + true + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + + temporally related to + + + + + + + + + + + + + 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. + Chris Mungall + consumes + + + has input + + + + + + + + + + + + + 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. + + acts upstream of + + + + + + + + + + + + + + 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 + + acts upstream of or within + + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + causally upstream of, negative effect + + + + + + + + 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 + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + + ecologically related to + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + 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 + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + + involved in + + + + + + + + + + + inverse of enables + Chris Mungall + + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + + positively regulated by + + + + + + + + + + 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 + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + Chris Mungall + + + + input of + + + + + + + + + + + + inverse of upstream of + Chris Mungall + + causally downstream of + + + + + + + + + + + + Chris Mungall + + immediately causally downstream of + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + 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. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + + involved in negative regulation of + + + + + + + + + + + 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 + Chris Mungall + involved in or reguates + + involved in or involved in regulation of + + + + + + + + + + + + + + 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. + Chris Mungall + executes activity in + enables activity in + + + is active in + + + + + + + + + true + + + + + 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. + GOC:cjm + GOC:dos + + + + + + + + + + + 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. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + 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. + Chris Mungall + binds + molecularly binds with + + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + + phosphorylates + + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + molecularly controls + + directly regulates activity of + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + directly inhibits + molecularly decreases activity of + + directly negatively regulates 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. + Chris Mungall + Vasundra Touré + directly activates + molecularly increases activity of + + directly positively regulates activity of + + + + + + + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + + helper property (not for use in curation) + + + + + + + + + + + + + + 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. + Chris Mungall + + + has part that occurs in + + + + + + + + + true + + + + + + + + + Chris Mungall + + is kinase activity + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + + causal agent in 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between processes + + + + + + + + + + + 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 + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between entities + + + + + + + + + + Chris Mungall + + causally influenced by (entity-centric) + + causally influenced by + + + + + + + + + Chris Mungall + + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + + molecular interaction relation helper property + + + + + + + + + + + + + + + + + + + + + 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). + Chris Mungall + Vasundra Touré + + causally influences (entity-centric) + + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + + directly regulates + + + + + + + + + + + + + + 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 + Chris Mungall + + has part structure that is capable of + + + + + + + + + + + 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. + Chris Mungall + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + + capable of negatively regulating + + + + + + + + + + + + + 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. + + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + + process has causal agent + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + + directly negatively regulates + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + + causally upstream of or within, positive effect + + + + + + + + + + + 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. + Vasundra Touré + + regulates activity of + + + + + + + + + + + + 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. + quality + decreased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + + decreased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + 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. + quality + different_in_magnitude_relative_to + + different_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + + + 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. + quality + increased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + + increased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + 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. + quality + reciprocal_of + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + + reciprocal_of + + + + + 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. + PATOC:CJM + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - continuant + entity - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + + + + + + + + + + + + continuant + Continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + @@ -986,6 +3284,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + @@ -993,8 +3303,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + occurrent Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. @@ -1057,6 +3380,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + ic @@ -1071,6 +3400,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] an organism the bottom right portion of a human torso the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) @@ -1119,6 +3449,26 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. + obsolete dependent continuant + true + + + + + + + + + spatial region + + + + @@ -1132,6 +3482,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the flight of a bird the life of an organism your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] @@ -1153,10 +3504,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + disposition + + + + + realizable RealizableEntity the disposition of this piece of metal to conduct electricity. @@ -1164,6 +3526,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet + 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. + https://orcid.org/0000-0001-8815-0078 To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] @@ -1198,10 +3562,25 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + quality + + + + + + + + + + sdc SpecificallyDependentContinuant @@ -1216,6 +3595,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the role of being a doctor the shape of this hole. the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. 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]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] @@ -1257,6 +3637,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the role of a stone in marking a property boundary the role of subject in a clinical trial the student role + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] @@ -1388,6 +3769,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] @@ -1408,6 +3790,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + function + + + + @@ -1427,6 +3818,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] an energy wave an epidemic the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. @@ -1491,6 +3883,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. + multicellular organism + Melissa Haendel + 9/18/11 + MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. + multicellular organism + + + + @@ -1512,75 +3919,39 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] organism mah 7.16.2011 - A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. organism - - - - - A feature that has been constructed by deliberate human effort. - "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference - constructed feature - construction - - - - - A feature that has been constructed by deliberate human effort. - MA:ma - - - - - + - - - A material entity which determines an environmental system. - ENVO - ENVO:00002297 - A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. - environmental feature + + + heterotroph that acquires nutrition from a symbiont + http://orcid.org/0000-0002-2908-3327 + symbiotroph - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - + - - - A system which has the disposition to environ one or more material entities. - 2013-09-23T16:04:08Z - EcoLexicon:environment - environment - In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. - environmental system + + + A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host + http://orcid.org/0000-0002-2908-3327 + https://www.wikidata.org/entity/Q10253316 + parasite - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. Subclasses will be added by inference. @@ -1595,24 +3966,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - A material part of an astronomical body. - envoAstro - envoPolar - astronomical body part - - - - - + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. - http://orcid.org/0000-0002-4366-3088 + CMECS:577 https://cmecscatalog.org/cmecs/classification/unit/577.html envoCmecs @@ -1623,14 +3982,37 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + molecular process + + molecular_function + + + + + + + + + + catalytic activity + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. - janelomax + jl 2012-09-20T14:06:08Z + GO:0023032 GO:0044708 + GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour @@ -1661,8 +4043,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - janelomax + jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 @@ -1683,7 +4066,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process @@ -1696,11 +4079,47 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + true + + + + kinase activity + + + + + + + + + + transferase activity + + + + + + + + + + transferase activity, transferring phosphorus-containing groups + + + + + - Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour @@ -1725,8 +4144,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + Any process in which an organism has an effect on an organism of a different species. + interaction with another species interspecies interaction interspecies interaction with other organisms @@ -1749,7 +4169,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + Any process in which an organism has an effect on an organism of the same species. intraspecies interaction with other organisms biological_process @@ -1770,7 +4190,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A biological process which involves another organism of the same or different species. GO:0051706 @@ -1793,45 +4212,30 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GO:0023032 - GO:0044709 - behavioral interaction between organisms - behavioral interaction with other organism - behavioural interaction between organisms - behavioural interaction with other organism - behavioral signaling - behavioral signalling - biological_process - GO:0051705 - - - multi-organism behavior - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GOC:ai - - - - - behavioral signalling - GOC:mah - - - - + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item @@ -1841,6 +4245,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + information content entity information content entity @@ -1881,13 +4286,32 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg + 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 data about an ontology part + + + + + measurement datum + Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + + measurement datum + + + + @@ -1927,11 +4351,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - denotator type + 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 + denotator type @@ -1940,12 +4365,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - cjm - 2018-05-20T20:55:03Z - ontology module + 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 + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module @@ -1954,10 +4378,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - cjm - 2018-05-20T20:55:30Z - base ontology module + 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. + base ontology module @@ -1967,11 +4390,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:55:47Z - editors ontology module + 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 + editors ontology module @@ -1980,11 +4402,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:56:13Z - main release 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 + main release ontology module @@ -1993,10 +4414,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - cjm - 2018-05-20T20:56:23Z - bridge ontology 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. + bridge ontology module @@ -2006,12 +4426,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:56:47Z - import ontology 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 + import ontology module @@ -2021,12 +4440,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - cjm - 2018-05-20T20:58:11Z - subset ontology module + 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 + subset ontology module @@ -2037,10 +4455,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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. - cjm - 2018-05-20T20:58:38Z - curation subset ontology module + 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. + curation subset ontology module @@ -2049,10 +4466,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is intended for usage in analysis or discovery applications. - cjm - 2018-05-20T20:58:49Z - analysis subset ontology module + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module @@ -2061,11 +4477,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:59:19Z - single layer subset ontology module + 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 + single layer subset ontology module @@ -2074,11 +4489,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - cjm - 2018-05-20T20:59:57Z - exclusion subset ontology module + 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 + exclusion subset ontology module @@ -2087,11 +4501,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - cjm - 2018-05-20T21:00:14Z - external import ontology module + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module @@ -2100,11 +4513,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - cjm - 2018-05-20T21:14:16Z - species subset ontology module + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module @@ -2114,10 +4526,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - cjm - 2018-05-20T21:20:33Z - reasoned ontology module + 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. + reasoned ontology module @@ -2127,11 +4538,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T21:21:12Z - generated ontology module + 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 + generated ontology module @@ -2140,10 +4550,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - cjm - 2018-05-20T21:21:21Z - template generated ontology module + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module @@ -2155,9 +4564,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - cjm - 2018-05-20T21:28:15Z - taxonomic bridge ontology module + taxonomic bridge ontology module + taxonomic bridge ontology module @@ -2166,9 +4574,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - cjm - 2018-05-22T04:15:54Z - ontology module subsetted by expressivity + ontology module subsetted by expressivity + ontology module subsetted by expressivity @@ -2177,7 +4584,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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. + 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). @@ -2193,9 +4601,7 @@ No qualifier lists No disjointness axioms No owl-axioms header No imports - cjm - 2018-05-22T04:16:10Z - obo basic subset ontology module + obo basic subset ontology module @@ -2205,9 +4611,8 @@ No imports - cjm - 2018-05-22T04:16:28Z - ontology module subsetted by OWL profile + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile @@ -2216,9 +4621,8 @@ No imports - cjm - 2018-05-22T04:16:48Z - EL++ ontology module + EL++ ontology module + EL++ ontology module @@ -2270,46 +4674,20 @@ No imports - - - NCBITaxon:40673 - GC_ID:1 - bony vertebrates - ncbi_taxonomy - - Euteleostomi - - - - - bony vertebrates - - - - - - - - - + + + NCBITaxon:40673 GC_ID:1 + bony vertebrates ncbi_taxonomy - Viroid - viroids - Viroids + Euteleostomi - - - Viroid - - - - - - viroids - + + + bony vertebrates + @@ -2320,22 +4698,22 @@ No imports GC_ID:1 + charophyte/embryophyte group ncbi_taxonomy Charophyta/Embryophyta group - charophyte/embryophyte group Streptophytina - - Charophyta/Embryophyta group - + + charophyte/embryophyte group + - charophyte/embryophyte group + Charophyta/Embryophyta group @@ -2429,7 +4807,9 @@ No imports PMID:12054223 PMID:2112744 PMID:270744 + PMID:7520741 PMID:8123559 + PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 @@ -2445,12 +4825,6 @@ No imports Bacteria - - - - prokaryotes - - @@ -2493,6 +4867,12 @@ No imports prokaryote + + + + prokaryotes + + @@ -2631,6 +5011,7 @@ No imports GC_ID:1 PMID:23020233 + PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy @@ -2886,7 +5267,7 @@ No imports Theria ncbi_taxonomy - Theria <Mammalia> + Theria <mammals> @@ -2903,11 +5284,14 @@ No imports GC_ID:1 + PMID:16248873 + PMID:30257078 + Chlorophyta/Embryophyta group + chlorophyte/embryophyte group green plants ncbi_taxonomy Chlorobionta - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group + Chloroplastida green plants Viridiplantae @@ -2915,25 +5299,31 @@ No imports - green plants - + Chlorophyta/Embryophyta group + - - Chlorobionta - + + chlorophyte/embryophyte group + + + + + + green plants + - Chlorophyta/Embryophyta group + Chlorobionta - chlorophyte/embryophyte group + Chloroplastida @@ -3047,15 +5437,17 @@ No imports + GC_ID:1 PMID:25249442 angiosperms flowering plants ncbi_taxonomy Angiospermae + Magnoliophyta flowering plants - Magnoliophyta + Magnoliopsida @@ -3075,6 +5467,12 @@ No imports Angiospermae + + + + Magnoliophyta + + @@ -3137,6 +5535,41 @@ No imports + + + + + + GC_ID:1 + PMID:11062127 + PMID:12684019 + ncbi_taxonomy + Mycota + fungi + + Fungi + + + + + Mycota + + + + + + fungi + + + + + + fungi + + + + + @@ -3238,7 +5671,7 @@ No imports ncbi_taxonomy vertebrates - Vertebrata <Metazoa> + Vertebrata <vertebrates> @@ -3270,7 +5703,7 @@ No imports jawed vertebrates ncbi_taxonomy - Gnathostomata <vertebrate> + Gnathostomata <vertebrates> @@ -3292,16 +5725,16 @@ No imports GC_ID:1 + euphyllophytes ncbi_taxonomy - euphyllophytes Euphyllophyta - + euphyllophytes - + @@ -3328,7 +5761,7 @@ No imports Craniata ncbi_taxonomy - Craniata <chordata> + Craniata <chordates> @@ -3489,19 +5922,6 @@ No imports human man ncbi_taxonomy - Home sapiens - Homo sampiens - Homo sapeins - Homo sapian - Homo sapians - Homo sapien - Homo sapience - Homo sapiense - Homo sapients - Homo sapines - Homo spaiens - Homo spiens - Humo sapiens Homo sapiens @@ -3517,124 +5937,340 @@ No imports man + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality (PATO) + PATO:0000072 + quality + PATO:0000001 + + quality + - - - Home sapiens - - - - - - Homo sampiens - - - - - - Homo sapeins - - - - - - Homo sapian - - - - - - Homo sapians - + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + quality + PATO:0000068 + TODO: define this or obsolete it and move children somewhere else. + + qualitative + + + + + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + quality + PATO:0000069 + + + deviation (from_normal) + - - - Homo sapien - + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + PATOC:GVG + + + + + + + + + + + + + + The number of entities of this type that are part of the whole organism. + PATO:0000053 + PATO:0000071 + PATO:0001169 + PATO:0001226 + presence or absence in organism + quantitative + quality + count in organism + number + presence + PATO:0000070 + + This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. + + amount + - - - Homo sapience - + + + The number of entities of this type that are part of the whole organism. + PATOC:GVG + + + + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + + rate + - - - Homo sapiense - + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + PATOC:melissa + + + + + + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + + quality + average + PATO:0000461 + + + + + normal + - - - Homo sapients - + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + PATOC:GVG + + + + + + + + A quality inhering in a bearer by virtue of the bearer's existence. + + quality + present in organism + PATO:0000467 + + + + present + - - - Homo sapines - + + + A quality inhering in a bearer by virtue of the bearer's existence. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + An amount which is relatively high. + + PATO:0000420 + PATO:0000650 + increased number + present in greater numbers in organism + supernumerary + quality + accessory + increased + PATO:0000470 + + + increased amount + - - - Homo spaiens - + + + An amount which is relatively high. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + A rate which is relatively low. + + slow rate + quality + PATO:0000911 + + + + decreased rate + - - - Homo spiens - + + + A rate which is relatively low. + PATO:GVG + + + + + + + + + + + + + + + + + + + + A rate which is relatively high. + + fast rate + high rate + quality + PATO:0000912 + + + + increased rate + - - - Humo sapiens - + + + A rate which is relatively high. + PATO:GVG - + - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 - trait + + + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + PATO:0002079 + Wikipedia:Physical_property + relational physical quality quality - PATO:0000001 + PATO:0001018 + - quality + physical quality - + - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG - + - - - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + + + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality - PATO:0000161 + density + PATO:0001019 - rate + mass density - + - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. - PATOC:melissa + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. + WordNet:WordNet + + + + + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + quality + PATO:0001164 + + + + dense + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + PATOC:GVG @@ -3643,6 +6279,7 @@ No imports + A quality which inheres in an process. PATO:0001239 PATO:0001240 @@ -3738,6 +6375,148 @@ No imports + + + + + + + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + OBO_REL:has_part + extra or missing physical or functional parts + has or lacks parts of type + mereological quality + number of + quality + cardinality + number + PATO:0001555 + + + + has number of + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + PATOC:CJM + + + + + + + + + + + + + + + + + + + + + A density which is higher relative to the normal or average. + + high density + quality + PATO:0001788 + + + increased mass density + + + + + A density which is higher relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A density which is lower relative to the normal or average. + + low density + quality + PATO:0001790 + + + decreased mass density + + + + + A density which is lower relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + An amount which is relatively low. + + PATO:0000419 + PATO:0000468 + decreased number + present in fewer numbers in organism + quality + decreased + reduced + subnumerary + PATO:0001997 + + + decreased amount + + + + + An amount which is relatively low. + PATOC:GVG + + + + @@ -3773,6 +6552,220 @@ No imports + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:39:43Z + quality + PATO:0002300 + + increased quality + + + + + A quality that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:40:15Z + quality + PATO:0002301 + + decreased quality + + + + + A quality that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:50:59Z + quality + PATO:0002302 + + decreased process quality + + + + + A quality of a process that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:51:54Z + quality + PATO:0002303 + + decreased object quality + + + + + A quality of an object that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:53:08Z + quality + PATO:0002304 + + increased process quality + + + + + A quality of a process that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:54:01Z + quality + PATO:0002305 + + increased object quality + + + + + A quality of an object that has a value that is increased compared to normal or average. + PATOC:GVG + + + + @@ -3799,6 +6792,12 @@ No imports + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. @@ -3830,18 +6829,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - 2 - - - - - + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 @@ -3873,8 +6861,9 @@ Classes for population already exist in IDO ('organism population', I - A quality that inheres in a biological population. + A quality that inheres in a population of organisms. See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community. Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. quality of a population @@ -3922,8 +6911,8 @@ Classes for population already exist in IDO ('organism population', I - A process that has as primary participant a population. - Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. + The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. population process @@ -3932,8 +6921,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of birth of a population of organisms. population birth rate @@ -3942,8 +6932,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of death of a population of organsisms. population death rate @@ -3952,9 +6943,9 @@ Classes for population already exist in IDO ('organism population', I - + - Is a rate a quality? Population growth rate may be better classified as a process profile. + The rate of growth of a population. population growth rate @@ -4023,30 +7014,51 @@ Classes for population already exist in IDO ('organism population', I - - - predator role + + Interactions are now covered in EcoCore ontology. + obsolete predator role + true + + + + true + + - - - prey role + + Interactions are now covered in EcoCore ontology. + obsolete prey role + true + + + + true + + - - - symbiont role + + Interactions are now covered in EcoCore ontology. + obsolete symbiont role + true + + + + true + + @@ -4054,9 +7066,15 @@ Classes for population already exist in IDO ('organism population', I + - A collection of organisms that has as parts every organism of given species and no organisms of any other species. + A collection of organisms that has as members every organism of given species and no organisms of any other species. + A collection of organisms that has as parts every organism of a species and no organisms of any other species. At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + + + + taxonomic group This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. species as a collection of organisms @@ -4073,25 +7091,26 @@ Classes for population already exist in IDO ('organism population', I - - - - - - 1 - - - - 2 + + + 1 + + + + + + + + A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -4156,7 +7175,7 @@ Classes for population already exist in IDO ('organism population', I If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. - A quality of a community that reflects how close in abundance all species in a community are. + A quality of an ecological community that reflects how close in abundance all species in a community are. adapted from http://en.wikipedia.org/wiki/Species_evenness community species evenness @@ -4166,7 +7185,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -4190,7 +7209,7 @@ Classes for population already exist in IDO ('organism population', I An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. - Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household household @@ -4203,7 +7222,7 @@ Classes for population already exist in IDO ('organism population', I This is an example population added to demonstrate the modeling pattern for collections of organisms. - red population + obsolete red population true @@ -4215,7 +7234,7 @@ Classes for population already exist in IDO ('organism population', I An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. - red organism + obsolete red organism true @@ -4264,7 +7283,7 @@ Classes for population already exist in IDO ('organism population', I Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). - community + obsolete community true @@ -4274,6 +7293,13 @@ Classes for population already exist in IDO ('organism population', I + + + + 2 + + + A collection of organisms that consists of two or more organisms from at least two species. Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". @@ -4372,34 +7398,336 @@ Classes for population already exist in IDO ('organism population', I + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 - A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. GenEpio curators potluck - + + + + + A human social gathering at which two people are married. May include a legal or social ceremony. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 + GenEpio curators + wedding + + + + + + + + + A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 + GenEpiO curators + baby shower + + + + + + + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community + + + + + + + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + microbial organism + microbe + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + + + + + + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + number of generations + number of generations of multicellular organism + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + + + + + + + + + + + + + + + + + + + + + + An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels. + + increased density of population + overcrowded population + + + + + + + + + + + + + + + + + + + + + + + + + + + A quality of a human population such that the density humans in an area is increased beyond sustainable levels. + + overcrowded human population + + + + + + + + + + A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations. + + + This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. + taxon as collection of organisms + + + + + + + + + + + An organism or virus or viroid that is a microbe and a parasite. + + microbial parasite + + + + + + + + + + + + + + + + + + A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations. + + VEuPathDB + parasite isolate population + + + + + + + + + + A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi). + + + Shannon entropy + Shannon's diversity index + Shannon-Wiener index + Shannon diversity index + + + + + - - - A human social gathering at which two people are married. May include a legal or social ceremony. - Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 - GenEpio curators - wedding + + + + A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi). + + + Simpson index + Simpson diversity index - + - - - A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. - Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 - GenEpiO curators - baby shower + + + + A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi). + + + inverse Simpson diversity index @@ -4408,12 +7736,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - @@ -4430,25 +7752,16 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 1 - - - - - - - + + + + 1 + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. pair of interacting organisms of the same species @@ -4525,7 +7838,7 @@ Classes for population already exist in IDO ('organism population', I - + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 @@ -4538,6 +7851,23 @@ Classes for population already exist in IDO ('organism population', I + + + + + a count of 4 resulting from counting limbs in humans + + a count is a data item denoted by an integer and represented the number of instances or occurences of an entity + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO + + count + + + + @@ -4551,55 +7881,10 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Obsolete Class @@ -4607,19 +7892,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 https://cmecscatalog.org/cmecs/classification/unit/577.html mangrove community tidal shrubland community - tidal mangrove shrubland community + obsolete tidal mangrove shrubland community + true @@ -4627,10 +7908,12 @@ Classes for population already exist in IDO ('organism population', I - + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO - invisible to unaided eye + obsolete invisible to unaided eye + true @@ -4638,15 +7921,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + + microbial organism - microbe + obsolete microbe + true @@ -4654,31 +7933,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - - - - - - - - + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 - collection of microbial organisms + obsolete collection of microbial organisms + true @@ -4686,11 +7946,12 @@ Classes for population already exist in IDO ('organism population', I - - + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 - multi-species collection of microbes + obsolete multi-species collection of microbes + true @@ -4698,36 +7959,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - 1 - - - - - - - 2 - - - - - - - + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 - single species collection of microbes + obsolete single species collection of microbes + true @@ -4735,18 +7972,13 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 microbiota - microbial population + obsolete microbial population + true @@ -4766,6 +7998,7 @@ Classes for population already exist in IDO ('organism population', I + example to be eventually removed example to be eventually removed @@ -4775,8 +8008,9 @@ Classes for population already exist in IDO ('organism population', I + 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 + Person:Alan Ruttenberg failed exploratory term @@ -4786,6 +8020,7 @@ Classes for population already exist in IDO ('organism population', I + 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. metadata complete @@ -4796,7 +8031,8 @@ Classes for population already exist in IDO ('organism population', I - term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -4806,6 +8042,7 @@ Classes for population already exist in IDO ('organism population', I + 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." ready for release @@ -4816,6 +8053,7 @@ Classes for population already exist in IDO ('organism population', I + metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -4826,6 +8064,7 @@ Classes for population already exist in IDO ('organism population', I + uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -4836,6 +8075,7 @@ Classes for population already exist in IDO ('organism population', I + 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. pending final vetting @@ -4845,11 +8085,12 @@ Classes for population already exist in IDO ('organism population', I - 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 - core + + obsolete_core + true @@ -4858,6 +8099,7 @@ Classes for population already exist in IDO ('organism population', I + placeholder removed placeholder removed @@ -4867,6 +8109,7 @@ Classes for population already exist in IDO ('organism population', I + terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -4877,6 +8120,7 @@ Classes for population already exist in IDO ('organism population', I + 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 imported @@ -4887,6 +8131,7 @@ Classes for population already exist in IDO ('organism population', I + 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. term split @@ -4897,10 +8142,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - universal + 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 + universal @@ -4909,10 +8155,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - defined class + 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 + defined class @@ -4921,10 +8168,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - named class expression + 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 + named class expression @@ -4933,6 +8181,7 @@ Classes for population already exist in IDO ('organism population', I + to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI @@ -4945,6 +8194,7 @@ Classes for population already exist in IDO ('organism population', I + 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 @@ -4961,6 +8211,39 @@ Classes for population already exist in IDO ('organism population', I /////////////////////////////////////////////////////////////////////////////////////// --> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4983,6 +8266,923 @@ Classes for population already exist in IDO ('organism population', I + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/pco.obo b/pco.obo index f15f70f..7b026ec 100644 --- a/pco.obo +++ b/pco.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2020-02-13 +data-version: releases/2020-08-26 remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -8,31 +8,35 @@ property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string -property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string +property_value: http://purl.org/dc/elements/1.1/description "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Population and Community Ontology" xsd:string +property_value: http://purl.org/dc/terms/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string +property_value: editor_note "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: editor_note "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000112 "Julius Caesar" xsd:string property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000002 name: continuant +def: "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." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent +relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string -property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: editor_note "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} @@ -46,13 +50,15 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000003 name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity +relationship: part_of BFO:0000003 ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string -property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} -property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: editor_note "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: editor_note "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: editor_note "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} @@ -63,10 +69,12 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string @@ -86,13 +94,27 @@ property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000005 +name: obsolete dependent continuant +def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true + +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity + [Term] id: BFO:0000015 name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string +property_value: editor_note "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string property_value: IAO:0000112 "a process of meiosis" xsd:string property_value: IAO:0000112 "a process of sleeping" xsd:string @@ -100,14 +122,21 @@ property_value: IAO:0000112 "the course of a disease" xsd:string property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + [Term] id: BFO:0000017 name: realizable entity +def: "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_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality property_value: BFO:0000179 "realizable" xsd:string property_value: BFO:0000180 "RealizableEntity" xsd:string property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string @@ -115,20 +144,29 @@ property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:str property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant + [Term] id: BFO:0000020 name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: part_of BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string @@ -140,16 +178,17 @@ property_value: IAO:0000112 "the pink color of a medium rare piece of grilled fi property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role +def: "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." [] is_a: BFO:0000017 ! realizable entity property_value: BFO:0000179 "role" xsd:string property_value: BFO:0000180 "Role" xsd:string +property_value: editor_note "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string property_value: IAO:0000112 "the priest role" xsd:string property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string @@ -157,7 +196,6 @@ property_value: IAO:0000112 "the role of a building in serving as a military tar property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl @@ -168,6 +206,9 @@ name: object aggregate is_a: BFO:0000040 ! material entity property_value: BFO:0000179 "object-aggregate" xsd:string property_value: BFO:0000180 "ObjectAggregate" xsd:string +property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: editor_note "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string property_value: IAO:0000112 "a symphony orchestra" xsd:string @@ -181,9 +222,6 @@ property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:stri property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} -property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} @@ -217,6 +255,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant property_value: BFO:0000179 "gdc" xsd:string @@ -227,13 +266,22 @@ property_value: IAO:0000112 "the sequence of this protein molecule; the sequence property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + [Term] id: BFO:0000040 name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "material" xsd:string property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: editor_note "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: editor_note "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: editor_note "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: IAO:0000112 "a flame" xsd:string property_value: IAO:0000112 "a forest fire" xsd:string property_value: IAO:0000112 "a human being" xsd:string @@ -246,9 +294,6 @@ property_value: IAO:0000112 "an aggregate of human beings." xsd:string property_value: IAO:0000112 "an energy wave" xsd:string property_value: IAO:0000112 "an epidemic" xsd:string property_value: IAO:0000112 "the undetached arm of a human being" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} @@ -263,9 +308,20 @@ name: immaterial entity is_a: BFO:0000004 ! independent continuant property_value: BFO:0000179 "immaterial" xsd:string property_value: BFO:0000180 "ImmaterialEntity" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string +property_value: editor_note "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: CARO:0000012 +name: multicellular organism +def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] +comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. +comment: MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. +is_a: CARO:0010004 ! organism +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "multicellular organism" xsd:string + [Term] id: CARO:0001010 name: organism or virus or viroid @@ -279,61 +335,34 @@ property_value: IAO:0000589 "organism or virus" xsd:string id: CARO:0010004 name: organism def: "An individual member of a clade." [] -comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. is_a: CARO:0001010 ! organism or virus or viroid property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string property_value: IAO:0000589 "organism" xsd:string [Term] -id: DbXref -is_a: IAO:0000102 ! data about an ontology part - -[Term] -id: Definition -is_a: IAO:0000102 ! data about an ontology part - -[Term] -id: ENVO:00000070 -name: construction -def: "A feature that has been constructed by deliberate human effort." [MA:ma] -synonym: "constructed feature" EXACT [] -is_a: ENVO:01000813 ! astronomical body part -property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string - -[Term] -id: ENVO:00002297 -name: environmental feature -namespace: ENVO -def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] -comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. -is_a: BFO:0000040 ! material entity +id: ECOCORE:00000045 +name: symbiotroph +def: "heterotroph that acquires nutrition from a symbiont" [] +is_a: CARO:0001010 ! organism or virus or viroid +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string [Term] -id: ENVO:01000254 -name: environmental system -def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] -comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. -synonym: "environment" EXACT [] -xref: EcoLexicon:environment -is_a: BFO:0000040 ! material entity -creation_date: 2013-09-23T16:04:08Z +id: ECOCORE:00000146 +name: parasite +def: "A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host" [] +xref: https://www.wikidata.org/entity/Q10253316 +is_a: ECOCORE:00000045 ! symbiotroph +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string [Term] id: ENVO:01000744 name: human dwelling def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] -is_a: ENVO:00000070 ! construction -property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string -property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string - -[Term] -id: ENVO:01000813 -name: astronomical body part -def: "A material part of an astronomical body." [] -subset: envoAstro -subset: envoPolar -is_a: ENVO:00002297 ! environmental feature +is_a: BFO:0000040 ! material entity +property_value: editor_note "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: editor_note "Subclasses will be added by inference." xsd:string [Term] id: ENVO:01001369 @@ -344,14 +373,29 @@ comment: This class aligns to the Coastal and Marine Ecological Classification S subset: envoCmecs subset: envoMarine xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ENVO:01000254 ! environmental system +is_a: BFO:0000040 ! material entity created_by: http://orcid.org/0000-0002-4366-3088 +[Term] +id: GO:0003674 +name: molecular_function +is_a: BFO:0000015 ! process +property_value: IAO:0000589 "molecular process" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0003824 +name: catalytic activity +is_a: GO:0003674 ! molecular_function +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0007610 name: behavior namespace: biological_process +alt_id: GO:0023032 alt_id: GO:0044708 +alt_id: GO:0044709 def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). subset: gocheck_do_not_manually_annotate @@ -364,7 +408,7 @@ synonym: "single-organism behavior" RELATED [] xref: Wikipedia:Behavior is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-20T14:06:08Z [Term] @@ -375,7 +419,7 @@ alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] -comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl @@ -390,10 +434,29 @@ synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-19T15:05:24Z +[Term] +id: GO:0016301 +name: kinase activity +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016740 +name: transferase activity +is_a: GO:0003824 ! catalytic activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +is_a: GO:0016740 ! transferase activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0035176 name: social behavior @@ -403,8 +466,8 @@ comment: Behavior such as predation which involves members of different species synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior +is_a: GO:0007610 ! behavior is_a: GO:0051703 ! intraspecies interaction between organisms -is_a: GO:0051705 ! multi-organism behavior property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -417,8 +480,9 @@ subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 @@ -427,7 +491,7 @@ namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] subset: goslim_pir synonym: "intraspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -441,46 +505,42 @@ subset: goslim_pir synonym: "interaction between organisms" EXACT [] synonym: "physiological interaction between organisms" EXACT [] synonym: "physiological interaction with other organism" EXACT [] -is_a: BFO:0000015 ! process is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -[Term] -id: GO:0051705 -name: multi-organism behavior -namespace: biological_process -alt_id: GO:0023032 -alt_id: GO:0044709 -def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] -subset: goslim_pir -synonym: "behavioral interaction between organisms" EXACT [] -synonym: "behavioral interaction with other organism" EXACT [] -synonym: "behavioral signaling" NARROW [] -synonym: "behavioral signalling" NARROW [GOC:mah] -synonym: "behavioural interaction between organisms" EXACT [] -synonym: "behavioural interaction with other organism" EXACT [] -is_a: GO:0007610 ! behavior -is_a: GO:0051704 ! multi-organism process -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - [Term] id: IAO:0000027 name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity +property_value: editor_note "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string +property_value: editor_note "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string +property_value: editor_note "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: editor_note "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: editor_note "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: IAO:0000030 name: information content entity is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000111 "information content entity" xsd:string [Term] id: IAO:0000078 name: curation status specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part +property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000111 "curation status specification" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 GROUP:OBI: xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string @@ -488,18 +548,33 @@ property_value: IAO:0000119 "OBI_0000266" xsd:string [Term] id: IAO:0000102 name: data about an ontology part -def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "data about an ontology part" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string +[Term] +id: IAO:0000109 +name: measurement datum +def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] +is_a: IAO:0000027 ! data item +property_value: editor_note "2/2/2009 is_specified_output of some assay?" xsd:string +property_value: IAO:0000111 "measurement datum" xsd:string +property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000119 group:OBI xsd:string +property_value: IAO:0000119 "OBI_0000305" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + [Term] id: IAO:0000225 name: obsolescence reason specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part +property_value: editor_note "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000111 "obsolescence reason specification" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string @@ -508,6 +583,7 @@ id: IAO:0000409 name: denotator type def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "denotator type" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string @@ -516,189 +592,168 @@ property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string id: IAO:8000000 name: ontology module is_a: IAO:0000102 ! data about an ontology part -property_value: IAO:0000116 "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." xsd:string +property_value: editor_note "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000111 "ontology module" xsd:string property_value: IAO:0000118 "ontology file" xsd:string property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string -created_by: cjm -creation_date: 2018-05-20T20:55:03Z [Term] id: IAO:8000001 name: base ontology module def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "base ontology module" xsd:string property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 -created_by: cjm -creation_date: 2018-05-20T20:55:30Z [Term] id: IAO:8000002 name: editors ontology module def: "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." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "editors ontology module" xsd:string property_value: IAO:0000118 "source ontology module" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:55:47Z [Term] id: IAO:8000003 name: main release ontology module def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] is_a: IAO:8000000 ! ontology module -property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:56:13Z +property_value: editor_note "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +property_value: IAO:0000111 "main release ontology module" xsd:string [Term] id: IAO:8000004 name: bridge ontology module def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "bridge ontology module" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies -created_by: cjm -creation_date: 2018-05-20T20:56:23Z [Term] id: IAO:8000005 name: import ontology module def: "A subset ontology module that is intended to be imported from another ontology." [] is_a: IAO:8000006 ! subset ontology module -property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: editor_note "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000111 "import ontology module" xsd:string property_value: IAO:0000118 "import file" xsd:string property_value: seeAlso http://robot.obolibrary.org/extract -created_by: cjm -creation_date: 2018-05-20T20:56:47Z [Term] id: IAO:8000006 name: subset ontology module def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "subset ontology module" xsd:string property_value: IAO:0000118 "ontology slim" xsd:string property_value: IAO:0000118 "subset ontology" xsd:string property_value: seeAlso http://robot.obolibrary.org/filter property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide -created_by: cjm -creation_date: 2018-05-20T20:58:11Z [Term] id: IAO:8000007 name: curation subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-20T20:58:38Z +property_value: IAO:0000111 "curation subset ontology module" xsd:string [Term] id: IAO:8000008 name: analysis subset ontology module def: "An ontology module that is intended for usage in analysis or discovery applications." [] is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-20T20:58:49Z +property_value: IAO:0000111 "analysis ontology module" xsd:string [Term] id: IAO:8000009 name: single layer subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "single layer ontology module" xsd:string property_value: IAO:0000118 "ribbon subset" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:59:19Z [Term] id: IAO:8000010 name: exclusion subset ontology module def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "exclusion subset ontology module" xsd:string property_value: IAO:0000118 "antislim" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:59:57Z [Term] id: IAO:8000011 name: external import ontology module def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000111 "external import ontology module" xsd:string property_value: IAO:0000118 "external import" xsd:string -created_by: cjm -creation_date: 2018-05-20T21:00:14Z [Term] id: IAO:8000012 name: species subset ontology module def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "species subset ontology module" xsd:string property_value: IAO:0000118 "taxon subset" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -created_by: cjm -creation_date: 2018-05-20T21:14:16Z [Term] id: IAO:8000013 name: reasoned ontology module def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "reasoned ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/reason -created_by: cjm -creation_date: 2018-05-20T21:20:33Z [Term] id: IAO:8000014 name: generated ontology module def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] is_a: IAO:8000000 ! ontology module -property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string -created_by: cjm -creation_date: 2018-05-20T21:21:12Z +property_value: editor_note "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +property_value: IAO:0000111 "generated ontology module" xsd:string [Term] id: IAO:8000015 name: template generated ontology module def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] is_a: IAO:8000014 ! generated ontology module +property_value: IAO:0000111 "template generated ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/template property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ -created_by: cjm -creation_date: 2018-05-20T21:21:21Z [Term] id: IAO:8000016 name: taxonomic bridge ontology module is_a: IAO:8000004 ! bridge ontology module -created_by: cjm -creation_date: 2018-05-20T21:28:15Z +property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string [Term] id: IAO:8000017 name: ontology module subsetted by expressivity is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-22T04:15:54Z +property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string [Term] id: IAO:8000018 name: obo basic subset ontology module def: "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "obo basic subset ontology module" xsd:string property_value: seeAlso "6.2" -created_by: cjm -creation_date: 2018-05-22T04:16:10Z [Term] id: IAO:8000019 name: ontology module subsetted by OWL profile is_a: IAO:8000017 ! ontology module subsetted by expressivity -created_by: cjm -creation_date: 2018-05-22T04:16:28Z +property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string [Term] id: IAO:8000020 name: EL++ ontology module is_a: IAO:8000019 ! ontology module subsetted by OWL profile -created_by: cjm -creation_date: 2018-05-22T04:16:48Z +property_value: IAO:0000111 "EL++ ontology module" xsd:string [Term] id: NCBITaxon:10239 @@ -716,7 +771,7 @@ id: NCBITaxon:117570 name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 -is_a: NCBITaxon:7776 ! Gnathostomata +is_a: NCBITaxon:7776 ! Gnathostomata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -729,22 +784,12 @@ xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl -[Term] -id: NCBITaxon:12884 -name: Viroids -namespace: ncbi_taxonomy -synonym: "Viroid" RELATED synonym [] -synonym: "viroids" RELATED blast_name [] -xref: GC_ID:1 -property_value: has_rank NCBITaxon:superkingdom -property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl - [Term] id: NCBITaxon:131221 name: Streptophytina namespace: ncbi_taxonomy synonym: "Charophyta/Embryophyta group" RELATED synonym [] -synonym: "charophyte/embryophyte group" RELATED synonym [] +synonym: "charophyte/embryophyte group" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:35493 ! Streptophyta property_value: has_rank NCBITaxon:subphylum @@ -817,7 +862,9 @@ xref: PMID:11760965 xref: PMID:12054223 xref: PMID:2112744 xref: PMID:270744 +xref: PMID:7520741 xref: PMID:8123559 +xref: PMID:8186100 xref: PMID:8590690 xref: PMID:9103655 xref: PMID:9336922 @@ -892,6 +939,7 @@ synonym: "eukaryotes" EXACT common_name [] synonym: "eukaryotes" RELATED blast_name [] xref: GC_ID:1 xref: PMID:23020233 +xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms property_value: has_rank NCBITaxon:superkingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -977,7 +1025,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32525 -name: Theria +name: Theria namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 @@ -989,11 +1037,14 @@ id: NCBITaxon:33090 name: Viridiplantae namespace: ncbi_taxonomy synonym: "Chlorobionta" RELATED synonym [] -synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] -synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name [] +synonym: "chlorophyte/embryophyte group" EXACT equivalent_name [] +synonym: "Chloroplastida" RELATED synonym [] synonym: "green plants" EXACT common_name [] synonym: "green plants" RELATED blast_name [] xref: GC_ID:1 +xref: PMID:16248873 +xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:kingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -1040,15 +1091,17 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:3398 -name: Magnoliophyta +name: Magnoliopsida namespace: ncbi_taxonomy synonym: "Angiospermae" RELATED synonym [] synonym: "angiosperms" EXACT common_name [] synonym: "flowering plants" EXACT genbank_common_name [] synonym: "flowering plants" RELATED blast_name [] +synonym: "Magnoliophyta" RELATED synonym [] xref: GC_ID:1 xref: PMID:25249442 is_a: NCBITaxon:58024 ! Spermatophyta +property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -1080,6 +1133,20 @@ is_a: NCBITaxon:32524 ! Amniota property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl +[Term] +id: NCBITaxon:4751 +name: Fungi +namespace: ncbi_taxonomy +synonym: "fungi" RELATED blast_name [] +synonym: "fungi" RELATED in_part [] +synonym: "Mycota" RELATED genbank_synonym [] +xref: GC_ID:1 +xref: PMID:11062127 +xref: PMID:12684019 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + [Term] id: NCBITaxon:58023 name: Tracheophyta @@ -1121,30 +1188,30 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7742 -name: Vertebrata +name: Vertebrata namespace: ncbi_taxonomy synonym: "Vertebrata" EXACT scientific_name [] synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:89593 ! Craniata +is_a: NCBITaxon:89593 ! Craniata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7776 -name: Gnathostomata +name: Gnathostomata namespace: ncbi_taxonomy synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 -is_a: NCBITaxon:7742 ! Vertebrata +is_a: NCBITaxon:7742 ! Vertebrata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:78536 name: Euphyllophyta namespace: ncbi_taxonomy -synonym: "euphyllophytes" RELATED synonym [] +synonym: "euphyllophytes" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:58023 ! Tracheophyta property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -1160,7 +1227,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:89593 -name: Craniata +name: Craniata namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 @@ -1178,7 +1245,7 @@ synonym: "Placentalia" RELATED synonym [] synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:32525 ! Theria +is_a: NCBITaxon:32525 ! Theria property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -1227,33 +1294,62 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl id: NCBITaxon:9606 name: Homo sapiens namespace: ncbi_taxonomy -synonym: "Home sapiens" RELATED misspelling [] -synonym: "Homo sampiens" RELATED misspelling [] -synonym: "Homo sapeins" RELATED misspelling [] -synonym: "Homo sapian" RELATED misspelling [] -synonym: "Homo sapians" RELATED misspelling [] -synonym: "Homo sapien" RELATED misspelling [] -synonym: "Homo sapience" RELATED misspelling [] -synonym: "Homo sapiense" RELATED misspelling [] -synonym: "Homo sapients" RELATED misspelling [] -synonym: "Homo sapines" RELATED misspelling [] -synonym: "Homo spaiens" RELATED misspelling [] -synonym: "Homo spiens" RELATED misspelling [] synonym: "human" EXACT genbank_common_name [] -synonym: "Humo sapiens" RELATED misspelling [] synonym: "man" EXACT common_name [] xref: GC_ID:1 is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl +[Term] +id: ObsoleteClass +name: Obsolete Class + [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -synonym: "trait" EXACT [] +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000068 +name: qualitative +namespace: quality +comment: TODO: define this or obsolete it and move children somewhere else. +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000069 +name: deviation (from_normal) +namespace: quality +def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000070 +name: amount +namespace: quality +alt_id: PATO:0000053 +alt_id: PATO:0000071 +alt_id: PATO:0001169 +alt_id: PATO:0001226 +def: "The number of entities of this type that are part of the whole organism." [PATOC:GVG] +comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. +subset: attribute_slim +synonym: "count in organism" RELATED [] +synonym: "number" RELATED [] +synonym: "presence" RELATED [] +synonym: "presence or absence in organism" EXACT [] +synonym: "quantitative" EXACT [] +is_a: PATO:0000068 ! qualitative +relationship: reciprocal_of PATO:0001555 ! has number of property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -1266,6 +1362,115 @@ subset: scalar_slim is_a: PATO:0002062 ! physical quality of a process property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0000461 +name: normal +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average." [PATOC:GVG] +subset: abnormal_slim +subset: mpath_slim +subset: value_slim +synonym: "average" RELATED [] +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000460 + +[Term] +id: PATO:0000467 +name: present +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's existence." [PATOC:GVG] +subset: absent_slim +subset: value_slim +synonym: "present in organism" RELATED [] +is_a: PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000462 + +[Term] +id: PATO:0000470 +name: increased amount +namespace: quality +alt_id: PATO:0000420 +alt_id: PATO:0000650 +def: "An amount which is relatively high." [PATOC:GVG] +subset: value_slim +synonym: "accessory" RELATED [] +synonym: "increased" RELATED [] +synonym: "increased number" EXACT [] +synonym: "present in greater numbers in organism" EXACT [] +synonym: "supernumerary" EXACT [] +is_a: PATO:0000467 ! present +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0000070 ! amount +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001997 + +[Term] +id: PATO:0000911 +name: decreased rate +namespace: quality +def: "A rate which is relatively low." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "slow rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002302 ! decreased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000912 + +[Term] +id: PATO:0000912 +name: increased rate +namespace: quality +def: "A rate which is relatively high." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "fast rate" EXACT [] +synonym: "high rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002304 ! increased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000911 + +[Term] +id: PATO:0001018 +name: physical quality +namespace: quality +alt_id: PATO:0002079 +def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] +subset: attribute_slim +synonym: "relational physical quality" EXACT [] +xref: Wikipedia:Physical_property +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001019 +name: mass density +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size." [WordNet:WordNet] +subset: attribute_slim +subset: scalar_slim +synonym: "density" RELATED [] +is_a: PATO:0001018 ! physical quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001164 +name: dense +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density." [PATOC:GVG] +subset: mpath_slim +subset: value_slim +is_a: PATO:0001019 ! mass density +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + [Term] id: PATO:0001236 name: process quality @@ -1279,6 +1484,7 @@ synonym: "quality of occurrent" EXACT [] synonym: "quality of process" EXACT [] synonym: "relational quality of occurrent" EXACT [] is_a: PATO:0000001 ! quality +disjoint_from: PATO:0001241 ! physical object quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -1321,6 +1527,72 @@ subset: scalar_slim is_a: PATO:0002003 ! population quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0001555 +name: has number of +namespace: quality +def: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts." [PATOC:CJM] +subset: attribute_slim +subset: relational_slim +synonym: "cardinality" RELATED [] +synonym: "extra or missing physical or functional parts" EXACT [] +synonym: "has or lacks parts of type" EXACT [] +synonym: "mereological quality" EXACT [] +synonym: "number" RELATED [] +synonym: "number of" EXACT [] +xref: OBO_REL:has_part +is_a: PATO:0001241 ! physical object quality +relationship: reciprocal_of PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001788 +name: increased mass density +namespace: quality +def: "A density which is higher relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "high density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002305 ! increased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001790 + +[Term] +id: PATO:0001790 +name: decreased mass density +namespace: quality +def: "A density which is lower relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "low density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002303 ! decreased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001788 + +[Term] +id: PATO:0001997 +name: decreased amount +namespace: quality +alt_id: PATO:0000419 +alt_id: PATO:0000468 +def: "An amount which is relatively low." [PATOC:GVG] +subset: value_slim +synonym: "decreased" RELATED [] +synonym: "decreased number" EXACT [] +synonym: "present in fewer numbers in organism" EXACT [] +synonym: "reduced" RELATED [] +synonym: "subnumerary" RELATED [] +is_a: PATO:0000467 ! present +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0000070 ! amount +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000470 + [Term] id: PATO:0002003 name: population quality @@ -1340,6 +1612,90 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl created_by: george creation_date: 2009-06-05T09:16:46Z +[Term] +id: PATO:0002300 +name: increased quality +namespace: quality +def: "A quality that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002301 +created_by: George Gkoutos +creation_date: 2011-06-16T06:39:43Z + +[Term] +id: PATO:0002301 +name: decreased quality +namespace: quality +def: "A quality that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002300 +created_by: George Gkoutos +creation_date: 2011-06-16T06:40:15Z + +[Term] +id: PATO:0002302 +name: decreased process quality +namespace: quality +def: "A quality of a process that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002304 +created_by: George Gkoutos +creation_date: 2011-06-16T06:50:59Z + +[Term] +id: PATO:0002303 +name: decreased object quality +namespace: quality +def: "A quality of an object that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002305 +created_by: George Gkoutos +creation_date: 2011-06-16T06:51:54Z + +[Term] +id: PATO:0002304 +name: increased process quality +namespace: quality +def: "A quality of a process that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002302 +created_by: George Gkoutos +creation_date: 2011-06-16T06:53:08Z + +[Term] +id: PATO:0002305 +name: increased object quality +namespace: quality +def: "A quality of an object that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002303 +created_by: George Gkoutos +creation_date: 2011-06-16T06:54:01Z + [Term] id: PCO:0000000 name: collection of organisms @@ -1347,9 +1703,10 @@ def: "A material entity that consists of two or more organisms, viruses, or viro comment: May be of the same or different species. is_a: BFO:0000027 ! object aggregate is_a: PCO:0000031 ! organismal entity -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "group of organism" xsd:string @@ -1371,20 +1728,22 @@ id: PCO:0000002 name: ecological community def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +is_a: PCO:0000029 ! multi-species collection of organisms property_value: IAO:0000118 "multispecies community" xsd:string property_value: IAO:0000119 ISBN:0865423504 xsd:string [Term] id: PCO:0000003 name: quality of a population -def: "A quality that inheres in a biological population." [] +def: "A quality that inheres in a population of organisms." [] comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. is_a: PATO:0002003 ! population quality intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000001 ! population of organisms -relationship: RO:0000052 PCO:0000001 ! population of organisms +intersection_of: RO:0000052 PCO:0000001 ! inheres in population of organisms +relationship: RO:0000052 PCO:0000001 ! inheres in population of organisms +property_value: editor_note "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string +property_value: editor_note "This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string [Term] id: PCO:0000004 @@ -1393,45 +1752,47 @@ def: "A quality that inheres in a community." [] comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. is_a: PATO:0002003 ! population quality intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000002 ! ecological community -relationship: RO:0000052 PCO:0000002 ! ecological community +intersection_of: RO:0000052 PCO:0000002 ! inheres in ecological community +relationship: RO:0000052 PCO:0000002 ! inheres in ecological community +property_value: editor_note "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string [Term] id: PCO:0000005 name: population process -def: "A process that has as primary participant a population. " [] -comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +def: "A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction." [] +comment: The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. is_a: BFO:0000015 ! process -relationship: RO:0000057 PCO:0000001 ! population of organisms +relationship: RO:0000057 PCO:0000001 ! has participant population of organisms property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000006 name: population birth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of birth of a population of organisms." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000007 name: population death rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of death of a population of organsisms." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000008 name: population growth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of growth of a population." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string [Term] id: PCO:0000009 name: obsolete carrying capacity def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] -is_a: ObsoleteClass -property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string property_value: IAO:0000119 ISBN:0878932739 xsd:string property_value: IAO:0000231 IAO:0000423 is_obsolete: true @@ -1441,8 +1802,8 @@ id: PCO:0000010 name: community species richness def: "The number of different species represented in an ecological community." [] is_a: PCO:0000004 ! quality of an ecological community +property_value: editor_note "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string [Term] @@ -1468,36 +1829,49 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 -name: predator role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete predator role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 -name: prey role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete prey role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 -name: symbiont role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete symbiont role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000017 name: species as a collection of organisms -def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as members every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as parts every organism of a species and no organisms of any other species." [] comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +synonym: "taxonomic group" EXACT [] +xref: GENO:0000113 +xref: Species +xref: TAXRANK:0000006 is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000059 ! taxon as collection of organisms +property_value: editor_note "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string [Term] id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms +intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid +relationship: PCO:0000055 PCO:0000017 ! has member of species as a collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -1507,8 +1881,8 @@ name: community species diversity def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. is_a: PCO:0000004 ! quality of an ecological community +property_value: editor_note "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string [Term] @@ -1517,8 +1891,8 @@ name: family def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. is_a: PCO:0000018 ! single-species collection of organisms +property_value: editor_note "Needs axioms for family relationships." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string [Term] @@ -1538,7 +1912,7 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000023 name: community species evenness -def: "A quality of a community that reflects how close in abundance all species in a community are." [] +def: "A quality of an ecological community that reflects how close in abundance all species in a community are." [] is_a: PCO:0000004 ! quality of an ecological community property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -1548,26 +1922,26 @@ property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_e id: PCO:0000024 name: household def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] -is_a: PCO:0000031 ! organismal entity -relationship: RO:0002321 ENVO:01000744 ! human dwelling -relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! Homo sapiens +is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002321 ENVO:01000744 ! ecologically related to human dwelling +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! has member Homo sapiens property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string [Term] id: PCO:0000025 -name: red population +name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000002 is_obsolete: true [Term] id: PCO:0000026 -name: red organism +name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1577,20 +1951,20 @@ name: collection of humans def: "A collection of organisms of the same species that has as members only humans." [] is_a: PCO:0000018 ! single-species collection of organisms intersection_of: PCO:0000018 ! single-species collection of organisms -intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! Homo sapiens -intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! Homo sapiens -relationship: RO:0002351 NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! has member Homo sapiens +relationship: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "human community" xsd:string property_value: IAO:0000118 "human population" xsd:string [Term] id: PCO:0000028 -name: community +name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). -is_a: ObsoleteClass -property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -1599,8 +1973,9 @@ id: PCO:0000029 name: multi-species collection of organisms def: "A collection of organisms that consists of two or more organisms from at least two species." [] is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 PCO:0000001 {minCardinality="2"} ! has member population of organisms +property_value: editor_note "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string [Term] id: PCO:0000030 @@ -1608,10 +1983,10 @@ name: agricultural household name: obsolete organismal entity def: "A household in which the majority of the income of its members is derived from agricultural activities." [] def: "A material entity that is one or more organisms, viruses or viroids." [] -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class is_a: PCO:0000024 ! household +property_value: editor_note "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000231 "wrong IRI form" xsd:string is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 @@ -1638,8 +2013,8 @@ id: PCO:0000033 name: human social gathering activity def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] is_a: GO:0035176 ! social behavior -relationship: RO:0000057 PCO:0000027 ! collection of humans -property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +relationship: RO:0000057 PCO:0000027 ! has participant collection of humans +property_value: editor_note "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] @@ -1647,7 +2022,7 @@ id: PCO:0000034 name: human community event def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1655,15 +2030,15 @@ id: PCO:0000035 name: party def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000037 name: potluck +def: "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string -property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1671,7 +2046,7 @@ id: PCO:0000038 name: wedding def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1679,90 +2054,244 @@ id: PCO:0000039 name: baby shower def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000040 +name: obsolete tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000041 +name: obsolete invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: ObsoleteClass ! Obsolete Class +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000042 +name: obsolete microbe +synonym: "microbial organism" EXACT [] +is_a: ObsoleteClass ! Obsolete Class +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000043 +name: obsolete collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000044 +name: obsolete multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000045 +name: obsolete single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000046 +name: obsolete microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000047 name: tidal mangrove shrubland community def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html is_a: PCO:0000002 ! ecological community -relationship: BFO:0000050 ENVO:01001369 ! tidal mangrove shrubland +relationship: part_of ENVO:01001369 ! tidal mangrove shrubland property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] -id: PCO:0000041 +id: PCO:0000048 name: invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO is_a: PATO:0001241 ! physical object quality [Term] -id: PCO:0000042 +id: PCO:0000049 name: microbe synonym: "microbial organism" EXACT [] is_a: CARO:0001010 ! organism or virus or viroid -relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye [Term] -id: PCO:0000043 +id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe -intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe -relationship: RO:0002351 PCO:0000042 ! microbe +intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! has member microbe +intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! has member microbe +relationship: RO:0002351 PCO:0000049 ! has member microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000044 +id: PCO:0000051 name: multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] is_a: PCO:0000029 ! multi-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000045 +id: PCO:0000052 name: single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] -is_a: PCO:0000018 ! single-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms +is_a: PCO:0000050 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000046 +id: PCO:0000053 name: microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] is_a: PCO:0000001 ! population of organisms -is_a: PCO:0000045 ! single species collection of microbes -relationship: RO:0002351 PCO:0000042 ! microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +[Term] +id: PCO:0000054 +name: number of generations of multicellular organism +def: "A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism." [] {comment="NCIT:C88214", comment="EFO:0000507"} +synonym: "number of generations" BROAD [] +is_a: STATO:0000047 ! count +relationship: IAO:0000136 CARO:0000012 ! is about multicellular organism +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 + +[Term] +id: PCO:0000057 +name: overcrowded population +def: "An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels." [] +synonym: "increased density of population" EXACT [] +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000058 +name: overcrowded human population +def: "A quality of a human population such that the density humans in an area is increased beyond sustainable levels." [] +is_a: PCO:0000057 ! overcrowded population +intersection_of: PCO:0000057 ! overcrowded population +intersection_of: RO:0000052 PCO:0000027 ! inheres in collection of humans +relationship: RO:0000052 PCO:0000027 ! inheres in collection of humans +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000059 +name: taxon as collection of organisms +def: "A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations." [] +comment: This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. +xref: data:1868 +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000060 +name: microbial parasite +def: "An organism or virus or viroid that is a microbe and a parasite." [] +is_a: ECOCORE:00000146 ! parasite +is_a: PCO:0000049 ! microbe +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000061 +name: parasite isolate population +def: "A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations." [] +is_a: PCO:0000050 ! collection of microbial organisms +is_a: PCO:0000053 ! microbial population +relationship: RO:0002351 PCO:0000060 ! has member microbial parasite +property_value: IAO:0000112 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811772/ +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "VEuPathDB" xsd:string + +[Term] +id: PCO:0000062 +name: Shannon diversity index +def: "A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi)." [] +synonym: "Shannon entropy" EXACT [] +synonym: "Shannon's diversity index" EXACT [] +synonym: "Shannon-Wiener index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html +property_value: IAO:0000119 "Shannon_index" + +[Term] +id: PCO:0000063 +name: Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi)." [] +synonym: "Simpson index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Simpson_index" + +[Term] +id: PCO:0000064 +name: inverse Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi)." [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Inverse_Simpson_index" + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: PCO:0000000 ! collection of organisms -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid [Term] id: PCO:0001001 name: pair of interacting organisms of the same species +def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms +relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms [Term] id: PCO:1000000 name: migratory population def: "A population which is participating in a migration process." [] is_a: PCO:0000001 ! population of organisms -relationship: RO:0000056 PCO:1000001 ! population migration +relationship: RO:0000056 PCO:1000001 ! participates in population migration property_value: IAO:0000114 IAO:0000123 [Term] @@ -1780,7 +2309,7 @@ name: human population migration def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration is_a: PCO:1000001 ! population migration -relationship: RO:0000057 PCO:0000027 ! collection of humans +relationship: RO:0000057 PCO:0000027 ! has participant collection of humans property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string @@ -1789,7 +2318,7 @@ id: PCO:1000003 name: human migratory population def: "A migratory population of humans, travelling with the intention of settling in a new area." [] is_a: PCO:0000027 ! collection of humans -relationship: RO:0000056 PCO:1000002 ! human population migration +relationship: RO:0000056 PCO:1000002 ! participates in human population migration property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string @@ -1800,21 +2329,1394 @@ def: "An ecological community which is composed of co-existing populations of mi comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. synonym: "microbiota" BROAD [] is_a: PCO:0000002 ! ecological community -is_a: PCO:0000044 ! multi-species collection of microbes +is_a: PCO:0000051 ! multi-species collection of microbes +property_value: editor_note "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string [Term] -id: Subset -is_a: IAO:0000102 ! data about an ontology part +id: STATO:0000047 +name: count +def: "a count is a data item denoted by an integer and represented the number of instances or occurences of an entity" [] +is_a: IAO:0000109 ! measurement datum +property_value: IAO:0000112 "a count of 4 resulting from counting limbs in humans" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string +property_value: IAO:0000117 "Orlaith Burke" xsd:string +property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string +property_value: IAO:0000119 "STATO" xsd:string +property_value: STATO:0000032 "" xsd:string + +[Typedef] +id: BFO:0000054 +name: realized in +comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realized in" xsd:string +property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string +property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string +property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string +property_value: IAO:0000118 "is realized by" xsd:string +property_value: IAO:0000118 "realized_in" xsd:string +property_value: IAO:0000600 "[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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +inverse_of: BFO:0000055 ! realizes + +[Typedef] +id: BFO:0000055 +name: realizes +comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realizes" xsd:string +property_value: IAO:0000112 "this disease course realizes this disease" xsd:string +property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string +property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string +property_value: IAO:0000600 "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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +domain: BFO:0000015 ! process +range: BFO:0000017 ! realizable entity + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "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." [] +subset: ro-eco +property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "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." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "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" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: part_of BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part_of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[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" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Term] -id: Synonym -is_a: IAO:0000102 ! data about an ontology part +[Typedef] +id: IAO:0000136 +name: is about +def: "A (currently) primitive relation that relates an information artifact to an entity." [] +property_value: editor_note "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string + +[Typedef] +id: PCO:0000055 +name: has member of +domain: PCO:0000000 ! collection of organisms + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: editor_note "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000079 +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 ! function +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000085 ! has function + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000085 +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000034 ! function +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +is_a: RO:0000052 ! inheres in + +[Typedef] +id: RO:0001000 +name: derives from +def: "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" [] +property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "derives_from" xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "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" [] +property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000111 "is location of" xsd:string +property_value: IAO:0000112 "my head is the location of my brain" xsd:string +property_value: IAO:0000112 "this cage is the location of this rat" xsd:string +property_value: IAO:0000118 "location_of" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string +property_value: IAO:0000111 "located in" xsd:string +property_value: IAO:0000112 "my brain is located in my head" xsd:string +property_value: IAO:0000112 "this rat is located in this cage" xsd:string +property_value: IAO:0000118 "located_in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true + +[Typedef] +id: RO:0002000 +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] +property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity + +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "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." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "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." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "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." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "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." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "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." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "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." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "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." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_functional: true +is_a: RO:0002017 ! has component activity +is_a: RO:0002211 ! regulates +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: has_part RO:0002131 +holds_over_chain: part_of part_of +is_a: RO:0002323 ! mereotopologically related to +transitive_over: part_of ! part_of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002180 +name: has component +def: "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." [] +subset: ro-eco +property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: has_part ! has part + +[Typedef] +id: RO:0002211 +name: regulates +def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string +property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002215 +name: capable of +def: "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. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of +expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process +expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002233 +name: has input +def: "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." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "consumes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "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." [] +property_value: IAO:0000112 "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." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "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." [] +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002321 +name: ecologically related to +def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] +subset: ro-eco +property_value: editor_note "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002327 +name: enables +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: has_part ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 part_of +is_a: RO:0000056 ! participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "regulated by (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part_of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +synonym: "affects" RELATED [] +property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "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" [] +property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "involved in or reguates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "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." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "executes activity in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso ECO:0000353 +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: editor_note "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: directly regulates activity of +def: "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0011002 ! regulates activity of + +[Typedef] +id: RO:0002449 +name: directly negatively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly inhibits" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002450 +name: directly positively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly activates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002464 +name: helper property (not for use in curation) +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "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." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} + +[Typedef] +id: RO:0002481 +name: is kinase activity +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002506 +name: causal relation between entities +property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002506 ! causal relation between entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002563 +name: interaction relation helper property +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +is_a: RO:0002464 ! helper property (not for use in curation) + +[Typedef] +id: RO:0002564 +name: molecular interaction relation helper property +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002566 +name: causally influences +def: "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)." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002506 ! causal relation between entities + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "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" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: has_part RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "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." [] +property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 has_part +is_a: RO:0002328 ! functionally related to +created_by: cjm +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "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" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: cjm +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "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" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: cjm +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0011002 +name: regulates activity of +def: "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." [] +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002566 ! causally influences + +[Typedef] +id: decreased_in_magnitude_relative_to +name: decreased_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: different_in_magnitude_relative_to +name: different_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality + +[Typedef] +id: editor_note +name: editor note +namespace: uberon +def: "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." [] +xref: IAO:0000116 +property_value: IAO:0000111 "editor note" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + +[Typedef] +id: has_part +name: has part +name: has_part +namespace: external +namespace: quality +def: "a core relation that holds between a whole and its part" [] +def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] +comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. +xref: BFO:0000051 +property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA 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'." xsd:string +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps -[Term] -id: SynonymType -is_a: IAO:0000102 ! data about an ontology part +[Typedef] +id: increased_in_magnitude_relative_to +name: increased_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: part_of +name: part of +name: part_of +namespace: external +namespace: quality +def: "a core relation that holds between a part and its whole" [] +xref: BFO:0000050 +property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA 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'." xsd:string +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: has_part ! has part + +[Typedef] +id: reciprocal_of +name: reciprocal_of +namespace: quality +def: "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." [PATOC:CJM] +comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl diff --git a/pco.owl b/pco.owl index 205fa6e..fc88485 100644 --- a/pco.owl +++ b/pco.owl @@ -1,26 +1,32 @@ - - - + + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg Ramona Walls - http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. + Population and Community Ontology + http://creativecommons.org/publicdomain/zero/1.0/ The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. @@ -62,12 +68,21 @@ + editor preferred label + editor preferred label + editor preferred term editor preferred term + editor preferred term~editor preferred label 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 label + editor preferred label + editor preferred term editor preferred term + editor preferred term~editor preferred label @@ -76,6 +91,7 @@ example + 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 @@ -106,6 +122,8 @@ PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 + + has curation status has curation status @@ -115,7 +133,10 @@ definition + definition + textual definition + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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 @@ -142,6 +163,7 @@ We also have the outstanding issue of how to aim different definitions to differ definition definition + textual definition @@ -154,6 +176,12 @@ We also have the outstanding issue of how to aim different definitions to differ 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.obfoundry.org/obo/obi> + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + IAO:0000116 + uberon + editor_note + true + editor_note editor note editor note @@ -170,6 +198,8 @@ We also have the outstanding issue of how to aim different definitions to differ 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 term editor @@ -183,6 +213,7 @@ We also have the outstanding issue of how to aim different definitions to differ An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + alternative term @@ -193,11 +224,14 @@ We also have the outstanding issue of how to aim different definitions to differ 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 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 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source definition source @@ -222,6 +256,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg + curator note @@ -230,13 +265,13 @@ We also have the outstanding issue of how to aim different definitions to differ - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + 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. + 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 @@ -245,10 +280,11 @@ We also have the outstanding issue of how to aim different definitions to differ + 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 + 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 The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester @@ -259,10 +295,10 @@ We also have the outstanding issue of how to aim different definitions to differ 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 - 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 + is denotator type @@ -276,6 +312,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from @@ -290,7 +327,8 @@ 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 + Chris Mungall + expand expression to @@ -326,7 +364,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. antisymmetric property part_of antisymmetric property xsd:true - use boolean value xsd:true to indicate that the property is an antisymmetric property + Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property @@ -339,12 +377,13 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. 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 . + 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/> + OBO foundry unique label @@ -353,14 +392,15 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 + 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 digit count @@ -369,12 +409,13 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Datatype: idrange:1 + 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 + 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 range allocated to @@ -383,15 +424,16 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 policy for + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for @@ -399,14 +441,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 + 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 ID prefix @@ -455,23 +498,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] is allocated id range - Add as annotation triples in the granting ontology 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 + Add as annotation triples in the granting ontology is allocated id range + + + + 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 + has ontology root term + + + + - 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 - #40 - VFB - 2018-09-21T16:43:39Z - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + 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 + #40 + VFB + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to @@ -480,6 +534,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + 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 https://github.com/geneontology/go-ontology/issues/15532 @@ -509,10 +564,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] term replaced by - Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by @@ -530,6 +585,94 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + is a defining property chain axiom + + + + + + + + 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. + + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + an alternative term used for STATO statistical ontology and ISA team + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO alternative term + + + + @@ -612,7 +755,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + + @@ -634,12 +779,36 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + @@ -675,6 +844,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + database_cross_reference @@ -700,7 +870,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - has_obo_namespace + has_obo_namespace @@ -739,6 +909,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + shorthand + + + + @@ -749,16 +934,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + - + + label + label @@ -771,6 +958,14 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -811,139 +1030,2218 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + + + + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + + + + + + + + BFO:0000050 + external + quality + part_of + part_of + + part of + part of + part_of + + + http://www.obofoundry.org/ro/#OBO_REL: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) + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + BFO:0000051 + external + quality + has_part + has_part + We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. + + has part + has part + has_part + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + PATOC:CJM + + + + + + + + + + + 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]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + + + 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]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + + + + + + + + + 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 + http://www.obofoundry.org/ro/#OBO_REL: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. + + + precedes + + + + + + + + + + + + + + + + + + + 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 + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs 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 + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + This document is about information artifacts and their representations + + A (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + + + + has member of + - + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + 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 + + bearer of + - + + + + + 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 + + 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 + http://www.obofoundry.org/ro/#OBO_REL:has_participant + + 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. + is concretized as + + + + + + + + + + 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. + concretizes + + + + + + + + + + + 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 + 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 + 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 + 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 + - + - + + + disposition of + - + - + + + 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 + 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 + derives into + - + - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - + + + + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + location_of + + location of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + located in + - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - + - - - - continuant - Continuant - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + 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 + + 2D boundary of + + + + + + + + + + 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 + + has 2D boundary + + + + + + + + + + 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. + dos + 2017-05-24T09:30:46Z + + has regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + + has negative regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + + has component activity + + + + + + + + + + + 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. + dos + 2017-05-24T09:49:21Z + + has component process + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:38Z + + directly negatively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:47Z + + directly positively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + + 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. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + + has 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. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + + immediately preceded by + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + + immediately precedes + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + overlaps + + + + + + + + + true + + + + + + + + + + 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. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + + has component + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + + positively regulates + + + + + + + + + + + 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. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + + capable of + + + + + + + + + + + + + + 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. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + + capable of part of + + + + + + + + + + true + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + + temporally related to + + + + + + + + + + + + + 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. + Chris Mungall + consumes + + + has input + + + + + + + + + + + + + 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. + + acts upstream of + + + + + + + + + + + + + + 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 + + acts upstream of or within + + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + causally upstream of, negative effect + + + + + + + + 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 + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + + ecologically related to + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + 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 + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + + involved in + + + + + + + + + + + inverse of enables + Chris Mungall + + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + + positively regulated by + + + + + + + + + + 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 + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + Chris Mungall + + + + input of + + + + + + + + + + + + inverse of upstream of + Chris Mungall + + causally downstream of + + + + + + + + + + + + Chris Mungall + + immediately causally downstream of + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + 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. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + + involved in negative regulation of + + + + + + + + + + + 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 + Chris Mungall + involved in or reguates + + involved in or involved in regulation of + + + + + + + + + + + + + + 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. + Chris Mungall + executes activity in + enables activity in + + + is active in + + + + + + + + + true + + + + + 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. + GOC:cjm + GOC:dos + + + + + + + + + + + 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. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + 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. + Chris Mungall + binds + molecularly binds with + + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + + phosphorylates + + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + molecularly controls + + directly regulates activity of + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + directly inhibits + molecularly decreases activity of + + directly negatively regulates 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. + Chris Mungall + Vasundra Touré + directly activates + molecularly increases activity of + + directly positively regulates activity of + + + + + + + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + + helper property (not for use in curation) + + + + + + + + + + + + + + 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. + Chris Mungall + + + has part that occurs in + + + + + + + + + true + + + + + + + + + Chris Mungall + + is kinase activity + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + + causal agent in 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between processes + + + + + + + + + + + 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 + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between entities + + + + + + + + + + Chris Mungall + + causally influenced by (entity-centric) + + causally influenced by + + + + + + + + + Chris Mungall + + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + + molecular interaction relation helper property + + + + + + + + + + + + + + + + + + + + + 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). + Chris Mungall + Vasundra Touré + + causally influences (entity-centric) + + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + + directly regulates + + + + + + + + + + + + + + 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 + Chris Mungall + + has part structure that is capable of + + + + + + + + + + + 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. + Chris Mungall + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + + capable of negatively regulating + + + + + + + + + + + + + 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. + + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + + process has causal agent + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + + directly negatively regulates + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + + causally upstream of or within, positive effect + + + + + + + + + + + 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. + Vasundra Touré + + regulates activity of + + + + + + + + + + + + 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. + quality + decreased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + + decreased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + 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. + quality + different_in_magnitude_relative_to + + different_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + + + 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. + quality + increased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + + increased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + 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. + quality + reciprocal_of + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + + reciprocal_of + + + + + 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. + PATOC:CJM + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - continuant + entity - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + + + + + + + + + + + + continuant + Continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + @@ -986,6 +3284,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + @@ -993,8 +3303,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + occurrent Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. @@ -1057,6 +3380,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + ic @@ -1071,6 +3400,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] an organism the bottom right portion of a human torso the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) @@ -1119,6 +3449,26 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. + obsolete dependent continuant + true + + + + + + + + + spatial region + + + + @@ -1132,6 +3482,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the flight of a bird the life of an organism your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] @@ -1153,10 +3504,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + disposition + + + + + realizable RealizableEntity the disposition of this piece of metal to conduct electricity. @@ -1164,6 +3526,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet + 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. + https://orcid.org/0000-0001-8815-0078 To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] @@ -1198,10 +3562,25 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + quality + + + + + + + + + + sdc SpecificallyDependentContinuant @@ -1216,6 +3595,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the role of being a doctor the shape of this hole. the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. 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]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] @@ -1257,6 +3637,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the role of a stone in marking a property boundary the role of subject in a clinical trial the student role + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] @@ -1388,6 +3769,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] @@ -1408,6 +3790,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + function + + + + @@ -1427,6 +3818,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] an energy wave an epidemic the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. @@ -1491,6 +3883,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. + multicellular organism + Melissa Haendel + 9/18/11 + MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. + multicellular organism + + + + @@ -1512,75 +3919,39 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] organism mah 7.16.2011 - A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. organism - - - - - A feature that has been constructed by deliberate human effort. - "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference - constructed feature - construction - - - - - A feature that has been constructed by deliberate human effort. - MA:ma - - - - - + - - - A material entity which determines an environmental system. - ENVO - ENVO:00002297 - A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. - environmental feature + + + heterotroph that acquires nutrition from a symbiont + http://orcid.org/0000-0002-2908-3327 + symbiotroph - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - + - - - A system which has the disposition to environ one or more material entities. - 2013-09-23T16:04:08Z - EcoLexicon:environment - environment - In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. - environmental system + + + A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host + http://orcid.org/0000-0002-2908-3327 + https://www.wikidata.org/entity/Q10253316 + parasite - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. Subclasses will be added by inference. @@ -1595,24 +3966,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - A material part of an astronomical body. - envoAstro - envoPolar - astronomical body part - - - - - + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. - http://orcid.org/0000-0002-4366-3088 + CMECS:577 https://cmecscatalog.org/cmecs/classification/unit/577.html envoCmecs @@ -1623,14 +3982,37 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + molecular process + + molecular_function + + + + + + + + + + catalytic activity + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. - janelomax + jl 2012-09-20T14:06:08Z + GO:0023032 GO:0044708 + GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour @@ -1661,8 +4043,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - janelomax + jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 @@ -1683,7 +4066,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process @@ -1696,11 +4079,47 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + true + + + + kinase activity + + + + + + + + + + transferase activity + + + + + + + + + + transferase activity, transferring phosphorus-containing groups + + + + + - Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour @@ -1725,8 +4144,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + Any process in which an organism has an effect on an organism of a different species. + interaction with another species interspecies interaction interspecies interaction with other organisms @@ -1749,7 +4169,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + Any process in which an organism has an effect on an organism of the same species. intraspecies interaction with other organisms biological_process @@ -1770,7 +4190,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A biological process which involves another organism of the same or different species. GO:0051706 @@ -1793,45 +4212,30 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GO:0023032 - GO:0044709 - behavioral interaction between organisms - behavioral interaction with other organism - behavioural interaction between organisms - behavioural interaction with other organism - behavioral signaling - behavioral signalling - biological_process - GO:0051705 - - - multi-organism behavior - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GOC:ai - - - - - behavioral signalling - GOC:mah - - - - + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item @@ -1841,6 +4245,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + information content entity information content entity @@ -1881,13 +4286,32 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg + 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 data about an ontology part + + + + + measurement datum + Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + + measurement datum + + + + @@ -1927,11 +4351,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - denotator type + 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 + denotator type @@ -1940,12 +4365,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - cjm - 2018-05-20T20:55:03Z - ontology module + 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 + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module @@ -1954,10 +4378,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - cjm - 2018-05-20T20:55:30Z - base ontology module + 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. + base ontology module @@ -1967,11 +4390,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:55:47Z - editors ontology module + 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 + editors ontology module @@ -1980,11 +4402,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:56:13Z - main release 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 + main release ontology module @@ -1993,10 +4414,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - cjm - 2018-05-20T20:56:23Z - bridge ontology 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. + bridge ontology module @@ -2006,12 +4426,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:56:47Z - import ontology 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 + import ontology module @@ -2021,12 +4440,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - cjm - 2018-05-20T20:58:11Z - subset ontology module + 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 + subset ontology module @@ -2037,10 +4455,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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. - cjm - 2018-05-20T20:58:38Z - curation subset ontology module + 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. + curation subset ontology module @@ -2049,10 +4466,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is intended for usage in analysis or discovery applications. - cjm - 2018-05-20T20:58:49Z - analysis subset ontology module + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module @@ -2061,11 +4477,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:59:19Z - single layer subset ontology module + 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 + single layer subset ontology module @@ -2074,11 +4489,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - cjm - 2018-05-20T20:59:57Z - exclusion subset ontology module + 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 + exclusion subset ontology module @@ -2087,11 +4501,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - cjm - 2018-05-20T21:00:14Z - external import ontology module + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module @@ -2100,11 +4513,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - cjm - 2018-05-20T21:14:16Z - species subset ontology module + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module @@ -2114,10 +4526,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - cjm - 2018-05-20T21:20:33Z - reasoned ontology module + 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. + reasoned ontology module @@ -2127,11 +4538,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T21:21:12Z - generated ontology module + 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 + generated ontology module @@ -2140,10 +4550,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - cjm - 2018-05-20T21:21:21Z - template generated ontology module + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module @@ -2155,9 +4564,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - cjm - 2018-05-20T21:28:15Z - taxonomic bridge ontology module + taxonomic bridge ontology module + taxonomic bridge ontology module @@ -2166,9 +4574,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - cjm - 2018-05-22T04:15:54Z - ontology module subsetted by expressivity + ontology module subsetted by expressivity + ontology module subsetted by expressivity @@ -2177,7 +4584,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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. + 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). @@ -2193,9 +4601,7 @@ No qualifier lists No disjointness axioms No owl-axioms header No imports - cjm - 2018-05-22T04:16:10Z - obo basic subset ontology module + obo basic subset ontology module @@ -2205,9 +4611,8 @@ No imports - cjm - 2018-05-22T04:16:28Z - ontology module subsetted by OWL profile + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile @@ -2216,9 +4621,8 @@ No imports - cjm - 2018-05-22T04:16:48Z - EL++ ontology module + EL++ ontology module + EL++ ontology module @@ -2270,46 +4674,20 @@ No imports - - - NCBITaxon:40673 - GC_ID:1 - bony vertebrates - ncbi_taxonomy - - Euteleostomi - - - - - bony vertebrates - - - - - - - - - + + + NCBITaxon:40673 GC_ID:1 + bony vertebrates ncbi_taxonomy - Viroid - viroids - Viroids + Euteleostomi - - - Viroid - - - - - - viroids - + + + bony vertebrates + @@ -2320,22 +4698,22 @@ No imports GC_ID:1 + charophyte/embryophyte group ncbi_taxonomy Charophyta/Embryophyta group - charophyte/embryophyte group Streptophytina - - Charophyta/Embryophyta group - + + charophyte/embryophyte group + - charophyte/embryophyte group + Charophyta/Embryophyta group @@ -2429,7 +4807,9 @@ No imports PMID:12054223 PMID:2112744 PMID:270744 + PMID:7520741 PMID:8123559 + PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 @@ -2445,12 +4825,6 @@ No imports Bacteria - - - - prokaryotes - - @@ -2493,6 +4867,12 @@ No imports prokaryote + + + + prokaryotes + + @@ -2631,6 +5011,7 @@ No imports GC_ID:1 PMID:23020233 + PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy @@ -2886,7 +5267,7 @@ No imports Theria ncbi_taxonomy - Theria <Mammalia> + Theria <mammals> @@ -2903,11 +5284,14 @@ No imports GC_ID:1 + PMID:16248873 + PMID:30257078 + Chlorophyta/Embryophyta group + chlorophyte/embryophyte group green plants ncbi_taxonomy Chlorobionta - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group + Chloroplastida green plants Viridiplantae @@ -2915,25 +5299,31 @@ No imports - green plants - + Chlorophyta/Embryophyta group + - - Chlorobionta - + + chlorophyte/embryophyte group + + + + + + green plants + - Chlorophyta/Embryophyta group + Chlorobionta - chlorophyte/embryophyte group + Chloroplastida @@ -3047,15 +5437,17 @@ No imports + GC_ID:1 PMID:25249442 angiosperms flowering plants ncbi_taxonomy Angiospermae + Magnoliophyta flowering plants - Magnoliophyta + Magnoliopsida @@ -3075,6 +5467,12 @@ No imports Angiospermae + + + + Magnoliophyta + + @@ -3137,6 +5535,41 @@ No imports + + + + + + GC_ID:1 + PMID:11062127 + PMID:12684019 + ncbi_taxonomy + Mycota + fungi + + Fungi + + + + + Mycota + + + + + + fungi + + + + + + fungi + + + + + @@ -3238,7 +5671,7 @@ No imports ncbi_taxonomy vertebrates - Vertebrata <Metazoa> + Vertebrata <vertebrates> @@ -3270,7 +5703,7 @@ No imports jawed vertebrates ncbi_taxonomy - Gnathostomata <vertebrate> + Gnathostomata <vertebrates> @@ -3292,16 +5725,16 @@ No imports GC_ID:1 + euphyllophytes ncbi_taxonomy - euphyllophytes Euphyllophyta - + euphyllophytes - + @@ -3328,7 +5761,7 @@ No imports Craniata ncbi_taxonomy - Craniata <chordata> + Craniata <chordates> @@ -3489,19 +5922,6 @@ No imports human man ncbi_taxonomy - Home sapiens - Homo sampiens - Homo sapeins - Homo sapian - Homo sapians - Homo sapien - Homo sapience - Homo sapiense - Homo sapients - Homo sapines - Homo spaiens - Homo spiens - Humo sapiens Homo sapiens @@ -3517,124 +5937,340 @@ No imports man + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality (PATO) + PATO:0000072 + quality + PATO:0000001 + + quality + - - - Home sapiens - - - - - - Homo sampiens - - - - - - Homo sapeins - - - - - - Homo sapian - - - - - - Homo sapians - + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + quality + PATO:0000068 + TODO: define this or obsolete it and move children somewhere else. + + qualitative + + + + + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + quality + PATO:0000069 + + + deviation (from_normal) + - - - Homo sapien - + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + PATOC:GVG + + + + + + + + + + + + + + The number of entities of this type that are part of the whole organism. + PATO:0000053 + PATO:0000071 + PATO:0001169 + PATO:0001226 + presence or absence in organism + quantitative + quality + count in organism + number + presence + PATO:0000070 + + This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. + + amount + - - - Homo sapience - + + + The number of entities of this type that are part of the whole organism. + PATOC:GVG + + + + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + + rate + - - - Homo sapiense - + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + PATOC:melissa + + + + + + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + + quality + average + PATO:0000461 + + + + + normal + - - - Homo sapients - + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + PATOC:GVG + + + + + + + + A quality inhering in a bearer by virtue of the bearer's existence. + + quality + present in organism + PATO:0000467 + + + + present + - - - Homo sapines - + + + A quality inhering in a bearer by virtue of the bearer's existence. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + An amount which is relatively high. + + PATO:0000420 + PATO:0000650 + increased number + present in greater numbers in organism + supernumerary + quality + accessory + increased + PATO:0000470 + + + increased amount + - - - Homo spaiens - + + + An amount which is relatively high. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + A rate which is relatively low. + + slow rate + quality + PATO:0000911 + + + + decreased rate + - - - Homo spiens - + + + A rate which is relatively low. + PATO:GVG + + + + + + + + + + + + + + + + + + + + A rate which is relatively high. + + fast rate + high rate + quality + PATO:0000912 + + + + increased rate + - - - Humo sapiens - + + + A rate which is relatively high. + PATO:GVG - + - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 - trait + + + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + PATO:0002079 + Wikipedia:Physical_property + relational physical quality quality - PATO:0000001 + PATO:0001018 + - quality + physical quality - + - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG - + - - - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + + + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality - PATO:0000161 + density + PATO:0001019 - rate + mass density - + - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. - PATOC:melissa + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. + WordNet:WordNet + + + + + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + quality + PATO:0001164 + + + + dense + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + PATOC:GVG @@ -3643,6 +6279,7 @@ No imports + A quality which inheres in an process. PATO:0001239 PATO:0001240 @@ -3738,6 +6375,148 @@ No imports + + + + + + + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + OBO_REL:has_part + extra or missing physical or functional parts + has or lacks parts of type + mereological quality + number of + quality + cardinality + number + PATO:0001555 + + + + has number of + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + PATOC:CJM + + + + + + + + + + + + + + + + + + + + + A density which is higher relative to the normal or average. + + high density + quality + PATO:0001788 + + + increased mass density + + + + + A density which is higher relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A density which is lower relative to the normal or average. + + low density + quality + PATO:0001790 + + + decreased mass density + + + + + A density which is lower relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + An amount which is relatively low. + + PATO:0000419 + PATO:0000468 + decreased number + present in fewer numbers in organism + quality + decreased + reduced + subnumerary + PATO:0001997 + + + decreased amount + + + + + An amount which is relatively low. + PATOC:GVG + + + + @@ -3773,6 +6552,220 @@ No imports + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:39:43Z + quality + PATO:0002300 + + increased quality + + + + + A quality that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:40:15Z + quality + PATO:0002301 + + decreased quality + + + + + A quality that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:50:59Z + quality + PATO:0002302 + + decreased process quality + + + + + A quality of a process that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:51:54Z + quality + PATO:0002303 + + decreased object quality + + + + + A quality of an object that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:53:08Z + quality + PATO:0002304 + + increased process quality + + + + + A quality of a process that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:54:01Z + quality + PATO:0002305 + + increased object quality + + + + + A quality of an object that has a value that is increased compared to normal or average. + PATOC:GVG + + + + @@ -3799,6 +6792,12 @@ No imports + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. @@ -3830,18 +6829,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - 2 - - - - - + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 @@ -3873,8 +6861,9 @@ Classes for population already exist in IDO ('organism population', I - A quality that inheres in a biological population. + A quality that inheres in a population of organisms. See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community. Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. quality of a population @@ -3922,8 +6911,8 @@ Classes for population already exist in IDO ('organism population', I - A process that has as primary participant a population. - Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. + The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. population process @@ -3932,8 +6921,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of birth of a population of organisms. population birth rate @@ -3942,8 +6932,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of death of a population of organsisms. population death rate @@ -3952,9 +6943,9 @@ Classes for population already exist in IDO ('organism population', I - + - Is a rate a quality? Population growth rate may be better classified as a process profile. + The rate of growth of a population. population growth rate @@ -4023,30 +7014,51 @@ Classes for population already exist in IDO ('organism population', I - - - predator role + + Interactions are now covered in EcoCore ontology. + obsolete predator role + true + + + + true + + - - - prey role + + Interactions are now covered in EcoCore ontology. + obsolete prey role + true + + + + true + + - - - symbiont role + + Interactions are now covered in EcoCore ontology. + obsolete symbiont role + true + + + + true + + @@ -4054,9 +7066,15 @@ Classes for population already exist in IDO ('organism population', I + - A collection of organisms that has as parts every organism of given species and no organisms of any other species. + A collection of organisms that has as members every organism of given species and no organisms of any other species. + A collection of organisms that has as parts every organism of a species and no organisms of any other species. At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + + + + taxonomic group This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. species as a collection of organisms @@ -4073,25 +7091,26 @@ Classes for population already exist in IDO ('organism population', I - - - - - - 1 - - - - 2 + + + 1 + + + + + + + + A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -4156,7 +7175,7 @@ Classes for population already exist in IDO ('organism population', I If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. - A quality of a community that reflects how close in abundance all species in a community are. + A quality of an ecological community that reflects how close in abundance all species in a community are. adapted from http://en.wikipedia.org/wiki/Species_evenness community species evenness @@ -4166,7 +7185,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -4190,7 +7209,7 @@ Classes for population already exist in IDO ('organism population', I An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. - Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household household @@ -4203,7 +7222,7 @@ Classes for population already exist in IDO ('organism population', I This is an example population added to demonstrate the modeling pattern for collections of organisms. - red population + obsolete red population true @@ -4215,7 +7234,7 @@ Classes for population already exist in IDO ('organism population', I An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. - red organism + obsolete red organism true @@ -4264,7 +7283,7 @@ Classes for population already exist in IDO ('organism population', I Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). - community + obsolete community true @@ -4274,6 +7293,13 @@ Classes for population already exist in IDO ('organism population', I + + + + 2 + + + A collection of organisms that consists of two or more organisms from at least two species. Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". @@ -4372,34 +7398,336 @@ Classes for population already exist in IDO ('organism population', I + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 - A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. GenEpio curators potluck - + + + + + A human social gathering at which two people are married. May include a legal or social ceremony. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 + GenEpio curators + wedding + + + + + + + + + A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 + GenEpiO curators + baby shower + + + + + + + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community + + + + + + + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + microbial organism + microbe + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + + + + + + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + number of generations + number of generations of multicellular organism + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + + + + + + + + + + + + + + + + + + + + + + An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels. + + increased density of population + overcrowded population + + + + + + + + + + + + + + + + + + + + + + + + + + + A quality of a human population such that the density humans in an area is increased beyond sustainable levels. + + overcrowded human population + + + + + + + + + + A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations. + + + This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. + taxon as collection of organisms + + + + + + + + + + + An organism or virus or viroid that is a microbe and a parasite. + + microbial parasite + + + + + + + + + + + + + + + + + + A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations. + + VEuPathDB + parasite isolate population + + + + + + + + + + A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi). + + + Shannon entropy + Shannon's diversity index + Shannon-Wiener index + Shannon diversity index + + + + + - - - A human social gathering at which two people are married. May include a legal or social ceremony. - Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 - GenEpio curators - wedding + + + + A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi). + + + Simpson index + Simpson diversity index - + - - - A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. - Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 - GenEpiO curators - baby shower + + + + A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi). + + + inverse Simpson diversity index @@ -4408,12 +7736,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - @@ -4430,25 +7752,16 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 1 - - - - - - - + + + + 1 + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. pair of interacting organisms of the same species @@ -4525,7 +7838,7 @@ Classes for population already exist in IDO ('organism population', I - + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 @@ -4538,6 +7851,23 @@ Classes for population already exist in IDO ('organism population', I + + + + + a count of 4 resulting from counting limbs in humans + + a count is a data item denoted by an integer and represented the number of instances or occurences of an entity + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO + + count + + + + @@ -4551,55 +7881,10 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Obsolete Class @@ -4607,19 +7892,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 https://cmecscatalog.org/cmecs/classification/unit/577.html mangrove community tidal shrubland community - tidal mangrove shrubland community + obsolete tidal mangrove shrubland community + true @@ -4627,10 +7908,12 @@ Classes for population already exist in IDO ('organism population', I - + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO - invisible to unaided eye + obsolete invisible to unaided eye + true @@ -4638,15 +7921,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + + microbial organism - microbe + obsolete microbe + true @@ -4654,31 +7933,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - - - - - - - - + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 - collection of microbial organisms + obsolete collection of microbial organisms + true @@ -4686,11 +7946,12 @@ Classes for population already exist in IDO ('organism population', I - - + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 - multi-species collection of microbes + obsolete multi-species collection of microbes + true @@ -4698,36 +7959,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - 1 - - - - - - - 2 - - - - - - - + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 - single species collection of microbes + obsolete single species collection of microbes + true @@ -4735,18 +7972,13 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 microbiota - microbial population + obsolete microbial population + true @@ -4766,6 +7998,7 @@ Classes for population already exist in IDO ('organism population', I + example to be eventually removed example to be eventually removed @@ -4775,8 +8008,9 @@ Classes for population already exist in IDO ('organism population', I + 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 + Person:Alan Ruttenberg failed exploratory term @@ -4786,6 +8020,7 @@ Classes for population already exist in IDO ('organism population', I + 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. metadata complete @@ -4796,7 +8031,8 @@ Classes for population already exist in IDO ('organism population', I - term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -4806,6 +8042,7 @@ Classes for population already exist in IDO ('organism population', I + 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." ready for release @@ -4816,6 +8053,7 @@ Classes for population already exist in IDO ('organism population', I + metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -4826,6 +8064,7 @@ Classes for population already exist in IDO ('organism population', I + uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -4836,6 +8075,7 @@ Classes for population already exist in IDO ('organism population', I + 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. pending final vetting @@ -4845,11 +8085,12 @@ Classes for population already exist in IDO ('organism population', I - 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 - core + + obsolete_core + true @@ -4858,6 +8099,7 @@ Classes for population already exist in IDO ('organism population', I + placeholder removed placeholder removed @@ -4867,6 +8109,7 @@ Classes for population already exist in IDO ('organism population', I + terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -4877,6 +8120,7 @@ Classes for population already exist in IDO ('organism population', I + 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 imported @@ -4887,6 +8131,7 @@ Classes for population already exist in IDO ('organism population', I + 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. term split @@ -4897,10 +8142,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - universal + 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 + universal @@ -4909,10 +8155,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - defined class + 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 + defined class @@ -4921,10 +8168,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - named class expression + 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 + named class expression @@ -4933,6 +8181,7 @@ Classes for population already exist in IDO ('organism population', I + to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI @@ -4945,6 +8194,7 @@ Classes for population already exist in IDO ('organism population', I + 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 @@ -4961,6 +8211,39 @@ Classes for population already exist in IDO ('organism population', I /////////////////////////////////////////////////////////////////////////////////////// --> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4983,9 +8266,926 @@ Classes for population already exist in IDO ('organism population', I + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + diff --git a/reports/pco-edit.owl-obo-report.tsv b/reports/pco-edit.owl-obo-report.tsv index 4d1219e..02983a2 100644 --- a/reports/pco-edit.owl-obo-report.tsv +++ b/reports/pco-edit.owl-obo-report.tsv @@ -1,24 +1,17 @@ Level Rule Name Subject Property Value +ERROR missing_label BFO:0000017 rdfs:label +ERROR missing_label ECOCORE:00000045 rdfs:label ERROR missing_label GO:0051704 rdfs:label ERROR missing_label IAO:0000030 rdfs:label -ERROR missing_ontology_description pco.owl dc11:description -ERROR missing_ontology_license pco.owl dc:license -ERROR missing_ontology_title pco.owl dc11:title +ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as members every organism of given species and no organisms of any other species.@en +ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as parts every organism of a species and no organisms of any other species.@en +WARN missing_definition BFO:0000017 IAO:0000115 +WARN missing_definition ECOCORE:00000045 IAO:0000115 WARN missing_definition GO:0051704 IAO:0000115 WARN missing_definition IAO:0000030 IAO:0000115 -WARN missing_definition PCO:0000006 IAO:0000115 -WARN missing_definition PCO:0000007 IAO:0000115 -WARN missing_definition PCO:0000008 IAO:0000115 -WARN missing_definition PCO:0000014 IAO:0000115 -WARN missing_definition PCO:0000015 IAO:0000115 -WARN missing_definition PCO:0000016 IAO:0000115 -WARN missing_definition PCO:0000037 IAO:0000115 -WARN missing_definition PCO:0001001 IAO:0000115 -WARN missing_definition https://purl.obolibrary.org/obo/PCO_0000042 IAO:0000115 -WARN missing_obsolete_label PCO:0000025 rdfs:label red population@en -WARN missing_obsolete_label PCO:0000026 rdfs:label red organism@en -WARN missing_obsolete_label PCO:0000028 rdfs:label community@en +WARN missing_definition PCO:0000049 IAO:0000115 +WARN missing_definition PCO:0000055 IAO:0000115 INFO missing_superclass PCO:0000003 rdfs:subClassOf INFO missing_superclass PCO:0000004 rdfs:subClassOf -INFO missing_superclass https://purl.obolibrary.org/obo/PCO_0000043 rdfs:subClassOf -INFO missing_superclass https://purl.obolibrary.org/obo/PCO_0000045 rdfs:subClassOf +INFO missing_superclass PCO:0000050 rdfs:subClassOf +INFO missing_superclass PCO:0000052 rdfs:subClassOf diff --git a/src/ontology/Makefile b/src/ontology/Makefile index db3aa85..ad89868 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -67,7 +67,7 @@ all_main: $(MAIN_FILES) ## By default this is the cross-product of IMPORT_MODULES x FORMATS -IMPORTS = bfo envo go pato ro +IMPORTS = bfo ecocore envo go iao ncbitaxon pato ro stato IMPORT_ROOTS = $(patsubst %, imports/%_import, $(IMPORTS)) IMPORT_FILES = $(foreach n,$(IMPORT_ROOTS), $(foreach f,$(FORMATS), $(n).$(f))) diff --git a/src/ontology/imports/ecocore_import.obo b/src/ontology/imports/ecocore_import.obo new file mode 100644 index 0000000..2dec575 --- /dev/null +++ b/src/ontology/imports/ecocore_import.obo @@ -0,0 +1,30 @@ +format-version: 1.2 +ontology: pco/imports/ecocore_import + +[Term] +id: ECOCORE:00000045 +name: symbiotroph +def: "heterotroph that acquires nutrition from a symbiont" [] +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string + +[Term] +id: ECOCORE:00000146 +name: parasite +def: "A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host" [] +xref: https://www.wikidata.org/entity/Q10253316 +is_a: ECOCORE:00000045 ! symbiotroph +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string + +[Typedef] +id: editor_note +name: editor note +namespace: uberon +def: "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." [] +xref: IAO:0000116 +property_value: IAO:0000111 "editor note" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + diff --git a/src/ontology/imports/envo_import.obo b/src/ontology/imports/envo_import.obo index 0e05ab0..8b04c52 100644 --- a/src/ontology/imports/envo_import.obo +++ b/src/ontology/imports/envo_import.obo @@ -1,62 +1,19 @@ format-version: 1.2 -default-namespace: ENVO -remark: ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. \n\nNew terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ \n\n\nPlease see www.environmentontology.org for more information and citations. -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 186 Logical Axioms: 30] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 114 Logical Axioms: 19] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 132 Logical Axioms: 23] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 40 Logical Axioms: 6] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 21 Logical Axioms: 2] ontology: pco/imports/envo_import -property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-4366-3088 xsd:string -property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-6601-2165 xsd:string -property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8343-612X xsd:string -property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0003-1604-1512 xsd:string -property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0002-6962-2807 xsd:string [Term] -id: ENVO:00000070 -name: construction -def: "A feature that has been constructed by deliberate human effort." [MA:ma] -synonym: "constructed feature" EXACT [] -is_a: BFO:0000040 -is_a: ENVO:00002297 ! environmental feature -is_a: ENVO:01000813 ! astronomical body part -property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string - -[Term] -id: ENVO:00002297 -name: environmental feature -def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] -comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. -is_a: BFO:0000040 - -[Term] -id: ENVO:01000254 -name: environmental system -def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] -comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. -synonym: "environment" EXACT [] -xref: EcoLexicon:environment -is_a: BFO:0000040 -creation_date: 2013-09-23T16:04:08Z +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] [Term] id: ENVO:01000744 name: human dwelling def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] -is_a: ENVO:00000070 ! construction +is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string -[Term] -id: ENVO:01000813 -name: astronomical body part -def: "A material part of an astronomical body." [] -subset: envoAstro -subset: envoPolar -is_a: BFO:0000040 -is_a: ENVO:00002297 ! environmental feature - [Term] id: ENVO:01001369 name: tidal mangrove shrubland @@ -66,6 +23,6 @@ comment: This class aligns to the Coastal and Marine Ecological Classification S subset: envoCmecs subset: envoMarine xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ENVO:01000254 ! environmental system +is_a: BFO:0000040 ! material entity created_by: http://orcid.org/0000-0002-4366-3088 diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl index 26bd646..48fc2f0 100644 --- a/src/ontology/imports/envo_import.owl +++ b/src/ontology/imports/envo_import.owl @@ -12,26 +12,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - - http://orcid.org/0000-0002-6601-2165 - http://orcid.org/0000-0002-8343-612X - http://orcid.org/0000-0003-1604-1512 - ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities - The Environment Ontology - https://creativecommons.org/publicdomain/zero/1.0/ - https://github.com/EnvironmentOntology/envo/ - https://github.com/EnvironmentOntology/envo/issues/ - ENVO - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 499 Logical Axioms: 88] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 114 Logical Axioms: 19] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 135 Logical Axioms: 22] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>) VersionIRI(<null>))) [Axioms: 40 Logical Axioms: 6] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>) VersionIRI(<null>))) [Axioms: 21 Logical Axioms: 2] - 2020-06-10 - http://environmentontology.org/ - + @@ -207,5 +188,5 @@ - + diff --git a/src/ontology/imports/go_import.obo b/src/ontology/imports/go_import.obo index 6c1fbb0..120b9b9 100644 --- a/src/ontology/imports/go_import.obo +++ b/src/ontology/imports/go_import.obo @@ -5,7 +5,9 @@ ontology: pco/imports/go_import id: GO:0007610 name: behavior namespace: biological_process +alt_id: GO:0023032 alt_id: GO:0044708 +alt_id: GO:0044709 def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). subset: gocheck_do_not_manually_annotate @@ -18,7 +20,7 @@ synonym: "single-organism behavior" RELATED [] xref: Wikipedia:Behavior is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-20T14:06:08Z [Term] @@ -29,7 +31,7 @@ alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] -comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl @@ -45,7 +47,7 @@ synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-19T15:05:24Z [Term] @@ -57,8 +59,8 @@ comment: Behavior such as predation which involves members of different species synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior +is_a: GO:0007610 ! behavior is_a: GO:0051703 ! intraspecies interaction between organisms -is_a: GO:0051705 ! multi-organism behavior property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -71,8 +73,9 @@ subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 @@ -81,7 +84,7 @@ namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] subset: goslim_pir synonym: "intraspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -98,21 +101,3 @@ synonym: "physiological interaction with other organism" EXACT [] is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -[Term] -id: GO:0051705 -name: multi-organism behavior -namespace: biological_process -alt_id: GO:0023032 -alt_id: GO:0044709 -def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] -subset: goslim_pir -synonym: "behavioral interaction between organisms" EXACT [] -synonym: "behavioral interaction with other organism" EXACT [] -synonym: "behavioral signaling" NARROW [] -synonym: "behavioral signalling" NARROW [GOC:mah] -synonym: "behavioural interaction between organisms" EXACT [] -synonym: "behavioural interaction with other organism" EXACT [] -is_a: GO:0007610 ! behavior -is_a: GO:0051704 ! multi-organism process -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - diff --git a/src/ontology/imports/iao_import.obo b/src/ontology/imports/iao_import.obo new file mode 100644 index 0000000..d60f8be --- /dev/null +++ b/src/ontology/imports/iao_import.obo @@ -0,0 +1,13 @@ +format-version: 1.2 +ontology: pco/imports/iao_import + +[Typedef] +id: IAO:0000136 +name: is about +def: "A (currently) primitive relation that relates an information artifact to an entity." [] +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string + diff --git a/src/ontology/imports/ncbitaxon_import.obo b/src/ontology/imports/ncbitaxon_import.obo index 3ba2b8c..3a99382 100644 --- a/src/ontology/imports/ncbitaxon_import.obo +++ b/src/ontology/imports/ncbitaxon_import.obo @@ -17,7 +17,7 @@ id: NCBITaxon:117570 name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 -is_a: NCBITaxon:7776 ! Gnathostomata +is_a: NCBITaxon:7776 ! Gnathostomata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -30,22 +30,12 @@ xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl -[Term] -id: NCBITaxon:12884 -name: Viroids -namespace: ncbi_taxonomy -synonym: "Viroid" RELATED synonym [] -synonym: "viroids" RELATED blast_name [] -xref: GC_ID:1 -property_value: has_rank NCBITaxon:superkingdom -property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl - [Term] id: NCBITaxon:131221 name: Streptophytina namespace: ncbi_taxonomy synonym: "Charophyta/Embryophyta group" RELATED synonym [] -synonym: "charophyte/embryophyte group" RELATED synonym [] +synonym: "charophyte/embryophyte group" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:35493 ! Streptophyta property_value: has_rank NCBITaxon:subphylum @@ -118,7 +108,9 @@ xref: PMID:11760965 xref: PMID:12054223 xref: PMID:2112744 xref: PMID:270744 +xref: PMID:7520741 xref: PMID:8123559 +xref: PMID:8186100 xref: PMID:8590690 xref: PMID:9103655 xref: PMID:9336922 @@ -193,6 +185,7 @@ synonym: "eukaryotes" EXACT common_name [] synonym: "eukaryotes" RELATED blast_name [] xref: GC_ID:1 xref: PMID:23020233 +xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms property_value: has_rank NCBITaxon:superkingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -278,7 +271,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32525 -name: Theria +name: Theria namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 @@ -290,11 +283,14 @@ id: NCBITaxon:33090 name: Viridiplantae namespace: ncbi_taxonomy synonym: "Chlorobionta" RELATED synonym [] -synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] -synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name [] +synonym: "chlorophyte/embryophyte group" EXACT equivalent_name [] +synonym: "Chloroplastida" RELATED synonym [] synonym: "green plants" EXACT common_name [] synonym: "green plants" RELATED blast_name [] xref: GC_ID:1 +xref: PMID:16248873 +xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:kingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -341,15 +337,17 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:3398 -name: Magnoliophyta +name: Magnoliopsida namespace: ncbi_taxonomy synonym: "Angiospermae" RELATED synonym [] synonym: "angiosperms" EXACT common_name [] synonym: "flowering plants" EXACT genbank_common_name [] synonym: "flowering plants" RELATED blast_name [] +synonym: "Magnoliophyta" RELATED synonym [] xref: GC_ID:1 xref: PMID:25249442 is_a: NCBITaxon:58024 ! Spermatophyta +property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -381,6 +379,20 @@ is_a: NCBITaxon:32524 ! Amniota property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl +[Term] +id: NCBITaxon:4751 +name: Fungi +namespace: ncbi_taxonomy +synonym: "fungi" RELATED blast_name [] +synonym: "fungi" RELATED in_part [] +synonym: "Mycota" RELATED genbank_synonym [] +xref: GC_ID:1 +xref: PMID:11062127 +xref: PMID:12684019 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + [Term] id: NCBITaxon:58023 name: Tracheophyta @@ -422,30 +434,30 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7742 -name: Vertebrata +name: Vertebrata namespace: ncbi_taxonomy synonym: "Vertebrata" EXACT scientific_name [] synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:89593 ! Craniata +is_a: NCBITaxon:89593 ! Craniata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7776 -name: Gnathostomata +name: Gnathostomata namespace: ncbi_taxonomy synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 -is_a: NCBITaxon:7742 ! Vertebrata +is_a: NCBITaxon:7742 ! Vertebrata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:78536 name: Euphyllophyta namespace: ncbi_taxonomy -synonym: "euphyllophytes" RELATED synonym [] +synonym: "euphyllophytes" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:58023 ! Tracheophyta property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -461,7 +473,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:89593 -name: Craniata +name: Craniata namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 @@ -479,7 +491,7 @@ synonym: "Placentalia" RELATED synonym [] synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:32525 ! Theria +is_a: NCBITaxon:32525 ! Theria property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -528,20 +540,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl id: NCBITaxon:9606 name: Homo sapiens namespace: ncbi_taxonomy -synonym: "Home sapiens" RELATED misspelling [] -synonym: "Homo sampiens" RELATED misspelling [] -synonym: "Homo sapeins" RELATED misspelling [] -synonym: "Homo sapian" RELATED misspelling [] -synonym: "Homo sapians" RELATED misspelling [] -synonym: "Homo sapien" RELATED misspelling [] -synonym: "Homo sapience" RELATED misspelling [] -synonym: "Homo sapiense" RELATED misspelling [] -synonym: "Homo sapients" RELATED misspelling [] -synonym: "Homo sapines" RELATED misspelling [] -synonym: "Homo spaiens" RELATED misspelling [] -synonym: "Homo spiens" RELATED misspelling [] synonym: "human" EXACT genbank_common_name [] -synonym: "Humo sapiens" RELATED misspelling [] synonym: "man" EXACT common_name [] xref: GC_ID:1 is_a: NCBITaxon:9605 ! Homo diff --git a/src/ontology/imports/ro_import.obo b/src/ontology/imports/ro_import.obo index 764b25d..685b747 100644 --- a/src/ontology/imports/ro_import.obo +++ b/src/ontology/imports/ro_import.obo @@ -1,696 +1,5 @@ format-version: 1.2 ontology: pco/imports/ro_import -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: ()\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) - -[Term] -id: BFO:0000002 -name: continuant -def: "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." [] -disjoint_from: BFO:0000003 ! occurrent -relationship: BFO:0000050 BFO:0000002 ! part of continuant -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000003 -name: occurrent -def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: BFO:0000050 BFO:0000003 ! part of occurrent -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000004 -name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] -is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000004 ! part of independent continuant -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000006 -name: spatial region -is_a: BFO:0000141 ! immaterial entity -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000015 -name: process -def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] -is_a: BFO:0000003 ! occurrent -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000019 -name: quality -is_a: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000019 ! part of quality -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000020 -name: specifically dependent continuant -def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -is_a: BFO:0000002 ! continuant -relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000040 -name: material entity -def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] -is_a: BFO:0000004 ! independent continuant -disjoint_from: BFO:0000141 ! immaterial entity -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: BFO:0000141 -name: immaterial entity -is_a: BFO:0000004 ! independent continuant -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Term] -id: GO:0003674 -name: molecular_function -is_a: BFO:0000015 ! process -property_value: IAO:0000589 "molecular process" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0003824 -name: catalytic activity -is_a: GO:0003674 ! molecular_function -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0008150 -name: biological_process -is_a: BFO:0000015 ! process -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0016301 -name: kinase activity -is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0016740 -name: transferase activity -is_a: GO:0003824 ! catalytic activity -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0016772 -name: transferase activity, transferring phosphorus-containing groups -is_a: GO:0016740 ! transferase activity -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - -[Typedef] -id: BFO:0000050 -name: part of -def: "a core relation that holds between a part and its whole" [] -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf -property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string -is_transitive: true -is_a: RO:0002131 ! overlaps -inverse_of: BFO:0000051 ! has part - -[Typedef] -id: BFO:0000051 -name: has part -def: "a core relation that holds between a whole and its part" [] -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000116 "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.)\n\nA 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'." xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: RO:0002131 ! overlaps - -[Typedef] -id: BFO:0000062 -name: preceded by -def: "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." [] -subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000062 -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - -[Typedef] -id: BFO:0000063 -name: precedes -def: "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." [] -subset: ro-eco -property_value: IAO:0000111 "precedes" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -holds_over_chain: BFO:0000050 BFO:0000063 -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: BFO:0000066 -name: occurs in -def: "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" [] -comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000050 BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[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" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: RO:0000052 -name: inheres in -def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string -property_value: IAO:0000112 "this red color inheres in this apple" xsd:string -property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -is_a: RO:0002314 ! inheres in part of -inverse_of: RO:0000053 ! bearer of - -[Typedef] -id: RO:0000053 -name: bearer of -def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant - -[Typedef] -id: RO:0000056 -name: participates in -def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000002 ! continuant -range: BFO:0000003 ! occurrent -inverse_of: RO:0000057 ! has participant - -[Typedef] -id: RO:0000057 -name: has participant -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: BFO:0000051 RO:0000057 - -[Typedef] -id: RO:0000080 -name: quality of -def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000052 ! inheres in -inverse_of: RO:0000086 ! has quality - -[Typedef] -id: RO:0000086 -name: has quality -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -range: BFO:0000019 ! quality -is_a: RO:0000053 ! bearer of - -[Typedef] -id: RO:0001015 -name: location of -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: RO:0001025 ! located in - -[Typedef] -id: RO:0001018 -name: contained in -subset: ro-eco -property_value: IAO:0000111 "contained in" xsd:string -property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string -property_value: IAO:0000116 "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):" xsd:string -property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string -property_value: IAO:0000118 "contained_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000004 ! independent continuant -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains - -[Typedef] -id: RO:0001019 -name: contains -subset: ro-eco -property_value: IAO:0000111 "contains" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 - -[Typedef] -id: RO:0001025 -name: located in -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true - -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "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." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: dos -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "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." [] -comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "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." [] -comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002018 ! has component process -created_by: dos -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "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." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: dos -creation_date: 2017-05-24T09:49:21Z - -[Typedef] -id: RO:0002019 -name: has ligand -def: "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." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002233 ! has input -created_by: dos -creation_date: 2017-07-19T17:30:36Z - -[Typedef] -id: RO:0002022 -name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002334 ! regulated by -inverse_of: RO:0002578 ! directly regulates -created_by: dos -creation_date: 2017-09-17T13:52:24Z - -[Typedef] -id: RO:0002023 -name: directly negatively regulated by -def: "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." [GOC:dos] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos -creation_date: 2017-09-17T13:52:38Z - -[Typedef] -id: RO:0002024 -name: directly positively regulated by -def: "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." [GOC:dos] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002629 ! directly positively regulates -created_by: dos -creation_date: 2017-09-17T13:52:47Z - -[Typedef] -id: RO:0002025 -name: has effector activity -def: "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." [GOC:dos] -comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_functional: true -is_a: RO:0002017 ! has component activity -is_a: RO:0002211 ! regulates -created_by: dos -creation_date: 2017-09-22T14:14:36Z - -[Typedef] -id: RO:0002086 -name: ends after -comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) -subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002087 -name: immediately preceded by -comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: BFO:0000062 ! preceded by -inverse_of: RO:0002090 ! immediately precedes - -[Typedef] -id: RO:0002090 -name: immediately precedes -comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) -subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0002575 BFO:0000063 -is_a: BFO:0000063 ! precedes - -[Typedef] -id: RO:0002131 -name: overlaps -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -subset: ro-eco -property_value: IAO:0000114 IAO:0000125 -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: BFO:0000051 RO:0002131 -is_a: RO:0002323 ! mereotopologically related to -transitive_over: BFO:0000050 ! part of -expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] - -[Typedef] -id: RO:0002180 -name: has component -def: "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." [] -subset: ro-eco -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002211 -name: regulates -def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -holds_over_chain: RO:0002578 RO:0002578 -is_transitive: true -is_a: RO:0002411 ! causally upstream of -inverse_of: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002212 -name: negatively regulates -def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002211 -is_a: RO:0002211 ! regulates -is_a: RO:0002305 ! causally upstream of, negative effect -inverse_of: RO:0002335 ! negatively regulated by - -[Typedef] -id: RO:0002213 -name: positively regulates -def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002211 -holds_over_chain: RO:0002212 RO:0002212 -is_transitive: true -is_a: RO:0002211 ! regulates -is_a: RO:0002304 ! causally upstream of, positive effect -inverse_of: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002215 -name: capable of -def: "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. " [] -subset: ro-eco -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process -is_a: RO:0002216 ! capable of part of -expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] - -[Typedef] -id: RO:0002216 -name: capable of part of -def: "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." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "has function in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso "defining-property-chains-involving-reflexivity" -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process -expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] - -[Typedef] -id: RO:0002217 -name: actively participates in -def: "x actively participates in y if and only if x participates in y and x realizes some active role" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "agent in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000056 ! participates in -inverse_of: RO:0002218 ! obsolete has active participant - -[Typedef] -id: RO:0002218 -name: obsolete has active participant -def: "x has participant y if and only if x realizes some active role that inheres in y" [] -subset: ro-eco -property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "has agent" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000057 ! has participant -is_obsolete: true - -[Typedef] -id: RO:0002222 -name: temporally related to -comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. -subset: ro-eco -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent - -[Typedef] -id: RO:0002233 -name: has input -def: "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." [] -subset: ro-eco -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "consumes" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000040 ! material entity -is_a: RO:0000057 ! has participant -inverse_of: RO:0002352 ! input of - -[Typedef] -id: RO:0002263 -name: acts upstream of -def: "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." [] -property_value: IAO:0000112 "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." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of -holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0002264 -name: acts upstream of or within -def: "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." [] -synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within -holds_over_chain: RO:0002327 RO:0002418 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002304 -name: causally upstream of, positive effect -comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002411 -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004047 ! causally upstream of or within, positive effect - -[Typedef] -id: RO:0002305 -name: causally upstream of, negative effect -comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002411 -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004046 ! causally upstream of or within, negative effect - -[Typedef] -id: RO:0002314 -name: inheres in part of -def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "defining-property-chains-involving-reflexivity" -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002502 ! depends on -transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002321 @@ -700,621 +9,4 @@ subset: ro-eco property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl - -[Typedef] -id: RO:0002323 -name: mereotopologically related to -def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 - -[Typedef] -id: RO:0002327 -name: enables -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string -property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002215 ! capable of -inverse_of: RO:0002333 ! enabled by -transitive_over: BFO:0000051 ! has part -transitive_over: RO:0002017 ! has component activity - -[Typedef] -id: RO:0002328 -name: functionally related to -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl - -[Typedef] -id: RO:0002329 -name: part of structure that is capable of -def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "false" xsd:boolean -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002331 -name: involved in -def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso Involved:in -holds_over_chain: RO:0002327 BFO:0000050 -is_a: RO:0002217 ! actively participates in -is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002333 -name: enabled by -def: "inverse of enables" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000057 ! has participant -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002334 -name: regulated by -def: "inverse of regulates" [] -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000589 "regulated by (processual)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_transitive: true -is_a: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002335 -name: negatively regulated by -def: "inverse of negatively regulates" [] -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002336 -name: positively regulated by -def: "inverse of positively regulates" [] -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002350 -name: member of -def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -is_a: BFO:0000050 ! part of -inverse_of: RO:0002351 ! has member - -[Typedef] -id: RO:0002351 -name: has member -def: "has member is a mereological relation between a collection and an item." [] -property_value: IAO:0000119 "SIO" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002352 -name: input of -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0000056 ! participates in -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002379 -name: spatially coextensive with -def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002404 -name: causally downstream of -def: "inverse of upstream of" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: BFO:0000062 ! preceded by -is_a: RO:0002427 ! causally downstream of or within -inverse_of: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002405 -name: immediately causally downstream of -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002087 ! immediately preceded by -is_a: RO:0002404 ! causally downstream of -inverse_of: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002410 -name: causally related to -def: "This relation groups causal relations between material entities and causal relations between processes" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "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.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl - -[Typedef] -id: RO:0002411 -name: causally upstream of -def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_transitive: true -is_a: BFO:0000063 ! precedes -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002412 -name: immediately causally upstream of -def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0002575 RO:0002411 -is_a: RO:0002090 ! immediately precedes -is_a: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002418 -name: causally upstream of or within -def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] -synonym: "affects" RELATED [] -property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "influences (processual)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_transitive: true -is_a: RO:0002501 ! causal relation between processes -inverse_of: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002427 -name: causally downstream of or within -def: "inverse of causally upstream of or within" [] -subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_transitive: true -is_a: RO:0002501 ! causal relation between processes - -[Typedef] -id: RO:0002428 -name: involved in regulation of -def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 RO:0002211 -holds_over_chain: RO:0002331 RO:0002211 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0002431 ! involved in or involved in regulation of - -[Typedef] -id: RO:0002429 -name: involved in positive regulation of -def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002428 -holds_over_chain: RO:0002327 RO:0002213 -holds_over_chain: RO:0002331 RO:0002213 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002430 -name: involved in negative regulation of -def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002428 -holds_over_chain: RO:0002327 RO:0002212 -holds_over_chain: RO:0002331 RO:0002212 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002431 -name: involved in or involved in regulation of -def: "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" [] -property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "involved in or reguates" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002264 ! acts upstream of or within -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002432 -name: is active in -def: "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." [GOC:cjm, GOC:dos] -synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "executes activity in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002131 ! overlaps -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002434 -name: interacts with -def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] -subset: ro-eco -synonym: "in pairwise interaction with" EXACT [] -property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI -property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: IAO:0000116 "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." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_symmetric: true - -[Typedef] -id: RO:0002436 -name: molecularly interacts with -def: "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." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso ECO:0000353 -property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -is_symmetric: true -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002447 -name: phosphorylates -property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002448 -name: activity directly regulates activity of -def: "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B." [] -synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002436 ! molecularly interacts with -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002449 -name: activity directly negatively regulates activity of -def: "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] -synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "inhibits" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002448 ! activity directly regulates activity of - -[Typedef] -id: RO:0002450 -name: activity directly positively regulates activity of -def: "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] -synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "activates" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002448 ! activity directly regulates activity of - -[Typedef] -id: RO:0002464 -name: helper property (not for use in curation) -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl - -[Typedef] -id: RO:0002479 -name: has part that occurs in -def: "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." [] -subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} - -[Typedef] -id: RO:0002481 -name: is kinase activity -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0002500 -name: causal agent in process -def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002595 ! causal relation between material entity and a process -inverse_of: RO:0002608 ! process has causal agent - -[Typedef] -id: RO:0002501 -name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002502 -name: depends on -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso BFO:0000169 - -[Typedef] -id: RO:0002506 -name: causal relation between material entities -property_value: IAO:0000116 "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" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002559 -name: causally influenced by -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (material entity to material entity)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002506 ! causal relation between material entities -inverse_of: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002563 -name: interaction relation helper property -property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -is_a: RO:0002464 ! helper property (not for use in curation) - -[Typedef] -id: RO:0002564 -name: molecular interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002563 ! interaction relation helper property - -[Typedef] -id: RO:0002566 -name: causally influences -def: "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (material entity to material entity)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002506 ! causal relation between material entities - -[Typedef] -id: RO:0002578 -name: directly regulates -def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0002575 RO:0002211 -is_a: RO:0002211 ! regulates -is_a: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002584 -name: has part structure that is capable of -def: "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" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: BFO:0000051 RO:0002215 -is_a: RO:0002328 ! functionally related to -is_a: RO:0002595 ! causal relation between material entity and a process - -[Typedef] -id: RO:0002595 -name: causal relation between material entity and a process -def: "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." [] -property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000040 ! material entity -range: BFO:0000015 ! process -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002596 -name: capable of regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002215 RO:0002211 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002597 -name: capable of negatively regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002215 RO:0002212 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002598 -name: capable of positively regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002215 RO:0002213 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002608 -name: process has causal agent -def: "Inverse of 'causal agent in process'" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002629 -name: directly positively regulates -def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002578 -is_a: RO:0002213 ! positively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002630 -name: directly negatively regulates -def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002578 -is_a: RO:0002212 ! negatively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0004031 -name: enables subfunction -def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 BFO:0000051 -is_a: RO:0002328 ! functionally related to -created_by: cjm -creation_date: 2018-01-25T23:20:13Z - -[Typedef] -id: RO:0004032 -name: acts upstream of or within, positive effect -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect -holds_over_chain: RO:0002327 RO:0004047 -is_a: RO:0002264 ! acts upstream of or within -created_by: cjm -creation_date: 2018-01-26T23:49:30Z - -[Typedef] -id: RO:0004033 -name: acts upstream of or within, negative effect -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002264 -holds_over_chain: RO:0002327 RO:0004046 -is_a: RO:0002264 ! acts upstream of or within -created_by: cjm -creation_date: 2018-01-26T23:49:51Z - -[Typedef] -id: RO:0004034 -name: acts upstream of, positive effect -def: "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" [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect -holds_over_chain: RO:0002327 RO:0002304 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: cjm -creation_date: 2018-01-26T23:53:14Z - -[Typedef] -id: RO:0004035 -name: acts upstream of, negative effect -def: "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" [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect -holds_over_chain: RO:0002327 RO:0002305 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: cjm -creation_date: 2018-01-26T23:53:22Z - -[Typedef] -id: RO:0004046 -name: causally upstream of or within, negative effect -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004050 RO:0002418 -is_a: RO:0002418 ! causally upstream of or within -created_by: cjm -creation_date: 2018-03-13T23:55:05Z - -[Typedef] -id: RO:0004047 -name: causally upstream of or within, positive effect -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0004049 RO:0002418 -is_a: RO:0002418 ! causally upstream of or within -created_by: cjm -creation_date: 2018-03-13T23:55:19Z diff --git a/src/ontology/imports/stato_import.obo b/src/ontology/imports/stato_import.obo new file mode 100644 index 0000000..faf4fd2 --- /dev/null +++ b/src/ontology/imports/stato_import.obo @@ -0,0 +1,48 @@ +format-version: 1.2 +ontology: pco/imports/stato_import + +[Term] +id: IAO:0000027 +name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string +property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string +property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + +[Term] +id: IAO:0000109 +name: measurement datum +def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "measurement datum" xsd:string +property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:string +property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000119 group:OBI xsd:string +property_value: IAO:0000119 "OBI_0000305" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + +[Term] +id: STATO:0000047 +name: count +def: "a count is a data item denoted by an integer and represented the number of instances or occurences of an entity" [] +is_a: IAO:0000109 ! measurement datum +property_value: IAO:0000112 "a count of 4 resulting from counting limbs in humans" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string +property_value: IAO:0000117 "Orlaith Burke" xsd:string +property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string +property_value: IAO:0000119 "STATO" xsd:string +property_value: STATO:0000032 "" xsd:string + diff --git a/src/ontology/pco-base.obo b/src/ontology/pco-base.obo index 1c082c0..89d34f8 100644 --- a/src/ontology/pco-base.obo +++ b/src/ontology/pco-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-02-13/pco-base.owl +data-version: pco/releases/2020-08-26/pco-base.owl remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco/pco-base property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -8,8 +8,21 @@ property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string -property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string +property_value: http://purl.org/dc/elements/1.1/description "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Population and Community Ontology" xsd:string property_value: http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 xsd:string +property_value: http://purl.org/dc/terms/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string + +[Term] +id: CARO:0000012 +name: multicellular organism +def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] +comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. +comment: MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. +is_a: CARO:0010004 ! organism +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "multicellular organism" xsd:string [Term] id: CARO:0001010 @@ -24,12 +37,16 @@ property_value: IAO:0000589 "organism or virus" xsd:string id: CARO:0010004 name: organism def: "An individual member of a clade." [] -comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. is_a: CARO:0001010 ! organism or virus or viroid property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string property_value: IAO:0000589 "organism" xsd:string +[Term] +id: ECOCORE:00000045 +is_a: CARO:0001010 ! organism or virus or viroid + [Term] id: GO:0051704 is_a: BFO:0000015 @@ -46,6 +63,7 @@ comment: May be of the same or different species. is_a: BFO:0000027 intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "group of organism" xsd:string @@ -67,18 +85,20 @@ id: PCO:0000002 name: ecological community def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +is_a: PCO:0000029 ! multi-species collection of organisms property_value: IAO:0000118 "multispecies community" xsd:string property_value: IAO:0000119 ISBN:0865423504 xsd:string [Term] id: PCO:0000003 name: quality of a population -def: "A quality that inheres in a biological population." [] +def: "A quality that inheres in a population of organisms." [] comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. intersection_of: PATO:0002003 intersection_of: RO:0000052 PCO:0000001 ! population of organisms property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string +property_value: IAO:0000116 "This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community." xsd:string [Term] id: PCO:0000004 @@ -93,8 +113,8 @@ property_value: IAO:0000116 "These may not belong under BFO:quality. May be bett [Term] id: PCO:0000005 name: population process -def: "A process that has as primary participant a population. " [] -comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +def: "A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction." [] +comment: The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. is_a: BFO:0000015 relationship: RO:0000057 PCO:0000001 ! population of organisms property_value: IAO:0000114 IAO:0000123 @@ -102,21 +122,23 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000006 name: population birth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of birth of a population of organisms." [] +is_a: PATO:0000161 property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000007 name: population death rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of death of a population of organsisms." [] +is_a: PATO:0000161 property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000008 name: population growth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of growth of a population." [] +is_a: PATO:0000161 property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string [Term] id: PCO:0000009 @@ -160,28 +182,37 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 -name: predator role -is_a: BFO:0000023 -property_value: IAO:0000114 IAO:0000124 +name: obsolete predator role +is_a: ObsoleteClass +property_value: IAO:0000116 "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 -name: prey role -is_a: BFO:0000023 -property_value: IAO:0000114 IAO:0000124 +name: obsolete prey role +is_a: ObsoleteClass +property_value: IAO:0000116 "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 -name: symbiont role -is_a: BFO:0000023 -property_value: IAO:0000114 IAO:0000124 +name: obsolete symbiont role +is_a: ObsoleteClass +property_value: IAO:0000116 "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000017 name: species as a collection of organisms -def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as members every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as parts every organism of a species and no organisms of any other species." [] comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +synonym: "taxonomic group" EXACT [] +xref: GENO:0000113 +xref: Species +xref: TAXRANK:0000006 is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000059 ! taxon as collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string @@ -190,6 +221,9 @@ id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms +intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -230,7 +264,7 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000023 name: community species evenness -def: "A quality of a community that reflects how close in abundance all species in a community are." [] +def: "A quality of an ecological community that reflects how close in abundance all species in a community are." [] is_a: PCO:0000004 ! quality of an ecological community property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -244,12 +278,12 @@ is_a: PCO:0000031 ! organismal entity relationship: RO:0002321 ENVO:01000744 relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string [Term] id: PCO:0000025 -name: red population +name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 @@ -257,7 +291,7 @@ is_obsolete: true [Term] id: PCO:0000026 -name: red organism +name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 @@ -277,7 +311,7 @@ property_value: IAO:0000118 "human population" xsd:string [Term] id: PCO:0000028 -name: community +name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). is_a: ObsoleteClass @@ -290,6 +324,7 @@ id: PCO:0000029 name: multi-species collection of organisms def: "A collection of organisms that consists of two or more organisms from at least two species." [] is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 PCO:0000001 {minCardinality="2"} ! population of organisms property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string @@ -352,9 +387,9 @@ property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000037 name: potluck +def: "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." [] is_a: PCO:0000033 ! human social gathering activity property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string -property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -375,6 +410,72 @@ property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000040 +name: obsolete tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000041 +name: obsolete invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000042 +name: obsolete microbe +synonym: "microbial organism" EXACT [] +is_a: ObsoleteClass +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000043 +name: obsolete collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000044 +name: obsolete multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000045 +name: obsolete single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000046 +name: obsolete microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: ObsoleteClass +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000047 name: tidal mangrove shrubland community def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] synonym: "mangrove community" RELATED [] @@ -385,62 +486,150 @@ relationship: BFO:0000050 ENVO:01001369 property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] -id: PCO:0000041 +id: PCO:0000048 name: invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO is_a: PATO:0001241 [Term] -id: PCO:0000042 +id: PCO:0000049 name: microbe synonym: "microbial organism" EXACT [] is_a: CARO:0001010 ! organism or virus or viroid -relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye [Term] -id: PCO:0000043 +id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe -intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe +intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! microbe +intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000044 +id: PCO:0000051 name: multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] is_a: PCO:0000029 ! multi-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000045 +id: PCO:0000052 name: single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000046 +id: PCO:0000053 name: microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] is_a: PCO:0000001 ! population of organisms -relationship: RO:0002351 PCO:0000042 ! microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +[Term] +id: PCO:0000054 +name: number of generations of multicellular organism +def: "A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism." [] {comment="NCIT:C88214", comment="EFO:0000507"} +synonym: "number of generations" BROAD [] +is_a: STATO:0000047 +relationship: IAO:0000136 CARO:0000012 ! multicellular organism +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 + +[Term] +id: PCO:0000057 +name: overcrowded population +def: "An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels." [] +synonym: "increased density of population" EXACT [] +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000058 +name: overcrowded human population +def: "A quality of a human population such that the density humans in an area is increased beyond sustainable levels." [] +is_a: PCO:0000057 ! overcrowded population +intersection_of: PCO:0000057 ! overcrowded population +intersection_of: RO:0000052 PCO:0000027 ! collection of humans +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000059 +name: taxon as collection of organisms +def: "A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations." [] +comment: This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. +xref: data:1868 +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000060 +name: microbial parasite +def: "An organism or virus or viroid that is a microbe and a parasite." [] +is_a: ECOCORE:00000146 +is_a: PCO:0000049 ! microbe +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000061 +name: parasite isolate population +def: "A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations." [] +is_a: PCO:0000053 ! microbial population +relationship: RO:0002351 PCO:0000060 ! microbial parasite +property_value: IAO:0000112 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811772/ +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "VEuPathDB" xsd:string + +[Term] +id: PCO:0000062 +name: Shannon diversity index +def: "A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi)." [] +synonym: "Shannon entropy" EXACT [] +synonym: "Shannon's diversity index" EXACT [] +synonym: "Shannon-Wiener index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html +property_value: IAO:0000119 "Shannon_index" + +[Term] +id: PCO:0000063 +name: Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi)." [] +synonym: "Simpson index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Simpson_index" + +[Term] +id: PCO:0000064 +name: inverse Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi)." [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Inverse_Simpson_index" + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: BFO:0000040 relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid [Term] id: PCO:0001001 name: pair of interacting organisms of the same species +def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0001000 ! pair of interacting organisms +relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms [Term] id: PCO:1000000 @@ -485,9 +674,14 @@ def: "An ecological community which is composed of co-existing populations of mi comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. synonym: "microbiota" BROAD [] is_a: PCO:0000002 ! ecological community -is_a: PCO:0000044 ! multi-species collection of microbes +is_a: PCO:0000051 ! multi-species collection of microbes property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string +[Typedef] +id: PCO:0000055 +name: has member of +domain: PCO:0000000 ! collection of organisms + diff --git a/src/ontology/pco-base.owl b/src/ontology/pco-base.owl index 37a491e..d554572 100644 --- a/src/ontology/pco-base.owl +++ b/src/ontology/pco-base.owl @@ -8,17 +8,20 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg Ramona Walls - http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. + Population and Community Ontology http://purl.obolibrary.org/obo/IAO_8000001 + http://creativecommons.org/publicdomain/zero/1.0/ The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. @@ -172,6 +175,24 @@ + + + + + + + + + + + + + + has member of + + + + @@ -267,6 +288,21 @@ + + + + + Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. + multicellular organism + Melissa Haendel + 9/18/11 + MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. + multicellular organism + + + + @@ -288,12 +324,26 @@ organism mah 7.16.2011 - A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. organism + + + + + + + + + + + + + + @@ -334,12 +384,24 @@ + + + + + + + + + + + + @@ -365,6 +427,12 @@ + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. @@ -396,18 +464,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - 2 - - - - - + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 @@ -432,8 +489,9 @@ Classes for population already exist in IDO ('organism population', I - A quality that inheres in a biological population. + A quality that inheres in a population of organisms. See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community. Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. quality of a population @@ -474,8 +532,8 @@ Classes for population already exist in IDO ('organism population', I - A process that has as primary participant a population. - Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. + The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. population process @@ -484,8 +542,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of birth of a population of organisms. population birth rate @@ -494,8 +553,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of death of a population of organsisms. population death rate @@ -504,9 +564,9 @@ Classes for population already exist in IDO ('organism population', I - + - Is a rate a quality? Population growth rate may be better classified as a process profile. + The rate of growth of a population. population growth rate @@ -575,30 +635,51 @@ Classes for population already exist in IDO ('organism population', I - - - predator role + + Interactions are now covered in EcoCore ontology. + obsolete predator role + true + + + + true + + - - - prey role + + Interactions are now covered in EcoCore ontology. + obsolete prey role + true + + + + true + + - - - symbiont role + + Interactions are now covered in EcoCore ontology. + obsolete symbiont role + true + + + + true + + @@ -606,9 +687,15 @@ Classes for population already exist in IDO ('organism population', I + - A collection of organisms that has as parts every organism of given species and no organisms of any other species. + A collection of organisms that has as members every organism of given species and no organisms of any other species. + A collection of organisms that has as parts every organism of a species and no organisms of any other species. At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + + + + taxonomic group This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. species as a collection of organisms @@ -625,21 +712,16 @@ Classes for population already exist in IDO ('organism population', I - - - - - - 1 - - - - 2 + + + 1 + + @@ -708,7 +790,7 @@ Classes for population already exist in IDO ('organism population', I If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. - A quality of a community that reflects how close in abundance all species in a community are. + A quality of an ecological community that reflects how close in abundance all species in a community are. adapted from http://en.wikipedia.org/wiki/Species_evenness community species evenness @@ -742,7 +824,7 @@ Classes for population already exist in IDO ('organism population', I An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. - Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household household @@ -755,7 +837,7 @@ Classes for population already exist in IDO ('organism population', I This is an example population added to demonstrate the modeling pattern for collections of organisms. - red population + obsolete red population true @@ -767,7 +849,7 @@ Classes for population already exist in IDO ('organism population', I An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. - red organism + obsolete red organism true @@ -810,7 +892,7 @@ Classes for population already exist in IDO ('organism population', I Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). - community + obsolete community true @@ -820,6 +902,13 @@ Classes for population already exist in IDO ('organism population', I + + + + 2 + + + A collection of organisms that consists of two or more organisms from at least two species. Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". @@ -918,8 +1007,8 @@ Classes for population already exist in IDO ('organism population', I + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 - A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. GenEpio curators potluck @@ -950,36 +1039,93 @@ Classes for population already exist in IDO ('organism population', I - + - - - - - - - - + + - - 2 - + + - A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. - pair of interacting organisms + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community - + - + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + microbial organism + microbe + + + + + + + - + + + + + + + 2 + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + @@ -990,10 +1136,225 @@ Classes for population already exist in IDO ('organism population', I + + + 2 + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + + + + + + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + number of generations + number of generations of multicellular organism + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + + + + + + + + + + + + + + + + + + + + + + An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels. + + increased density of population + overcrowded population + + + + + + + + + + + + + + + + + + + + + A quality of a human population such that the density humans in an area is increased beyond sustainable levels. + + overcrowded human population + + + + + + + + + + A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations. + + + This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. + taxon as collection of organisms + + + + + + + + + + + An organism or virus or viroid that is a microbe and a parasite. + + microbial parasite + + + + + + + + + + + + + + + + + A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations. + + VEuPathDB + parasite isolate population + + + + + + + + + + A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi). + + + Shannon entropy + Shannon's diversity index + Shannon-Wiener index + Shannon diversity index + + + + + + + + + + A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi). + + + Simpson index + Simpson diversity index + + + + + + + + + + A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi). + + + inverse Simpson diversity index + + + + + + + + + + + + 2 + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + 1 + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. pair of interacting organisms of the same species @@ -1070,7 +1431,7 @@ Classes for population already exist in IDO ('organism population', I - + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 @@ -1083,6 +1444,12 @@ Classes for population already exist in IDO ('organism population', I + + + + + + @@ -1105,19 +1472,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 https://cmecscatalog.org/cmecs/classification/unit/577.html mangrove community tidal shrubland community - tidal mangrove shrubland community + obsolete tidal mangrove shrubland community + true @@ -1125,10 +1488,12 @@ Classes for population already exist in IDO ('organism population', I - + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO - invisible to unaided eye + obsolete invisible to unaided eye + true @@ -1136,15 +1501,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + + microbial organism - microbe + obsolete microbe + true @@ -1152,24 +1513,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 - collection of microbial organisms + obsolete collection of microbial organisms + true @@ -1177,11 +1526,12 @@ Classes for population already exist in IDO ('organism population', I - - + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 - multi-species collection of microbes + obsolete multi-species collection of microbes + true @@ -1189,34 +1539,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - 1 - - - - - - - 2 - - - - - + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 - single species collection of microbes + obsolete single species collection of microbes + true @@ -1224,18 +1552,28 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 microbiota - microbial population + obsolete microbial population + true + + + + + + + https://orcid.org/0000-0001-8815-0078 + diff --git a/src/ontology/pco-edit.owl b/src/ontology/pco-edit.owl index 9c6c4ae..32c7cdc 100644 --- a/src/ontology/pco-edit.owl +++ b/src/ontology/pco-edit.owl @@ -292,8 +292,7 @@ obo:PCO_0000005 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/PCO_0000006 obo:PCO_0000006 rdf:type owl:Class ; - rdfs:subClassOf obo:PATO_0000161 , - obo:PCO_0000003 ; + rdfs:subClassOf obo:PATO_0000161 ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "The rate of birth of a population of organisms." ; rdfs:label "population birth rate"@en . @@ -301,8 +300,7 @@ obo:PCO_0000006 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/PCO_0000007 obo:PCO_0000007 rdf:type owl:Class ; - rdfs:subClassOf obo:PATO_0000161 , - obo:PCO_0000003 ; + rdfs:subClassOf obo:PATO_0000161 ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "The rate of death of a population of organsisms." ; rdfs:label "population death rate"@en . @@ -310,8 +308,7 @@ obo:PCO_0000007 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/PCO_0000008 obo:PCO_0000008 rdf:type owl:Class ; - rdfs:subClassOf obo:PATO_0000161 , - obo:PCO_0000003 ; + rdfs:subClassOf obo:PATO_0000161 ; obo:IAO_0000114 obo:IAO_0000123 ; obo:IAO_0000115 "The rate of growth of a population." ; rdfs:label "population growth rate"@en . diff --git a/src/ontology/pco-full.obo b/src/ontology/pco-full.obo index 84df48c..08e5f17 100644 --- a/src/ontology/pco-full.obo +++ b/src/ontology/pco-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-02-13/pco-full.owl +data-version: pco/releases/2020-08-26/pco-full.owl remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco/pco-full property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -8,31 +8,35 @@ property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string -property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string +property_value: http://purl.org/dc/elements/1.1/description "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Population and Community Ontology" xsd:string +property_value: http://purl.org/dc/terms/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string +property_value: editor_note "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: editor_note "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000112 "Julius Caesar" xsd:string property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000002 name: continuant +def: "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." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent +relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string -property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: editor_note "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} @@ -46,13 +50,15 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000003 name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity +relationship: part_of BFO:0000003 ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string -property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} -property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: editor_note "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: editor_note "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: editor_note "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} @@ -63,10 +69,12 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string @@ -86,13 +94,27 @@ property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000005 +name: obsolete dependent continuant +def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true + +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity + [Term] id: BFO:0000015 name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string +property_value: editor_note "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string property_value: IAO:0000112 "a process of meiosis" xsd:string property_value: IAO:0000112 "a process of sleeping" xsd:string @@ -100,14 +122,21 @@ property_value: IAO:0000112 "the course of a disease" xsd:string property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + [Term] id: BFO:0000017 name: realizable entity +def: "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_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality property_value: BFO:0000179 "realizable" xsd:string property_value: BFO:0000180 "RealizableEntity" xsd:string property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string @@ -115,20 +144,29 @@ property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:str property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant + [Term] id: BFO:0000020 name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: part_of BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string @@ -140,16 +178,17 @@ property_value: IAO:0000112 "the pink color of a medium rare piece of grilled fi property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role +def: "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." [] is_a: BFO:0000017 ! realizable entity property_value: BFO:0000179 "role" xsd:string property_value: BFO:0000180 "Role" xsd:string +property_value: editor_note "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string property_value: IAO:0000112 "the priest role" xsd:string property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string @@ -157,7 +196,6 @@ property_value: IAO:0000112 "the role of a building in serving as a military tar property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl @@ -168,6 +206,9 @@ name: object aggregate is_a: BFO:0000040 ! material entity property_value: BFO:0000179 "object-aggregate" xsd:string property_value: BFO:0000180 "ObjectAggregate" xsd:string +property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: editor_note "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string property_value: IAO:0000112 "a symphony orchestra" xsd:string @@ -181,9 +222,6 @@ property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:stri property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} -property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} @@ -217,6 +255,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant property_value: BFO:0000179 "gdc" xsd:string @@ -227,13 +266,22 @@ property_value: IAO:0000112 "the sequence of this protein molecule; the sequence property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + [Term] id: BFO:0000040 name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "material" xsd:string property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: editor_note "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: editor_note "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: editor_note "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: IAO:0000112 "a flame" xsd:string property_value: IAO:0000112 "a forest fire" xsd:string property_value: IAO:0000112 "a human being" xsd:string @@ -246,9 +294,6 @@ property_value: IAO:0000112 "an aggregate of human beings." xsd:string property_value: IAO:0000112 "an energy wave" xsd:string property_value: IAO:0000112 "an epidemic" xsd:string property_value: IAO:0000112 "the undetached arm of a human being" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} @@ -263,9 +308,20 @@ name: immaterial entity is_a: BFO:0000004 ! independent continuant property_value: BFO:0000179 "immaterial" xsd:string property_value: BFO:0000180 "ImmaterialEntity" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string +property_value: editor_note "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: CARO:0000012 +name: multicellular organism +def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] +comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. +comment: MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. +is_a: CARO:0010004 ! organism +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "multicellular organism" xsd:string + [Term] id: CARO:0001010 name: organism or virus or viroid @@ -279,61 +335,34 @@ property_value: IAO:0000589 "organism or virus" xsd:string id: CARO:0010004 name: organism def: "An individual member of a clade." [] -comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. is_a: CARO:0001010 ! organism or virus or viroid property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string property_value: IAO:0000589 "organism" xsd:string [Term] -id: DbXref -is_a: IAO:0000102 ! data about an ontology part - -[Term] -id: Definition -is_a: IAO:0000102 ! data about an ontology part - -[Term] -id: ENVO:00000070 -name: construction -def: "A feature that has been constructed by deliberate human effort." [MA:ma] -synonym: "constructed feature" EXACT [] -is_a: ENVO:01000813 ! astronomical body part -property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string - -[Term] -id: ENVO:00002297 -name: environmental feature -namespace: ENVO -def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] -comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. -is_a: BFO:0000040 ! material entity +id: ECOCORE:00000045 +name: symbiotroph +def: "heterotroph that acquires nutrition from a symbiont" [] +is_a: CARO:0001010 ! organism or virus or viroid +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string [Term] -id: ENVO:01000254 -name: environmental system -def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] -comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. -synonym: "environment" EXACT [] -xref: EcoLexicon:environment -is_a: BFO:0000040 ! material entity -creation_date: 2013-09-23T16:04:08Z +id: ECOCORE:00000146 +name: parasite +def: "A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host" [] +xref: https://www.wikidata.org/entity/Q10253316 +is_a: ECOCORE:00000045 ! symbiotroph +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string [Term] id: ENVO:01000744 name: human dwelling def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] -is_a: ENVO:00000070 ! construction -property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string -property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string - -[Term] -id: ENVO:01000813 -name: astronomical body part -def: "A material part of an astronomical body." [] -subset: envoAstro -subset: envoPolar -is_a: ENVO:00002297 ! environmental feature +is_a: BFO:0000040 ! material entity +property_value: editor_note "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: editor_note "Subclasses will be added by inference." xsd:string [Term] id: ENVO:01001369 @@ -344,14 +373,29 @@ comment: This class aligns to the Coastal and Marine Ecological Classification S subset: envoCmecs subset: envoMarine xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ENVO:01000254 ! environmental system +is_a: BFO:0000040 ! material entity created_by: http://orcid.org/0000-0002-4366-3088 +[Term] +id: GO:0003674 +name: molecular_function +is_a: BFO:0000015 ! process +property_value: IAO:0000589 "molecular process" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0003824 +name: catalytic activity +is_a: GO:0003674 ! molecular_function +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0007610 name: behavior namespace: biological_process +alt_id: GO:0023032 alt_id: GO:0044708 +alt_id: GO:0044709 def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). subset: gocheck_do_not_manually_annotate @@ -364,7 +408,7 @@ synonym: "single-organism behavior" RELATED [] xref: Wikipedia:Behavior is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-20T14:06:08Z [Term] @@ -375,7 +419,7 @@ alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] -comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl @@ -390,10 +434,29 @@ synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-19T15:05:24Z +[Term] +id: GO:0016301 +name: kinase activity +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016740 +name: transferase activity +is_a: GO:0003824 ! catalytic activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +is_a: GO:0016740 ! transferase activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0035176 name: social behavior @@ -403,8 +466,8 @@ comment: Behavior such as predation which involves members of different species synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior +is_a: GO:0007610 ! behavior is_a: GO:0051703 ! intraspecies interaction between organisms -is_a: GO:0051705 ! multi-organism behavior property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -417,8 +480,9 @@ subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 @@ -427,7 +491,7 @@ namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] subset: goslim_pir synonym: "intraspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -441,46 +505,42 @@ subset: goslim_pir synonym: "interaction between organisms" EXACT [] synonym: "physiological interaction between organisms" EXACT [] synonym: "physiological interaction with other organism" EXACT [] -is_a: BFO:0000015 ! process is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -[Term] -id: GO:0051705 -name: multi-organism behavior -namespace: biological_process -alt_id: GO:0023032 -alt_id: GO:0044709 -def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] -subset: goslim_pir -synonym: "behavioral interaction between organisms" EXACT [] -synonym: "behavioral interaction with other organism" EXACT [] -synonym: "behavioral signaling" NARROW [] -synonym: "behavioral signalling" NARROW [GOC:mah] -synonym: "behavioural interaction between organisms" EXACT [] -synonym: "behavioural interaction with other organism" EXACT [] -is_a: GO:0007610 ! behavior -is_a: GO:0051704 ! multi-organism process -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - [Term] id: IAO:0000027 name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity +property_value: editor_note "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string +property_value: editor_note "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string +property_value: editor_note "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: editor_note "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: editor_note "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: IAO:0000030 name: information content entity is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000111 "information content entity" xsd:string [Term] id: IAO:0000078 name: curation status specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part +property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000111 "curation status specification" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 GROUP:OBI: xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string @@ -488,18 +548,33 @@ property_value: IAO:0000119 "OBI_0000266" xsd:string [Term] id: IAO:0000102 name: data about an ontology part -def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "data about an ontology part" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string +[Term] +id: IAO:0000109 +name: measurement datum +def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] +is_a: IAO:0000027 ! data item +property_value: editor_note "2/2/2009 is_specified_output of some assay?" xsd:string +property_value: IAO:0000111 "measurement datum" xsd:string +property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000119 group:OBI xsd:string +property_value: IAO:0000119 "OBI_0000305" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + [Term] id: IAO:0000225 name: obsolescence reason specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part +property_value: editor_note "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000111 "obsolescence reason specification" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string @@ -508,6 +583,7 @@ id: IAO:0000409 name: denotator type def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "denotator type" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string @@ -516,189 +592,168 @@ property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string id: IAO:8000000 name: ontology module is_a: IAO:0000102 ! data about an ontology part -property_value: IAO:0000116 "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." xsd:string +property_value: editor_note "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000111 "ontology module" xsd:string property_value: IAO:0000118 "ontology file" xsd:string property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string -created_by: cjm -creation_date: 2018-05-20T20:55:03Z [Term] id: IAO:8000001 name: base ontology module def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "base ontology module" xsd:string property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 -created_by: cjm -creation_date: 2018-05-20T20:55:30Z [Term] id: IAO:8000002 name: editors ontology module def: "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." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "editors ontology module" xsd:string property_value: IAO:0000118 "source ontology module" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:55:47Z [Term] id: IAO:8000003 name: main release ontology module def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] is_a: IAO:8000000 ! ontology module -property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:56:13Z +property_value: editor_note "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +property_value: IAO:0000111 "main release ontology module" xsd:string [Term] id: IAO:8000004 name: bridge ontology module def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "bridge ontology module" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies -created_by: cjm -creation_date: 2018-05-20T20:56:23Z [Term] id: IAO:8000005 name: import ontology module def: "A subset ontology module that is intended to be imported from another ontology." [] is_a: IAO:8000006 ! subset ontology module -property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: editor_note "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000111 "import ontology module" xsd:string property_value: IAO:0000118 "import file" xsd:string property_value: seeAlso http://robot.obolibrary.org/extract -created_by: cjm -creation_date: 2018-05-20T20:56:47Z [Term] id: IAO:8000006 name: subset ontology module def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "subset ontology module" xsd:string property_value: IAO:0000118 "ontology slim" xsd:string property_value: IAO:0000118 "subset ontology" xsd:string property_value: seeAlso http://robot.obolibrary.org/filter property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide -created_by: cjm -creation_date: 2018-05-20T20:58:11Z [Term] id: IAO:8000007 name: curation subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-20T20:58:38Z +property_value: IAO:0000111 "curation subset ontology module" xsd:string [Term] id: IAO:8000008 name: analysis subset ontology module def: "An ontology module that is intended for usage in analysis or discovery applications." [] is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-20T20:58:49Z +property_value: IAO:0000111 "analysis ontology module" xsd:string [Term] id: IAO:8000009 name: single layer subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "single layer ontology module" xsd:string property_value: IAO:0000118 "ribbon subset" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:59:19Z [Term] id: IAO:8000010 name: exclusion subset ontology module def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "exclusion subset ontology module" xsd:string property_value: IAO:0000118 "antislim" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:59:57Z [Term] id: IAO:8000011 name: external import ontology module def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000111 "external import ontology module" xsd:string property_value: IAO:0000118 "external import" xsd:string -created_by: cjm -creation_date: 2018-05-20T21:00:14Z [Term] id: IAO:8000012 name: species subset ontology module def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "species subset ontology module" xsd:string property_value: IAO:0000118 "taxon subset" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -created_by: cjm -creation_date: 2018-05-20T21:14:16Z [Term] id: IAO:8000013 name: reasoned ontology module def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "reasoned ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/reason -created_by: cjm -creation_date: 2018-05-20T21:20:33Z [Term] id: IAO:8000014 name: generated ontology module def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] is_a: IAO:8000000 ! ontology module -property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string -created_by: cjm -creation_date: 2018-05-20T21:21:12Z +property_value: editor_note "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +property_value: IAO:0000111 "generated ontology module" xsd:string [Term] id: IAO:8000015 name: template generated ontology module def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] is_a: IAO:8000014 ! generated ontology module +property_value: IAO:0000111 "template generated ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/template property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ -created_by: cjm -creation_date: 2018-05-20T21:21:21Z [Term] id: IAO:8000016 name: taxonomic bridge ontology module is_a: IAO:8000004 ! bridge ontology module -created_by: cjm -creation_date: 2018-05-20T21:28:15Z +property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string [Term] id: IAO:8000017 name: ontology module subsetted by expressivity is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-22T04:15:54Z +property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string [Term] id: IAO:8000018 name: obo basic subset ontology module def: "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "obo basic subset ontology module" xsd:string property_value: seeAlso "6.2" -created_by: cjm -creation_date: 2018-05-22T04:16:10Z [Term] id: IAO:8000019 name: ontology module subsetted by OWL profile is_a: IAO:8000017 ! ontology module subsetted by expressivity -created_by: cjm -creation_date: 2018-05-22T04:16:28Z +property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string [Term] id: IAO:8000020 name: EL++ ontology module is_a: IAO:8000019 ! ontology module subsetted by OWL profile -created_by: cjm -creation_date: 2018-05-22T04:16:48Z +property_value: IAO:0000111 "EL++ ontology module" xsd:string [Term] id: NCBITaxon:10239 @@ -716,7 +771,7 @@ id: NCBITaxon:117570 name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 -is_a: NCBITaxon:7776 ! Gnathostomata +is_a: NCBITaxon:7776 ! Gnathostomata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -729,22 +784,12 @@ xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl -[Term] -id: NCBITaxon:12884 -name: Viroids -namespace: ncbi_taxonomy -synonym: "Viroid" RELATED synonym [] -synonym: "viroids" RELATED blast_name [] -xref: GC_ID:1 -property_value: has_rank NCBITaxon:superkingdom -property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl - [Term] id: NCBITaxon:131221 name: Streptophytina namespace: ncbi_taxonomy synonym: "Charophyta/Embryophyta group" RELATED synonym [] -synonym: "charophyte/embryophyte group" RELATED synonym [] +synonym: "charophyte/embryophyte group" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:35493 ! Streptophyta property_value: has_rank NCBITaxon:subphylum @@ -817,7 +862,9 @@ xref: PMID:11760965 xref: PMID:12054223 xref: PMID:2112744 xref: PMID:270744 +xref: PMID:7520741 xref: PMID:8123559 +xref: PMID:8186100 xref: PMID:8590690 xref: PMID:9103655 xref: PMID:9336922 @@ -892,6 +939,7 @@ synonym: "eukaryotes" EXACT common_name [] synonym: "eukaryotes" RELATED blast_name [] xref: GC_ID:1 xref: PMID:23020233 +xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms property_value: has_rank NCBITaxon:superkingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -977,7 +1025,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32525 -name: Theria +name: Theria namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 @@ -989,11 +1037,14 @@ id: NCBITaxon:33090 name: Viridiplantae namespace: ncbi_taxonomy synonym: "Chlorobionta" RELATED synonym [] -synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] -synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name [] +synonym: "chlorophyte/embryophyte group" EXACT equivalent_name [] +synonym: "Chloroplastida" RELATED synonym [] synonym: "green plants" EXACT common_name [] synonym: "green plants" RELATED blast_name [] xref: GC_ID:1 +xref: PMID:16248873 +xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:kingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -1040,15 +1091,17 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:3398 -name: Magnoliophyta +name: Magnoliopsida namespace: ncbi_taxonomy synonym: "Angiospermae" RELATED synonym [] synonym: "angiosperms" EXACT common_name [] synonym: "flowering plants" EXACT genbank_common_name [] synonym: "flowering plants" RELATED blast_name [] +synonym: "Magnoliophyta" RELATED synonym [] xref: GC_ID:1 xref: PMID:25249442 is_a: NCBITaxon:58024 ! Spermatophyta +property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -1080,6 +1133,20 @@ is_a: NCBITaxon:32524 ! Amniota property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl +[Term] +id: NCBITaxon:4751 +name: Fungi +namespace: ncbi_taxonomy +synonym: "fungi" RELATED in_part [] +synonym: "fungi" RELATED blast_name [] +synonym: "Mycota" RELATED genbank_synonym [] +xref: GC_ID:1 +xref: PMID:11062127 +xref: PMID:12684019 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + [Term] id: NCBITaxon:58023 name: Tracheophyta @@ -1121,30 +1188,30 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7742 -name: Vertebrata +name: Vertebrata namespace: ncbi_taxonomy synonym: "Vertebrata" EXACT scientific_name [] synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:89593 ! Craniata +is_a: NCBITaxon:89593 ! Craniata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7776 -name: Gnathostomata +name: Gnathostomata namespace: ncbi_taxonomy synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 -is_a: NCBITaxon:7742 ! Vertebrata +is_a: NCBITaxon:7742 ! Vertebrata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:78536 name: Euphyllophyta namespace: ncbi_taxonomy -synonym: "euphyllophytes" RELATED synonym [] +synonym: "euphyllophytes" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:58023 ! Tracheophyta property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -1160,7 +1227,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:89593 -name: Craniata +name: Craniata namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 @@ -1178,7 +1245,7 @@ synonym: "Placentalia" RELATED synonym [] synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:32525 ! Theria +is_a: NCBITaxon:32525 ! Theria property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -1227,33 +1294,62 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl id: NCBITaxon:9606 name: Homo sapiens namespace: ncbi_taxonomy -synonym: "Home sapiens" RELATED misspelling [] -synonym: "Homo sampiens" RELATED misspelling [] -synonym: "Homo sapeins" RELATED misspelling [] -synonym: "Homo sapian" RELATED misspelling [] -synonym: "Homo sapians" RELATED misspelling [] -synonym: "Homo sapien" RELATED misspelling [] -synonym: "Homo sapience" RELATED misspelling [] -synonym: "Homo sapiense" RELATED misspelling [] -synonym: "Homo sapients" RELATED misspelling [] -synonym: "Homo sapines" RELATED misspelling [] -synonym: "Homo spaiens" RELATED misspelling [] -synonym: "Homo spiens" RELATED misspelling [] synonym: "human" EXACT genbank_common_name [] -synonym: "Humo sapiens" RELATED misspelling [] synonym: "man" EXACT common_name [] xref: GC_ID:1 is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl +[Term] +id: ObsoleteClass +name: Obsolete Class + [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -synonym: "trait" EXACT [] +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000068 +name: qualitative +namespace: quality +comment: TODO: define this or obsolete it and move children somewhere else. +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000069 +name: deviation (from_normal) +namespace: quality +def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000070 +name: amount +namespace: quality +alt_id: PATO:0000053 +alt_id: PATO:0000071 +alt_id: PATO:0001169 +alt_id: PATO:0001226 +def: "The number of entities of this type that are part of the whole organism." [PATOC:GVG] +comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. +subset: attribute_slim +synonym: "count in organism" RELATED [] +synonym: "number" RELATED [] +synonym: "presence" RELATED [] +synonym: "presence or absence in organism" EXACT [] +synonym: "quantitative" EXACT [] +is_a: PATO:0000068 ! qualitative +relationship: reciprocal_of PATO:0001555 ! has number of property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -1266,6 +1362,115 @@ subset: scalar_slim is_a: PATO:0002062 ! physical quality of a process property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0000461 +name: normal +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average." [PATOC:GVG] +subset: abnormal_slim +subset: mpath_slim +subset: value_slim +synonym: "average" RELATED [] +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000460 + +[Term] +id: PATO:0000467 +name: present +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's existence." [PATOC:GVG] +subset: absent_slim +subset: value_slim +synonym: "present in organism" RELATED [] +is_a: PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000462 + +[Term] +id: PATO:0000470 +name: increased amount +namespace: quality +alt_id: PATO:0000420 +alt_id: PATO:0000650 +def: "An amount which is relatively high." [PATOC:GVG] +subset: value_slim +synonym: "accessory" RELATED [] +synonym: "increased" RELATED [] +synonym: "increased number" EXACT [] +synonym: "present in greater numbers in organism" EXACT [] +synonym: "supernumerary" EXACT [] +is_a: PATO:0000467 ! present +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0000070 ! amount +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001997 + +[Term] +id: PATO:0000911 +name: decreased rate +namespace: quality +def: "A rate which is relatively low." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "slow rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002302 ! decreased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000912 + +[Term] +id: PATO:0000912 +name: increased rate +namespace: quality +def: "A rate which is relatively high." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "fast rate" EXACT [] +synonym: "high rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002304 ! increased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000911 + +[Term] +id: PATO:0001018 +name: physical quality +namespace: quality +alt_id: PATO:0002079 +def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] +subset: attribute_slim +synonym: "relational physical quality" EXACT [] +xref: Wikipedia:Physical_property +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001019 +name: mass density +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size." [WordNet:WordNet] +subset: attribute_slim +subset: scalar_slim +synonym: "density" RELATED [] +is_a: PATO:0001018 ! physical quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001164 +name: dense +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density." [PATOC:GVG] +subset: mpath_slim +subset: value_slim +is_a: PATO:0001019 ! mass density +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + [Term] id: PATO:0001236 name: process quality @@ -1279,6 +1484,7 @@ synonym: "quality of occurrent" EXACT [] synonym: "quality of process" EXACT [] synonym: "relational quality of occurrent" EXACT [] is_a: PATO:0000001 ! quality +disjoint_from: PATO:0001241 ! physical object quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -1321,6 +1527,72 @@ subset: scalar_slim is_a: PATO:0002003 ! population quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0001555 +name: has number of +namespace: quality +def: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts." [PATOC:CJM] +subset: attribute_slim +subset: relational_slim +synonym: "cardinality" RELATED [] +synonym: "extra or missing physical or functional parts" EXACT [] +synonym: "has or lacks parts of type" EXACT [] +synonym: "mereological quality" EXACT [] +synonym: "number" RELATED [] +synonym: "number of" EXACT [] +xref: OBO_REL:has_part +is_a: PATO:0001241 ! physical object quality +relationship: reciprocal_of PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001788 +name: increased mass density +namespace: quality +def: "A density which is higher relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "high density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002305 ! increased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001790 + +[Term] +id: PATO:0001790 +name: decreased mass density +namespace: quality +def: "A density which is lower relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "low density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002303 ! decreased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001788 + +[Term] +id: PATO:0001997 +name: decreased amount +namespace: quality +alt_id: PATO:0000419 +alt_id: PATO:0000468 +def: "An amount which is relatively low." [PATOC:GVG] +subset: value_slim +synonym: "decreased" RELATED [] +synonym: "decreased number" EXACT [] +synonym: "present in fewer numbers in organism" EXACT [] +synonym: "reduced" RELATED [] +synonym: "subnumerary" RELATED [] +is_a: PATO:0000467 ! present +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0000070 ! amount +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000470 + [Term] id: PATO:0002003 name: population quality @@ -1340,6 +1612,90 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl created_by: george creation_date: 2009-06-05T09:16:46Z +[Term] +id: PATO:0002300 +name: increased quality +namespace: quality +def: "A quality that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002301 +created_by: George Gkoutos +creation_date: 2011-06-16T06:39:43Z + +[Term] +id: PATO:0002301 +name: decreased quality +namespace: quality +def: "A quality that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002300 +created_by: George Gkoutos +creation_date: 2011-06-16T06:40:15Z + +[Term] +id: PATO:0002302 +name: decreased process quality +namespace: quality +def: "A quality of a process that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002304 +created_by: George Gkoutos +creation_date: 2011-06-16T06:50:59Z + +[Term] +id: PATO:0002303 +name: decreased object quality +namespace: quality +def: "A quality of an object that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002305 +created_by: George Gkoutos +creation_date: 2011-06-16T06:51:54Z + +[Term] +id: PATO:0002304 +name: increased process quality +namespace: quality +def: "A quality of a process that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002302 +created_by: George Gkoutos +creation_date: 2011-06-16T06:53:08Z + +[Term] +id: PATO:0002305 +name: increased object quality +namespace: quality +def: "A quality of an object that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002303 +created_by: George Gkoutos +creation_date: 2011-06-16T06:54:01Z + [Term] id: PCO:0000000 name: collection of organisms @@ -1347,9 +1703,10 @@ def: "A material entity that consists of two or more organisms, viruses, or viro comment: May be of the same or different species. is_a: BFO:0000027 ! object aggregate is_a: PCO:0000031 ! organismal entity -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "group of organism" xsd:string @@ -1371,20 +1728,22 @@ id: PCO:0000002 name: ecological community def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +is_a: PCO:0000029 ! multi-species collection of organisms property_value: IAO:0000118 "multispecies community" xsd:string property_value: IAO:0000119 ISBN:0865423504 xsd:string [Term] id: PCO:0000003 name: quality of a population -def: "A quality that inheres in a biological population." [] +def: "A quality that inheres in a population of organisms." [] comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. is_a: PATO:0002003 ! population quality intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000001 ! population of organisms -relationship: RO:0000052 PCO:0000001 ! population of organisms +intersection_of: RO:0000052 PCO:0000001 ! inheres in population of organisms +relationship: RO:0000052 PCO:0000001 ! inheres in population of organisms +property_value: editor_note "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string +property_value: editor_note "This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string [Term] id: PCO:0000004 @@ -1393,45 +1752,47 @@ def: "A quality that inheres in a community." [] comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. is_a: PATO:0002003 ! population quality intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000002 ! ecological community -relationship: RO:0000052 PCO:0000002 ! ecological community +intersection_of: RO:0000052 PCO:0000002 ! inheres in ecological community +relationship: RO:0000052 PCO:0000002 ! inheres in ecological community +property_value: editor_note "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string [Term] id: PCO:0000005 name: population process -def: "A process that has as primary participant a population. " [] -comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +def: "A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction." [] +comment: The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. is_a: BFO:0000015 ! process -relationship: RO:0000057 PCO:0000001 ! population of organisms +relationship: RO:0000057 PCO:0000001 ! has participant population of organisms property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000006 name: population birth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of birth of a population of organisms." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000007 name: population death rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of death of a population of organsisms." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000008 name: population growth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of growth of a population." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string [Term] id: PCO:0000009 name: obsolete carrying capacity def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] -is_a: ObsoleteClass -property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string property_value: IAO:0000119 ISBN:0878932739 xsd:string property_value: IAO:0000231 IAO:0000423 is_obsolete: true @@ -1441,8 +1802,8 @@ id: PCO:0000010 name: community species richness def: "The number of different species represented in an ecological community." [] is_a: PCO:0000004 ! quality of an ecological community +property_value: editor_note "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string [Term] @@ -1468,36 +1829,49 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 -name: predator role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete predator role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 -name: prey role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete prey role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 -name: symbiont role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete symbiont role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000017 name: species as a collection of organisms -def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as members every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as parts every organism of a species and no organisms of any other species." [] comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +synonym: "taxonomic group" EXACT [] +xref: GENO:0000113 +xref: Species +xref: TAXRANK:0000006 is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000059 ! taxon as collection of organisms +property_value: editor_note "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string [Term] id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms +intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid +relationship: PCO:0000055 PCO:0000017 ! has member of species as a collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -1507,8 +1881,8 @@ name: community species diversity def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. is_a: PCO:0000004 ! quality of an ecological community +property_value: editor_note "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string [Term] @@ -1517,8 +1891,8 @@ name: family def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. is_a: PCO:0000018 ! single-species collection of organisms +property_value: editor_note "Needs axioms for family relationships." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string [Term] @@ -1538,7 +1912,7 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000023 name: community species evenness -def: "A quality of a community that reflects how close in abundance all species in a community are." [] +def: "A quality of an ecological community that reflects how close in abundance all species in a community are." [] is_a: PCO:0000004 ! quality of an ecological community property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -1548,26 +1922,26 @@ property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_e id: PCO:0000024 name: household def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] -is_a: PCO:0000031 ! organismal entity -relationship: RO:0002321 ENVO:01000744 ! human dwelling -relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! Homo sapiens +is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002321 ENVO:01000744 ! ecologically related to human dwelling +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! has member Homo sapiens property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string [Term] id: PCO:0000025 -name: red population +name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000002 is_obsolete: true [Term] id: PCO:0000026 -name: red organism +name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1577,20 +1951,20 @@ name: collection of humans def: "A collection of organisms of the same species that has as members only humans." [] is_a: PCO:0000018 ! single-species collection of organisms intersection_of: PCO:0000018 ! single-species collection of organisms -intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! Homo sapiens -intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! Homo sapiens -relationship: RO:0002351 NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! has member Homo sapiens +relationship: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "human community" xsd:string property_value: IAO:0000118 "human population" xsd:string [Term] id: PCO:0000028 -name: community +name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). -is_a: ObsoleteClass -property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -1599,8 +1973,9 @@ id: PCO:0000029 name: multi-species collection of organisms def: "A collection of organisms that consists of two or more organisms from at least two species." [] is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 PCO:0000001 {minCardinality="2"} ! has member population of organisms +property_value: editor_note "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string [Term] id: PCO:0000030 @@ -1608,10 +1983,10 @@ name: agricultural household name: obsolete organismal entity def: "A household in which the majority of the income of its members is derived from agricultural activities." [] def: "A material entity that is one or more organisms, viruses or viroids." [] -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class is_a: PCO:0000024 ! household +property_value: editor_note "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000231 "wrong IRI form" xsd:string is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 @@ -1638,8 +2013,8 @@ id: PCO:0000033 name: human social gathering activity def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] is_a: GO:0035176 ! social behavior -relationship: RO:0000057 PCO:0000027 ! collection of humans -property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +relationship: RO:0000057 PCO:0000027 ! has participant collection of humans +property_value: editor_note "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] @@ -1647,7 +2022,7 @@ id: PCO:0000034 name: human community event def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1655,15 +2030,15 @@ id: PCO:0000035 name: party def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000037 name: potluck +def: "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string -property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1671,7 +2046,7 @@ id: PCO:0000038 name: wedding def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1679,90 +2054,244 @@ id: PCO:0000039 name: baby shower def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000040 +name: obsolete tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000041 +name: obsolete invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: ObsoleteClass ! Obsolete Class +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000042 +name: obsolete microbe +synonym: "microbial organism" EXACT [] +is_a: ObsoleteClass ! Obsolete Class +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000043 +name: obsolete collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000044 +name: obsolete multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000045 +name: obsolete single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000046 +name: obsolete microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000047 name: tidal mangrove shrubland community def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html is_a: PCO:0000002 ! ecological community -relationship: BFO:0000050 ENVO:01001369 ! tidal mangrove shrubland +relationship: part_of ENVO:01001369 ! tidal mangrove shrubland property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] -id: PCO:0000041 +id: PCO:0000048 name: invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO is_a: PATO:0001241 ! physical object quality [Term] -id: PCO:0000042 +id: PCO:0000049 name: microbe synonym: "microbial organism" EXACT [] is_a: CARO:0001010 ! organism or virus or viroid -relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye [Term] -id: PCO:0000043 +id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe -intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe -relationship: RO:0002351 PCO:0000042 ! microbe +intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! has member microbe +intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! has member microbe +relationship: RO:0002351 PCO:0000049 ! has member microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000044 +id: PCO:0000051 name: multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] is_a: PCO:0000029 ! multi-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000045 +id: PCO:0000052 name: single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] -is_a: PCO:0000018 ! single-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms +is_a: PCO:0000050 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000046 +id: PCO:0000053 name: microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] is_a: PCO:0000001 ! population of organisms -is_a: PCO:0000045 ! single species collection of microbes -relationship: RO:0002351 PCO:0000042 ! microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +[Term] +id: PCO:0000054 +name: number of generations of multicellular organism +def: "A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism." [] {comment="NCIT:C88214", comment="EFO:0000507"} +synonym: "number of generations" BROAD [] +is_a: STATO:0000047 ! count +relationship: IAO:0000136 CARO:0000012 ! is about multicellular organism +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 + +[Term] +id: PCO:0000057 +name: overcrowded population +def: "An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels." [] +synonym: "increased density of population" EXACT [] +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000058 +name: overcrowded human population +def: "A quality of a human population such that the density humans in an area is increased beyond sustainable levels." [] +is_a: PCO:0000057 ! overcrowded population +intersection_of: PCO:0000057 ! overcrowded population +intersection_of: RO:0000052 PCO:0000027 ! inheres in collection of humans +relationship: RO:0000052 PCO:0000027 ! inheres in collection of humans +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000059 +name: taxon as collection of organisms +def: "A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations." [] +comment: This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. +xref: data:1868 +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000060 +name: microbial parasite +def: "An organism or virus or viroid that is a microbe and a parasite." [] +is_a: ECOCORE:00000146 ! parasite +is_a: PCO:0000049 ! microbe +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000061 +name: parasite isolate population +def: "A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations." [] +is_a: PCO:0000050 ! collection of microbial organisms +is_a: PCO:0000053 ! microbial population +relationship: RO:0002351 PCO:0000060 ! has member microbial parasite +property_value: IAO:0000112 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811772/ +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "VEuPathDB" xsd:string + +[Term] +id: PCO:0000062 +name: Shannon diversity index +def: "A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi)." [] +synonym: "Shannon entropy" EXACT [] +synonym: "Shannon's diversity index" EXACT [] +synonym: "Shannon-Wiener index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html +property_value: IAO:0000119 "Shannon_index" + +[Term] +id: PCO:0000063 +name: Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi)." [] +synonym: "Simpson index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Simpson_index" + +[Term] +id: PCO:0000064 +name: inverse Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi)." [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Inverse_Simpson_index" + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: PCO:0000000 ! collection of organisms -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid [Term] id: PCO:0001001 name: pair of interacting organisms of the same species +def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms +relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms [Term] id: PCO:1000000 name: migratory population def: "A population which is participating in a migration process." [] is_a: PCO:0000001 ! population of organisms -relationship: RO:0000056 PCO:1000001 ! population migration +relationship: RO:0000056 PCO:1000001 ! participates in population migration property_value: IAO:0000114 IAO:0000123 [Term] @@ -1780,7 +2309,7 @@ name: human population migration def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration is_a: PCO:1000001 ! population migration -relationship: RO:0000057 PCO:0000027 ! collection of humans +relationship: RO:0000057 PCO:0000027 ! has participant collection of humans property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string @@ -1789,7 +2318,7 @@ id: PCO:1000003 name: human migratory population def: "A migratory population of humans, travelling with the intention of settling in a new area." [] is_a: PCO:0000027 ! collection of humans -relationship: RO:0000056 PCO:1000002 ! human population migration +relationship: RO:0000056 PCO:1000002 ! participates in human population migration property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string @@ -1800,21 +2329,1394 @@ def: "An ecological community which is composed of co-existing populations of mi comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. synonym: "microbiota" BROAD [] is_a: PCO:0000002 ! ecological community -is_a: PCO:0000044 ! multi-species collection of microbes +is_a: PCO:0000051 ! multi-species collection of microbes +property_value: editor_note "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string [Term] -id: Subset -is_a: IAO:0000102 ! data about an ontology part +id: STATO:0000047 +name: count +def: "a count is a data item denoted by an integer and represented the number of instances or occurences of an entity" [] +is_a: IAO:0000109 ! measurement datum +property_value: IAO:0000112 "a count of 4 resulting from counting limbs in humans" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string +property_value: IAO:0000117 "Orlaith Burke" xsd:string +property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string +property_value: IAO:0000119 "STATO" xsd:string +property_value: STATO:0000032 "" xsd:string + +[Typedef] +id: BFO:0000054 +name: realized in +comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realized in" xsd:string +property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string +property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string +property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string +property_value: IAO:0000118 "is realized by" xsd:string +property_value: IAO:0000118 "realized_in" xsd:string +property_value: IAO:0000600 "[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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +inverse_of: BFO:0000055 ! realizes + +[Typedef] +id: BFO:0000055 +name: realizes +comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realizes" xsd:string +property_value: IAO:0000112 "this disease course realizes this disease" xsd:string +property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string +property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string +property_value: IAO:0000600 "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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +domain: BFO:0000015 ! process +range: BFO:0000017 ! realizable entity + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "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." [] +subset: ro-eco +property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "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." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "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" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: part_of BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part_of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[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" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Term] -id: Synonym -is_a: IAO:0000102 ! data about an ontology part +[Typedef] +id: IAO:0000136 +name: is about +def: "A (currently) primitive relation that relates an information artifact to an entity." [] +property_value: editor_note "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string + +[Typedef] +id: PCO:0000055 +name: has member of +domain: PCO:0000000 ! collection of organisms + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: editor_note "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000079 +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 ! function +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000085 ! has function + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000085 +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000034 ! function +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +is_a: RO:0000052 ! inheres in + +[Typedef] +id: RO:0001000 +name: derives from +def: "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" [] +property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "derives_from" xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "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" [] +property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000111 "is location of" xsd:string +property_value: IAO:0000112 "my head is the location of my brain" xsd:string +property_value: IAO:0000112 "this cage is the location of this rat" xsd:string +property_value: IAO:0000118 "location_of" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string +property_value: IAO:0000111 "located in" xsd:string +property_value: IAO:0000112 "my brain is located in my head" xsd:string +property_value: IAO:0000112 "this rat is located in this cage" xsd:string +property_value: IAO:0000118 "located_in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true + +[Typedef] +id: RO:0002000 +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] +property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity + +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "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." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "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." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "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." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "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." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "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." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "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." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "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." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_functional: true +is_a: RO:0002017 ! has component activity +is_a: RO:0002211 ! regulates +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: has_part RO:0002131 +holds_over_chain: part_of part_of +is_a: RO:0002323 ! mereotopologically related to +transitive_over: part_of ! part_of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002180 +name: has component +def: "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." [] +subset: ro-eco +property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: has_part ! has part + +[Typedef] +id: RO:0002211 +name: regulates +def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string +property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002215 +name: capable of +def: "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. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of +expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process +expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002233 +name: has input +def: "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." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "consumes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "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." [] +property_value: IAO:0000112 "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." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "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." [] +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002321 +name: ecologically related to +def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] +subset: ro-eco +property_value: editor_note "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002327 +name: enables +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: has_part ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 part_of +is_a: RO:0000056 ! participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "regulated by (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part_of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +synonym: "affects" RELATED [] +property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "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" [] +property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "involved in or reguates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "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." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "executes activity in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso ECO:0000353 +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: editor_note "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: directly regulates activity of +def: "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0011002 ! regulates activity of + +[Typedef] +id: RO:0002449 +name: directly negatively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly inhibits" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002450 +name: directly positively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly activates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002464 +name: helper property (not for use in curation) +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "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." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} + +[Typedef] +id: RO:0002481 +name: is kinase activity +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002506 +name: causal relation between entities +property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002506 ! causal relation between entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002563 +name: interaction relation helper property +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +is_a: RO:0002464 ! helper property (not for use in curation) + +[Typedef] +id: RO:0002564 +name: molecular interaction relation helper property +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002566 +name: causally influences +def: "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)." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002506 ! causal relation between entities + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "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" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: has_part RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "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." [] +property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 has_part +is_a: RO:0002328 ! functionally related to +created_by: cjm +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "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" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: cjm +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "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" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: cjm +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0011002 +name: regulates activity of +def: "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." [] +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002566 ! causally influences + +[Typedef] +id: decreased_in_magnitude_relative_to +name: decreased_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: different_in_magnitude_relative_to +name: different_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality + +[Typedef] +id: editor_note +name: editor note +namespace: uberon +def: "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." [] +xref: IAO:0000116 +property_value: IAO:0000111 "editor note" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + +[Typedef] +id: has_part +name: has part +name: has_part +namespace: external +namespace: quality +def: "a core relation that holds between a whole and its part" [] +def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] +comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. +xref: BFO:0000051 +property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA 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'." xsd:string +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps -[Term] -id: SynonymType -is_a: IAO:0000102 ! data about an ontology part +[Typedef] +id: increased_in_magnitude_relative_to +name: increased_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: part_of +name: part of +name: part_of +namespace: external +namespace: quality +def: "a core relation that holds between a part and its whole" [] +xref: BFO:0000050 +property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA 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'." xsd:string +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: has_part ! has part + +[Typedef] +id: reciprocal_of +name: reciprocal_of +namespace: quality +def: "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." [PATOC:CJM] +comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl diff --git a/src/ontology/pco-full.owl b/src/ontology/pco-full.owl index c95c12c..b73706e 100644 --- a/src/ontology/pco-full.owl +++ b/src/ontology/pco-full.owl @@ -7,20 +7,26 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:swrl="http://www.w3.org/2003/11/swrl#" + xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" + xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg Ramona Walls - http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. + Population and Community Ontology + http://creativecommons.org/publicdomain/zero/1.0/ The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. @@ -62,12 +68,21 @@ + editor preferred label + editor preferred label + editor preferred term editor preferred term + editor preferred term~editor preferred label 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 label + editor preferred label + editor preferred term editor preferred term + editor preferred term~editor preferred label @@ -76,6 +91,7 @@ example + 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 @@ -106,6 +122,8 @@ PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 + + has curation status has curation status @@ -115,7 +133,10 @@ definition + definition + textual definition + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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 @@ -142,6 +163,7 @@ We also have the outstanding issue of how to aim different definitions to differ definition definition + textual definition @@ -154,6 +176,12 @@ We also have the outstanding issue of how to aim different definitions to differ 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.obfoundry.org/obo/obi> + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + IAO:0000116 + uberon + editor_note + true + editor_note editor note editor note @@ -170,6 +198,8 @@ We also have the outstanding issue of how to aim different definitions to differ 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 term editor @@ -183,6 +213,7 @@ We also have the outstanding issue of how to aim different definitions to differ An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + alternative term @@ -193,11 +224,14 @@ We also have the outstanding issue of how to aim different definitions to differ 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 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 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source definition source @@ -222,6 +256,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg + curator note @@ -230,13 +265,13 @@ We also have the outstanding issue of how to aim different definitions to differ - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + 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. + 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 @@ -245,10 +280,11 @@ We also have the outstanding issue of how to aim different definitions to differ + 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 + 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 The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester @@ -259,10 +295,10 @@ We also have the outstanding issue of how to aim different definitions to differ 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 - 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 + is denotator type @@ -276,6 +312,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from @@ -290,7 +327,8 @@ 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 + Chris Mungall + expand expression to @@ -326,7 +364,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. antisymmetric property part_of antisymmetric property xsd:true - use boolean value xsd:true to indicate that the property is an antisymmetric property + Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property @@ -339,12 +377,13 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. 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 . + 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/> + OBO foundry unique label @@ -353,14 +392,15 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 + 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 digit count @@ -369,12 +409,13 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Datatype: idrange:1 + 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 + 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 range allocated to @@ -383,15 +424,16 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 policy for + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for @@ -399,14 +441,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 + 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 ID prefix @@ -455,23 +498,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] is allocated id range - Add as annotation triples in the granting ontology 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 + Add as annotation triples in the granting ontology is allocated id range + + + + 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 + has ontology root term + + + + - 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 - #40 - VFB - 2018-09-21T16:43:39Z - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + 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 + #40 + VFB + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to @@ -480,6 +534,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + 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 https://github.com/geneontology/go-ontology/issues/15532 @@ -509,10 +564,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] term replaced by - Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by @@ -530,6 +585,94 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + is a defining property chain axiom + + + + + + + + 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. + + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + an alternative term used for STATO statistical ontology and ISA team + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO alternative term + + + + @@ -612,7 +755,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + + @@ -634,12 +779,36 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + @@ -675,6 +844,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + database_cross_reference @@ -700,7 +870,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - has_obo_namespace + has_obo_namespace @@ -739,6 +909,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + shorthand + + + + @@ -749,16 +934,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + - + + label + label @@ -771,6 +958,14 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -811,139 +1030,2218 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + + + + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + + + + + + + + BFO:0000050 + external + quality + part_of + part_of + + part of + part of + part_of + + + http://www.obofoundry.org/ro/#OBO_REL: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) + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + BFO:0000051 + external + quality + has_part + has_part + We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. + + has part + has part + has_part + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + PATOC:CJM + + + + + + + + + + + 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]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + + + 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]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + + + + + + + + + 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 + http://www.obofoundry.org/ro/#OBO_REL: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. + + + precedes + + + + + + + + + + + + + + + + + + + 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 + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs 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 + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + This document is about information artifacts and their representations + + A (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + + + + has member of + - + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + 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 + + bearer of + - + + + + + 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 + + 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 + http://www.obofoundry.org/ro/#OBO_REL:has_participant + + 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. + is concretized as + + + + + + + + + + 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. + concretizes + + + + + + + + + + + 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 + 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 + 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 + 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 + - + - + + + disposition of + - + - + + + 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 + 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 + derives into + - + - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - + + + + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + location_of + + location of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + located in + - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - + - - - - continuant - Continuant - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + 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 + + 2D boundary of + + + + + + + + + + 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 + + has 2D boundary + + + + + + + + + + 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. + dos + 2017-05-24T09:30:46Z + + has regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + + has negative regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + + has component activity + + + + + + + + + + + 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. + dos + 2017-05-24T09:49:21Z + + has component process + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:38Z + + directly negatively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:47Z + + directly positively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + + 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. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + + has 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. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + + immediately preceded by + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + + immediately precedes + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + overlaps + + + + + + + + + true + + + + + + + + + + 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. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + + has component + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + + positively regulates + + + + + + + + + + + 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. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + + capable of + + + + + + + + + + + + + + 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. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + + capable of part of + + + + + + + + + + true + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + + temporally related to + + + + + + + + + + + + + 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. + Chris Mungall + consumes + + + has input + + + + + + + + + + + + + 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. + + acts upstream of + + + + + + + + + + + + + + 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 + + acts upstream of or within + + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + causally upstream of, negative effect + + + + + + + + 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 + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + + ecologically related to + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + 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 + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + + involved in + + + + + + + + + + + inverse of enables + Chris Mungall + + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + + positively regulated by + + + + + + + + + + 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 + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + Chris Mungall + + + + input of + + + + + + + + + + + + inverse of upstream of + Chris Mungall + + causally downstream of + + + + + + + + + + + + Chris Mungall + + immediately causally downstream of + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + 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. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + + involved in negative regulation of + + + + + + + + + + + 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 + Chris Mungall + involved in or reguates + + involved in or involved in regulation of + + + + + + + + + + + + + + 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. + Chris Mungall + executes activity in + enables activity in + + + is active in + + + + + + + + + true + + + + + 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. + GOC:cjm + GOC:dos + + + + + + + + + + + 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. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + 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. + Chris Mungall + binds + molecularly binds with + + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + + phosphorylates + + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + molecularly controls + + directly regulates activity of + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + directly inhibits + molecularly decreases activity of + + directly negatively regulates 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. + Chris Mungall + Vasundra Touré + directly activates + molecularly increases activity of + + directly positively regulates activity of + + + + + + + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + + helper property (not for use in curation) + + + + + + + + + + + + + + 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. + Chris Mungall + + + has part that occurs in + + + + + + + + + true + + + + + + + + + Chris Mungall + + is kinase activity + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + + causal agent in 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between processes + + + + + + + + + + + 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 + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between entities + + + + + + + + + + Chris Mungall + + causally influenced by (entity-centric) + + causally influenced by + + + + + + + + + Chris Mungall + + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + + molecular interaction relation helper property + + + + + + + + + + + + + + + + + + + + + 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). + Chris Mungall + Vasundra Touré + + causally influences (entity-centric) + + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + + directly regulates + + + + + + + + + + + + + + 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 + Chris Mungall + + has part structure that is capable of + + + + + + + + + + + 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. + Chris Mungall + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + + capable of negatively regulating + + + + + + + + + + + + + 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. + + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + + process has causal agent + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + + directly negatively regulates + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + + causally upstream of or within, positive effect + + + + + + + + + + + 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. + Vasundra Touré + + regulates activity of + + + + + + + + + + + + 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. + quality + decreased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + + decreased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + 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. + quality + different_in_magnitude_relative_to + + different_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + + + 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. + quality + increased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + + increased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + 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. + quality + reciprocal_of + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + + reciprocal_of + + + + + 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. + PATOC:CJM + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - continuant + entity - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + + + + + + + + + + + + continuant + Continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + @@ -986,6 +3284,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + @@ -993,8 +3303,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + occurrent Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. @@ -1057,6 +3380,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + ic @@ -1071,6 +3400,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] an organism the bottom right portion of a human torso the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) @@ -1119,6 +3449,26 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. + obsolete dependent continuant + true + + + + + + + + + spatial region + + + + @@ -1132,6 +3482,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the flight of a bird the life of an organism your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] @@ -1153,10 +3504,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + disposition + + + + + realizable RealizableEntity the disposition of this piece of metal to conduct electricity. @@ -1164,6 +3526,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet + 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. + https://orcid.org/0000-0001-8815-0078 To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] @@ -1198,10 +3562,25 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + quality + + + + + + + + + + sdc SpecificallyDependentContinuant @@ -1216,6 +3595,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the role of being a doctor the shape of this hole. the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. 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]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] @@ -1257,6 +3637,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the role of a stone in marking a property boundary the role of subject in a clinical trial the student role + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] @@ -1388,6 +3769,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] @@ -1408,6 +3790,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + function + + + + @@ -1427,6 +3818,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] an energy wave an epidemic the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. @@ -1491,6 +3883,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. + multicellular organism + Melissa Haendel + 9/18/11 + MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. + multicellular organism + + + + @@ -1512,75 +3919,39 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] organism mah 7.16.2011 - A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. organism - - - - - A feature that has been constructed by deliberate human effort. - "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference - constructed feature - construction - - - - - A feature that has been constructed by deliberate human effort. - MA:ma - - - - - + - - - A material entity which determines an environmental system. - ENVO - ENVO:00002297 - A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. - environmental feature + + + heterotroph that acquires nutrition from a symbiont + http://orcid.org/0000-0002-2908-3327 + symbiotroph - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - + - - - A system which has the disposition to environ one or more material entities. - 2013-09-23T16:04:08Z - EcoLexicon:environment - environment - In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. - environmental system + + + A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host + http://orcid.org/0000-0002-2908-3327 + https://www.wikidata.org/entity/Q10253316 + parasite - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. Subclasses will be added by inference. @@ -1595,24 +3966,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - A material part of an astronomical body. - envoAstro - envoPolar - astronomical body part - - - - - + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. - http://orcid.org/0000-0002-4366-3088 + CMECS:577 https://cmecscatalog.org/cmecs/classification/unit/577.html envoCmecs @@ -1623,14 +3982,37 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + molecular process + + molecular_function + + + + + + + + + + catalytic activity + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. - janelomax + jl 2012-09-20T14:06:08Z + GO:0023032 GO:0044708 + GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour @@ -1661,8 +4043,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - janelomax + jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 @@ -1683,7 +4066,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process @@ -1696,11 +4079,47 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + true + + + + kinase activity + + + + + + + + + + transferase activity + + + + + + + + + + transferase activity, transferring phosphorus-containing groups + + + + + - Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour @@ -1725,8 +4144,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + Any process in which an organism has an effect on an organism of a different species. + interaction with another species interspecies interaction interspecies interaction with other organisms @@ -1749,7 +4169,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + Any process in which an organism has an effect on an organism of the same species. intraspecies interaction with other organisms biological_process @@ -1770,7 +4190,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A biological process which involves another organism of the same or different species. GO:0051706 @@ -1793,45 +4212,30 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GO:0023032 - GO:0044709 - behavioral interaction between organisms - behavioral interaction with other organism - behavioural interaction between organisms - behavioural interaction with other organism - behavioral signaling - behavioral signalling - biological_process - GO:0051705 - - - multi-organism behavior - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GOC:ai - - - - - behavioral signalling - GOC:mah - - - - + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item @@ -1841,6 +4245,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + information content entity information content entity @@ -1881,13 +4286,32 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg + 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 data about an ontology part + + + + + measurement datum + Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + + measurement datum + + + + @@ -1927,11 +4351,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - denotator type + 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 + denotator type @@ -1940,12 +4365,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - cjm - 2018-05-20T20:55:03Z - ontology module + 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 + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module @@ -1954,10 +4378,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - cjm - 2018-05-20T20:55:30Z - base ontology module + 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. + base ontology module @@ -1967,11 +4390,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:55:47Z - editors ontology module + 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 + editors ontology module @@ -1980,11 +4402,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:56:13Z - main release 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 + main release ontology module @@ -1993,10 +4414,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - cjm - 2018-05-20T20:56:23Z - bridge ontology 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. + bridge ontology module @@ -2006,12 +4426,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:56:47Z - import ontology 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 + import ontology module @@ -2021,12 +4440,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - cjm - 2018-05-20T20:58:11Z - subset ontology module + 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 + subset ontology module @@ -2037,10 +4455,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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. - cjm - 2018-05-20T20:58:38Z - curation subset ontology module + 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. + curation subset ontology module @@ -2049,10 +4466,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is intended for usage in analysis or discovery applications. - cjm - 2018-05-20T20:58:49Z - analysis subset ontology module + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module @@ -2061,11 +4477,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:59:19Z - single layer subset ontology module + 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 + single layer subset ontology module @@ -2074,11 +4489,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - cjm - 2018-05-20T20:59:57Z - exclusion subset ontology module + 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 + exclusion subset ontology module @@ -2087,11 +4501,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - cjm - 2018-05-20T21:00:14Z - external import ontology module + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module @@ -2100,11 +4513,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - cjm - 2018-05-20T21:14:16Z - species subset ontology module + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module @@ -2114,10 +4526,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - cjm - 2018-05-20T21:20:33Z - reasoned ontology module + 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. + reasoned ontology module @@ -2127,11 +4538,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T21:21:12Z - generated ontology module + 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 + generated ontology module @@ -2140,10 +4550,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - cjm - 2018-05-20T21:21:21Z - template generated ontology module + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module @@ -2155,9 +4564,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - cjm - 2018-05-20T21:28:15Z - taxonomic bridge ontology module + taxonomic bridge ontology module + taxonomic bridge ontology module @@ -2166,9 +4574,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - cjm - 2018-05-22T04:15:54Z - ontology module subsetted by expressivity + ontology module subsetted by expressivity + ontology module subsetted by expressivity @@ -2177,7 +4584,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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. + 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). @@ -2193,9 +4601,7 @@ No qualifier lists No disjointness axioms No owl-axioms header No imports - cjm - 2018-05-22T04:16:10Z - obo basic subset ontology module + obo basic subset ontology module @@ -2205,9 +4611,8 @@ No imports - cjm - 2018-05-22T04:16:28Z - ontology module subsetted by OWL profile + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile @@ -2216,9 +4621,8 @@ No imports - cjm - 2018-05-22T04:16:48Z - EL++ ontology module + EL++ ontology module + EL++ ontology module @@ -2270,46 +4674,20 @@ No imports - - - NCBITaxon:40673 - GC_ID:1 - bony vertebrates - ncbi_taxonomy - - Euteleostomi - - - - - bony vertebrates - - - - - - - - - + + + NCBITaxon:40673 GC_ID:1 + bony vertebrates ncbi_taxonomy - Viroid - viroids - Viroids + Euteleostomi - - - Viroid - - - - - - viroids - + + + bony vertebrates + @@ -2320,22 +4698,22 @@ No imports GC_ID:1 + charophyte/embryophyte group ncbi_taxonomy Charophyta/Embryophyta group - charophyte/embryophyte group Streptophytina - - Charophyta/Embryophyta group - + + charophyte/embryophyte group + - charophyte/embryophyte group + Charophyta/Embryophyta group @@ -2429,7 +4807,9 @@ No imports PMID:12054223 PMID:2112744 PMID:270744 + PMID:7520741 PMID:8123559 + PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 @@ -2445,12 +4825,6 @@ No imports Bacteria - - - - prokaryotes - - @@ -2493,6 +4867,12 @@ No imports prokaryote + + + + prokaryotes + + @@ -2631,6 +5011,7 @@ No imports GC_ID:1 PMID:23020233 + PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy @@ -2886,7 +5267,7 @@ No imports Theria ncbi_taxonomy - Theria <Mammalia> + Theria <mammals> @@ -2903,11 +5284,14 @@ No imports GC_ID:1 + PMID:16248873 + PMID:30257078 + Chlorophyta/Embryophyta group + chlorophyte/embryophyte group green plants ncbi_taxonomy Chlorobionta - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group + Chloroplastida green plants Viridiplantae @@ -2915,25 +5299,31 @@ No imports - green plants - + Chlorophyta/Embryophyta group + - - Chlorobionta - + + chlorophyte/embryophyte group + + + + + + green plants + - Chlorophyta/Embryophyta group + Chlorobionta - chlorophyte/embryophyte group + Chloroplastida @@ -3047,15 +5437,17 @@ No imports + GC_ID:1 PMID:25249442 angiosperms flowering plants ncbi_taxonomy Angiospermae + Magnoliophyta flowering plants - Magnoliophyta + Magnoliopsida @@ -3075,6 +5467,12 @@ No imports Angiospermae + + + + Magnoliophyta + + @@ -3137,6 +5535,41 @@ No imports + + + + + + GC_ID:1 + PMID:11062127 + PMID:12684019 + ncbi_taxonomy + Mycota + fungi + + Fungi + + + + + Mycota + + + + + + fungi + + + + + + fungi + + + + + @@ -3238,7 +5671,7 @@ No imports ncbi_taxonomy vertebrates - Vertebrata <Metazoa> + Vertebrata <vertebrates> @@ -3270,7 +5703,7 @@ No imports jawed vertebrates ncbi_taxonomy - Gnathostomata <vertebrate> + Gnathostomata <vertebrates> @@ -3292,16 +5725,16 @@ No imports GC_ID:1 + euphyllophytes ncbi_taxonomy - euphyllophytes Euphyllophyta - + euphyllophytes - + @@ -3328,7 +5761,7 @@ No imports Craniata ncbi_taxonomy - Craniata <chordata> + Craniata <chordates> @@ -3489,19 +5922,6 @@ No imports human man ncbi_taxonomy - Home sapiens - Homo sampiens - Homo sapeins - Homo sapian - Homo sapians - Homo sapien - Homo sapience - Homo sapiense - Homo sapients - Homo sapines - Homo spaiens - Homo spiens - Humo sapiens Homo sapiens @@ -3517,124 +5937,340 @@ No imports man + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality (PATO) + PATO:0000072 + quality + PATO:0000001 + + quality + - - - Home sapiens - - - - - - Homo sampiens - - - - - - Homo sapeins - - - - - - Homo sapian - - - - - - Homo sapians - + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + quality + PATO:0000068 + TODO: define this or obsolete it and move children somewhere else. + + qualitative + + + + + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + quality + PATO:0000069 + + + deviation (from_normal) + - - - Homo sapien - + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + PATOC:GVG + + + + + + + + + + + + + + The number of entities of this type that are part of the whole organism. + PATO:0000053 + PATO:0000071 + PATO:0001169 + PATO:0001226 + presence or absence in organism + quantitative + quality + count in organism + number + presence + PATO:0000070 + + This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. + + amount + - - - Homo sapience - + + + The number of entities of this type that are part of the whole organism. + PATOC:GVG + + + + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + + rate + - - - Homo sapiense - + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + PATOC:melissa + + + + + + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + + quality + average + PATO:0000461 + + + + + normal + - - - Homo sapients - + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + PATOC:GVG + + + + + + + + A quality inhering in a bearer by virtue of the bearer's existence. + + quality + present in organism + PATO:0000467 + + + + present + - - - Homo sapines - + + + A quality inhering in a bearer by virtue of the bearer's existence. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + An amount which is relatively high. + + PATO:0000420 + PATO:0000650 + increased number + present in greater numbers in organism + supernumerary + quality + accessory + increased + PATO:0000470 + + + increased amount + - - - Homo spaiens - + + + An amount which is relatively high. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + A rate which is relatively low. + + slow rate + quality + PATO:0000911 + + + + decreased rate + - - - Homo spiens - + + + A rate which is relatively low. + PATO:GVG + + + + + + + + + + + + + + + + + + + + A rate which is relatively high. + + fast rate + high rate + quality + PATO:0000912 + + + + increased rate + - - - Humo sapiens - + + + A rate which is relatively high. + PATO:GVG - + - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 - trait + + + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + PATO:0002079 + Wikipedia:Physical_property + relational physical quality quality - PATO:0000001 + PATO:0001018 + - quality + physical quality - + - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG - + - - - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + + + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality - PATO:0000161 + density + PATO:0001019 - rate + mass density - + - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. - PATOC:melissa + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. + WordNet:WordNet + + + + + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + quality + PATO:0001164 + + + + dense + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + PATOC:GVG @@ -3643,6 +6279,7 @@ No imports + A quality which inheres in an process. PATO:0001239 PATO:0001240 @@ -3738,6 +6375,148 @@ No imports + + + + + + + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + OBO_REL:has_part + extra or missing physical or functional parts + has or lacks parts of type + mereological quality + number of + quality + cardinality + number + PATO:0001555 + + + + has number of + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + PATOC:CJM + + + + + + + + + + + + + + + + + + + + + A density which is higher relative to the normal or average. + + high density + quality + PATO:0001788 + + + increased mass density + + + + + A density which is higher relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A density which is lower relative to the normal or average. + + low density + quality + PATO:0001790 + + + decreased mass density + + + + + A density which is lower relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + An amount which is relatively low. + + PATO:0000419 + PATO:0000468 + decreased number + present in fewer numbers in organism + quality + decreased + reduced + subnumerary + PATO:0001997 + + + decreased amount + + + + + An amount which is relatively low. + PATOC:GVG + + + + @@ -3773,6 +6552,220 @@ No imports + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:39:43Z + quality + PATO:0002300 + + increased quality + + + + + A quality that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:40:15Z + quality + PATO:0002301 + + decreased quality + + + + + A quality that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:50:59Z + quality + PATO:0002302 + + decreased process quality + + + + + A quality of a process that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:51:54Z + quality + PATO:0002303 + + decreased object quality + + + + + A quality of an object that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:53:08Z + quality + PATO:0002304 + + increased process quality + + + + + A quality of a process that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:54:01Z + quality + PATO:0002305 + + increased object quality + + + + + A quality of an object that has a value that is increased compared to normal or average. + PATOC:GVG + + + + @@ -3799,6 +6792,12 @@ No imports + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. @@ -3830,18 +6829,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - 2 - - - - - + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 @@ -3873,8 +6861,9 @@ Classes for population already exist in IDO ('organism population', I - A quality that inheres in a biological population. + A quality that inheres in a population of organisms. See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community. Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. quality of a population @@ -3922,8 +6911,8 @@ Classes for population already exist in IDO ('organism population', I - A process that has as primary participant a population. - Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. + The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. population process @@ -3932,8 +6921,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of birth of a population of organisms. population birth rate @@ -3942,8 +6932,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of death of a population of organsisms. population death rate @@ -3952,9 +6943,9 @@ Classes for population already exist in IDO ('organism population', I - + - Is a rate a quality? Population growth rate may be better classified as a process profile. + The rate of growth of a population. population growth rate @@ -4023,30 +7014,51 @@ Classes for population already exist in IDO ('organism population', I - - - predator role + + Interactions are now covered in EcoCore ontology. + obsolete predator role + true + + + + true + + - - - prey role + + Interactions are now covered in EcoCore ontology. + obsolete prey role + true + + + + true + + - - - symbiont role + + Interactions are now covered in EcoCore ontology. + obsolete symbiont role + true + + + + true + + @@ -4054,9 +7066,15 @@ Classes for population already exist in IDO ('organism population', I + - A collection of organisms that has as parts every organism of given species and no organisms of any other species. + A collection of organisms that has as members every organism of given species and no organisms of any other species. + A collection of organisms that has as parts every organism of a species and no organisms of any other species. At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + + + + taxonomic group This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. species as a collection of organisms @@ -4073,25 +7091,26 @@ Classes for population already exist in IDO ('organism population', I - - - - - - 1 - - - - 2 + + + 1 + + + + + + + + A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -4156,7 +7175,7 @@ Classes for population already exist in IDO ('organism population', I If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. - A quality of a community that reflects how close in abundance all species in a community are. + A quality of an ecological community that reflects how close in abundance all species in a community are. adapted from http://en.wikipedia.org/wiki/Species_evenness community species evenness @@ -4166,7 +7185,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -4190,7 +7209,7 @@ Classes for population already exist in IDO ('organism population', I An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. - Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household household @@ -4203,7 +7222,7 @@ Classes for population already exist in IDO ('organism population', I This is an example population added to demonstrate the modeling pattern for collections of organisms. - red population + obsolete red population true @@ -4215,7 +7234,7 @@ Classes for population already exist in IDO ('organism population', I An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. - red organism + obsolete red organism true @@ -4264,7 +7283,7 @@ Classes for population already exist in IDO ('organism population', I Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). - community + obsolete community true @@ -4274,6 +7293,13 @@ Classes for population already exist in IDO ('organism population', I + + + + 2 + + + A collection of organisms that consists of two or more organisms from at least two species. Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". @@ -4372,34 +7398,336 @@ Classes for population already exist in IDO ('organism population', I + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 - A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. GenEpio curators potluck - + + + + + A human social gathering at which two people are married. May include a legal or social ceremony. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 + GenEpio curators + wedding + + + + + + + + + A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 + GenEpiO curators + baby shower + + + + + + + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community + + + + + + + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + microbial organism + microbe + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + + + + + + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + number of generations + number of generations of multicellular organism + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + + + + + + + + + + + + + + + + + + + + + + An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels. + + increased density of population + overcrowded population + + + + + + + + + + + + + + + + + + + + + + + + + + + A quality of a human population such that the density humans in an area is increased beyond sustainable levels. + + overcrowded human population + + + + + + + + + + A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations. + + + This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. + taxon as collection of organisms + + + + + + + + + + + An organism or virus or viroid that is a microbe and a parasite. + + microbial parasite + + + + + + + + + + + + + + + + + + A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations. + + VEuPathDB + parasite isolate population + + + + + + + + + + A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi). + + + Shannon entropy + Shannon's diversity index + Shannon-Wiener index + Shannon diversity index + + + + + - - - A human social gathering at which two people are married. May include a legal or social ceremony. - Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 - GenEpio curators - wedding + + + + A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi). + + + Simpson index + Simpson diversity index - + - - - A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. - Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 - GenEpiO curators - baby shower + + + + A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi). + + + inverse Simpson diversity index @@ -4408,12 +7736,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - @@ -4430,25 +7752,16 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 1 - - - - - - - + + + + 1 + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. pair of interacting organisms of the same species @@ -4525,7 +7838,7 @@ Classes for population already exist in IDO ('organism population', I - + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 @@ -4538,6 +7851,23 @@ Classes for population already exist in IDO ('organism population', I + + + + + a count of 4 resulting from counting limbs in humans + + a count is a data item denoted by an integer and represented the number of instances or occurences of an entity + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO + + count + + + + @@ -4551,55 +7881,10 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Obsolete Class @@ -4607,19 +7892,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 https://cmecscatalog.org/cmecs/classification/unit/577.html mangrove community tidal shrubland community - tidal mangrove shrubland community + obsolete tidal mangrove shrubland community + true @@ -4627,10 +7908,12 @@ Classes for population already exist in IDO ('organism population', I - + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO - invisible to unaided eye + obsolete invisible to unaided eye + true @@ -4638,15 +7921,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + + microbial organism - microbe + obsolete microbe + true @@ -4654,31 +7933,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - - - - - - - - + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 - collection of microbial organisms + obsolete collection of microbial organisms + true @@ -4686,11 +7946,12 @@ Classes for population already exist in IDO ('organism population', I - - + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 - multi-species collection of microbes + obsolete multi-species collection of microbes + true @@ -4698,36 +7959,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - 1 - - - - - - - 2 - - - - - - - + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 - single species collection of microbes + obsolete single species collection of microbes + true @@ -4735,18 +7972,13 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 microbiota - microbial population + obsolete microbial population + true @@ -4766,6 +7998,7 @@ Classes for population already exist in IDO ('organism population', I + example to be eventually removed example to be eventually removed @@ -4775,8 +8008,9 @@ Classes for population already exist in IDO ('organism population', I + 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 + Person:Alan Ruttenberg failed exploratory term @@ -4786,6 +8020,7 @@ Classes for population already exist in IDO ('organism population', I + 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. metadata complete @@ -4796,7 +8031,8 @@ Classes for population already exist in IDO ('organism population', I - term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -4806,6 +8042,7 @@ Classes for population already exist in IDO ('organism population', I + 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." ready for release @@ -4816,6 +8053,7 @@ Classes for population already exist in IDO ('organism population', I + metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -4826,6 +8064,7 @@ Classes for population already exist in IDO ('organism population', I + uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -4836,6 +8075,7 @@ Classes for population already exist in IDO ('organism population', I + 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. pending final vetting @@ -4845,11 +8085,12 @@ Classes for population already exist in IDO ('organism population', I - 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 - core + + obsolete_core + true @@ -4858,6 +8099,7 @@ Classes for population already exist in IDO ('organism population', I + placeholder removed placeholder removed @@ -4867,6 +8109,7 @@ Classes for population already exist in IDO ('organism population', I + terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -4877,6 +8120,7 @@ Classes for population already exist in IDO ('organism population', I + 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 imported @@ -4887,6 +8131,7 @@ Classes for population already exist in IDO ('organism population', I + 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. term split @@ -4897,10 +8142,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - universal + 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 + universal @@ -4909,10 +8155,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - defined class + 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 + defined class @@ -4921,10 +8168,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - named class expression + 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 + named class expression @@ -4933,6 +8181,7 @@ Classes for population already exist in IDO ('organism population', I + to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI @@ -4945,6 +8194,7 @@ Classes for population already exist in IDO ('organism population', I + 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 @@ -4961,6 +8211,39 @@ Classes for population already exist in IDO ('organism population', I /////////////////////////////////////////////////////////////////////////////////////// --> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4983,6 +8266,923 @@ Classes for population already exist in IDO ('organism population', I + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/pco.obo b/src/ontology/pco.obo index f15f70f..7b026ec 100644 --- a/src/ontology/pco.obo +++ b/src/ontology/pco.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2020-02-13 +data-version: releases/2020-08-26 remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -8,31 +8,35 @@ property_value: http://purl.org/dc/elements/1.1/creator "David Osumi-Sutherland" property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Pier Luigi Buttigieg" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Ramona Walls" xsd:string -property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string +property_value: http://purl.org/dc/elements/1.1/description "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Population and Community Ontology" xsd:string +property_value: http://purl.org/dc/terms/license http://creativecommons.org/publicdomain/zero/1.0/ xsd:string [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string +property_value: editor_note "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: editor_note "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000112 "Julius Caesar" xsd:string property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000002 name: continuant +def: "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." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent +relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string -property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: editor_note "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} @@ -46,13 +50,15 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000003 name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity +relationship: part_of BFO:0000003 ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string -property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} -property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string +property_value: editor_note "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string +property_value: editor_note "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: editor_note "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} @@ -63,10 +69,12 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string @@ -86,13 +94,27 @@ property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000005 +name: obsolete dependent continuant +def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true + +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity + [Term] id: BFO:0000015 name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string +property_value: editor_note "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string property_value: IAO:0000112 "a process of meiosis" xsd:string property_value: IAO:0000112 "a process of sleeping" xsd:string @@ -100,14 +122,21 @@ property_value: IAO:0000112 "the course of a disease" xsd:string property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + [Term] id: BFO:0000017 name: realizable entity +def: "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_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality property_value: BFO:0000179 "realizable" xsd:string property_value: BFO:0000180 "RealizableEntity" xsd:string property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string @@ -115,20 +144,29 @@ property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:str property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant + [Term] id: BFO:0000020 name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: part_of BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string @@ -140,16 +178,17 @@ property_value: IAO:0000112 "the pink color of a medium rare piece of grilled fi property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000023 name: role +def: "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." [] is_a: BFO:0000017 ! realizable entity property_value: BFO:0000179 "role" xsd:string property_value: BFO:0000180 "Role" xsd:string +property_value: editor_note "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string property_value: IAO:0000112 "the priest role" xsd:string property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string @@ -157,7 +196,6 @@ property_value: IAO:0000112 "the role of a building in serving as a military tar property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl @@ -168,6 +206,9 @@ name: object aggregate is_a: BFO:0000040 ! material entity property_value: BFO:0000179 "object-aggregate" xsd:string property_value: BFO:0000180 "ObjectAggregate" xsd:string +property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: editor_note "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: editor_note "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000112 "a collection of cells in a blood biobank." xsd:string property_value: IAO:0000112 "a swarm of bees is an aggregate of members who are linked together through natural bonds" xsd:string property_value: IAO:0000112 "a symphony orchestra" xsd:string @@ -181,9 +222,6 @@ property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:stri property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} -property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} @@ -217,6 +255,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] def: "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])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant property_value: BFO:0000179 "gdc" xsd:string @@ -227,13 +266,22 @@ property_value: IAO:0000112 "the sequence of this protein molecule; the sequence property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + [Term] id: BFO:0000040 name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "material" xsd:string property_value: BFO:0000180 "MaterialEntity" xsd:string +property_value: editor_note "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string +property_value: editor_note "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string +property_value: editor_note "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: IAO:0000112 "a flame" xsd:string property_value: IAO:0000112 "a forest fire" xsd:string property_value: IAO:0000112 "a human being" xsd:string @@ -246,9 +294,6 @@ property_value: IAO:0000112 "an aggregate of human beings." xsd:string property_value: IAO:0000112 "an energy wave" xsd:string property_value: IAO:0000112 "an epidemic" xsd:string property_value: IAO:0000112 "the undetached arm of a human being" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string -property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} @@ -263,9 +308,20 @@ name: immaterial entity is_a: BFO:0000004 ! independent continuant property_value: BFO:0000179 "immaterial" xsd:string property_value: BFO:0000180 "ImmaterialEntity" xsd:string -property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string +property_value: editor_note "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Term] +id: CARO:0000012 +name: multicellular organism +def: "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell." [] +comment: MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. +comment: MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. +is_a: CARO:0010004 ! organism +property_value: http://purl.obolibrary.org/obo/IAO_created_by "Melissa Haendel" xsd:string +property_value: http://purl.obolibrary.org/obo/IAO_creation_date "9/18/11" xsd:string +property_value: IAO:0000589 "multicellular organism" xsd:string + [Term] id: CARO:0001010 name: organism or virus or viroid @@ -279,61 +335,34 @@ property_value: IAO:0000589 "organism or virus" xsd:string id: CARO:0010004 name: organism def: "An individual member of a clade." [] -comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. +comment: A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. is_a: CARO:0001010 ! organism or virus or viroid property_value: http://purl.obolibrary.org/obo/IAO_created_by "mah" xsd:string property_value: http://purl.obolibrary.org/obo/IAO_creation_date "7.16.2011" xsd:string property_value: IAO:0000589 "organism" xsd:string [Term] -id: DbXref -is_a: IAO:0000102 ! data about an ontology part - -[Term] -id: Definition -is_a: IAO:0000102 ! data about an ontology part - -[Term] -id: ENVO:00000070 -name: construction -def: "A feature that has been constructed by deliberate human effort." [MA:ma] -synonym: "constructed feature" EXACT [] -is_a: ENVO:01000813 ! astronomical body part -property_value: IAO:0000116 "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference" xsd:string - -[Term] -id: ENVO:00002297 -name: environmental feature -namespace: ENVO -def: "A material entity which determines an environmental system." [DOI:10.1186/2041-1480-4-43, NM:nm, ORCID:0000-0002-4366-3088] -comment: A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. -is_a: BFO:0000040 ! material entity +id: ECOCORE:00000045 +name: symbiotroph +def: "heterotroph that acquires nutrition from a symbiont" [] +is_a: CARO:0001010 ! organism or virus or viroid +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string [Term] -id: ENVO:01000254 -name: environmental system -def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] -comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. -synonym: "environment" EXACT [] -xref: EcoLexicon:environment -is_a: BFO:0000040 ! material entity -creation_date: 2013-09-23T16:04:08Z +id: ECOCORE:00000146 +name: parasite +def: "A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host" [] +xref: https://www.wikidata.org/entity/Q10253316 +is_a: ECOCORE:00000045 ! symbiotroph +property_value: IAO:0000117 http://orcid.org/0000-0002-2908-3327 xsd:string [Term] id: ENVO:01000744 name: human dwelling def: "A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning." [https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015] -is_a: ENVO:00000070 ! construction -property_value: IAO:0000116 "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string -property_value: IAO:0000116 "Subclasses will be added by inference." xsd:string - -[Term] -id: ENVO:01000813 -name: astronomical body part -def: "A material part of an astronomical body." [] -subset: envoAstro -subset: envoPolar -is_a: ENVO:00002297 ! environmental feature +is_a: BFO:0000040 ! material entity +property_value: editor_note "See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work." xsd:string +property_value: editor_note "Subclasses will be added by inference." xsd:string [Term] id: ENVO:01001369 @@ -344,14 +373,29 @@ comment: This class aligns to the Coastal and Marine Ecological Classification S subset: envoCmecs subset: envoMarine xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ENVO:01000254 ! environmental system +is_a: BFO:0000040 ! material entity created_by: http://orcid.org/0000-0002-4366-3088 +[Term] +id: GO:0003674 +name: molecular_function +is_a: BFO:0000015 ! process +property_value: IAO:0000589 "molecular process" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0003824 +name: catalytic activity +is_a: GO:0003674 ! molecular_function +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0007610 name: behavior namespace: biological_process +alt_id: GO:0023032 alt_id: GO:0044708 +alt_id: GO:0044709 def: "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." [GOC:ems, GOC:jl, ISBN:0395448956, PMID:20160973] comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). subset: gocheck_do_not_manually_annotate @@ -364,7 +408,7 @@ synonym: "single-organism behavior" RELATED [] xref: Wikipedia:Behavior is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-20T14:06:08Z [Term] @@ -375,7 +419,7 @@ alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] -comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl @@ -390,10 +434,29 @@ synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -created_by: janelomax +created_by: jl creation_date: 2012-09-19T15:05:24Z +[Term] +id: GO:0016301 +name: kinase activity +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016740 +name: transferase activity +is_a: GO:0003824 ! catalytic activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +is_a: GO:0016740 ! transferase activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + [Term] id: GO:0035176 name: social behavior @@ -403,8 +466,8 @@ comment: Behavior such as predation which involves members of different species synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior +is_a: GO:0007610 ! behavior is_a: GO:0051703 ! intraspecies interaction between organisms -is_a: GO:0051705 ! multi-organism behavior property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -417,8 +480,9 @@ subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 @@ -427,7 +491,7 @@ namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] subset: goslim_pir synonym: "intraspecies interaction with other organisms" EXACT [] -is_a: GO:0051704 ! multi-organism process +is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -441,46 +505,42 @@ subset: goslim_pir synonym: "interaction between organisms" EXACT [] synonym: "physiological interaction between organisms" EXACT [] synonym: "physiological interaction with other organism" EXACT [] -is_a: BFO:0000015 ! process is_a: GO:0008150 ! biological_process property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl -[Term] -id: GO:0051705 -name: multi-organism behavior -namespace: biological_process -alt_id: GO:0023032 -alt_id: GO:0044709 -def: "Any process in which an organism has a behavioral effect on another organism of the same or different species." [GOC:ai] -subset: goslim_pir -synonym: "behavioral interaction between organisms" EXACT [] -synonym: "behavioral interaction with other organism" EXACT [] -synonym: "behavioral signaling" NARROW [] -synonym: "behavioral signalling" NARROW [GOC:mah] -synonym: "behavioural interaction between organisms" EXACT [] -synonym: "behavioural interaction with other organism" EXACT [] -is_a: GO:0007610 ! behavior -is_a: GO:0051704 ! multi-organism process -property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl - [Term] id: IAO:0000027 name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity +property_value: editor_note "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string +property_value: editor_note "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string +property_value: editor_note "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: editor_note "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: editor_note "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: IAO:0000030 name: information content entity is_a: BFO:0000031 ! generically dependent continuant +property_value: IAO:0000111 "information content entity" xsd:string [Term] id: IAO:0000078 name: curation status specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part +property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000111 "curation status specification" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 GROUP:OBI: xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string @@ -488,18 +548,33 @@ property_value: IAO:0000119 "OBI_0000266" xsd:string [Term] id: IAO:0000102 name: data about an ontology part -def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "data about an ontology part" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string +[Term] +id: IAO:0000109 +name: measurement datum +def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] +is_a: IAO:0000027 ! data item +property_value: editor_note "2/2/2009 is_specified_output of some assay?" xsd:string +property_value: IAO:0000111 "measurement datum" xsd:string +property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string +property_value: IAO:0000119 group:OBI xsd:string +property_value: IAO:0000119 "OBI_0000305" xsd:string +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + [Term] id: IAO:0000225 name: obsolescence reason specification def: "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." [] is_a: IAO:0000102 ! data about an ontology part +property_value: editor_note "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000111 "obsolescence reason specification" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string @@ -508,6 +583,7 @@ id: IAO:0000409 name: denotator type def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "denotator type" xsd:string property_value: IAO:0000112 "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." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string @@ -516,189 +592,168 @@ property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string id: IAO:8000000 name: ontology module is_a: IAO:0000102 ! data about an ontology part -property_value: IAO:0000116 "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." xsd:string +property_value: editor_note "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." xsd:string +property_value: IAO:0000111 "ontology module" xsd:string property_value: IAO:0000118 "ontology file" xsd:string property_value: IAO:0000232 "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." xsd:string -created_by: cjm -creation_date: 2018-05-20T20:55:03Z [Term] id: IAO:8000001 name: base ontology module def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "base ontology module" xsd:string property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 -created_by: cjm -creation_date: 2018-05-20T20:55:30Z [Term] id: IAO:8000002 name: editors ontology module def: "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." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "editors ontology module" xsd:string property_value: IAO:0000118 "source ontology module" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:55:47Z [Term] id: IAO:8000003 name: main release ontology module def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] is_a: IAO:8000000 ! ontology module -property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:56:13Z +property_value: editor_note "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string +property_value: IAO:0000111 "main release ontology module" xsd:string [Term] id: IAO:8000004 name: bridge ontology module def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "bridge ontology module" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies -created_by: cjm -creation_date: 2018-05-20T20:56:23Z [Term] id: IAO:8000005 name: import ontology module def: "A subset ontology module that is intended to be imported from another ontology." [] is_a: IAO:8000006 ! subset ontology module -property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: editor_note "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000111 "import ontology module" xsd:string property_value: IAO:0000118 "import file" xsd:string property_value: seeAlso http://robot.obolibrary.org/extract -created_by: cjm -creation_date: 2018-05-20T20:56:47Z [Term] id: IAO:8000006 name: subset ontology module def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "subset ontology module" xsd:string property_value: IAO:0000118 "ontology slim" xsd:string property_value: IAO:0000118 "subset ontology" xsd:string property_value: seeAlso http://robot.obolibrary.org/filter property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide -created_by: cjm -creation_date: 2018-05-20T20:58:11Z [Term] id: IAO:8000007 name: curation subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-20T20:58:38Z +property_value: IAO:0000111 "curation subset ontology module" xsd:string [Term] id: IAO:8000008 name: analysis subset ontology module def: "An ontology module that is intended for usage in analysis or discovery applications." [] is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-20T20:58:49Z +property_value: IAO:0000111 "analysis ontology module" xsd:string [Term] id: IAO:8000009 name: single layer subset ontology module def: "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." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "single layer ontology module" xsd:string property_value: IAO:0000118 "ribbon subset" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:59:19Z [Term] id: IAO:8000010 name: exclusion subset ontology module def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "exclusion subset ontology module" xsd:string property_value: IAO:0000118 "antislim" xsd:string -created_by: cjm -creation_date: 2018-05-20T20:59:57Z [Term] id: IAO:8000011 name: external import ontology module def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000111 "external import ontology module" xsd:string property_value: IAO:0000118 "external import" xsd:string -created_by: cjm -creation_date: 2018-05-20T21:00:14Z [Term] id: IAO:8000012 name: species subset ontology module def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "species subset ontology module" xsd:string property_value: IAO:0000118 "taxon subset" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -created_by: cjm -creation_date: 2018-05-20T21:14:16Z [Term] id: IAO:8000013 name: reasoned ontology module def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "reasoned ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/reason -created_by: cjm -creation_date: 2018-05-20T21:20:33Z [Term] id: IAO:8000014 name: generated ontology module def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] is_a: IAO:8000000 ! ontology module -property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string -created_by: cjm -creation_date: 2018-05-20T21:21:12Z +property_value: editor_note "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string +property_value: IAO:0000111 "generated ontology module" xsd:string [Term] id: IAO:8000015 name: template generated ontology module def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] is_a: IAO:8000014 ! generated ontology module +property_value: IAO:0000111 "template generated ontology module" xsd:string property_value: seeAlso http://robot.obolibrary.org/template property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ -created_by: cjm -creation_date: 2018-05-20T21:21:21Z [Term] id: IAO:8000016 name: taxonomic bridge ontology module is_a: IAO:8000004 ! bridge ontology module -created_by: cjm -creation_date: 2018-05-20T21:28:15Z +property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string [Term] id: IAO:8000017 name: ontology module subsetted by expressivity is_a: IAO:8000006 ! subset ontology module -created_by: cjm -creation_date: 2018-05-22T04:15:54Z +property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string [Term] id: IAO:8000018 name: obo basic subset ontology module def: "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "obo basic subset ontology module" xsd:string property_value: seeAlso "6.2" -created_by: cjm -creation_date: 2018-05-22T04:16:10Z [Term] id: IAO:8000019 name: ontology module subsetted by OWL profile is_a: IAO:8000017 ! ontology module subsetted by expressivity -created_by: cjm -creation_date: 2018-05-22T04:16:28Z +property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string [Term] id: IAO:8000020 name: EL++ ontology module is_a: IAO:8000019 ! ontology module subsetted by OWL profile -created_by: cjm -creation_date: 2018-05-22T04:16:48Z +property_value: IAO:0000111 "EL++ ontology module" xsd:string [Term] id: NCBITaxon:10239 @@ -716,7 +771,7 @@ id: NCBITaxon:117570 name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 -is_a: NCBITaxon:7776 ! Gnathostomata +is_a: NCBITaxon:7776 ! Gnathostomata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -729,22 +784,12 @@ xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl -[Term] -id: NCBITaxon:12884 -name: Viroids -namespace: ncbi_taxonomy -synonym: "Viroid" RELATED synonym [] -synonym: "viroids" RELATED blast_name [] -xref: GC_ID:1 -property_value: has_rank NCBITaxon:superkingdom -property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl - [Term] id: NCBITaxon:131221 name: Streptophytina namespace: ncbi_taxonomy synonym: "Charophyta/Embryophyta group" RELATED synonym [] -synonym: "charophyte/embryophyte group" RELATED synonym [] +synonym: "charophyte/embryophyte group" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:35493 ! Streptophyta property_value: has_rank NCBITaxon:subphylum @@ -817,7 +862,9 @@ xref: PMID:11760965 xref: PMID:12054223 xref: PMID:2112744 xref: PMID:270744 +xref: PMID:7520741 xref: PMID:8123559 +xref: PMID:8186100 xref: PMID:8590690 xref: PMID:9103655 xref: PMID:9336922 @@ -892,6 +939,7 @@ synonym: "eukaryotes" EXACT common_name [] synonym: "eukaryotes" RELATED blast_name [] xref: GC_ID:1 xref: PMID:23020233 +xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms property_value: has_rank NCBITaxon:superkingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -977,7 +1025,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32525 -name: Theria +name: Theria namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 @@ -989,11 +1037,14 @@ id: NCBITaxon:33090 name: Viridiplantae namespace: ncbi_taxonomy synonym: "Chlorobionta" RELATED synonym [] -synonym: "Chlorophyta/Embryophyta group" RELATED synonym [] -synonym: "chlorophyte/embryophyte group" RELATED synonym [] +synonym: "Chlorophyta/Embryophyta group" EXACT equivalent_name [] +synonym: "chlorophyte/embryophyte group" EXACT equivalent_name [] +synonym: "Chloroplastida" RELATED synonym [] synonym: "green plants" EXACT common_name [] synonym: "green plants" RELATED blast_name [] xref: GC_ID:1 +xref: PMID:16248873 +xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota property_value: has_rank NCBITaxon:kingdom property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -1040,15 +1091,17 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:3398 -name: Magnoliophyta +name: Magnoliopsida namespace: ncbi_taxonomy synonym: "Angiospermae" RELATED synonym [] synonym: "angiosperms" EXACT common_name [] synonym: "flowering plants" EXACT genbank_common_name [] synonym: "flowering plants" RELATED blast_name [] +synonym: "Magnoliophyta" RELATED synonym [] xref: GC_ID:1 xref: PMID:25249442 is_a: NCBITaxon:58024 ! Spermatophyta +property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -1080,6 +1133,20 @@ is_a: NCBITaxon:32524 ! Amniota property_value: has_rank NCBITaxon:class property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl +[Term] +id: NCBITaxon:4751 +name: Fungi +namespace: ncbi_taxonomy +synonym: "fungi" RELATED blast_name [] +synonym: "fungi" RELATED in_part [] +synonym: "Mycota" RELATED genbank_synonym [] +xref: GC_ID:1 +xref: PMID:11062127 +xref: PMID:12684019 +is_a: NCBITaxon:33154 ! Opisthokonta +property_value: has_rank NCBITaxon:kingdom +property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl + [Term] id: NCBITaxon:58023 name: Tracheophyta @@ -1121,30 +1188,30 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7742 -name: Vertebrata +name: Vertebrata namespace: ncbi_taxonomy synonym: "Vertebrata" EXACT scientific_name [] synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:89593 ! Craniata +is_a: NCBITaxon:89593 ! Craniata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7776 -name: Gnathostomata +name: Gnathostomata namespace: ncbi_taxonomy synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 -is_a: NCBITaxon:7742 ! Vertebrata +is_a: NCBITaxon:7742 ! Vertebrata property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:78536 name: Euphyllophyta namespace: ncbi_taxonomy -synonym: "euphyllophytes" RELATED synonym [] +synonym: "euphyllophytes" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:58023 ! Tracheophyta property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl @@ -1160,7 +1227,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:89593 -name: Craniata +name: Craniata namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 @@ -1178,7 +1245,7 @@ synonym: "Placentalia" RELATED synonym [] synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:32525 ! Theria +is_a: NCBITaxon:32525 ! Theria property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] @@ -1227,33 +1294,62 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl id: NCBITaxon:9606 name: Homo sapiens namespace: ncbi_taxonomy -synonym: "Home sapiens" RELATED misspelling [] -synonym: "Homo sampiens" RELATED misspelling [] -synonym: "Homo sapeins" RELATED misspelling [] -synonym: "Homo sapian" RELATED misspelling [] -synonym: "Homo sapians" RELATED misspelling [] -synonym: "Homo sapien" RELATED misspelling [] -synonym: "Homo sapience" RELATED misspelling [] -synonym: "Homo sapiense" RELATED misspelling [] -synonym: "Homo sapients" RELATED misspelling [] -synonym: "Homo sapines" RELATED misspelling [] -synonym: "Homo spaiens" RELATED misspelling [] -synonym: "Homo spiens" RELATED misspelling [] synonym: "human" EXACT genbank_common_name [] -synonym: "Humo sapiens" RELATED misspelling [] synonym: "man" EXACT common_name [] xref: GC_ID:1 is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl +[Term] +id: ObsoleteClass +name: Obsolete Class + [Term] id: PATO:0000001 name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -synonym: "trait" EXACT [] +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000068 +name: qualitative +namespace: quality +comment: TODO: define this or obsolete it and move children somewhere else. +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000069 +name: deviation (from_normal) +namespace: quality +def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000070 +name: amount +namespace: quality +alt_id: PATO:0000053 +alt_id: PATO:0000071 +alt_id: PATO:0001169 +alt_id: PATO:0001226 +def: "The number of entities of this type that are part of the whole organism." [PATOC:GVG] +comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. +subset: attribute_slim +synonym: "count in organism" RELATED [] +synonym: "number" RELATED [] +synonym: "presence" RELATED [] +synonym: "presence or absence in organism" EXACT [] +synonym: "quantitative" EXACT [] +is_a: PATO:0000068 ! qualitative +relationship: reciprocal_of PATO:0001555 ! has number of property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -1266,6 +1362,115 @@ subset: scalar_slim is_a: PATO:0002062 ! physical quality of a process property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0000461 +name: normal +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average." [PATOC:GVG] +subset: abnormal_slim +subset: mpath_slim +subset: value_slim +synonym: "average" RELATED [] +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000460 + +[Term] +id: PATO:0000467 +name: present +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's existence." [PATOC:GVG] +subset: absent_slim +subset: value_slim +synonym: "present in organism" RELATED [] +is_a: PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000462 + +[Term] +id: PATO:0000470 +name: increased amount +namespace: quality +alt_id: PATO:0000420 +alt_id: PATO:0000650 +def: "An amount which is relatively high." [PATOC:GVG] +subset: value_slim +synonym: "accessory" RELATED [] +synonym: "increased" RELATED [] +synonym: "increased number" EXACT [] +synonym: "present in greater numbers in organism" EXACT [] +synonym: "supernumerary" EXACT [] +is_a: PATO:0000467 ! present +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0000070 ! amount +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001997 + +[Term] +id: PATO:0000911 +name: decreased rate +namespace: quality +def: "A rate which is relatively low." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "slow rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002302 ! decreased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000912 + +[Term] +id: PATO:0000912 +name: increased rate +namespace: quality +def: "A rate which is relatively high." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "fast rate" EXACT [] +synonym: "high rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002304 ! increased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000911 + +[Term] +id: PATO:0001018 +name: physical quality +namespace: quality +alt_id: PATO:0002079 +def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] +subset: attribute_slim +synonym: "relational physical quality" EXACT [] +xref: Wikipedia:Physical_property +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001019 +name: mass density +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size." [WordNet:WordNet] +subset: attribute_slim +subset: scalar_slim +synonym: "density" RELATED [] +is_a: PATO:0001018 ! physical quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001164 +name: dense +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density." [PATOC:GVG] +subset: mpath_slim +subset: value_slim +is_a: PATO:0001019 ! mass density +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + [Term] id: PATO:0001236 name: process quality @@ -1279,6 +1484,7 @@ synonym: "quality of occurrent" EXACT [] synonym: "quality of process" EXACT [] synonym: "relational quality of occurrent" EXACT [] is_a: PATO:0000001 ! quality +disjoint_from: PATO:0001241 ! physical object quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -1321,6 +1527,72 @@ subset: scalar_slim is_a: PATO:0002003 ! population quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0001555 +name: has number of +namespace: quality +def: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts." [PATOC:CJM] +subset: attribute_slim +subset: relational_slim +synonym: "cardinality" RELATED [] +synonym: "extra or missing physical or functional parts" EXACT [] +synonym: "has or lacks parts of type" EXACT [] +synonym: "mereological quality" EXACT [] +synonym: "number" RELATED [] +synonym: "number of" EXACT [] +xref: OBO_REL:has_part +is_a: PATO:0001241 ! physical object quality +relationship: reciprocal_of PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001788 +name: increased mass density +namespace: quality +def: "A density which is higher relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "high density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002305 ! increased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001790 + +[Term] +id: PATO:0001790 +name: decreased mass density +namespace: quality +def: "A density which is lower relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "low density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002303 ! decreased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001788 + +[Term] +id: PATO:0001997 +name: decreased amount +namespace: quality +alt_id: PATO:0000419 +alt_id: PATO:0000468 +def: "An amount which is relatively low." [PATOC:GVG] +subset: value_slim +synonym: "decreased" RELATED [] +synonym: "decreased number" EXACT [] +synonym: "present in fewer numbers in organism" EXACT [] +synonym: "reduced" RELATED [] +synonym: "subnumerary" RELATED [] +is_a: PATO:0000467 ! present +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0000070 ! amount +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000470 + [Term] id: PATO:0002003 name: population quality @@ -1340,6 +1612,90 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl created_by: george creation_date: 2009-06-05T09:16:46Z +[Term] +id: PATO:0002300 +name: increased quality +namespace: quality +def: "A quality that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002301 +created_by: George Gkoutos +creation_date: 2011-06-16T06:39:43Z + +[Term] +id: PATO:0002301 +name: decreased quality +namespace: quality +def: "A quality that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002300 +created_by: George Gkoutos +creation_date: 2011-06-16T06:40:15Z + +[Term] +id: PATO:0002302 +name: decreased process quality +namespace: quality +def: "A quality of a process that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002304 +created_by: George Gkoutos +creation_date: 2011-06-16T06:50:59Z + +[Term] +id: PATO:0002303 +name: decreased object quality +namespace: quality +def: "A quality of an object that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002305 +created_by: George Gkoutos +creation_date: 2011-06-16T06:51:54Z + +[Term] +id: PATO:0002304 +name: increased process quality +namespace: quality +def: "A quality of a process that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002302 +created_by: George Gkoutos +creation_date: 2011-06-16T06:53:08Z + +[Term] +id: PATO:0002305 +name: increased object quality +namespace: quality +def: "A quality of an object that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002303 +created_by: George Gkoutos +creation_date: 2011-06-16T06:54:01Z + [Term] id: PCO:0000000 name: collection of organisms @@ -1347,9 +1703,10 @@ def: "A material entity that consists of two or more organisms, viruses, or viro comment: May be of the same or different species. is_a: BFO:0000027 ! object aggregate is_a: PCO:0000031 ! organismal entity -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid +relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid property_value: IAO:0000112 "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "group of organism" xsd:string @@ -1371,20 +1728,22 @@ id: PCO:0000002 name: ecological community def: "A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members." [] comment: Ecological community is defined broadly here, but includes both ecological interactions (inherited from parent term community) and spatial co-existence. It may be used to describe every organisms living in an area, but is often used to refer only to organisms of a particular taxon or guild (e.g., the plant community, the insect community, the herbivore community). The word community, as it often used to describe a group of humans living together, is a type of single-species collection of organisms, not an ecological community. +is_a: PCO:0000029 ! multi-species collection of organisms property_value: IAO:0000118 "multispecies community" xsd:string property_value: IAO:0000119 ISBN:0865423504 xsd:string [Term] id: PCO:0000003 name: quality of a population -def: "A quality that inheres in a biological population." [] +def: "A quality that inheres in a population of organisms." [] comment: Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. is_a: PATO:0002003 ! population quality intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000001 ! population of organisms -relationship: RO:0000052 PCO:0000001 ! population of organisms +intersection_of: RO:0000052 PCO:0000001 ! inheres in population of organisms +relationship: RO:0000052 PCO:0000001 ! inheres in population of organisms +property_value: editor_note "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string +property_value: editor_note "This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string [Term] id: PCO:0000004 @@ -1393,45 +1752,47 @@ def: "A quality that inheres in a community." [] comment: Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. is_a: PATO:0002003 ! population quality intersection_of: PATO:0002003 ! population quality -intersection_of: RO:0000052 PCO:0000002 ! ecological community -relationship: RO:0000052 PCO:0000002 ! ecological community +intersection_of: RO:0000052 PCO:0000002 ! inheres in ecological community +relationship: RO:0000052 PCO:0000002 ! inheres in ecological community +property_value: editor_note "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000116 "These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2." xsd:string [Term] id: PCO:0000005 name: population process -def: "A process that has as primary participant a population. " [] -comment: Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms \{e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. +def: "A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction." [] +comment: The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. is_a: BFO:0000015 ! process -relationship: RO:0000057 PCO:0000001 ! population of organisms +relationship: RO:0000057 PCO:0000001 ! has participant population of organisms property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000006 name: population birth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of birth of a population of organisms." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000007 name: population death rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of death of a population of organsisms." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000008 name: population growth rate -is_a: PCO:0000003 ! quality of a population +def: "The rate of growth of a population." [] +is_a: PATO:0000161 ! rate property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Is a rate a quality? Population growth rate may be better classified as a process profile." xsd:string [Term] id: PCO:0000009 name: obsolete carrying capacity def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] -is_a: ObsoleteClass -property_value: IAO:0000116 "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string property_value: IAO:0000119 ISBN:0878932739 xsd:string property_value: IAO:0000231 IAO:0000423 is_obsolete: true @@ -1441,8 +1802,8 @@ id: PCO:0000010 name: community species richness def: "The number of different species represented in an ecological community." [] is_a: PCO:0000004 ! quality of an ecological community +property_value: editor_note "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019)." xsd:string property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_richness" xsd:string [Term] @@ -1468,36 +1829,49 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 -name: predator role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete predator role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 -name: prey role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete prey role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 -name: symbiont role -is_a: BFO:0000023 ! role -property_value: IAO:0000114 IAO:0000124 +name: obsolete symbiont role +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string +is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000017 name: species as a collection of organisms -def: "A collection of organisms that has as parts every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as members every organism of given species and no organisms of any other species." [] +def: "A collection of organisms that has as parts every organism of a species and no organisms of any other species." [] comment: This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. +synonym: "taxonomic group" EXACT [] +xref: GENO:0000113 +xref: Species +xref: TAXRANK:0000006 is_a: PCO:0000018 ! single-species collection of organisms +is_a: PCO:0000059 ! taxon as collection of organisms +property_value: editor_note "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible." xsd:string [Term] id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms +intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid +intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid +relationship: PCO:0000055 PCO:0000017 ! has member of species as a collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -1507,8 +1881,8 @@ name: community species diversity def: "The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness." [] comment: The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. is_a: PCO:0000004 ! quality of an ecological community +property_value: editor_note "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string property_value: IAO:0000114 IAO:0000120 -property_value: IAO:0000116 "If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity." xsd:string property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_diversity" xsd:string [Term] @@ -1517,8 +1891,8 @@ name: family def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. is_a: PCO:0000018 ! single-species collection of organisms +property_value: editor_note "Needs axioms for family relationships." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string property_value: IAO:0000119 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 xsd:string [Term] @@ -1538,7 +1912,7 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000023 name: community species evenness -def: "A quality of a community that reflects how close in abundance all species in a community are." [] +def: "A quality of an ecological community that reflects how close in abundance all species in a community are." [] is_a: PCO:0000004 ! quality of an ecological community property_value: IAO:0000112 "If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -1548,26 +1922,26 @@ property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_e id: PCO:0000024 name: household def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] -is_a: PCO:0000031 ! organismal entity -relationship: RO:0002321 ENVO:01000744 ! human dwelling -relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! Homo sapiens +is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002321 ENVO:01000744 ! ecologically related to human dwelling +relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! has member Homo sapiens property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000117 "Person: Jie Zheng" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:string [Term] id: PCO:0000025 -name: red population +name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000002 is_obsolete: true [Term] id: PCO:0000026 -name: red organism +name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1577,20 +1951,20 @@ name: collection of humans def: "A collection of organisms of the same species that has as members only humans." [] is_a: PCO:0000018 ! single-species collection of organisms intersection_of: PCO:0000018 ! single-species collection of organisms -intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! Homo sapiens -intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! Homo sapiens -relationship: RO:0002351 NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens +intersection_of: RO:0002351 NCBITaxon:9606 {minCardinality="2"} ! has member Homo sapiens +relationship: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "human community" xsd:string property_value: IAO:0000118 "human population" xsd:string [Term] id: PCO:0000028 -name: community +name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). -is_a: ObsoleteClass -property_value: IAO:0000116 "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string +is_a: ObsoleteClass ! Obsolete Class +property_value: editor_note "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -1599,8 +1973,9 @@ id: PCO:0000029 name: multi-species collection of organisms def: "A collection of organisms that consists of two or more organisms from at least two species." [] is_a: PCO:0000000 ! collection of organisms +relationship: RO:0002351 PCO:0000001 {minCardinality="2"} ! has member population of organisms +property_value: editor_note "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say \"('has member' only ('member of' min 2 'species as a collection of organisms'))\"." xsd:string [Term] id: PCO:0000030 @@ -1608,10 +1983,10 @@ name: agricultural household name: obsolete organismal entity def: "A household in which the majority of the income of its members is derived from agricultural activities." [] def: "A material entity that is one or more organisms, viruses or viroids." [] -is_a: ObsoleteClass +is_a: ObsoleteClass ! Obsolete Class is_a: PCO:0000024 ! household +property_value: editor_note "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000231 "wrong IRI form" xsd:string is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/PCO_0000031 @@ -1638,8 +2013,8 @@ id: PCO:0000033 name: human social gathering activity def: "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially." [] is_a: GO:0035176 ! social behavior -relationship: RO:0000057 PCO:0000027 ! collection of humans -property_value: IAO:0000116 "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string +relationship: RO:0000057 PCO:0000027 ! has participant collection of humans +property_value: editor_note "Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] @@ -1647,7 +2022,7 @@ id: PCO:0000034 name: human community event def: "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1655,15 +2030,15 @@ id: PCO:0000035 name: party def: "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000037 name: potluck +def: "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string -property_value: IAO:0000119 "A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering." xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1671,7 +2046,7 @@ id: PCO:0000038 name: wedding def: "A human social gathering at which two people are married. May include a legal or social ceremony." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031" xsd:string property_value: IAO:0000119 "GenEpio curators" xsd:string [Term] @@ -1679,90 +2054,244 @@ id: PCO:0000039 name: baby shower def: "A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby." [] is_a: PCO:0000033 ! human social gathering activity -property_value: IAO:0000116 "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string +property_value: editor_note "Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032" xsd:string property_value: IAO:0000119 "GenEpiO curators" xsd:string [Term] id: PCO:0000040 +name: obsolete tidal mangrove shrubland community +def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] +synonym: "mangrove community" RELATED [] +synonym: "tidal shrubland community" RELATED [] +xref: https://cmecscatalog.org/cmecs/classification/unit/577.html +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000041 +name: obsolete invisible to unaided eye +def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] +comment: should move to PATO +is_a: ObsoleteClass ! Obsolete Class +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000042 +name: obsolete microbe +synonym: "microbial organism" EXACT [] +is_a: ObsoleteClass ! Obsolete Class +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000043 +name: obsolete collection of microbial organisms +def: "A collection of organisms consisting of two or more microbes." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000044 +name: obsolete multi-species collection of microbes +def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000045 +name: obsolete single species collection of microbes +def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000046 +name: obsolete microbial population +def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] +synonym: "microbiota" BROAD [] +is_a: ObsoleteClass ! Obsolete Class +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true + +[Term] +id: PCO:0000047 name: tidal mangrove shrubland community def: "An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima." [] synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html is_a: PCO:0000002 ! ecological community -relationship: BFO:0000050 ENVO:01001369 ! tidal mangrove shrubland +relationship: part_of ENVO:01001369 ! tidal mangrove shrubland property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] -id: PCO:0000041 +id: PCO:0000048 name: invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO is_a: PATO:0001241 ! physical object quality [Term] -id: PCO:0000042 +id: PCO:0000049 name: microbe synonym: "microbial organism" EXACT [] is_a: CARO:0001010 ! organism or virus or viroid -relationship: RO:0000086 PCO:0000041 ! invisible to unaided eye [Term] -id: PCO:0000043 +id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: RO:0002351 PCO:0000042 {all_only="true"} ! microbe -intersection_of: RO:0002351 PCO:0000042 {minCardinality="2"} ! microbe -relationship: RO:0002351 PCO:0000042 ! microbe +intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! has member microbe +intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! has member microbe +relationship: RO:0002351 PCO:0000049 ! has member microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000044 +id: PCO:0000051 name: multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] is_a: PCO:0000029 ! multi-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000045 +id: PCO:0000052 name: single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] -is_a: PCO:0000018 ! single-species collection of organisms -is_a: PCO:0000043 ! collection of microbial organisms +is_a: PCO:0000050 ! collection of microbial organisms property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string [Term] -id: PCO:0000046 +id: PCO:0000053 name: microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] is_a: PCO:0000001 ! population of organisms -is_a: PCO:0000045 ! single species collection of microbes -relationship: RO:0002351 PCO:0000042 ! microbe property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string +[Term] +id: PCO:0000054 +name: number of generations of multicellular organism +def: "A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism." [] {comment="NCIT:C88214", comment="EFO:0000507"} +synonym: "number of generations" BROAD [] +is_a: STATO:0000047 ! count +relationship: IAO:0000136 CARO:0000012 ! is about multicellular organism +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-2999-0103 + +[Term] +id: PCO:0000057 +name: overcrowded population +def: "An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels." [] +synonym: "increased density of population" EXACT [] +is_a: PCO:0000003 ! quality of a population +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000058 +name: overcrowded human population +def: "A quality of a human population such that the density humans in an area is increased beyond sustainable levels." [] +is_a: PCO:0000057 ! overcrowded population +intersection_of: PCO:0000057 ! overcrowded population +intersection_of: RO:0000052 PCO:0000027 ! inheres in collection of humans +relationship: RO:0000052 PCO:0000027 ! inheres in collection of humans +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000059 +name: taxon as collection of organisms +def: "A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations." [] +comment: This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. +xref: data:1868 +is_a: PCO:0000000 ! collection of organisms +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000060 +name: microbial parasite +def: "An organism or virus or viroid that is a microbe and a parasite." [] +is_a: ECOCORE:00000146 ! parasite +is_a: PCO:0000049 ! microbe +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000061 +name: parasite isolate population +def: "A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations." [] +is_a: PCO:0000050 ! collection of microbial organisms +is_a: PCO:0000053 ! microbial population +relationship: RO:0002351 PCO:0000060 ! has member microbial parasite +property_value: IAO:0000112 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811772/ +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "VEuPathDB" xsd:string + +[Term] +id: PCO:0000062 +name: Shannon diversity index +def: "A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi)." [] +synonym: "Shannon entropy" EXACT [] +synonym: "Shannon's diversity index" EXACT [] +synonym: "Shannon-Wiener index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shannonDI.html +property_value: IAO:0000119 "Shannon_index" + +[Term] +id: PCO:0000063 +name: Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi)." [] +synonym: "Simpson index" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Simpson_index" + +[Term] +id: PCO:0000064 +name: inverse Simpson diversity index +def: "A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi)." [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html +property_value: IAO:0000119 "Inverse_Simpson_index" + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: PCO:0000000 ! collection of organisms -relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid +relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid [Term] id: PCO:0001001 name: pair of interacting organisms of the same species +def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms +relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms [Term] id: PCO:1000000 name: migratory population def: "A population which is participating in a migration process." [] is_a: PCO:0000001 ! population of organisms -relationship: RO:0000056 PCO:1000001 ! population migration +relationship: RO:0000056 PCO:1000001 ! participates in population migration property_value: IAO:0000114 IAO:0000123 [Term] @@ -1780,7 +2309,7 @@ name: human population migration def: "A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location." [] comment: The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration is_a: PCO:1000001 ! population migration -relationship: RO:0000057 PCO:0000027 ! collection of humans +relationship: RO:0000057 PCO:0000027 ! has participant collection of humans property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string @@ -1789,7 +2318,7 @@ id: PCO:1000003 name: human migratory population def: "A migratory population of humans, travelling with the intention of settling in a new area." [] is_a: PCO:0000027 ! collection of humans -relationship: RO:0000056 PCO:1000002 ! human population migration +relationship: RO:0000056 PCO:1000002 ! participates in human population migration property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Human_migration xsd:string @@ -1800,21 +2329,1394 @@ def: "An ecological community which is composed of co-existing populations of mi comment: The definition of a microbial species is deeply debated, however, units of phylogenetic and functional diversity are recognised with respect to their varying roles in an ecosystem. In turn, there exist multiple operational definitions of microbial community, such as local, phenomenological, and indexical communities. This class seeks to capture microbial communities in a very broad sense, as collections of phylogenetically and functionally divergent microbial organisms co-existing, potentially interacting, and competing for niche space in the same ecosystem over a period of time in which their causal footprints overlap one another. synonym: "microbiota" BROAD [] is_a: PCO:0000002 ! ecological community -is_a: PCO:0000044 ! multi-species collection of microbes +is_a: PCO:0000051 ! multi-species collection of microbes +property_value: editor_note "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "A class for a collection of organisms considered \"microbial\" and an accompanying quality in PATO (e.g. \"microscopic\") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22" xsd:string property_value: IAO:0000117 http://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string [Term] -id: Subset -is_a: IAO:0000102 ! data about an ontology part +id: STATO:0000047 +name: count +def: "a count is a data item denoted by an integer and represented the number of instances or occurences of an entity" [] +is_a: IAO:0000109 ! measurement datum +property_value: IAO:0000112 "a count of 4 resulting from counting limbs in humans" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "Alejandra Gonzalez-Beltran" xsd:string +property_value: IAO:0000117 "Orlaith Burke" xsd:string +property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string +property_value: IAO:0000119 "STATO" xsd:string +property_value: STATO:0000032 "" xsd:string + +[Typedef] +id: BFO:0000054 +name: realized in +comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realized in" xsd:string +property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string +property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string +property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string +property_value: IAO:0000118 "is realized by" xsd:string +property_value: IAO:0000118 "realized_in" xsd:string +property_value: IAO:0000600 "[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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +inverse_of: BFO:0000055 ! realizes + +[Typedef] +id: BFO:0000055 +name: realizes +comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realizes" xsd:string +property_value: IAO:0000112 "this disease course realizes this disease" xsd:string +property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string +property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string +property_value: IAO:0000600 "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])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +domain: BFO:0000015 ! process +range: BFO:0000017 ! realizable entity + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "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." [] +subset: ro-eco +property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "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." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: part_of BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "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" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: part_of BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part_of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[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" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -[Term] -id: Synonym -is_a: IAO:0000102 ! data about an ontology part +[Typedef] +id: IAO:0000136 +name: is about +def: "A (currently) primitive relation that relates an information artifact to an entity." [] +property_value: editor_note "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string + +[Typedef] +id: PCO:0000055 +name: has member of +domain: PCO:0000000 ! collection of organisms + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: editor_note "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "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." [] +property_value: IAO:0000112 "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)." xsd:string +property_value: IAO:0000112 "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)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000079 +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 ! function +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000085 ! has function + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! inheres in +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000085 +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000034 ! function +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! bearer of +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +is_a: RO:0000052 ! inheres in + +[Typedef] +id: RO:0001000 +name: derives from +def: "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" [] +property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "derives_from" xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "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" [] +property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000111 "is location of" xsd:string +property_value: IAO:0000112 "my head is the location of my brain" xsd:string +property_value: IAO:0000112 "this cage is the location of this rat" xsd:string +property_value: IAO:0000118 "location_of" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string +property_value: IAO:0000111 "located in" xsd:string +property_value: IAO:0000112 "my brain is located in my head" xsd:string +property_value: IAO:0000112 "this rat is located in this cage" xsd:string +property_value: IAO:0000118 "located_in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true + +[Typedef] +id: RO:0002000 +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] +property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity + +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "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." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "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." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "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." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "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." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "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." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "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." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "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." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_functional: true +is_a: RO:0002017 ! has component activity +is_a: RO:0002211 ! regulates +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: has_part RO:0002131 +holds_over_chain: part_of part_of +is_a: RO:0002323 ! mereotopologically related to +transitive_over: part_of ! part_of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002180 +name: has component +def: "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." [] +subset: ro-eco +property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: has_part ! has part + +[Typedef] +id: RO:0002211 +name: regulates +def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string +property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002215 +name: capable of +def: "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. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of +expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso "defining-property-chains-involving-reflexivity" +holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process +expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002233 +name: has input +def: "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." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "consumes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "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." [] +property_value: IAO:0000112 "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." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "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." [] +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002321 +name: ecologically related to +def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] +subset: ro-eco +property_value: editor_note "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002327 +name: enables +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: has_part ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 part_of +is_a: RO:0000056 ! participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: part_of ! part_of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "regulated by (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part_of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +synonym: "affects" RELATED [] +property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "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" [] +property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "involved in or reguates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "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." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "executes activity in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "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." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso ECO:0000353 +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: editor_note "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: directly regulates activity of +def: "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0011002 ! regulates activity of + +[Typedef] +id: RO:0002449 +name: directly negatively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly inhibits" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002450 +name: directly positively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly activates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002464 +name: helper property (not for use in curation) +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "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." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} + +[Typedef] +id: RO:0002481 +name: is kinase activity +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002506 +name: causal relation between entities +property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002506 ! causal relation between entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002563 +name: interaction relation helper property +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +is_a: RO:0002464 ! helper property (not for use in curation) + +[Typedef] +id: RO:0002564 +name: molecular interaction relation helper property +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002566 +name: causally influences +def: "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)." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002506 ! causal relation between entities + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "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" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: has_part RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "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." [] +property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 has_part +is_a: RO:0002328 ! functionally related to +created_by: cjm +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "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" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: cjm +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "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" [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: cjm +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0011002 +name: regulates activity of +def: "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." [] +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002566 ! causally influences + +[Typedef] +id: decreased_in_magnitude_relative_to +name: decreased_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: different_in_magnitude_relative_to +name: different_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality + +[Typedef] +id: editor_note +name: editor note +namespace: uberon +def: "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." [] +xref: IAO:0000116 +property_value: IAO:0000111 "editor note" xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +is_metadata_tag: true + +[Typedef] +id: has_part +name: has part +name: has_part +namespace: external +namespace: quality +def: "a core relation that holds between a whole and its part" [] +def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] +comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. +xref: BFO:0000051 +property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA 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'." xsd:string +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps -[Term] -id: SynonymType -is_a: IAO:0000102 ! data about an ontology part +[Typedef] +id: increased_in_magnitude_relative_to +name: increased_in_magnitude_relative_to +namespace: quality +def: "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." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: part_of +name: part of +name: part_of +namespace: external +namespace: quality +def: "a core relation that holds between a part and its whole" [] +xref: BFO:0000050 +property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA 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'." xsd:string +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: has_part ! has part + +[Typedef] +id: reciprocal_of +name: reciprocal_of +namespace: quality +def: "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." [PATOC:CJM] +comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl diff --git a/src/ontology/pco.owl b/src/ontology/pco.owl index 4ce4e18..fc88485 100644 --- a/src/ontology/pco.owl +++ b/src/ontology/pco.owl @@ -7,20 +7,26 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:swrl="http://www.w3.org/2003/11/swrl#" + xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" + xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg Ramona Walls - http://creativecommons.org/publicdomain/zero/1.0/ + The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. + Population and Community Ontology + http://creativecommons.org/publicdomain/zero/1.0/ The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. @@ -62,12 +68,21 @@ + editor preferred label + editor preferred label + editor preferred term editor preferred term + editor preferred term~editor preferred label 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 label + editor preferred label + editor preferred term editor preferred term + editor preferred term~editor preferred label @@ -76,6 +91,7 @@ example + 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 @@ -106,6 +122,8 @@ PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 + + has curation status has curation status @@ -115,7 +133,10 @@ definition + definition + textual definition + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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 @@ -142,6 +163,7 @@ We also have the outstanding issue of how to aim different definitions to differ definition definition + textual definition @@ -154,6 +176,12 @@ We also have the outstanding issue of how to aim different definitions to differ 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.obfoundry.org/obo/obi> + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + IAO:0000116 + uberon + editor_note + true + editor_note editor note editor note @@ -170,6 +198,8 @@ We also have the outstanding issue of how to aim different definitions to differ 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 term editor @@ -183,6 +213,7 @@ We also have the outstanding issue of how to aim different definitions to differ An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + alternative term @@ -193,11 +224,14 @@ We also have the outstanding issue of how to aim different definitions to differ 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 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 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition source definition source @@ -222,6 +256,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg + curator note @@ -230,13 +265,13 @@ We also have the outstanding issue of how to aim different definitions to differ - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + 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. + 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 @@ -245,10 +280,11 @@ We also have the outstanding issue of how to aim different definitions to differ + 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 + 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 The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester @@ -259,10 +295,10 @@ We also have the outstanding issue of how to aim different definitions to differ 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 - 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 + is denotator type @@ -276,6 +312,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + imported from @@ -290,7 +327,8 @@ 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 + Chris Mungall + expand expression to @@ -326,7 +364,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. antisymmetric property part_of antisymmetric property xsd:true - use boolean value xsd:true to indicate that the property is an antisymmetric property + Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property @@ -339,12 +377,13 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. 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 . + 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/> + OBO foundry unique label @@ -353,14 +392,15 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 + 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 digit count @@ -369,12 +409,13 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Datatype: idrange:1 + 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 + 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 range allocated to @@ -383,15 +424,16 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 policy for + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for @@ -399,14 +441,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + 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 + 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 ID prefix @@ -455,23 +498,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] is allocated id range - Add as annotation triples in the granting ontology 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 + Add as annotation triples in the granting ontology is allocated id range + + + + 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 + has ontology root term + + + + - 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 - #40 - VFB - 2018-09-21T16:43:39Z - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + 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 + #40 + VFB + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to @@ -480,6 +534,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + 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 https://github.com/geneontology/go-ontology/issues/15532 @@ -509,10 +564,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] term replaced by - Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by @@ -530,6 +585,94 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + is a defining property chain axiom + + + + + + + + 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. + + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + an alternative term used for STATO statistical ontology and ISA team + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO alternative term + + + + @@ -612,7 +755,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + + @@ -634,12 +779,36 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + @@ -675,6 +844,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + database_cross_reference @@ -700,7 +870,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - has_obo_namespace + has_obo_namespace @@ -739,6 +909,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + shorthand + + + + @@ -749,16 +934,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + - + + label + label @@ -771,6 +958,14 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -811,139 +1030,2218 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + + + + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + + + + + + + + BFO:0000050 + external + quality + part_of + part_of + + part of + part of + part_of + + + http://www.obofoundry.org/ro/#OBO_REL: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) + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + 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 + + BFO:0000051 + external + quality + has_part + has_part + We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. + + has part + has part + has_part + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + PATOC:CJM + + + + + + + + + + + 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]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + + + 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]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + + + + + + + + + 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 + http://www.obofoundry.org/ro/#OBO_REL: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. + + + precedes + + + + + + + + + + + + + + + + + + + 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 + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs 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 + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + This document is about information artifacts and their representations + + A (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + + + + has member of + - + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + 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 + + bearer of + - + + + + + 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 + + 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 + http://www.obofoundry.org/ro/#OBO_REL:has_participant + + 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. + is concretized as + + + + + + + + + + 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. + concretizes + + + + + + + + + + + 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 + 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 + 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 + 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 + - + - + + + disposition of + - + - + + + 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 + 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 + derives into + - + - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - + + + + 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 https://code.google.com/p/obo-relations/wiki/ROAndTime + location_of + + location of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + located in + - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - + - - - - continuant - Continuant - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + 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 + + 2D boundary of + + + + + + + + + + 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 + + has 2D boundary + + + + + + + + + + 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. + dos + 2017-05-24T09:30:46Z + + has regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + + has negative regulatory component activity + + + + + + + + + + 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. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + + has component activity + + + + + + + + + + + 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. + dos + 2017-05-24T09:49:21Z + + has component process + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:38Z + + directly negatively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + 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. + dos + 2017-09-17T13:52:47Z + + directly positively regulated by + + + + + 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. + GOC:dos + + + + + + + + + + + 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. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + + has 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. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + + immediately preceded by + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + + immediately precedes + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + overlaps + + + + + + + + + true + + + + + + + + + + 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. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + + has component + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + + positively regulates + + + + + + + + + + + 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. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + + capable of + + + + + + + + + + + + + + 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. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + + capable of part of + + + + + + + + + + true + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + + temporally related to + + + + + + + + + + + + + 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. + Chris Mungall + consumes + + + has input + + + + + + + + + + + + + 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. + + acts upstream of + + + + + + + + + + + + + + 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 + + acts upstream of or within + + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + + causally upstream of, negative effect + + + + + + + + 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 + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + + ecologically related to + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + 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 + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + + involved in + + + + + + + + + + + inverse of enables + Chris Mungall + + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + + positively regulated by + + + + + + + + + + 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 + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + Chris Mungall + + + + input of + + + + + + + + + + + + inverse of upstream of + Chris Mungall + + causally downstream of + + + + + + + + + + + + Chris Mungall + + immediately causally downstream of + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + 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. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + + involved in negative regulation of + + + + + + + + + + + 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 + Chris Mungall + involved in or reguates + + involved in or involved in regulation of + + + + + + + + + + + + + + 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. + Chris Mungall + executes activity in + enables activity in + + + is active in + + + + + + + + + true + + + + + 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. + GOC:cjm + GOC:dos + + + + + + + + + + + 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. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + 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. + Chris Mungall + binds + molecularly binds with + + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + Axiomatization to GO to be added later + Chris Mungall + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + + phosphorylates + + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + molecularly controls + + directly regulates activity of + + + + + + + + + + + + + + + + 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. + Chris Mungall + Vasundra Touré + directly inhibits + molecularly decreases activity of + + directly negatively regulates 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. + Chris Mungall + Vasundra Touré + directly activates + molecularly increases activity of + + directly positively regulates activity of + + + + + + + + Chris Mungall + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + + helper property (not for use in curation) + + + + + + + + + + + + + + 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. + Chris Mungall + + + has part that occurs in + + + + + + + + + true + + + + + + + + + Chris Mungall + + is kinase activity + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + + causal agent in 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between processes + + + + + + + + + + + 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 + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + causal relation between entities + + + + + + + + + + Chris Mungall + + causally influenced by (entity-centric) + + causally influenced by + + + + + + + + + Chris Mungall + + interaction relation helper property + + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + Chris Mungall + + molecular interaction relation helper property + + + + + + + + + + + + + + + + + + + + + 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). + Chris Mungall + Vasundra Touré + + causally influences (entity-centric) + + causally influences + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + + directly regulates + + + + + + + + + + + + + + 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 + Chris Mungall + + has part structure that is capable of + + + + + + + + + + + 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. + Chris Mungall + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + + capable of negatively regulating + + + + + + + + + + + + + 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. + + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + + process has causal agent + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + + directly negatively regulates + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + 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 + + cjm + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + + causally upstream of or within, positive effect + + + + + + + + + + + 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. + Vasundra Touré + + regulates activity of + + + + + + + + + + + + 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. + quality + decreased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + + decreased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + 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. + quality + different_in_magnitude_relative_to + + different_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + + + + + 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. + quality + increased_in_magnitude_relative_to + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + + increased_in_magnitude_relative_to + + + + + 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. + PATOC:CJM + + + + + + + + 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. + quality + reciprocal_of + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + + reciprocal_of + + + + + 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. + PATOC:CJM + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - continuant + entity - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + + + + + + + + + + + + continuant + Continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + @@ -986,6 +3284,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + @@ -993,8 +3303,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + occurrent Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. @@ -1057,6 +3380,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + ic @@ -1071,6 +3400,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] an organism the bottom right portion of a human torso the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) @@ -1119,6 +3449,26 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. + obsolete dependent continuant + true + + + + + + + + + spatial region + + + + @@ -1132,6 +3482,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the flight of a bird the life of an organism your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] @@ -1153,10 +3504,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + disposition + + + + + realizable RealizableEntity the disposition of this piece of metal to conduct electricity. @@ -1164,6 +3526,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet + 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. + https://orcid.org/0000-0001-8815-0078 To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] @@ -1198,10 +3562,25 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + quality + + + + + + + + + + sdc SpecificallyDependentContinuant @@ -1216,6 +3595,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the role of being a doctor the shape of this hole. the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. 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]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] @@ -1257,6 +3637,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] the role of a stone in marking a property boundary the role of subject in a clinical trial the student role + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] @@ -1388,6 +3769,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] @@ -1408,6 +3790,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + function + + + + @@ -1427,6 +3818,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] an energy wave an epidemic the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. @@ -1491,6 +3883,21 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell. + multicellular organism + Melissa Haendel + 9/18/11 + MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. + MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities. + multicellular organism + + + + @@ -1512,75 +3919,39 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] organism mah 7.16.2011 - A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. + A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. So, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. organism - - - - - A feature that has been constructed by deliberate human effort. - "constructed" should probably be made something like a quality and this class obsoleted or filled only by inference - constructed feature - construction - - - - - A feature that has been constructed by deliberate human effort. - MA:ma - - - - - + - - - A material entity which determines an environmental system. - ENVO - ENVO:00002297 - A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised. - environmental feature + + + heterotroph that acquires nutrition from a symbiont + http://orcid.org/0000-0002-2908-3327 + symbiotroph - - - - A material entity which determines an environmental system. - DOI:10.1186/2041-1480-4-43 - NM:nm - ORCID:0000-0002-4366-3088 - - + - - - A system which has the disposition to environ one or more material entities. - 2013-09-23T16:04:08Z - EcoLexicon:environment - environment - In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. - environmental system + + + A symbiotroph that reduces the fitness, survival, or growth of its symbiont, often called a host + http://orcid.org/0000-0002-2908-3327 + https://www.wikidata.org/entity/Q10253316 + parasite - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - + A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. Subclasses will be added by inference. @@ -1595,24 +3966,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - A material part of an astronomical body. - envoAstro - envoPolar - astronomical body part - - - - - + A shrubland biome which is densely vegetated by dwarf or short mangroves (and associates) that are generally less than 6 meters in height, is tidally influenced, is located in tropical or subtropical areas. - http://orcid.org/0000-0002-4366-3088 + CMECS:577 https://cmecscatalog.org/cmecs/classification/unit/577.html envoCmecs @@ -1623,14 +3982,37 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + molecular process + + molecular_function + + + + + + + + + + catalytic activity + + + + The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. - janelomax + jl 2012-09-20T14:06:08Z + GO:0023032 GO:0044708 + GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour @@ -1661,8 +4043,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - janelomax + jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 @@ -1683,7 +4066,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process @@ -1696,11 +4079,47 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + true + + + + kinase activity + + + + + + + + + + transferase activity + + + + + + + + + + transferase activity, transferring phosphorus-containing groups + + + + + - Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour @@ -1725,8 +4144,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + Any process in which an organism has an effect on an organism of a different species. + interaction with another species interspecies interaction interspecies interaction with other organisms @@ -1749,7 +4169,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + Any process in which an organism has an effect on an organism of the same species. intraspecies interaction with other organisms biological_process @@ -1770,7 +4190,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A biological process which involves another organism of the same or different species. GO:0051706 @@ -1793,45 +4212,30 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GO:0023032 - GO:0044709 - behavioral interaction between organisms - behavioral interaction with other organism - behavioural interaction between organisms - behavioural interaction with other organism - behavioral signaling - behavioral signalling - biological_process - GO:0051705 - - - multi-organism behavior - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - GOC:ai - - - - - behavioral signalling - GOC:mah - - - - + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item @@ -1841,6 +4245,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + information content entity information content entity @@ -1881,13 +4286,32 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg + 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 data about an ontology part + + + + + measurement datum + Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + + measurement datum + + + + @@ -1927,11 +4351,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - denotator type + 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 + denotator type @@ -1940,12 +4365,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - cjm - 2018-05-20T20:55:03Z - ontology module + 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 + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module @@ -1954,10 +4378,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - cjm - 2018-05-20T20:55:30Z - base ontology module + 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. + base ontology module @@ -1967,11 +4390,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:55:47Z - editors ontology module + 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 + editors ontology module @@ -1980,11 +4402,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:56:13Z - main release 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 + main release ontology module @@ -1993,10 +4414,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - cjm - 2018-05-20T20:56:23Z - bridge ontology 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. + bridge ontology module @@ -2006,12 +4426,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:56:47Z - import ontology 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 + import ontology module @@ -2021,12 +4440,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - cjm - 2018-05-20T20:58:11Z - subset ontology module + 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 + subset ontology module @@ -2037,10 +4455,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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. - cjm - 2018-05-20T20:58:38Z - curation subset ontology module + 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. + curation subset ontology module @@ -2049,10 +4466,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is intended for usage in analysis or discovery applications. - cjm - 2018-05-20T20:58:49Z - analysis subset ontology module + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module @@ -2061,11 +4477,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T20:59:19Z - single layer subset ontology module + 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 + single layer subset ontology module @@ -2074,11 +4489,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - cjm - 2018-05-20T20:59:57Z - exclusion subset ontology module + 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 + exclusion subset ontology module @@ -2087,11 +4501,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - cjm - 2018-05-20T21:00:14Z - external import ontology module + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module @@ -2100,11 +4513,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - cjm - 2018-05-20T21:14:16Z - species subset ontology module + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module @@ -2114,10 +4526,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - cjm - 2018-05-20T21:20:33Z - reasoned ontology module + 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. + reasoned ontology module @@ -2127,11 +4538,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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 - cjm - 2018-05-20T21:21:12Z - generated ontology module + 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 + generated ontology module @@ -2140,10 +4550,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - cjm - 2018-05-20T21:21:21Z - template generated ontology module + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module @@ -2155,9 +4564,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - cjm - 2018-05-20T21:28:15Z - taxonomic bridge ontology module + taxonomic bridge ontology module + taxonomic bridge ontology module @@ -2166,9 +4574,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - cjm - 2018-05-22T04:15:54Z - ontology module subsetted by expressivity + ontology module subsetted by expressivity + ontology module subsetted by expressivity @@ -2177,7 +4584,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - 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. + 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). @@ -2193,9 +4601,7 @@ No qualifier lists No disjointness axioms No owl-axioms header No imports - cjm - 2018-05-22T04:16:10Z - obo basic subset ontology module + obo basic subset ontology module @@ -2205,9 +4611,8 @@ No imports - cjm - 2018-05-22T04:16:28Z - ontology module subsetted by OWL profile + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile @@ -2216,9 +4621,8 @@ No imports - cjm - 2018-05-22T04:16:48Z - EL++ ontology module + EL++ ontology module + EL++ ontology module @@ -2270,46 +4674,20 @@ No imports - - - NCBITaxon:40673 - GC_ID:1 - bony vertebrates - ncbi_taxonomy - - Euteleostomi - - - - - bony vertebrates - - - - - - - - - + + + NCBITaxon:40673 GC_ID:1 + bony vertebrates ncbi_taxonomy - Viroid - viroids - Viroids + Euteleostomi - - - Viroid - - - - - - viroids - + + + bony vertebrates + @@ -2320,22 +4698,22 @@ No imports GC_ID:1 + charophyte/embryophyte group ncbi_taxonomy Charophyta/Embryophyta group - charophyte/embryophyte group Streptophytina - - Charophyta/Embryophyta group - + + charophyte/embryophyte group + - charophyte/embryophyte group + Charophyta/Embryophyta group @@ -2429,7 +4807,9 @@ No imports PMID:12054223 PMID:2112744 PMID:270744 + PMID:7520741 PMID:8123559 + PMID:8186100 PMID:8590690 PMID:9103655 PMID:9336922 @@ -2445,12 +4825,6 @@ No imports Bacteria - - - - prokaryotes - - @@ -2493,6 +4867,12 @@ No imports prokaryote + + + + prokaryotes + + @@ -2631,6 +5011,7 @@ No imports GC_ID:1 PMID:23020233 + PMID:30257078 eucaryotes eukaryotes ncbi_taxonomy @@ -2886,7 +5267,7 @@ No imports Theria ncbi_taxonomy - Theria <Mammalia> + Theria <mammals> @@ -2903,11 +5284,14 @@ No imports GC_ID:1 + PMID:16248873 + PMID:30257078 + Chlorophyta/Embryophyta group + chlorophyte/embryophyte group green plants ncbi_taxonomy Chlorobionta - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group + Chloroplastida green plants Viridiplantae @@ -2915,25 +5299,31 @@ No imports - green plants - + Chlorophyta/Embryophyta group + - - Chlorobionta - + + chlorophyte/embryophyte group + + + + + + green plants + - Chlorophyta/Embryophyta group + Chlorobionta - chlorophyte/embryophyte group + Chloroplastida @@ -3047,15 +5437,17 @@ No imports + GC_ID:1 PMID:25249442 angiosperms flowering plants ncbi_taxonomy Angiospermae + Magnoliophyta flowering plants - Magnoliophyta + Magnoliopsida @@ -3075,6 +5467,12 @@ No imports Angiospermae + + + + Magnoliophyta + + @@ -3137,6 +5535,41 @@ No imports + + + + + + GC_ID:1 + PMID:11062127 + PMID:12684019 + ncbi_taxonomy + Mycota + fungi + + Fungi + + + + + Mycota + + + + + + fungi + + + + + + fungi + + + + + @@ -3238,7 +5671,7 @@ No imports ncbi_taxonomy vertebrates - Vertebrata <Metazoa> + Vertebrata <vertebrates> @@ -3270,7 +5703,7 @@ No imports jawed vertebrates ncbi_taxonomy - Gnathostomata <vertebrate> + Gnathostomata <vertebrates> @@ -3292,16 +5725,16 @@ No imports GC_ID:1 + euphyllophytes ncbi_taxonomy - euphyllophytes Euphyllophyta - + euphyllophytes - + @@ -3328,7 +5761,7 @@ No imports Craniata ncbi_taxonomy - Craniata <chordata> + Craniata <chordates> @@ -3489,19 +5922,6 @@ No imports human man ncbi_taxonomy - Home sapiens - Homo sampiens - Homo sapeins - Homo sapian - Homo sapians - Homo sapien - Homo sapience - Homo sapiense - Homo sapients - Homo sapines - Homo spaiens - Homo spiens - Humo sapiens Homo sapiens @@ -3517,124 +5937,340 @@ No imports man + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + quality (PATO) + PATO:0000072 + quality + PATO:0000001 + + quality + - - - Home sapiens - - - - - - Homo sampiens - - - - - - Homo sapeins - - - - - - Homo sapian - - - - - - Homo sapians - + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + quality + PATO:0000068 + TODO: define this or obsolete it and move children somewhere else. + + qualitative + + + + + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + quality + PATO:0000069 + + + deviation (from_normal) + - - - Homo sapien - + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + PATOC:GVG + + + + + + + + + + + + + + The number of entities of this type that are part of the whole organism. + PATO:0000053 + PATO:0000071 + PATO:0001169 + PATO:0001226 + presence or absence in organism + quantitative + quality + count in organism + number + presence + PATO:0000070 + + This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. + + amount + - - - Homo sapience - + + + The number of entities of this type that are part of the whole organism. + PATOC:GVG + + + + + + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + quality + PATO:0000161 + + + + rate + - - - Homo sapiense - + + + A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + PATOC:melissa + + + + + + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + + quality + average + PATO:0000461 + + + + + normal + - - - Homo sapients - + + + A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. + PATOC:GVG + + + + + + + + A quality inhering in a bearer by virtue of the bearer's existence. + + quality + present in organism + PATO:0000467 + + + + present + - - - Homo sapines - + + + A quality inhering in a bearer by virtue of the bearer's existence. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + An amount which is relatively high. + + PATO:0000420 + PATO:0000650 + increased number + present in greater numbers in organism + supernumerary + quality + accessory + increased + PATO:0000470 + + + increased amount + - - - Homo spaiens - + + + An amount which is relatively high. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + A rate which is relatively low. + + slow rate + quality + PATO:0000911 + + + + decreased rate + - - - Homo spiens - + + + A rate which is relatively low. + PATO:GVG + + + + + + + + + + + + + + + + + + + + A rate which is relatively high. + + fast rate + high rate + quality + PATO:0000912 + + + + increased rate + - - - Humo sapiens - + + + A rate which is relatively high. + PATO:GVG - + - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000072 - trait + + + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + PATO:0002079 + Wikipedia:Physical_property + relational physical quality quality - PATO:0000001 + PATO:0001018 + - quality + physical quality - + - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG - + - - - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. + + + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality - PATO:0000161 + density + PATO:0001019 - rate + mass density - + - A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. - PATOC:melissa + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. + WordNet:WordNet + + + + + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + quality + PATO:0001164 + + + + dense + + + + + A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. + PATOC:GVG @@ -3643,6 +6279,7 @@ No imports + A quality which inheres in an process. PATO:0001239 PATO:0001240 @@ -3738,6 +6375,148 @@ No imports + + + + + + + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + OBO_REL:has_part + extra or missing physical or functional parts + has or lacks parts of type + mereological quality + number of + quality + cardinality + number + PATO:0001555 + + + + has number of + + + + + The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. + PATOC:CJM + + + + + + + + + + + + + + + + + + + + + A density which is higher relative to the normal or average. + + high density + quality + PATO:0001788 + + + increased mass density + + + + + A density which is higher relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A density which is lower relative to the normal or average. + + low density + quality + PATO:0001790 + + + decreased mass density + + + + + A density which is lower relative to the normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + An amount which is relatively low. + + PATO:0000419 + PATO:0000468 + decreased number + present in fewer numbers in organism + quality + decreased + reduced + subnumerary + PATO:0001997 + + + decreased amount + + + + + An amount which is relatively low. + PATOC:GVG + + + + @@ -3773,6 +6552,220 @@ No imports + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:39:43Z + quality + PATO:0002300 + + increased quality + + + + + A quality that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + + + + + + A quality that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:40:15Z + quality + PATO:0002301 + + decreased quality + + + + + A quality that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:50:59Z + quality + PATO:0002302 + + decreased process quality + + + + + A quality of a process that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is decreased compared to normal or average. + + George Gkoutos + 2011-06-16T06:51:54Z + quality + PATO:0002303 + + decreased object quality + + + + + A quality of an object that has a value that is decreased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of a process that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:53:08Z + quality + PATO:0002304 + + increased process quality + + + + + A quality of a process that has a value that is increased compared to normal or average. + PATOC:GVG + + + + + + + + + + + + + + + + + + + + + A quality of an object that has a value that is increased compared to normal or average. + + George Gkoutos + 2011-06-16T06:54:01Z + quality + PATO:0002305 + + increased object quality + + + + + A quality of an object that has a value that is increased compared to normal or average. + PATOC:GVG + + + + @@ -3799,6 +6792,12 @@ No imports + + + + + + Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. @@ -3830,18 +6829,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - 2 - - - - - + A multi-species collection of organisms of at least two different species, living in a particular area. Must have at least two populations of different species as members. multispecies community ISBN:0865423504 @@ -3873,8 +6861,9 @@ Classes for population already exist in IDO ('organism population', I - A quality that inheres in a biological population. + A quality that inheres in a population of organisms. See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. + This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community. Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. quality of a population @@ -3922,8 +6911,8 @@ Classes for population already exist in IDO ('organism population', I - A process that has as primary participant a population. - Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but tPCOhese categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. + A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. + The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. population process @@ -3932,8 +6921,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of birth of a population of organisms. population birth rate @@ -3942,8 +6932,9 @@ Classes for population already exist in IDO ('organism population', I - + + The rate of death of a population of organsisms. population death rate @@ -3952,9 +6943,9 @@ Classes for population already exist in IDO ('organism population', I - + - Is a rate a quality? Population growth rate may be better classified as a process profile. + The rate of growth of a population. population growth rate @@ -4023,30 +7014,51 @@ Classes for population already exist in IDO ('organism population', I - - - predator role + + Interactions are now covered in EcoCore ontology. + obsolete predator role + true + + + + true + + - - - prey role + + Interactions are now covered in EcoCore ontology. + obsolete prey role + true + + + + true + + - - - symbiont role + + Interactions are now covered in EcoCore ontology. + obsolete symbiont role + true + + + + true + + @@ -4054,9 +7066,15 @@ Classes for population already exist in IDO ('organism population', I + - A collection of organisms that has as parts every organism of given species and no organisms of any other species. + A collection of organisms that has as members every organism of given species and no organisms of any other species. + A collection of organisms that has as parts every organism of a species and no organisms of any other species. At the moment there is no way to specify in an OWL axiom that the collection includes every individual of a species. This should be added, if possible. + + + + taxonomic group This term is neutral with respect to which organisms are included in a species. Membership will depend on the species concept and the taxonomic assertions used to define the species. These criteria must be specified by the user. species as a collection of organisms @@ -4073,25 +7091,26 @@ Classes for population already exist in IDO ('organism population', I - - - - - - 1 - - - - 2 + + + 1 + + + + + + + + A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -4156,7 +7175,7 @@ Classes for population already exist in IDO ('organism population', I If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. - A quality of a community that reflects how close in abundance all species in a community are. + A quality of an ecological community that reflects how close in abundance all species in a community are. adapted from http://en.wikipedia.org/wiki/Species_evenness community species evenness @@ -4166,7 +7185,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -4190,7 +7209,7 @@ Classes for population already exist in IDO ('organism population', I An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. - Person: Jie Zheng + WEB: http://en.wikipedia.org/wiki/Household household @@ -4203,7 +7222,7 @@ Classes for population already exist in IDO ('organism population', I This is an example population added to demonstrate the modeling pattern for collections of organisms. - red population + obsolete red population true @@ -4215,7 +7234,7 @@ Classes for population already exist in IDO ('organism population', I An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. - red organism + obsolete red organism true @@ -4264,7 +7283,7 @@ Classes for population already exist in IDO ('organism population', I Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete. These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). - community + obsolete community true @@ -4274,6 +7293,13 @@ Classes for population already exist in IDO ('organism population', I + + + + 2 + + + A collection of organisms that consists of two or more organisms from at least two species. Need to add axiom to specify that it has at a mimum members of two different species, but not sure how to specify that. Can't say "('has member' only ('member of' min 2 'species as a collection of organisms'))". @@ -4372,34 +7398,336 @@ Classes for population already exist in IDO ('organism population', I + A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 - A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. GenEpio curators potluck - + + + + + A human social gathering at which two people are married. May include a legal or social ceremony. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 + GenEpio curators + wedding + + + + + + + + + A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. + Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 + GenEpiO curators + baby shower + + + + + + + + + + + + + + + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 + https://cmecscatalog.org/cmecs/classification/unit/577.html + mangrove community + tidal shrubland community + tidal mangrove shrubland community + + + + + + + + + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO + invisible to unaided eye + + + + + + + + + microbial organism + microbe + + + + + + + + + + + + + + + + + 2 + + + + + + + + + + + + + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 + collection of microbial organisms + + + + + + + + + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 + multi-species collection of microbes + + + + + + + + + + + + + + + + + + + + 1 + + + + + + + 2 + + + + + + + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 + single species collection of microbes + + + + + + + + + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 + microbiota + microbial population + + + + + + + + + + + + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + number of generations + number of generations of multicellular organism + + + + + A count data item of the number of steps in the line of descent from a common ancestor for a multicellular organism. + + + + + + + + + + + + + + + + + + + + + + + An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels. + + increased density of population + overcrowded population + + + + + + + + + + + + + + + + + + + + + + + + + + + A quality of a human population such that the density humans in an area is increased beyond sustainable levels. + + overcrowded human population + + + + + + + + + + A collection of organisms that has as members every organism of a taxon and no organisms of any other equal or higher ranked taxon. The taxon may be at any level. If the taxon is species, then this is the same as the class species as a collection of organisms. When defining a taxon, it is generally understood that members include both living organisms and dead organisms that are known through specimens or observations. + + + This term is neutral with respect to which organisms are included in a taxon. Membership will depend on the taxon concept and the assertions used to define the taxon. These criteria must be specified by the user. The best practice is to refer to a formal taxon description, rather than informal names "Genus species" without an authority. + taxon as collection of organisms + + + + + + + + + + + An organism or virus or viroid that is a microbe and a parasite. + + microbial parasite + + + + + + + + + + + + + + + + + + A microbial population of parasites that is defined by shared features such as genetic markers reflecting a common origin and distinguishing the population from other related parasite populations. + + VEuPathDB + parasite isolate population + + + + + + + + + + A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi). + + + Shannon entropy + Shannon's diversity index + Shannon-Wiener index + Shannon diversity index + + + + + - - - A human social gathering at which two people are married. May include a legal or social ceremony. - Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 - GenEpio curators - wedding + + + + A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi). + + + Simpson index + Simpson diversity index - + - - - A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. - Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 - GenEpiO curators - baby shower + + + + A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi). + + + inverse Simpson diversity index @@ -4408,12 +7736,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - @@ -4430,25 +7752,16 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 1 - - - - - - - + + + + 1 + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. pair of interacting organisms of the same species @@ -4525,7 +7838,7 @@ Classes for population already exist in IDO ('organism population', I - + An ecological community which is composed of co-existing populations of microbial organisms that interact, directly or indirectly, such that they impact one another's ecological fitness. A class for a collection of organisms considered "microbial" and an accompanying quality in PATO (e.g. "microscopic") would be useful to better axiomatise this class. See https://github.com/PopulationAndCommunityOntology/pco/issues/22 @@ -4538,6 +7851,23 @@ Classes for population already exist in IDO ('organism population', I + + + + + a count of 4 resulting from counting limbs in humans + + a count is a data item denoted by an integer and represented the number of instances or occurences of an entity + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO + + count + + + + @@ -4551,55 +7881,10 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Obsolete Class @@ -4607,19 +7892,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + An ecological community which is composed primarily of dwarf or short mangroves, often populations of Laguncularia racemosa, Avicennia germinans, Sarcocornia pacifica, or Batis maritima. + https://orcid.org/0000-0002-4366-3088 https://cmecscatalog.org/cmecs/classification/unit/577.html mangrove community tidal shrubland community - tidal mangrove shrubland community + obsolete tidal mangrove shrubland community + true @@ -4627,10 +7908,12 @@ Classes for population already exist in IDO ('organism population', I - + A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. + should move to PATO - invisible to unaided eye + obsolete invisible to unaided eye + true @@ -4638,15 +7921,11 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - + + microbial organism - microbe + obsolete microbe + true @@ -4654,31 +7933,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - - - - - - - - + A collection of organisms consisting of two or more microbes. + https://orcid.org/0000-0001-8815-0078 - collection of microbial organisms + obsolete collection of microbial organisms + true @@ -4686,11 +7946,12 @@ Classes for population already exist in IDO ('organism population', I - - + A multi-species collection of organisms that consists of two or more microbes from at least two species. + https://orcid.org/0000-0001-8815-0078 - multi-species collection of microbes + obsolete multi-species collection of microbes + true @@ -4698,36 +7959,12 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - 1 - - - - - - - 2 - - - - - - - + A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species. + https://orcid.org/0000-0001-8815-0078 - single species collection of microbes + obsolete single species collection of microbes + true @@ -4735,18 +7972,13 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - + A population of organisms consisting of only microbes of the same species, that live in the same place. + https://orcid.org/0000-0001-8815-0078 microbiota - microbial population + obsolete microbial population + true @@ -4766,6 +7998,7 @@ Classes for population already exist in IDO ('organism population', I + example to be eventually removed example to be eventually removed @@ -4775,8 +8008,9 @@ Classes for population already exist in IDO ('organism population', I + 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 + Person:Alan Ruttenberg failed exploratory term @@ -4786,6 +8020,7 @@ Classes for population already exist in IDO ('organism population', I + 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. metadata complete @@ -4796,7 +8031,8 @@ Classes for population already exist in IDO ('organism population', I - term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -4806,6 +8042,7 @@ Classes for population already exist in IDO ('organism population', I + 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." ready for release @@ -4816,6 +8053,7 @@ Classes for population already exist in IDO ('organism population', I + metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -4826,6 +8064,7 @@ Classes for population already exist in IDO ('organism population', I + uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -4836,6 +8075,7 @@ Classes for population already exist in IDO ('organism population', I + 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. pending final vetting @@ -4845,11 +8085,12 @@ Classes for population already exist in IDO ('organism population', I - 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 - core + + obsolete_core + true @@ -4858,6 +8099,7 @@ Classes for population already exist in IDO ('organism population', I + placeholder removed placeholder removed @@ -4867,6 +8109,7 @@ Classes for population already exist in IDO ('organism population', I + terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -4877,6 +8120,7 @@ Classes for population already exist in IDO ('organism population', I + 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 imported @@ -4887,6 +8131,7 @@ Classes for population already exist in IDO ('organism population', I + 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. term split @@ -4897,10 +8142,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - universal + 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 + universal @@ -4909,10 +8155,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - defined class + 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 + defined class @@ -4921,10 +8168,11 @@ Classes for population already exist in IDO ('organism population', I - 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 - named class expression + 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 + named class expression @@ -4933,6 +8181,7 @@ Classes for population already exist in IDO ('organism population', I + to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI @@ -4945,6 +8194,7 @@ Classes for population already exist in IDO ('organism population', I + 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 @@ -4961,6 +8211,39 @@ Classes for population already exist in IDO ('organism population', I /////////////////////////////////////////////////////////////////////////////////////// --> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -4983,6 +8266,923 @@ Classes for population already exist in IDO ('organism population', I + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/reports/pco-edit.owl-obo-report.tsv b/src/ontology/reports/pco-edit.owl-obo-report.tsv index 4d1219e..02983a2 100644 --- a/src/ontology/reports/pco-edit.owl-obo-report.tsv +++ b/src/ontology/reports/pco-edit.owl-obo-report.tsv @@ -1,24 +1,17 @@ Level Rule Name Subject Property Value +ERROR missing_label BFO:0000017 rdfs:label +ERROR missing_label ECOCORE:00000045 rdfs:label ERROR missing_label GO:0051704 rdfs:label ERROR missing_label IAO:0000030 rdfs:label -ERROR missing_ontology_description pco.owl dc11:description -ERROR missing_ontology_license pco.owl dc:license -ERROR missing_ontology_title pco.owl dc11:title +ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as members every organism of given species and no organisms of any other species.@en +ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as parts every organism of a species and no organisms of any other species.@en +WARN missing_definition BFO:0000017 IAO:0000115 +WARN missing_definition ECOCORE:00000045 IAO:0000115 WARN missing_definition GO:0051704 IAO:0000115 WARN missing_definition IAO:0000030 IAO:0000115 -WARN missing_definition PCO:0000006 IAO:0000115 -WARN missing_definition PCO:0000007 IAO:0000115 -WARN missing_definition PCO:0000008 IAO:0000115 -WARN missing_definition PCO:0000014 IAO:0000115 -WARN missing_definition PCO:0000015 IAO:0000115 -WARN missing_definition PCO:0000016 IAO:0000115 -WARN missing_definition PCO:0000037 IAO:0000115 -WARN missing_definition PCO:0001001 IAO:0000115 -WARN missing_definition https://purl.obolibrary.org/obo/PCO_0000042 IAO:0000115 -WARN missing_obsolete_label PCO:0000025 rdfs:label red population@en -WARN missing_obsolete_label PCO:0000026 rdfs:label red organism@en -WARN missing_obsolete_label PCO:0000028 rdfs:label community@en +WARN missing_definition PCO:0000049 IAO:0000115 +WARN missing_definition PCO:0000055 IAO:0000115 INFO missing_superclass PCO:0000003 rdfs:subClassOf INFO missing_superclass PCO:0000004 rdfs:subClassOf -INFO missing_superclass https://purl.obolibrary.org/obo/PCO_0000043 rdfs:subClassOf -INFO missing_superclass https://purl.obolibrary.org/obo/PCO_0000045 rdfs:subClassOf +INFO missing_superclass PCO:0000050 rdfs:subClassOf +INFO missing_superclass PCO:0000052 rdfs:subClassOf