From 8256ce0148eda51e225f6a562987c62b316697f7 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Wed, 8 Jul 2015 17:59:49 -0700 Subject: [PATCH] initial checkin --- .../{README-editors.txt => README-editors.md} | 0 src/ontology/README.txt | 17 - src/ontology/md/BFO/02/BFO_0000002.md | 51 ++ src/ontology/md/BFO/03/BFO_0000003.md | 52 ++ src/ontology/md/BFO/04/BFO_0000004.md | 59 ++ src/ontology/md/BFO/05/BFO_0000005.md | 39 ++ src/ontology/md/BFO/15/BFO_0000015.md | 57 ++ src/ontology/md/BFO/17/BFO_0000017.md | 42 ++ src/ontology/md/BFO/19/BFO_0000019.md | 38 ++ src/ontology/md/BFO/20/BFO_0000020.md | 45 ++ src/ontology/md/BFO/23/BFO_0000023.md | 39 ++ src/ontology/md/BFO/31/BFO_0000031.md | 40 ++ src/ontology/md/BFO/34/BFO_0000034.md | 38 ++ src/ontology/md/BFO/40/BFO_0000040.md | 68 ++ src/ontology/md/BFO/41/BFO_0000141.md | 42 ++ src/ontology/md/BFO/50/BFO_0000050.md | 113 ++++ src/ontology/md/BFO/51/BFO_0000051.md | 74 +++ src/ontology/md/BFO/54/BFO_0000054.md | 50 ++ 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create mode 100644 src/ontology/md/ym/oboInOwl#hasExactSynonym.md create mode 100644 src/ontology/md/ym/oboInOwl#hasRelatedSynonym.md diff --git a/src/ontology/README-editors.txt b/src/ontology/README-editors.md similarity index 100% rename from src/ontology/README-editors.txt rename to src/ontology/README-editors.md diff --git a/src/ontology/README.txt b/src/ontology/README.txt deleted file mode 100644 index a59fdf97..00000000 --- a/src/ontology/README.txt +++ /dev/null @@ -1,17 +0,0 @@ -OBO Relation Ontology -===================== - -This is the replacement ontology for the deprecated OBO_REL. - -See this announcement: - http://groups.google.com/group/obo-relations/browse_thread/thread/29fc616eb570f7dc/fc0647f190b5f178 - -Project page: - - http://code.google.com/p/obo-relations - -Ontology PURLs: - - http://purl.obolibrary.org/obo/ro.owl - http://purl.obolibrary.org/obo/ro.obo - diff --git a/src/ontology/md/BFO/02/BFO_0000002.md b/src/ontology/md/BFO/02/BFO_0000002.md new file mode 100644 index 00000000..6109dcb9 --- /dev/null +++ b/src/ontology/md/BFO/02/BFO_0000002.md @@ -0,0 +1,51 @@ + +## Class : continuant + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000002 + * *Label* = continuant + * *Definition* = An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = continuant + +## Usage + + * - + * [coincident with](../../RO/08/RO_0002008.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [coincident with](../../RO/08/RO_0002008.md) Range [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [expressed in](../../RO/06/RO_0002206.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [gene product of](../../RO/04/RO_0002204.md) Range [continuant](../../BFO/02/BFO_0000002.md) + * [generically dependent continuant](../../BFO/31/BFO_0000031.md) SubClassOf [continuant](../../BFO/02/BFO_0000002.md) + * [genomically related to](../../RO/30/RO_0002330.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [genomically related to](../../RO/30/RO_0002330.md) Range [continuant](../../BFO/02/BFO_0000002.md) + * [has gene product](../../RO/05/RO_0002205.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [has participant](../../RO/57/RO_0000057.md) Range [continuant](../../BFO/02/BFO_0000002.md) + * [has phenotype](../../RO/00/RO_0002200.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [independent continuant](../../BFO/04/BFO_0000004.md) SubClassOf [continuant](../../BFO/02/BFO_0000002.md) + * [participates in](../../RO/56/RO_0000056.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [related via localization to](../../RO/37/RO_0002337.md) Range [continuant](../../BFO/02/BFO_0000002.md) + * [relation between structure and stage](../../RO/87/RO_0002487.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [specifically dependent continuant](../../BFO/20/BFO_0000020.md) SubClassOf [continuant](../../BFO/02/BFO_0000002.md) + +## External Comments + diff --git a/src/ontology/md/BFO/03/BFO_0000003.md b/src/ontology/md/BFO/03/BFO_0000003.md new file mode 100644 index 00000000..09e27226 --- /dev/null +++ b/src/ontology/md/BFO/03/BFO_0000003.md @@ -0,0 +1,52 @@ + +## Class : occurrent + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000003 + * *Label* = occurrent + * *Definition* = An entity that has temporal parts and that happens, unfolds or develops through time. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An entity that has temporal parts and that happens, unfolds or develops through time. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = occurrent + +## Usage + + * - + * [causal relation between processes](../../RO/01/RO_0002501.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [causal relation between processes](../../RO/01/RO_0002501.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [has part that occurs in](../../RO/79/RO_0002479.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [has participant](../../RO/57/RO_0000057.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [occurs in](../../BFO/66/BFO_0000066.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [participates in](../../RO/56/RO_0000056.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [preceded by](../../BFO/62/BFO_0000062.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [preceded by](../../BFO/62/BFO_0000062.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [precedes](../../BFO/63/BFO_0000063.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [precedes](../../BFO/63/BFO_0000063.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [process](../../BFO/15/BFO_0000015.md) SubClassOf [occurrent](../../BFO/03/BFO_0000003.md) + * [relation between structure and stage](../../RO/87/RO_0002487.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [starts during](../../RO/91/RO_0002091.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [starts during](../../RO/91/RO_0002091.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [temporally related to](../../RO/22/RO_0002222.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [temporally related to](../../RO/22/RO_0002222.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + +## External Comments + diff --git a/src/ontology/md/BFO/04/BFO_0000004.md b/src/ontology/md/BFO/04/BFO_0000004.md new file mode 100644 index 00000000..82907bae --- /dev/null +++ b/src/ontology/md/BFO/04/BFO_0000004.md @@ -0,0 +1,59 @@ + +## Class : independent continuant + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000004 + * *Label* = independent continuant + * *Definition* = A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [continuant](../../BFO/02/BFO_0000002.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = independent continuant + +## Usage + + * - + * [adjacent to](../../RO/20/RO_0002220.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [adjacent to](../../RO/20/RO_0002220.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [capable of](../../RO/15/RO_0002215.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [connects](../../RO/76/RO_0002176.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [contained in](../../RO/18/RO_0001018.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [continuous with](../../RO/50/RO_0002150.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [continuous with](../../RO/50/RO_0002150.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [develops from](../../RO/02/RO_0002202.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [develops from](../../RO/02/RO_0002202.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [differs in attribute of](../../RO/25/RO_0002425.md) Range [independent continuant](../../BFO/04/BFO_0000004.md)or[process](../../BFO/15/BFO_0000015.md) + * [expressed in](../../RO/06/RO_0002206.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [gene product of](../../RO/04/RO_0002204.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [has end location](../../RO/32/RO_0002232.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has gene product](../../RO/05/RO_0002205.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has part that occurs in](../../RO/79/RO_0002479.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has role](../../RO/87/RO_0000087.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [has start location](../../RO/31/RO_0002231.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [immaterial entity](../../BFO/41/BFO_0000141.md) SubClassOf [independent continuant](../../BFO/04/BFO_0000004.md) + * [in taxon](../../RO/62/RO_0002162.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [independent continuant](../../BFO/04/BFO_0000004.md) SubClassOf [continuant](../../BFO/02/BFO_0000002.md) + * [material entity](../../BFO/40/BFO_0000040.md) SubClassOf [independent continuant](../../BFO/04/BFO_0000004.md) + * [occurs in](../../BFO/66/BFO_0000066.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + +## External Comments + diff --git a/src/ontology/md/BFO/05/BFO_0000005.md b/src/ontology/md/BFO/05/BFO_0000005.md new file mode 100644 index 00000000..451e142e --- /dev/null +++ b/src/ontology/md/BFO/05/BFO_0000005.md @@ -0,0 +1,39 @@ + +## Class : obsolete dependent continuant + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000005 + * *Label* = obsolete dependent continuant + * *Definition* = A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [Obsolete Class](../../ss/oboInOwl#ObsoleteClass.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = obsolete dependent continuant + * *[owl#deprecated](../../ed/owl#deprecated.md)* = true + +## Usage + + * - + * [obsolete dependent continuant](../../BFO/05/BFO_0000005.md) SubClassOf [Obsolete Class](../../ss/oboInOwl#ObsoleteClass.md) + +## External Comments + diff --git a/src/ontology/md/BFO/15/BFO_0000015.md b/src/ontology/md/BFO/15/BFO_0000015.md new file mode 100644 index 00000000..23d6d46e --- /dev/null +++ b/src/ontology/md/BFO/15/BFO_0000015.md @@ -0,0 +1,57 @@ + +## Class : process + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000015 + * *Label* = process + * *Definition* = An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [occurrent](../../BFO/03/BFO_0000003.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = process + +## Usage + + * - + * [biological_process](../../GO/50/GO_0008150.md) SubClassOf [process](../../BFO/15/BFO_0000015.md) + * [capable of](../../RO/15/RO_0002215.md) Range [process](../../BFO/15/BFO_0000015.md) + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) Range [process](../../BFO/15/BFO_0000015.md) + * [causally influences](../../RO/66/RO_0002566.md) some [material entity](../../BFO/40/BFO_0000040.md) SubClassOf [capable of](../../RO/15/RO_0002215.md) some [participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md)or[participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md) + * [differs in attribute of](../../RO/25/RO_0002425.md) Range [independent continuant](../../BFO/04/BFO_0000004.md)or[process](../../BFO/15/BFO_0000015.md) + * [has end location](../../RO/32/RO_0002232.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [has start location](../../RO/31/RO_0002231.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [molecular_function](../../GO/74/GO_0003674.md) SubClassOf [process](../../BFO/15/BFO_0000015.md) + * [process](../../BFO/15/BFO_0000015.md) SubClassOf [occurrent](../../BFO/03/BFO_0000003.md) + * [realized in](../../BFO/54/BFO_0000054.md) Range [process](../../BFO/15/BFO_0000015.md) + * [realizes](../../BFO/55/BFO_0000055.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulated by](../../RO/34/RO_0002334.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulated by](../../RO/34/RO_0002334.md) Range [process](../../BFO/15/BFO_0000015.md) + * [regulates in other organism](../../RO/10/RO_0002010.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulates in other organism](../../RO/10/RO_0002010.md) Range [process](../../BFO/15/BFO_0000015.md) + * [regulates](../../RO/11/RO_0002211.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulates](../../RO/11/RO_0002211.md) Range [process](../../BFO/15/BFO_0000015.md) + * [related via localization to](../../RO/37/RO_0002337.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) Range [process](../../BFO/15/BFO_0000015.md) + +## External Comments + diff --git a/src/ontology/md/BFO/17/BFO_0000017.md b/src/ontology/md/BFO/17/BFO_0000017.md new file mode 100644 index 00000000..dbc1f110 --- /dev/null +++ b/src/ontology/md/BFO/17/BFO_0000017.md @@ -0,0 +1,42 @@ + +## Class : realizable entity + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000017 + * *Label* = realizable entity + * *Definition* = A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = realizable entity + +## Usage + + * - + * [function](../../BFO/34/BFO_0000034.md) SubClassOf [realizable entity](../../BFO/17/BFO_0000017.md) + * [realizable entity](../../BFO/17/BFO_0000017.md) SubClassOf [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [realized in](../../BFO/54/BFO_0000054.md) Domain [realizable entity](../../BFO/17/BFO_0000017.md) + * [realizes](../../BFO/55/BFO_0000055.md) Range [realizable entity](../../BFO/17/BFO_0000017.md) + * [role](../../BFO/23/BFO_0000023.md) SubClassOf [realizable entity](../../BFO/17/BFO_0000017.md) + +## External Comments + diff --git a/src/ontology/md/BFO/19/BFO_0000019.md b/src/ontology/md/BFO/19/BFO_0000019.md new file mode 100644 index 00000000..461d7be0 --- /dev/null +++ b/src/ontology/md/BFO/19/BFO_0000019.md @@ -0,0 +1,38 @@ + +## Class : quality + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000019 + * *Label* = quality + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = quality + +## Usage + + * - + * [has quality](../../RO/86/RO_0000086.md) Range [quality](../../BFO/19/BFO_0000019.md) + * [morphology](../../PATO/51/PATO_0000051.md) SubClassOf [quality](../../BFO/19/BFO_0000019.md) + * [quality](../../BFO/19/BFO_0000019.md) SubClassOf [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + +## External Comments + diff --git a/src/ontology/md/BFO/20/BFO_0000020.md b/src/ontology/md/BFO/20/BFO_0000020.md new file mode 100644 index 00000000..061b2d26 --- /dev/null +++ b/src/ontology/md/BFO/20/BFO_0000020.md @@ -0,0 +1,45 @@ + +## Class : specifically dependent continuant + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000020 + * *Label* = specifically dependent continuant + * *Definition* = A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [continuant](../../BFO/02/BFO_0000002.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = specifically dependent continuant + +## Usage + + * - + * [bearer of](../../RO/53/RO_0000053.md) Range [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [concretizes](../../RO/59/RO_0000059.md) Domain [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [differs in attribute](../../RO/26/RO_0002426.md) Range [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [is concretized as](../../RO/58/RO_0000058.md) Range [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [quality](../../BFO/19/BFO_0000019.md) SubClassOf [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [quality](../../PATO/01/PATO_0000001.md) SubClassOf [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [realizable entity](../../BFO/17/BFO_0000017.md) SubClassOf [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [specifically dependent continuant](../../BFO/20/BFO_0000020.md) SubClassOf [continuant](../../BFO/02/BFO_0000002.md) + +## External Comments + diff --git a/src/ontology/md/BFO/23/BFO_0000023.md b/src/ontology/md/BFO/23/BFO_0000023.md new file mode 100644 index 00000000..d3821125 --- /dev/null +++ b/src/ontology/md/BFO/23/BFO_0000023.md @@ -0,0 +1,39 @@ + +## Class : role + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000023 + * *Label* = role + * *Definition* = A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [realizable entity](../../BFO/17/BFO_0000017.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = role + +## Usage + + * - + * [has role](../../RO/87/RO_0000087.md) Range [role](../../BFO/23/BFO_0000023.md) + * [role](../../BFO/23/BFO_0000023.md) SubClassOf [realizable entity](../../BFO/17/BFO_0000017.md) + +## External Comments + diff --git a/src/ontology/md/BFO/31/BFO_0000031.md b/src/ontology/md/BFO/31/BFO_0000031.md new file mode 100644 index 00000000..f5986e12 --- /dev/null +++ b/src/ontology/md/BFO/31/BFO_0000031.md @@ -0,0 +1,40 @@ + +## Class : generically dependent continuant + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000031 + * *Label* = generically dependent continuant + * *Definition* = A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [continuant](../../BFO/02/BFO_0000002.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = generically dependent continuant + +## Usage + + * - + * [concretizes](../../RO/59/RO_0000059.md) Range [generically dependent continuant](../../BFO/31/BFO_0000031.md) + * [generically dependent continuant](../../BFO/31/BFO_0000031.md) SubClassOf [continuant](../../BFO/02/BFO_0000002.md) + * [is concretized as](../../RO/58/RO_0000058.md) Domain [generically dependent continuant](../../BFO/31/BFO_0000031.md) + +## External Comments + diff --git a/src/ontology/md/BFO/34/BFO_0000034.md b/src/ontology/md/BFO/34/BFO_0000034.md new file mode 100644 index 00000000..5c65f1a6 --- /dev/null +++ b/src/ontology/md/BFO/34/BFO_0000034.md @@ -0,0 +1,38 @@ + +## Class : function + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000034 + * *Label* = function + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [realizable entity](../../BFO/17/BFO_0000017.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = function + +## Usage + + * - + * [function of](../../RO/79/RO_0000079.md) Domain [function](../../BFO/34/BFO_0000034.md) + * [function](../../BFO/34/BFO_0000034.md) SubClassOf [realizable entity](../../BFO/17/BFO_0000017.md) + * [has function](../../RO/85/RO_0000085.md) Range [function](../../BFO/34/BFO_0000034.md) + +## External Comments + diff --git a/src/ontology/md/BFO/40/BFO_0000040.md b/src/ontology/md/BFO/40/BFO_0000040.md new file mode 100644 index 00000000..c7f4e158 --- /dev/null +++ b/src/ontology/md/BFO/40/BFO_0000040.md @@ -0,0 +1,68 @@ + +## Class : material entity + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000040 + * *Label* = material entity + * *Definition* = An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [independent continuant](../../BFO/04/BFO_0000004.md) + +## Equivalencies + + +## Other Logical Axioms + + * DisjointClasses( ObjectSomeValuesFrom( )) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = material entity + +## Usage + + * - + * DisjointClasses( ObjectSomeValuesFrom( )) + * DisjointClasses( ObjectSomeValuesFrom( )) + * [biotically interacts with](../../RO/37/RO_0002437.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [bounding layer of](../../RO/07/RO_0002007.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [laminar](../../PATO/24/PATO_0002124.md) and [material entity](../../BFO/40/BFO_0000040.md) + * [bounding layer of](../../RO/07/RO_0002007.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [causal relation between material entities](../../RO/06/RO_0002506.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [causal relation between material entities](../../RO/06/RO_0002506.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [causally influences](../../RO/66/RO_0002566.md) some [material entity](../../BFO/40/BFO_0000040.md) SubClassOf [capable of](../../RO/15/RO_0002215.md) some [participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md)or[participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md) + * [colocalizes with](../../RO/25/RO_0002325.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [colocalizes with](../../RO/25/RO_0002325.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [conduit for](../../RO/70/RO_0002570.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [conduit for](../../RO/70/RO_0002570.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [contained in](../../RO/18/RO_0001018.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [determined by part of](../../RO/09/RO_0002509.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [determined by](../../RO/07/RO_0002507.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [interacts with](../../RO/34/RO_0002434.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [interacts with](../../RO/34/RO_0002434.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [lumen of](../../RO/71/RO_0002571.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [material anatomical entity](../../CARO/06/CARO_0000006.md) SubClassOf [material entity](../../BFO/40/BFO_0000040.md) + * [material entity](../../BFO/40/BFO_0000040.md) SubClassOf [independent continuant](../../BFO/04/BFO_0000004.md) + * [produced by](../../RO/01/RO_0003001.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [produced by](../../RO/01/RO_0003001.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [produces](../../RO/00/RO_0003000.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [produces](../../RO/00/RO_0003000.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [system](../../RO/77/RO_0002577.md) SubClassOf [material entity](../../BFO/40/BFO_0000040.md) + +## External Comments + diff --git a/src/ontology/md/BFO/41/BFO_0000141.md b/src/ontology/md/BFO/41/BFO_0000141.md new file mode 100644 index 00000000..44cb4bb1 --- /dev/null +++ b/src/ontology/md/BFO/41/BFO_0000141.md @@ -0,0 +1,42 @@ + +## Class : immaterial entity + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000141 + * *Label* = immaterial entity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [independent continuant](../../BFO/04/BFO_0000004.md) + +## Equivalencies + + +## Other Logical Axioms + + * DisjointClasses( ObjectSomeValuesFrom( )) + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = immaterial entity + +## Usage + + * - + * DisjointClasses( ObjectSomeValuesFrom( )) + * DisjointClasses( ObjectSomeValuesFrom( )) + * [has 2D boundary](../../RO/02/RO_0002002.md) Range [immaterial entity](../../BFO/41/BFO_0000141.md) + * [immaterial anatomical entity](../../CARO/07/CARO_0000007.md) SubClassOf [immaterial entity](../../BFO/41/BFO_0000141.md) + * [immaterial entity](../../BFO/41/BFO_0000141.md) SubClassOf [independent continuant](../../BFO/04/BFO_0000004.md) + * [luminal space of](../../RO/72/RO_0002572.md) Domain [immaterial entity](../../BFO/41/BFO_0000141.md) + +## External Comments + diff --git a/src/ontology/md/BFO/50/BFO_0000050.md b/src/ontology/md/BFO/50/BFO_0000050.md new file mode 100644 index 00000000..d38ae4e6 --- /dev/null +++ b/src/ontology/md/BFO/50/BFO_0000050.md @@ -0,0 +1,113 @@ + +## Class : part of + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000050 + * *Label* = part of + * *Definition* = a core relation that holds between a part and its whole + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [part of](../../BFO/50/BFO_0000050.md) + * [part of](../../BFO/50/BFO_0000050.md) InverseOf [has part](../../BFO/51/BFO_0000051.md) + * [part of](../../BFO/50/BFO_0000050.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = is part of + * *[example of usage](../../IAO/12/IAO_0000112.md)* = my brain is part of my body (continuant parthood, two material entities) + * *[example of usage](../../IAO/12/IAO_0000112.md)* = my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this day is part of this year (occurrent parthood) + * *[definition](../../IAO/15/IAO_0000115.md)* = a core relation that holds between a part and its whole + * *[editor note](../../IAO/16/IAO_0000116.md)* = Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + * *[editor note](../../IAO/16/IAO_0000116.md)* = Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = part_of + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = part of + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://ontologydesignpatterns.org/wiki/Submissions:PartOf + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://www.obofoundry.org/ro/#OBO_REL:part_of + +## Usage + + * - + * DisjointClasses( ObjectSomeValuesFrom( )) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [part of](../../BFO/50/BFO_0000050.md) + * [bounding layer of](../../RO/07/RO_0002007.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [branching part of](../../RO/80/RO_0002380.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [connected to](../../RO/70/RO_0002170.md) Domain [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connected to](../../RO/70/RO_0002170.md) Range [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connects](../../RO/76/RO_0002176.md) Range [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [determined by](../../RO/07/RO_0002507.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [ends](../../RO/29/RO_0002229.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [fasciculates with](../../RO/01/RO_0002101.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) Range [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has presynaptic terminal in](../../RO/13/RO_0002113.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has synaptic terminal in](../../RO/30/RO_0002130.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [is subsequence of](../../RO/25/RO_0002525.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [lumen of](../../RO/71/RO_0002571.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [member of](../../RO/50/RO_0002350.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [part of](../../BFO/50/BFO_0000050.md) InverseOf [has part](../../BFO/51/BFO_0000051.md) + * [part of](../../BFO/50/BFO_0000050.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [skeleton of](../../RO/76/RO_0002576.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [starts](../../RO/23/RO_0002223.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [synapsed by](../../RO/03/RO_0002103.md) Range [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [synapsed to](../../RO/20/RO_0002120.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + +## External Comments + diff --git a/src/ontology/md/BFO/51/BFO_0000051.md b/src/ontology/md/BFO/51/BFO_0000051.md new file mode 100644 index 00000000..24f4482d --- /dev/null +++ b/src/ontology/md/BFO/51/BFO_0000051.md @@ -0,0 +1,74 @@ + +## Class : has part + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000051 + * *Label* = has part + * *Definition* = a core relation that holds between a whole and its part + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [has part](../../BFO/51/BFO_0000051.md) + * [has part](../../BFO/51/BFO_0000051.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [part of](../../BFO/50/BFO_0000050.md) InverseOf [has part](../../BFO/51/BFO_0000051.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = has part + * *[example of usage](../../IAO/12/IAO_0000112.md)* = my body has part my brain (continuant parthood, two material entities) + * *[example of usage](../../IAO/12/IAO_0000112.md)* = my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this year has part this day (occurrent parthood) + * *[definition](../../IAO/15/IAO_0000115.md)* = a core relation that holds between a whole and its part + * *[editor note](../../IAO/16/IAO_0000116.md)* = Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + * *[editor note](../../IAO/16/IAO_0000116.md)* = Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has_part + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has part + +## Usage + + * - + * DisjointClasses( ObjectSomeValuesFrom( )) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [has part](../../BFO/51/BFO_0000051.md) + * [composed primarily of](../../RO/73/RO_0002473.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [ends with](../../RO/30/RO_0002230.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [has component](../../RO/80/RO_0002180.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [has member](../../RO/51/RO_0002351.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [has part](../../BFO/51/BFO_0000051.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has plasma membrane part](../../RO/04/RO_0002104.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [has skeleton](../../RO/51/RO_0002551.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [has subsequence](../../RO/24/RO_0002524.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [part of](../../BFO/50/BFO_0000050.md) InverseOf [has part](../../BFO/51/BFO_0000051.md) + * [starts with](../../RO/24/RO_0002224.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + +## External Comments + diff --git a/src/ontology/md/BFO/54/BFO_0000054.md b/src/ontology/md/BFO/54/BFO_0000054.md new file mode 100644 index 00000000..f792461d --- /dev/null +++ b/src/ontology/md/BFO/54/BFO_0000054.md @@ -0,0 +1,50 @@ + +## Class : realized in + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000054 + * *Label* = 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 + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [realized in](../../BFO/54/BFO_0000054.md) Domain [realizable entity](../../BFO/17/BFO_0000017.md) + * [realized in](../../BFO/54/BFO_0000054.md) Range [process](../../BFO/15/BFO_0000015.md) + * [realizes](../../BFO/55/BFO_0000055.md) InverseOf [realized in](../../BFO/54/BFO_0000054.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = realized in + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this disease is realized in this disease course + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this fragility is realized in this shattering + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this investigator role is realized in this investigation + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is realized by + * *[alternative term](../../IAO/18/IAO_0000118.md)* = realized_in + * *[elucidation](../../IAO/00/IAO_0000600.md)* = [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]) + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = 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 + * *[rdf-schema#isDefinedBy](../../By/rdf-schema#isDefinedBy.md)* = http://purl.obolibrary.org/obo/bfo.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = realized in + +## Usage + + * - + * [realized in](../../BFO/54/BFO_0000054.md) Domain [realizable entity](../../BFO/17/BFO_0000017.md) + * [realized in](../../BFO/54/BFO_0000054.md) Range [process](../../BFO/15/BFO_0000015.md) + * [realizes](../../BFO/55/BFO_0000055.md) InverseOf [realized in](../../BFO/54/BFO_0000054.md) + +## External Comments + diff --git a/src/ontology/md/BFO/55/BFO_0000055.md b/src/ontology/md/BFO/55/BFO_0000055.md new file mode 100644 index 00000000..bd877d63 --- /dev/null +++ b/src/ontology/md/BFO/55/BFO_0000055.md @@ -0,0 +1,49 @@ + +## Class : realizes + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000055 + * *Label* = 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 + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [realizes](../../BFO/55/BFO_0000055.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [realizes](../../BFO/55/BFO_0000055.md) InverseOf [realized in](../../BFO/54/BFO_0000054.md) + * [realizes](../../BFO/55/BFO_0000055.md) Range [realizable entity](../../BFO/17/BFO_0000017.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = realizes + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this disease course realizes this disease + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this investigation realizes this investigator role + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this shattering realizes this fragility + * *[elucidation](../../IAO/00/IAO_0000600.md)* = 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]) + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = 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 + * *[rdf-schema#isDefinedBy](../../By/rdf-schema#isDefinedBy.md)* = http://purl.obolibrary.org/obo/iao.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = realizes + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [realizes](../../BFO/55/BFO_0000055.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [realizes](../../BFO/55/BFO_0000055.md) InverseOf [realized in](../../BFO/54/BFO_0000054.md) + * [realizes](../../BFO/55/BFO_0000055.md) Range [realizable entity](../../BFO/17/BFO_0000017.md) + +## External Comments + diff --git a/src/ontology/md/BFO/60/BFO_0000060.md b/src/ontology/md/BFO/60/BFO_0000060.md new file mode 100644 index 00000000..1dfae1b5 --- /dev/null +++ b/src/ontology/md/BFO/60/BFO_0000060.md @@ -0,0 +1,41 @@ + +## Class : obsolete preceded by + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000060 + * *Label* = obsolete preceded by + * *Comment* = accidentally included in BFO 1.2 proposal + - should have been BFO_0000062 + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [obsolete preceded by](../../BFO/60/BFO_0000060.md) + +## Other Annotations + + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = accidentally included in BFO 1.2 proposal + - should have been BFO_0000062 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = obsolete preceded by + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [obsolete preceded by](../../BFO/60/BFO_0000060.md) + +## External Comments + diff --git a/src/ontology/md/BFO/62/BFO_0000062.md b/src/ontology/md/BFO/62/BFO_0000062.md new file mode 100644 index 00000000..670ac1fd --- /dev/null +++ b/src/ontology/md/BFO/62/BFO_0000062.md @@ -0,0 +1,62 @@ + +## Class : preceded by + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000062 + * *Label* = preceded by + * *Definition* = x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [ends after](../../RO/86/RO_0002086.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [preceded by](../../BFO/62/BFO_0000062.md) + * [preceded by](../../BFO/62/BFO_0000062.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [preceded by](../../BFO/62/BFO_0000062.md) InverseOf [precedes](../../BFO/63/BFO_0000063.md) + * [preceded by](../../BFO/62/BFO_0000062.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [preceded by](../../BFO/62/BFO_0000062.md) SubPropertyOf [ends after](../../RO/86/RO_0002086.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = preceded by + * *[definition](../../IAO/15/IAO_0000115.md)* = x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + * *[editor note](../../IAO/16/IAO_0000116.md)* = An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is preceded by + * *[alternative term](../../IAO/18/IAO_0000118.md)* = preceded_by + * *[source](../../ce/source.md)* = http://www.obofoundry.org/ro/#OBO_REL:preceded_by + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = preceded by + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * TransitiveObjectProperty [preceded by](../../BFO/62/BFO_0000062.md) + * [causally downstream of](../../RO/04/RO_0002404.md) SubPropertyOf [preceded by](../../BFO/62/BFO_0000062.md) + * [immediately preceded by](../../RO/87/RO_0002087.md) SubPropertyOf [preceded by](../../BFO/62/BFO_0000062.md) + * [preceded by](../../BFO/62/BFO_0000062.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [preceded by](../../BFO/62/BFO_0000062.md) InverseOf [precedes](../../BFO/63/BFO_0000063.md) + * [preceded by](../../BFO/62/BFO_0000062.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [preceded by](../../BFO/62/BFO_0000062.md) SubPropertyOf [ends after](../../RO/86/RO_0002086.md) + * [transformation of](../../RO/94/RO_0002494.md) SubPropertyOf [preceded by](../../BFO/62/BFO_0000062.md) + +## External Comments + diff --git a/src/ontology/md/BFO/63/BFO_0000063.md b/src/ontology/md/BFO/63/BFO_0000063.md new file mode 100644 index 00000000..34229703 --- /dev/null +++ b/src/ontology/md/BFO/63/BFO_0000063.md @@ -0,0 +1,54 @@ + +## Class : precedes + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000063 + * *Label* = precedes + * *Definition* = x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [precedes](../../BFO/63/BFO_0000063.md) + * [preceded by](../../BFO/62/BFO_0000062.md) InverseOf [precedes](../../BFO/63/BFO_0000063.md) + * [precedes](../../BFO/63/BFO_0000063.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [precedes](../../BFO/63/BFO_0000063.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [precedes](../../BFO/63/BFO_0000063.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = precedes + * *[definition](../../IAO/15/IAO_0000115.md)* = x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = precedes + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * TransitiveObjectProperty [precedes](../../BFO/63/BFO_0000063.md) + * [causally upstream of](../../RO/11/RO_0002411.md) SubPropertyOf [precedes](../../BFO/63/BFO_0000063.md) + * [immediately precedes](../../RO/90/RO_0002090.md) SubPropertyOf [precedes](../../BFO/63/BFO_0000063.md) + * [preceded by](../../BFO/62/BFO_0000062.md) InverseOf [precedes](../../BFO/63/BFO_0000063.md) + * [precedes](../../BFO/63/BFO_0000063.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [precedes](../../BFO/63/BFO_0000063.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [precedes](../../BFO/63/BFO_0000063.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## External Comments + diff --git a/src/ontology/md/BFO/66/BFO_0000066.md b/src/ontology/md/BFO/66/BFO_0000066.md new file mode 100644 index 00000000..35ce4f45 --- /dev/null +++ b/src/ontology/md/BFO/66/BFO_0000066.md @@ -0,0 +1,56 @@ + +## Class : occurs in + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000066 + * *Label* = occurs in + * *Definition* = b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + * *Comment* = Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [occurs in](../../BFO/66/BFO_0000066.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [occurs in](../../BFO/66/BFO_0000066.md) InverseOf [contains process](../../BFO/67/BFO_0000067.md) + * [occurs in](../../BFO/66/BFO_0000066.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = occurs in + * *[definition](../../IAO/15/IAO_0000115.md)* = b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + * *[alternative term](../../IAO/18/IAO_0000118.md)* = occurs_in + * *[alternative term](../../IAO/18/IAO_0000118.md)* = unfolds in + * *[alternative term](../../IAO/18/IAO_0000118.md)* = unfolds_in + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + * *[rdf-schema#isDefinedBy](../../By/rdf-schema#isDefinedBy.md)* = http://purl.obolibrary.org/obo/bfo.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = occurs in + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [occurs in](../../BFO/66/BFO_0000066.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [occurs in](../../BFO/66/BFO_0000066.md) InverseOf [contains process](../../BFO/67/BFO_0000067.md) + * [occurs in](../../BFO/66/BFO_0000066.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + +## External Comments + diff --git a/src/ontology/md/BFO/67/BFO_0000067.md b/src/ontology/md/BFO/67/BFO_0000067.md new file mode 100644 index 00000000..537071fc --- /dev/null +++ b/src/ontology/md/BFO/67/BFO_0000067.md @@ -0,0 +1,42 @@ + +## Class : contains process + + * *IRI* = http://purl.obolibrary.org/obo/BFO_0000067 + * *Label* = contains process + * *Definition* = [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + * *Comment* = Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [occurs in](../../BFO/66/BFO_0000066.md) InverseOf [contains process](../../BFO/67/BFO_0000067.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = site of + * *[definition](../../IAO/15/IAO_0000115.md)* = [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 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + * *[rdf-schema#isDefinedBy](../../By/rdf-schema#isDefinedBy.md)* = http://purl.obolibrary.org/obo/bfo.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = contains process + +## Usage + + * - + * [occurs in](../../BFO/66/BFO_0000066.md) InverseOf [contains process](../../BFO/67/BFO_0000067.md) + +## External Comments + diff --git a/src/ontology/md/By/rdf-schema#isDefinedBy.md b/src/ontology/md/By/rdf-schema#isDefinedBy.md new file mode 100644 index 00000000..79b6588c --- /dev/null +++ b/src/ontology/md/By/rdf-schema#isDefinedBy.md @@ -0,0 +1,36 @@ + +## Class : null + + * *IRI* = http://www.w3.org/2000/01/rdf-schema#isDefinedBy + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = is defined by + +## Usage + + * http://purl.obolibrary.org/obo/BFO_0000054 [rdf-schema#isDefinedBy](../../By/rdf-schema#isDefinedBy.md) http://purl.obolibrary.org/obo/bfo.owl + * http://purl.obolibrary.org/obo/BFO_0000055 [rdf-schema#isDefinedBy](../../By/rdf-schema#isDefinedBy.md) http://purl.obolibrary.org/obo/iao.owl + * http://purl.obolibrary.org/obo/BFO_0000066 [rdf-schema#isDefinedBy](../../By/rdf-schema#isDefinedBy.md) http://purl.obolibrary.org/obo/bfo.owl + * http://purl.obolibrary.org/obo/BFO_0000067 [rdf-schema#isDefinedBy](../../By/rdf-schema#isDefinedBy.md) http://purl.obolibrary.org/obo/bfo.owl + +## External Comments + diff --git a/src/ontology/md/CARO/00/CARO_0001000.md b/src/ontology/md/CARO/00/CARO_0001000.md new file mode 100644 index 00000000..f4eca21b --- /dev/null +++ b/src/ontology/md/CARO/00/CARO_0001000.md @@ -0,0 +1,38 @@ + +## Class : multi-cell-part structure + + * *IRI* = http://purl.obolibrary.org/obo/CARO_0001000 + * *Label* = multi-cell-part structure + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [anatomical structure](../../CARO/03/CARO_0000003.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/caro.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = multi-cell-part structure + +## Usage + + * - + * [multi-cell-part structure](../../CARO/00/CARO_0001000.md) SubClassOf [anatomical structure](../../CARO/03/CARO_0000003.md) + * [neuron projection bundle](../../CARO/01/CARO_0001001.md) SubClassOf [multi-cell-part structure](../../CARO/00/CARO_0001000.md) + +## External Comments + diff --git a/src/ontology/md/CARO/00/CARO_0010000.md b/src/ontology/md/CARO/00/CARO_0010000.md new file mode 100644 index 00000000..f4096b74 --- /dev/null +++ b/src/ontology/md/CARO/00/CARO_0010000.md @@ -0,0 +1,41 @@ + +## Class : multicellular anatomical structure + + * *IRI* = http://purl.obolibrary.org/obo/CARO_0010000 + * *Label* = multicellular anatomical structure + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [anatomical structure](../../CARO/03/CARO_0000003.md) + +## Equivalencies + + +## Other Logical Axioms + + * [multicellular anatomical structure](../../CARO/00/CARO_0010000.md) SubClassOf [directly develops from](../../RO/07/RO_0002207.md) only [multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/caro.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = multicellular anatomical structure + +## Usage + + * - + * [directly develops from](../../RO/07/RO_0002207.md) Domain [cell](../../CL/00/CL_0000000.md)or[multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + * [directly develops from](../../RO/07/RO_0002207.md) Range [cell](../../CL/00/CL_0000000.md)or[multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + * [multicellular anatomical structure](../../CARO/00/CARO_0010000.md) SubClassOf [anatomical structure](../../CARO/03/CARO_0000003.md) + * [multicellular anatomical structure](../../CARO/00/CARO_0010000.md) SubClassOf [directly develops from](../../RO/07/RO_0002207.md) only [multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + +## External Comments + diff --git a/src/ontology/md/CARO/01/CARO_0001001.md b/src/ontology/md/CARO/01/CARO_0001001.md new file mode 100644 index 00000000..b0771453 --- /dev/null +++ b/src/ontology/md/CARO/01/CARO_0001001.md @@ -0,0 +1,40 @@ + +## Class : neuron projection bundle + + * *IRI* = http://purl.obolibrary.org/obo/CARO_0001001 + * *Label* = neuron projection bundle + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [multi-cell-part structure](../../CARO/00/CARO_0001000.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/caro.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = neuron projection bundle + +## Usage + + * - + * [fasciculates with](../../RO/01/RO_0002101.md) Range [neuron projection bundle](../../CARO/01/CARO_0001001.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) Domain [neuron projection bundle](../../CARO/01/CARO_0001001.md) + * [innervates](../../RO/34/RO_0002134.md) Domain [neuron projection bundle](../../CARO/01/CARO_0001001.md) + * [neuron projection bundle](../../CARO/01/CARO_0001001.md) SubClassOf [multi-cell-part structure](../../CARO/00/CARO_0001000.md) + +## External Comments + diff --git a/src/ontology/md/CARO/03/CARO_0000003.md b/src/ontology/md/CARO/03/CARO_0000003.md new file mode 100644 index 00000000..5cf60788 --- /dev/null +++ b/src/ontology/md/CARO/03/CARO_0000003.md @@ -0,0 +1,49 @@ + +## Class : anatomical structure + + * *IRI* = http://purl.obolibrary.org/obo/CARO_0000003 + * *Label* = anatomical structure + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [material anatomical entity](../../CARO/06/CARO_0000006.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/caro.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = anatomical structure + +## Usage + + * - + * [anatomical structure](../../CARO/03/CARO_0000003.md) SubClassOf [material anatomical entity](../../CARO/06/CARO_0000006.md) + * [cell part](../../CARO/14/CARO_0000014.md) SubClassOf [anatomical structure](../../CARO/03/CARO_0000003.md) + * [cell](../../CL/00/CL_0000000.md) SubClassOf [anatomical structure](../../CARO/03/CARO_0000003.md) + * [developmentally induced by](../../RO/56/RO_0002256.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [developmentally induced by](../../RO/56/RO_0002256.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [develops in](../../RO/26/RO_0002226.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [has developmental contribution from](../../RO/54/RO_0002254.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [has developmental contribution from](../../RO/54/RO_0002254.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [multi-cell-part structure](../../CARO/00/CARO_0001000.md) SubClassOf [anatomical structure](../../CARO/03/CARO_0000003.md) + * [multicellular anatomical structure](../../CARO/00/CARO_0010000.md) SubClassOf [anatomical structure](../../CARO/03/CARO_0000003.md) + * [results in developmental progression of](../../RO/95/RO_0002295.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [skeleton of](../../RO/76/RO_0002576.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [skeleton of](../../RO/76/RO_0002576.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + +## External Comments + diff --git a/src/ontology/md/CARO/06/CARO_0000006.md b/src/ontology/md/CARO/06/CARO_0000006.md new file mode 100644 index 00000000..2d83d4a0 --- /dev/null +++ b/src/ontology/md/CARO/06/CARO_0000006.md @@ -0,0 +1,40 @@ + +## Class : material anatomical entity + + * *IRI* = http://purl.obolibrary.org/obo/CARO_0000006 + * *Label* = material anatomical entity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [material entity](../../BFO/40/BFO_0000040.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/caro.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = material anatomical entity + +## Usage + + * - + * [anatomical structure](../../CARO/03/CARO_0000003.md) SubClassOf [material anatomical entity](../../CARO/06/CARO_0000006.md) + * [connected anatomical system](../../CARO/11/CARO_0000011.md) SubClassOf [material anatomical entity](../../CARO/06/CARO_0000006.md) + * [has habitat](../../RO/03/RO_0002303.md) Domain [material anatomical entity](../../CARO/06/CARO_0000006.md) + * [material anatomical entity](../../CARO/06/CARO_0000006.md) SubClassOf [material entity](../../BFO/40/BFO_0000040.md) + +## External Comments + diff --git a/src/ontology/md/CARO/07/CARO_0000007.md b/src/ontology/md/CARO/07/CARO_0000007.md new file mode 100644 index 00000000..77df695d --- /dev/null +++ b/src/ontology/md/CARO/07/CARO_0000007.md @@ -0,0 +1,36 @@ + +## Class : immaterial anatomical entity + + * *IRI* = http://purl.obolibrary.org/obo/CARO_0000007 + * *Label* = immaterial anatomical entity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [immaterial entity](../../BFO/41/BFO_0000141.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = immaterial anatomical entity + +## Usage + + * - + * [immaterial anatomical entity](../../CARO/07/CARO_0000007.md) SubClassOf [immaterial entity](../../BFO/41/BFO_0000141.md) + +## External Comments + diff --git a/src/ontology/md/CARO/11/CARO_0000011.md b/src/ontology/md/CARO/11/CARO_0000011.md new file mode 100644 index 00000000..77bd8639 --- /dev/null +++ b/src/ontology/md/CARO/11/CARO_0000011.md @@ -0,0 +1,38 @@ + +## Class : connected anatomical system + + * *IRI* = http://purl.obolibrary.org/obo/CARO_0000011 + * *Label* = connected anatomical system + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [material anatomical entity](../../CARO/06/CARO_0000006.md) + * [system](../../RO/77/RO_0002577.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = connected anatomical system + +## Usage + + * - + * [connected anatomical system](../../CARO/11/CARO_0000011.md) SubClassOf [material anatomical entity](../../CARO/06/CARO_0000006.md) + * [connected anatomical system](../../CARO/11/CARO_0000011.md) SubClassOf [system](../../RO/77/RO_0002577.md) + +## External Comments + diff --git a/src/ontology/md/CARO/14/CARO_0000014.md b/src/ontology/md/CARO/14/CARO_0000014.md new file mode 100644 index 00000000..b03ac81c --- /dev/null +++ b/src/ontology/md/CARO/14/CARO_0000014.md @@ -0,0 +1,41 @@ + +## Class : cell part + + * *IRI* = http://purl.obolibrary.org/obo/CARO_0000014 + * *Label* = cell part + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [anatomical structure](../../CARO/03/CARO_0000003.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/caro.owl + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = cell part (CARO) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = cell part + +## Usage + + * - + * [cell part](../../CARO/14/CARO_0000014.md) SubClassOf [anatomical structure](../../CARO/03/CARO_0000003.md) + * [cell part](../../GO/64/GO_0044464.md) SubClassOf [cell part](../../CARO/14/CARO_0000014.md) + * [synapse part](../../GO/56/GO_0044456.md) SubClassOf [cell part](../../CARO/14/CARO_0000014.md) + * [synapse](../../GO/02/GO_0045202.md) SubClassOf [cell part](../../CARO/14/CARO_0000014.md) + +## External Comments + diff --git a/src/ontology/md/CL/00/CL_0000000.md b/src/ontology/md/CL/00/CL_0000000.md new file mode 100644 index 00000000..71c52d7a --- /dev/null +++ b/src/ontology/md/CL/00/CL_0000000.md @@ -0,0 +1,47 @@ + +## Class : cell + + * *IRI* = http://purl.obolibrary.org/obo/CL_0000000 + * *Label* = cell + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [anatomical structure](../../CARO/03/CARO_0000003.md) + +## Equivalencies + + +## Other Logical Axioms + + * [cell](../../CL/00/CL_0000000.md) SubClassOf [directly develops from](../../RO/07/RO_0002207.md) only [cell](../../CL/00/CL_0000000.md) + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/cl.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = cell + +## Usage + + * - + * [cell expresses](../../RO/09/RO_0002009.md) Domain [cell](../../CL/00/CL_0000000.md) + * [cell](../../CL/00/CL_0000000.md) SubClassOf [anatomical structure](../../CARO/03/CARO_0000003.md) + * [cell](../../CL/00/CL_0000000.md) SubClassOf [directly develops from](../../RO/07/RO_0002207.md) only [cell](../../CL/00/CL_0000000.md) + * [directly develops from](../../RO/07/RO_0002207.md) Domain [cell](../../CL/00/CL_0000000.md)or[multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + * [directly develops from](../../RO/07/RO_0002207.md) Range [cell](../../CL/00/CL_0000000.md)or[multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + * [neuron](../../CL/40/CL_0000540.md) SubClassOf [cell](../../CL/00/CL_0000000.md) + * [results in acquisition of features of](../../RO/15/RO_0002315.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in commitment to](../../RO/48/RO_0002348.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in determination of](../../RO/49/RO_0002349.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in specification of](../../RO/56/RO_0002356.md) Range [cell](../../CL/00/CL_0000000.md) + +## External Comments + diff --git a/src/ontology/md/CL/40/CL_0000540.md b/src/ontology/md/CL/40/CL_0000540.md new file mode 100644 index 00000000..90daf589 --- /dev/null +++ b/src/ontology/md/CL/40/CL_0000540.md @@ -0,0 +1,47 @@ + +## Class : neuron + + * *IRI* = http://purl.obolibrary.org/obo/CL_0000540 + * *Label* = neuron + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [cell](../../CL/00/CL_0000000.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/cl.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = neuron + +## Usage + + * - + * [axon synapses in](../../RO/02/RO_0002102.md) Domain [neuron](../../CL/40/CL_0000540.md) + * [dendrite synapsed in](../../RO/21/RO_0002121.md) Domain [neuron](../../CL/40/CL_0000540.md) + * [fasciculates with](../../RO/01/RO_0002101.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) Range [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has presynaptic terminal in](../../RO/13/RO_0002113.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has soma location](../../RO/00/RO_0002100.md) Domain [neuron](../../CL/40/CL_0000540.md) + * [has synaptic terminal in](../../RO/30/RO_0002130.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [neuron](../../CL/40/CL_0000540.md) SubClassOf [cell](../../CL/00/CL_0000000.md) + * [synapsed by](../../RO/03/RO_0002103.md) Range [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [synapsed to](../../RO/20/RO_0002120.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + +## External Comments + diff --git a/src/ontology/md/ENVO/28/ENVO_00000428.md b/src/ontology/md/ENVO/28/ENVO_00000428.md new file mode 100644 index 00000000..1905b629 --- /dev/null +++ b/src/ontology/md/ENVO/28/ENVO_00000428.md @@ -0,0 +1,36 @@ + +## Class : biome + + * *IRI* = http://purl.obolibrary.org/obo/ENVO_00000428 + * *Label* = biome + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [environmental system](../../ENVO/54/ENVO_01000254.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = biome + +## Usage + + * - + * [biome](../../ENVO/28/ENVO_00000428.md) SubClassOf [environmental system](../../ENVO/54/ENVO_01000254.md) + +## External Comments + diff --git a/src/ontology/md/ENVO/36/ENVO_00002036.md b/src/ontology/md/ENVO/36/ENVO_00002036.md new file mode 100644 index 00000000..0749ce4b --- /dev/null +++ b/src/ontology/md/ENVO/36/ENVO_00002036.md @@ -0,0 +1,36 @@ + +## Class : habitat + + * *IRI* = http://purl.obolibrary.org/obo/ENVO_00002036 + * *Label* = habitat + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [environmental system](../../ENVO/54/ENVO_01000254.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = habitat + +## Usage + + * - + * [habitat](../../ENVO/36/ENVO_00002036.md) SubClassOf [environmental system](../../ENVO/54/ENVO_01000254.md) + +## External Comments + diff --git a/src/ontology/md/ENVO/54/ENVO_01000254.md b/src/ontology/md/ENVO/54/ENVO_01000254.md new file mode 100644 index 00000000..f1c56a51 --- /dev/null +++ b/src/ontology/md/ENVO/54/ENVO_01000254.md @@ -0,0 +1,39 @@ + +## Class : environmental system + + * *IRI* = http://purl.obolibrary.org/obo/ENVO_01000254 + * *Label* = environmental system + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [system](../../RO/77/RO_0002577.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = environmental system + +## Usage + + * - + * [biome](../../ENVO/28/ENVO_00000428.md) SubClassOf [environmental system](../../ENVO/54/ENVO_01000254.md) + * [environmental system](../../ENVO/54/ENVO_01000254.md) SubClassOf [system](../../RO/77/RO_0002577.md) + * [habitat](../../ENVO/36/ENVO_00002036.md) SubClassOf [environmental system](../../ENVO/54/ENVO_01000254.md) + * [has habitat](../../RO/03/RO_0002303.md) Range [environmental system](../../ENVO/54/ENVO_01000254.md) + +## External Comments + diff --git a/src/ontology/md/GO/01/GO_0016301.md b/src/ontology/md/GO/01/GO_0016301.md new file mode 100644 index 00000000..18e6b7ec --- /dev/null +++ b/src/ontology/md/GO/01/GO_0016301.md @@ -0,0 +1,38 @@ + +## Class : kinase activity + + * *IRI* = http://purl.obolibrary.org/obo/GO_0016301 + * *Label* = kinase activity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [transferase activity, transferring phosphorus-containing groups](../../GO/72/GO_0016772.md) + +## Equivalencies + + +## Other Logical Axioms + + * [kinase activity](../../GO/01/GO_0016301.md) SubClassOf ObjectHasSelf() + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = kinase activity + +## Usage + + * - + * [kinase activity](../../GO/01/GO_0016301.md) SubClassOf ObjectHasSelf() + * [kinase activity](../../GO/01/GO_0016301.md) SubClassOf [transferase activity, transferring phosphorus-containing groups](../../GO/72/GO_0016772.md) + +## External Comments + diff --git a/src/ontology/md/GO/02/GO_0045202.md b/src/ontology/md/GO/02/GO_0045202.md new file mode 100644 index 00000000..af655ff5 --- /dev/null +++ b/src/ontology/md/GO/02/GO_0045202.md @@ -0,0 +1,37 @@ + +## Class : synapse + + * *IRI* = http://purl.obolibrary.org/obo/GO_0045202 + * *Label* = synapse + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [cell part](../../CARO/14/CARO_0000014.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapse + +## Usage + + * - + * [synapse](../../GO/02/GO_0045202.md) SubClassOf [cell part](../../CARO/14/CARO_0000014.md) + +## External Comments + diff --git a/src/ontology/md/GO/02/GO_0051702.md b/src/ontology/md/GO/02/GO_0051702.md new file mode 100644 index 00000000..a20e7e52 --- /dev/null +++ b/src/ontology/md/GO/02/GO_0051702.md @@ -0,0 +1,37 @@ + +## Class : interaction with symbiont + + * *IRI* = http://purl.obolibrary.org/obo/GO_0051702 + * *Label* = interaction with symbiont + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [interspecies interaction between organisms](../../GO/19/GO_0044419.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = interaction with symbiont + +## Usage + + * - + * [acquisition of nutrients from symbiont](../../GO/50/GO_0051850.md) SubClassOf [interaction with symbiont](../../GO/02/GO_0051702.md) + * [interaction with symbiont](../../GO/02/GO_0051702.md) SubClassOf [interspecies interaction between organisms](../../GO/19/GO_0044419.md) + +## External Comments + diff --git a/src/ontology/md/GO/03/GO_0044403.md b/src/ontology/md/GO/03/GO_0044403.md new file mode 100644 index 00000000..eb2bc952 --- /dev/null +++ b/src/ontology/md/GO/03/GO_0044403.md @@ -0,0 +1,41 @@ + +## Class : symbiosis, encompassing mutualism through parasitism + + * *IRI* = http://purl.obolibrary.org/obo/GO_0044403 + * *Label* = symbiosis, encompassing mutualism through parasitism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [interspecies interaction between organisms](../../GO/19/GO_0044419.md) + +## Equivalencies + + +## Other Logical Axioms + + * [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) SubClassOf ObjectHasSelf() + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = symbiosis, encompassing mutualism through parasitism + +## Usage + + * - + * [commensalism](../../GO/31/GO_0085031.md) SubClassOf [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) + * [mutualism](../../GO/30/GO_0085030.md) SubClassOf [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) + * [parasitism](../../GO/19/GO_0072519.md) SubClassOf [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) + * [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) SubClassOf ObjectHasSelf() + * [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) SubClassOf [interspecies interaction between organisms](../../GO/19/GO_0044419.md) + +## External Comments + diff --git a/src/ontology/md/GO/04/GO_0051704.md b/src/ontology/md/GO/04/GO_0051704.md new file mode 100644 index 00000000..f594abd3 --- /dev/null +++ b/src/ontology/md/GO/04/GO_0051704.md @@ -0,0 +1,38 @@ + +## Class : multi-organism process + + * *IRI* = http://purl.obolibrary.org/obo/GO_0051704 + * *Label* = multi-organism process + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [biological_process](../../GO/50/GO_0008150.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = multi-organism process + +## Usage + + * - + * [interspecies interaction between organisms](../../GO/19/GO_0044419.md) SubClassOf [multi-organism process](../../GO/04/GO_0051704.md) + * [multi-organism behavior](../../GO/05/GO_0051705.md) SubClassOf [multi-organism process](../../GO/04/GO_0051704.md) + * [multi-organism process](../../GO/04/GO_0051704.md) SubClassOf [biological_process](../../GO/50/GO_0008150.md) + +## External Comments + diff --git a/src/ontology/md/GO/05/GO_0043005.md b/src/ontology/md/GO/05/GO_0043005.md new file mode 100644 index 00000000..fcfbf332 --- /dev/null +++ b/src/ontology/md/GO/05/GO_0043005.md @@ -0,0 +1,39 @@ + +## Class : neuron projection + + * *IRI* = http://purl.obolibrary.org/obo/GO_0043005 + * *Label* = neuron projection + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [cell projection](../../GO/95/GO_0042995.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = neuron projection + +## Usage + + * - + * [axon](../../GO/24/GO_0030424.md) SubClassOf [neuron projection](../../GO/05/GO_0043005.md) + * [dendrite](../../GO/25/GO_0030425.md) SubClassOf [neuron projection](../../GO/05/GO_0043005.md) + * [neuron projection](../../GO/05/GO_0043005.md) SubClassOf [cell projection](../../GO/95/GO_0042995.md) + +## External Comments + diff --git a/src/ontology/md/GO/05/GO_0051705.md b/src/ontology/md/GO/05/GO_0051705.md new file mode 100644 index 00000000..90f991a8 --- /dev/null +++ b/src/ontology/md/GO/05/GO_0051705.md @@ -0,0 +1,39 @@ + +## Class : multi-organism behavior + + * *IRI* = http://purl.obolibrary.org/obo/GO_0051705 + * *Label* = multi-organism behavior + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [behavior](../../GO/10/GO_0007610.md) + * [multi-organism process](../../GO/04/GO_0051704.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = multi-organism behavior + +## Usage + + * - + * [acquisition of nutrients from symbiont](../../GO/50/GO_0051850.md) SubClassOf [multi-organism behavior](../../GO/05/GO_0051705.md) + * [multi-organism behavior](../../GO/05/GO_0051705.md) SubClassOf [behavior](../../GO/10/GO_0007610.md) + * [multi-organism behavior](../../GO/05/GO_0051705.md) SubClassOf [multi-organism process](../../GO/04/GO_0051704.md) + +## External Comments + diff --git a/src/ontology/md/GO/10/GO_0007610.md b/src/ontology/md/GO/10/GO_0007610.md new file mode 100644 index 00000000..e523b09d --- /dev/null +++ b/src/ontology/md/GO/10/GO_0007610.md @@ -0,0 +1,38 @@ + +## Class : behavior + + * *IRI* = http://purl.obolibrary.org/obo/GO_0007610 + * *Label* = behavior + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [response to stimulus](../../GO/96/GO_0050896.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = behavior + +## Usage + + * - + * [behavior](../../GO/10/GO_0007610.md) SubClassOf [response to stimulus](../../GO/96/GO_0050896.md) + * [feeding behavior](../../GO/31/GO_0007631.md) SubClassOf [behavior](../../GO/10/GO_0007610.md) + * [multi-organism behavior](../../GO/05/GO_0051705.md) SubClassOf [behavior](../../GO/10/GO_0007610.md) + +## External Comments + diff --git a/src/ontology/md/GO/11/GO_0040011.md b/src/ontology/md/GO/11/GO_0040011.md new file mode 100644 index 00000000..3e507f4b --- /dev/null +++ b/src/ontology/md/GO/11/GO_0040011.md @@ -0,0 +1,33 @@ + +## Class : null + + * *IRI* = http://purl.obolibrary.org/obo/GO_0040011 + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * [results in movement of](../../RO/65/RO_0002565.md) Domain [GO_0040011](../../GO/11/GO_0040011.md) + +## External Comments + diff --git a/src/ontology/md/GO/11/GO_0045211.md b/src/ontology/md/GO/11/GO_0045211.md new file mode 100644 index 00000000..c6bfc881 --- /dev/null +++ b/src/ontology/md/GO/11/GO_0045211.md @@ -0,0 +1,39 @@ + +## Class : postsynaptic membrane + + * *IRI* = http://purl.obolibrary.org/obo/GO_0045211 + * *Label* = postsynaptic membrane + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [membrane](../../GO/20/GO_0016020.md) + * [synapse part](../../GO/56/GO_0044456.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = postsynaptic membrane + +## Usage + + * - + * [postsynaptic membrane](../../GO/11/GO_0045211.md) SubClassOf [membrane](../../GO/20/GO_0016020.md) + * [postsynaptic membrane](../../GO/11/GO_0045211.md) SubClassOf [synapse part](../../GO/56/GO_0044456.md) + +## External Comments + diff --git a/src/ontology/md/GO/16/GO_0051816.md b/src/ontology/md/GO/16/GO_0051816.md new file mode 100644 index 00000000..b974222b --- /dev/null +++ b/src/ontology/md/GO/16/GO_0051816.md @@ -0,0 +1,37 @@ + +## Class : acquisition of nutrients from other organism during symbiotic interaction + + * *IRI* = http://purl.obolibrary.org/obo/GO_0051816 + * *Label* = acquisition of nutrients from other organism during symbiotic interaction + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [feeding behavior](../../GO/31/GO_0007631.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = acquisition of nutrients from other organism during symbiotic interaction + +## Usage + + * - + * [acquisition of nutrients from other organism during symbiotic interaction](../../GO/16/GO_0051816.md) SubClassOf [feeding behavior](../../GO/31/GO_0007631.md) + * [acquisition of nutrients from symbiont](../../GO/50/GO_0051850.md) SubClassOf [acquisition of nutrients from other organism during symbiotic interaction](../../GO/16/GO_0051816.md) + +## External Comments + diff --git a/src/ontology/md/GO/19/GO_0044419.md b/src/ontology/md/GO/19/GO_0044419.md new file mode 100644 index 00000000..b6e5c682 --- /dev/null +++ b/src/ontology/md/GO/19/GO_0044419.md @@ -0,0 +1,38 @@ + +## Class : interspecies interaction between organisms + + * *IRI* = http://purl.obolibrary.org/obo/GO_0044419 + * *Label* = interspecies interaction between organisms + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [multi-organism process](../../GO/04/GO_0051704.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = interspecies interaction between organisms + +## Usage + + * - + * [interaction with symbiont](../../GO/02/GO_0051702.md) SubClassOf [interspecies interaction between organisms](../../GO/19/GO_0044419.md) + * [interspecies interaction between organisms](../../GO/19/GO_0044419.md) SubClassOf [multi-organism process](../../GO/04/GO_0051704.md) + * [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) SubClassOf [interspecies interaction between organisms](../../GO/19/GO_0044419.md) + +## External Comments + diff --git a/src/ontology/md/GO/19/GO_0072519.md b/src/ontology/md/GO/19/GO_0072519.md new file mode 100644 index 00000000..0ba729bf --- /dev/null +++ b/src/ontology/md/GO/19/GO_0072519.md @@ -0,0 +1,38 @@ + +## Class : parasitism + + * *IRI* = http://purl.obolibrary.org/obo/GO_0072519 + * *Label* = parasitism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) + +## Equivalencies + + +## Other Logical Axioms + + * [parasitism](../../GO/19/GO_0072519.md) SubClassOf ObjectHasSelf() + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = parasitism + +## Usage + + * - + * [parasitism](../../GO/19/GO_0072519.md) SubClassOf ObjectHasSelf() + * [parasitism](../../GO/19/GO_0072519.md) SubClassOf [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) + +## External Comments + diff --git a/src/ontology/md/GO/20/GO_0016020.md b/src/ontology/md/GO/20/GO_0016020.md new file mode 100644 index 00000000..0f9a6aa8 --- /dev/null +++ b/src/ontology/md/GO/20/GO_0016020.md @@ -0,0 +1,39 @@ + +## Class : membrane + + * *IRI* = http://purl.obolibrary.org/obo/GO_0016020 + * *Label* = membrane + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [cell part](../../GO/64/GO_0044464.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = membrane + +## Usage + + * - + * [membrane](../../GO/20/GO_0016020.md) SubClassOf [cell part](../../GO/64/GO_0044464.md) + * [postsynaptic membrane](../../GO/11/GO_0045211.md) SubClassOf [membrane](../../GO/20/GO_0016020.md) + * [presynaptic membrane](../../GO/34/GO_0042734.md) SubClassOf [membrane](../../GO/20/GO_0016020.md) + +## External Comments + diff --git a/src/ontology/md/GO/24/GO_0003824.md b/src/ontology/md/GO/24/GO_0003824.md new file mode 100644 index 00000000..6ca32e06 --- /dev/null +++ b/src/ontology/md/GO/24/GO_0003824.md @@ -0,0 +1,38 @@ + +## Class : catalytic activity + + * *IRI* = http://purl.obolibrary.org/obo/GO_0003824 + * *Label* = catalytic activity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [molecular_function](../../GO/74/GO_0003674.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = catalytic activity + +## Usage + + * - + * [catalytic activity](../../GO/24/GO_0003824.md) SubClassOf [molecular_function](../../GO/74/GO_0003674.md) + * [ligase activity](../../GO/74/GO_0016874.md) SubClassOf [catalytic activity](../../GO/24/GO_0003824.md) + * [transferase activity](../../GO/40/GO_0016740.md) SubClassOf [catalytic activity](../../GO/24/GO_0003824.md) + +## External Comments + diff --git a/src/ontology/md/GO/24/GO_0030424.md b/src/ontology/md/GO/24/GO_0030424.md new file mode 100644 index 00000000..8aa05af5 --- /dev/null +++ b/src/ontology/md/GO/24/GO_0030424.md @@ -0,0 +1,37 @@ + +## Class : axon + + * *IRI* = http://purl.obolibrary.org/obo/GO_0030424 + * *Label* = axon + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [neuron projection](../../GO/05/GO_0043005.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = axon + +## Usage + + * - + * [axon](../../GO/24/GO_0030424.md) SubClassOf [neuron projection](../../GO/05/GO_0043005.md) + +## External Comments + diff --git a/src/ontology/md/GO/25/GO_0030425.md b/src/ontology/md/GO/25/GO_0030425.md new file mode 100644 index 00000000..e9bd99c9 --- /dev/null +++ b/src/ontology/md/GO/25/GO_0030425.md @@ -0,0 +1,37 @@ + +## Class : dendrite + + * *IRI* = http://purl.obolibrary.org/obo/GO_0030425 + * *Label* = dendrite + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [neuron projection](../../GO/05/GO_0043005.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = dendrite + +## Usage + + * - + * [dendrite](../../GO/25/GO_0030425.md) SubClassOf [neuron projection](../../GO/05/GO_0043005.md) + +## External Comments + diff --git a/src/ontology/md/GO/30/GO_0085030.md b/src/ontology/md/GO/30/GO_0085030.md new file mode 100644 index 00000000..10f6ab0f --- /dev/null +++ b/src/ontology/md/GO/30/GO_0085030.md @@ -0,0 +1,38 @@ + +## Class : mutualism + + * *IRI* = http://purl.obolibrary.org/obo/GO_0085030 + * *Label* = mutualism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) + +## Equivalencies + + +## Other Logical Axioms + + * [mutualism](../../GO/30/GO_0085030.md) SubClassOf ObjectHasSelf() + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = mutualism + +## Usage + + * - + * [mutualism](../../GO/30/GO_0085030.md) SubClassOf ObjectHasSelf() + * [mutualism](../../GO/30/GO_0085030.md) SubClassOf [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) + +## External Comments + diff --git a/src/ontology/md/GO/31/GO_0007631.md b/src/ontology/md/GO/31/GO_0007631.md new file mode 100644 index 00000000..6379c559 --- /dev/null +++ b/src/ontology/md/GO/31/GO_0007631.md @@ -0,0 +1,37 @@ + +## Class : feeding behavior + + * *IRI* = http://purl.obolibrary.org/obo/GO_0007631 + * *Label* = feeding behavior + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [behavior](../../GO/10/GO_0007610.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = feeding behavior + +## Usage + + * - + * [acquisition of nutrients from other organism during symbiotic interaction](../../GO/16/GO_0051816.md) SubClassOf [feeding behavior](../../GO/31/GO_0007631.md) + * [feeding behavior](../../GO/31/GO_0007631.md) SubClassOf [behavior](../../GO/10/GO_0007610.md) + +## External Comments + diff --git a/src/ontology/md/GO/31/GO_0085031.md b/src/ontology/md/GO/31/GO_0085031.md new file mode 100644 index 00000000..85300bf7 --- /dev/null +++ b/src/ontology/md/GO/31/GO_0085031.md @@ -0,0 +1,38 @@ + +## Class : commensalism + + * *IRI* = http://purl.obolibrary.org/obo/GO_0085031 + * *Label* = commensalism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) + +## Equivalencies + + +## Other Logical Axioms + + * [commensalism](../../GO/31/GO_0085031.md) SubClassOf ObjectHasSelf() + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = commensalism + +## Usage + + * - + * [commensalism](../../GO/31/GO_0085031.md) SubClassOf ObjectHasSelf() + * [commensalism](../../GO/31/GO_0085031.md) SubClassOf [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) + +## External Comments + diff --git a/src/ontology/md/GO/34/GO_0005634.md b/src/ontology/md/GO/34/GO_0005634.md new file mode 100644 index 00000000..43cd04f4 --- /dev/null +++ b/src/ontology/md/GO/34/GO_0005634.md @@ -0,0 +1,39 @@ + +## Class : nucleus + + * *IRI* = http://purl.obolibrary.org/obo/GO_0005634 + * *Label* = nucleus + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [cell part](../../GO/64/GO_0044464.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = nucleus + +## Usage + + * - + * [child nucleus of](../../RO/76/RO_0002476.md) Domain [nucleus](../../GO/34/GO_0005634.md) + * [child nucleus of](../../RO/76/RO_0002476.md) Range [nucleus](../../GO/34/GO_0005634.md) + * [nucleus](../../GO/34/GO_0005634.md) SubClassOf [cell part](../../GO/64/GO_0044464.md) + +## External Comments + diff --git a/src/ontology/md/GO/34/GO_0042734.md b/src/ontology/md/GO/34/GO_0042734.md new file mode 100644 index 00000000..b6bdbee8 --- /dev/null +++ b/src/ontology/md/GO/34/GO_0042734.md @@ -0,0 +1,39 @@ + +## Class : presynaptic membrane + + * *IRI* = http://purl.obolibrary.org/obo/GO_0042734 + * *Label* = presynaptic membrane + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [membrane](../../GO/20/GO_0016020.md) + * [synapse part](../../GO/56/GO_0044456.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = presynaptic membrane + +## Usage + + * - + * [presynaptic membrane](../../GO/34/GO_0042734.md) SubClassOf [membrane](../../GO/20/GO_0016020.md) + * [presynaptic membrane](../../GO/34/GO_0042734.md) SubClassOf [synapse part](../../GO/56/GO_0044456.md) + +## External Comments + diff --git a/src/ontology/md/GO/40/GO_0016740.md b/src/ontology/md/GO/40/GO_0016740.md new file mode 100644 index 00000000..58506109 --- /dev/null +++ b/src/ontology/md/GO/40/GO_0016740.md @@ -0,0 +1,37 @@ + +## Class : transferase activity + + * *IRI* = http://purl.obolibrary.org/obo/GO_0016740 + * *Label* = transferase activity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [catalytic activity](../../GO/24/GO_0003824.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = transferase activity + +## Usage + + * - + * [transferase activity, transferring phosphorus-containing groups](../../GO/72/GO_0016772.md) SubClassOf [transferase activity](../../GO/40/GO_0016740.md) + * [transferase activity](../../GO/40/GO_0016740.md) SubClassOf [catalytic activity](../../GO/24/GO_0003824.md) + +## External Comments + diff --git a/src/ontology/md/GO/42/GO_0004842.md b/src/ontology/md/GO/42/GO_0004842.md new file mode 100644 index 00000000..4295d92b --- /dev/null +++ b/src/ontology/md/GO/42/GO_0004842.md @@ -0,0 +1,38 @@ + +## Class : ubiquitin-protein ligase activity + + * *IRI* = http://purl.obolibrary.org/obo/GO_0004842 + * *Label* = ubiquitin-protein ligase activity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [small conjugating protein ligase activity](../../GO/87/GO_0019787.md) + +## Equivalencies + + +## Other Logical Axioms + + * [ubiquitin-protein ligase activity](../../GO/42/GO_0004842.md) SubClassOf ObjectHasSelf() + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ubiquitin-protein ligase activity + +## Usage + + * - + * [ubiquitin-protein ligase activity](../../GO/42/GO_0004842.md) SubClassOf ObjectHasSelf() + * [ubiquitin-protein ligase activity](../../GO/42/GO_0004842.md) SubClassOf [small conjugating protein ligase activity](../../GO/87/GO_0019787.md) + +## External Comments + diff --git a/src/ontology/md/GO/50/GO_0008150.md b/src/ontology/md/GO/50/GO_0008150.md new file mode 100644 index 00000000..4969e8a4 --- /dev/null +++ b/src/ontology/md/GO/50/GO_0008150.md @@ -0,0 +1,39 @@ + +## Class : biological_process + + * *IRI* = http://purl.obolibrary.org/obo/GO_0008150 + * *Label* = biological_process + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [process](../../BFO/15/BFO_0000015.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = biological_process + +## Usage + + * - + * [biological_process](../../GO/50/GO_0008150.md) SubClassOf [process](../../BFO/15/BFO_0000015.md) + * [multi-organism process](../../GO/04/GO_0051704.md) SubClassOf [biological_process](../../GO/50/GO_0008150.md) + * [response to stimulus](../../GO/96/GO_0050896.md) SubClassOf [biological_process](../../GO/50/GO_0008150.md) + * [results in developmental progression of](../../RO/95/RO_0002295.md) Domain [biological_process](../../GO/50/GO_0008150.md) + +## External Comments + diff --git a/src/ontology/md/GO/50/GO_0051850.md b/src/ontology/md/GO/50/GO_0051850.md new file mode 100644 index 00000000..a6dbefc7 --- /dev/null +++ b/src/ontology/md/GO/50/GO_0051850.md @@ -0,0 +1,40 @@ + +## Class : acquisition of nutrients from symbiont + + * *IRI* = http://purl.obolibrary.org/obo/GO_0051850 + * *Label* = acquisition of nutrients from symbiont + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [interaction with symbiont](../../GO/02/GO_0051702.md) + * [multi-organism behavior](../../GO/05/GO_0051705.md) + * [acquisition of nutrients from other organism during symbiotic interaction](../../GO/16/GO_0051816.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = acquisition of nutrients from symbiont + +## Usage + + * - + * [acquisition of nutrients from symbiont](../../GO/50/GO_0051850.md) SubClassOf [acquisition of nutrients from other organism during symbiotic interaction](../../GO/16/GO_0051816.md) + * [acquisition of nutrients from symbiont](../../GO/50/GO_0051850.md) SubClassOf [interaction with symbiont](../../GO/02/GO_0051702.md) + * [acquisition of nutrients from symbiont](../../GO/50/GO_0051850.md) SubClassOf [multi-organism behavior](../../GO/05/GO_0051705.md) + +## External Comments + diff --git a/src/ontology/md/GO/56/GO_0044456.md b/src/ontology/md/GO/56/GO_0044456.md new file mode 100644 index 00000000..2be0ce76 --- /dev/null +++ b/src/ontology/md/GO/56/GO_0044456.md @@ -0,0 +1,39 @@ + +## Class : synapse part + + * *IRI* = http://purl.obolibrary.org/obo/GO_0044456 + * *Label* = synapse part + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [cell part](../../CARO/14/CARO_0000014.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapse part + +## Usage + + * - + * [postsynaptic membrane](../../GO/11/GO_0045211.md) SubClassOf [synapse part](../../GO/56/GO_0044456.md) + * [presynaptic membrane](../../GO/34/GO_0042734.md) SubClassOf [synapse part](../../GO/56/GO_0044456.md) + * [synapse part](../../GO/56/GO_0044456.md) SubClassOf [cell part](../../CARO/14/CARO_0000014.md) + +## External Comments + diff --git a/src/ontology/md/GO/64/GO_0044464.md b/src/ontology/md/GO/64/GO_0044464.md new file mode 100644 index 00000000..ecca964e --- /dev/null +++ b/src/ontology/md/GO/64/GO_0044464.md @@ -0,0 +1,40 @@ + +## Class : cell part + + * *IRI* = http://purl.obolibrary.org/obo/GO_0044464 + * *Label* = cell part + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [cell part](../../CARO/14/CARO_0000014.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = cell part + +## Usage + + * - + * [cell part](../../GO/64/GO_0044464.md) SubClassOf [cell part](../../CARO/14/CARO_0000014.md) + * [cell projection](../../GO/95/GO_0042995.md) SubClassOf [cell part](../../GO/64/GO_0044464.md) + * [membrane](../../GO/20/GO_0016020.md) SubClassOf [cell part](../../GO/64/GO_0044464.md) + * [nucleus](../../GO/34/GO_0005634.md) SubClassOf [cell part](../../GO/64/GO_0044464.md) + +## External Comments + diff --git a/src/ontology/md/GO/72/GO_0016772.md b/src/ontology/md/GO/72/GO_0016772.md new file mode 100644 index 00000000..016c9f24 --- /dev/null +++ b/src/ontology/md/GO/72/GO_0016772.md @@ -0,0 +1,37 @@ + +## Class : transferase activity, transferring phosphorus-containing groups + + * *IRI* = http://purl.obolibrary.org/obo/GO_0016772 + * *Label* = transferase activity, transferring phosphorus-containing groups + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [transferase activity](../../GO/40/GO_0016740.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = transferase activity, transferring phosphorus-containing groups + +## Usage + + * - + * [kinase activity](../../GO/01/GO_0016301.md) SubClassOf [transferase activity, transferring phosphorus-containing groups](../../GO/72/GO_0016772.md) + * [transferase activity, transferring phosphorus-containing groups](../../GO/72/GO_0016772.md) SubClassOf [transferase activity](../../GO/40/GO_0016740.md) + +## External Comments + diff --git a/src/ontology/md/GO/74/GO_0003674.md b/src/ontology/md/GO/74/GO_0003674.md new file mode 100644 index 00000000..8b06b242 --- /dev/null +++ b/src/ontology/md/GO/74/GO_0003674.md @@ -0,0 +1,38 @@ + +## Class : molecular_function + + * *IRI* = http://purl.obolibrary.org/obo/GO_0003674 + * *Label* = molecular_function + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [process](../../BFO/15/BFO_0000015.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = molecular process + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = molecular_function + +## Usage + + * - + * [catalytic activity](../../GO/24/GO_0003824.md) SubClassOf [molecular_function](../../GO/74/GO_0003674.md) + * [molecular_function](../../GO/74/GO_0003674.md) SubClassOf [process](../../BFO/15/BFO_0000015.md) + +## External Comments + diff --git a/src/ontology/md/GO/74/GO_0016874.md b/src/ontology/md/GO/74/GO_0016874.md new file mode 100644 index 00000000..3de7e600 --- /dev/null +++ b/src/ontology/md/GO/74/GO_0016874.md @@ -0,0 +1,37 @@ + +## Class : ligase activity + + * *IRI* = http://purl.obolibrary.org/obo/GO_0016874 + * *Label* = ligase activity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [catalytic activity](../../GO/24/GO_0003824.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ligase activity + +## Usage + + * - + * [ligase activity, forming carbon-nitrogen bonds](../../GO/79/GO_0016879.md) SubClassOf [ligase activity](../../GO/74/GO_0016874.md) + * [ligase activity](../../GO/74/GO_0016874.md) SubClassOf [catalytic activity](../../GO/24/GO_0003824.md) + +## External Comments + diff --git a/src/ontology/md/GO/79/GO_0016879.md b/src/ontology/md/GO/79/GO_0016879.md new file mode 100644 index 00000000..509c9271 --- /dev/null +++ b/src/ontology/md/GO/79/GO_0016879.md @@ -0,0 +1,37 @@ + +## Class : ligase activity, forming carbon-nitrogen bonds + + * *IRI* = http://purl.obolibrary.org/obo/GO_0016879 + * *Label* = ligase activity, forming carbon-nitrogen bonds + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [ligase activity](../../GO/74/GO_0016874.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ligase activity, forming carbon-nitrogen bonds + +## Usage + + * - + * [acid-amino acid ligase activity](../../GO/81/GO_0016881.md) SubClassOf [ligase activity, forming carbon-nitrogen bonds](../../GO/79/GO_0016879.md) + * [ligase activity, forming carbon-nitrogen bonds](../../GO/79/GO_0016879.md) SubClassOf [ligase activity](../../GO/74/GO_0016874.md) + +## External Comments + diff --git a/src/ontology/md/GO/81/GO_0016881.md b/src/ontology/md/GO/81/GO_0016881.md new file mode 100644 index 00000000..4577ddc7 --- /dev/null +++ b/src/ontology/md/GO/81/GO_0016881.md @@ -0,0 +1,37 @@ + +## Class : acid-amino acid ligase activity + + * *IRI* = http://purl.obolibrary.org/obo/GO_0016881 + * *Label* = acid-amino acid ligase activity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [ligase activity, forming carbon-nitrogen bonds](../../GO/79/GO_0016879.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = acid-amino acid ligase activity + +## Usage + + * - + * [acid-amino acid ligase activity](../../GO/81/GO_0016881.md) SubClassOf [ligase activity, forming carbon-nitrogen bonds](../../GO/79/GO_0016879.md) + * [small conjugating protein ligase activity](../../GO/87/GO_0019787.md) SubClassOf [acid-amino acid ligase activity](../../GO/81/GO_0016881.md) + +## External Comments + diff --git a/src/ontology/md/GO/87/GO_0019787.md b/src/ontology/md/GO/87/GO_0019787.md new file mode 100644 index 00000000..2bd07170 --- /dev/null +++ b/src/ontology/md/GO/87/GO_0019787.md @@ -0,0 +1,37 @@ + +## Class : small conjugating protein ligase activity + + * *IRI* = http://purl.obolibrary.org/obo/GO_0019787 + * *Label* = small conjugating protein ligase activity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [acid-amino acid ligase activity](../../GO/81/GO_0016881.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = small conjugating protein ligase activity + +## Usage + + * - + * [small conjugating protein ligase activity](../../GO/87/GO_0019787.md) SubClassOf [acid-amino acid ligase activity](../../GO/81/GO_0016881.md) + * [ubiquitin-protein ligase activity](../../GO/42/GO_0004842.md) SubClassOf [small conjugating protein ligase activity](../../GO/87/GO_0019787.md) + +## External Comments + diff --git a/src/ontology/md/GO/95/GO_0042995.md b/src/ontology/md/GO/95/GO_0042995.md new file mode 100644 index 00000000..de1f67d3 --- /dev/null +++ b/src/ontology/md/GO/95/GO_0042995.md @@ -0,0 +1,38 @@ + +## Class : cell projection + + * *IRI* = http://purl.obolibrary.org/obo/GO_0042995 + * *Label* = cell projection + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [cell part](../../GO/64/GO_0044464.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[imported from](../../IAO/12/IAO_0000412.md)* = http://purl.obolibrary.org/obo/go.owl + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = cell projection + +## Usage + + * - + * [cell projection](../../GO/95/GO_0042995.md) SubClassOf [cell part](../../GO/64/GO_0044464.md) + * [neuron projection](../../GO/05/GO_0043005.md) SubClassOf [cell projection](../../GO/95/GO_0042995.md) + +## External Comments + diff --git a/src/ontology/md/GO/96/GO_0050896.md b/src/ontology/md/GO/96/GO_0050896.md new file mode 100644 index 00000000..6b9936e0 --- /dev/null +++ b/src/ontology/md/GO/96/GO_0050896.md @@ -0,0 +1,37 @@ + +## Class : response to stimulus + + * *IRI* = http://purl.obolibrary.org/obo/GO_0050896 + * *Label* = response to stimulus + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [biological_process](../../GO/50/GO_0008150.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = response to stimulus + +## Usage + + * - + * [behavior](../../GO/10/GO_0007610.md) SubClassOf [response to stimulus](../../GO/96/GO_0050896.md) + * [response to stimulus](../../GO/96/GO_0050896.md) SubClassOf [biological_process](../../GO/50/GO_0008150.md) + +## External Comments + diff --git a/src/ontology/md/IAO/00/IAO_0000600.md b/src/ontology/md/IAO/00/IAO_0000600.md new file mode 100644 index 00000000..e967b643 --- /dev/null +++ b/src/ontology/md/IAO/00/IAO_0000600.md @@ -0,0 +1,37 @@ + +## Class : elucidation + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000600 + * *Label* = elucidation + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = elucidation + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000054 [elucidation](../../IAO/00/IAO_0000600.md) [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]) + * http://purl.obolibrary.org/obo/BFO_0000055 [elucidation](../../IAO/00/IAO_0000600.md) 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]) + * http://purl.obolibrary.org/obo/RO_0002211 [elucidation](../../IAO/00/IAO_0000600.md) false + +## External Comments + diff --git a/src/ontology/md/IAO/11/IAO_0000111.md b/src/ontology/md/IAO/11/IAO_0000111.md new file mode 100644 index 00000000..42a8c4ab --- /dev/null +++ b/src/ontology/md/IAO/11/IAO_0000111.md @@ -0,0 +1,50 @@ + +## Class : editor preferred term + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000111 + * *Label* = editor preferred term + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = editor preferred term + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000050 [editor preferred term](../../IAO/11/IAO_0000111.md) is part of + * http://purl.obolibrary.org/obo/BFO_0000051 [editor preferred term](../../IAO/11/IAO_0000111.md) has part + * http://purl.obolibrary.org/obo/BFO_0000054 [editor preferred term](../../IAO/11/IAO_0000111.md) realized in + * http://purl.obolibrary.org/obo/BFO_0000055 [editor preferred term](../../IAO/11/IAO_0000111.md) realizes + * http://purl.obolibrary.org/obo/BFO_0000062 [editor preferred term](../../IAO/11/IAO_0000111.md) preceded by + * http://purl.obolibrary.org/obo/BFO_0000063 [editor preferred term](../../IAO/11/IAO_0000111.md) precedes + * http://purl.obolibrary.org/obo/BFO_0000066 [editor preferred term](../../IAO/11/IAO_0000111.md) occurs in + * http://purl.obolibrary.org/obo/BFO_0000067 [editor preferred term](../../IAO/11/IAO_0000111.md) site of + * http://purl.obolibrary.org/obo/RO_0000052 [editor preferred term](../../IAO/11/IAO_0000111.md) inheres in + * http://purl.obolibrary.org/obo/RO_0000053 [editor preferred term](../../IAO/11/IAO_0000111.md) bearer of + * http://purl.obolibrary.org/obo/RO_0000056 [editor preferred term](../../IAO/11/IAO_0000111.md) participates in + * http://purl.obolibrary.org/obo/RO_0000057 [editor preferred term](../../IAO/11/IAO_0000111.md) has participant + * http://purl.obolibrary.org/obo/RO_0001015 [editor preferred term](../../IAO/11/IAO_0000111.md) is location of + * http://purl.obolibrary.org/obo/RO_0001018 [editor preferred term](../../IAO/11/IAO_0000111.md) contained in + * http://purl.obolibrary.org/obo/RO_0001019 [editor preferred term](../../IAO/11/IAO_0000111.md) contains + * http://purl.obolibrary.org/obo/RO_0001025 [editor preferred term](../../IAO/11/IAO_0000111.md) located in + +## External Comments + diff --git a/src/ontology/md/IAO/12/IAO_0000112.md b/src/ontology/md/IAO/12/IAO_0000112.md new file mode 100644 index 00000000..d16ad926 --- /dev/null +++ b/src/ontology/md/IAO/12/IAO_0000112.md @@ -0,0 +1,152 @@ + +## Class : example of usage + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000112 + * *Label* = example of usage + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000122 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = example of usage + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000050 [example of usage](../../IAO/12/IAO_0000112.md) my brain is part of my body (continuant parthood, two material entities) + * http://purl.obolibrary.org/obo/BFO_0000050 [example of usage](../../IAO/12/IAO_0000112.md) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + * http://purl.obolibrary.org/obo/BFO_0000050 [example of usage](../../IAO/12/IAO_0000112.md) this day is part of this year (occurrent parthood) + * http://purl.obolibrary.org/obo/BFO_0000051 [example of usage](../../IAO/12/IAO_0000112.md) my body has part my brain (continuant parthood, two material entities) + * http://purl.obolibrary.org/obo/BFO_0000051 [example of usage](../../IAO/12/IAO_0000112.md) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + * http://purl.obolibrary.org/obo/BFO_0000051 [example of usage](../../IAO/12/IAO_0000112.md) this year has part this day (occurrent parthood) + * http://purl.obolibrary.org/obo/BFO_0000054 [example of usage](../../IAO/12/IAO_0000112.md) this disease is realized in this disease course + * http://purl.obolibrary.org/obo/BFO_0000054 [example of usage](../../IAO/12/IAO_0000112.md) this fragility is realized in this shattering + * http://purl.obolibrary.org/obo/BFO_0000054 [example of usage](../../IAO/12/IAO_0000112.md) this investigator role is realized in this investigation + * http://purl.obolibrary.org/obo/BFO_0000055 [example of usage](../../IAO/12/IAO_0000112.md) this disease course realizes this disease + * http://purl.obolibrary.org/obo/BFO_0000055 [example of usage](../../IAO/12/IAO_0000112.md) this investigation realizes this investigator role + * http://purl.obolibrary.org/obo/BFO_0000055 [example of usage](../../IAO/12/IAO_0000112.md) this shattering realizes this fragility + * http://purl.obolibrary.org/obo/RO_0000052 [example of usage](../../IAO/12/IAO_0000112.md) this fragility inheres in this vase + * http://purl.obolibrary.org/obo/RO_0000052 [example of usage](../../IAO/12/IAO_0000112.md) this red color inheres in this apple + * http://purl.obolibrary.org/obo/RO_0000053 [example of usage](../../IAO/12/IAO_0000112.md) this apple is bearer of this red color + * http://purl.obolibrary.org/obo/RO_0000053 [example of usage](../../IAO/12/IAO_0000112.md) this vase is bearer of this fragility + * http://purl.obolibrary.org/obo/RO_0000056 [example of usage](../../IAO/12/IAO_0000112.md) this blood clot participates in this blood coagulation + * http://purl.obolibrary.org/obo/RO_0000056 [example of usage](../../IAO/12/IAO_0000112.md) this input material (or this output material) participates in this process + * http://purl.obolibrary.org/obo/RO_0000056 [example of usage](../../IAO/12/IAO_0000112.md) this investigator participates in this investigation + * http://purl.obolibrary.org/obo/RO_0000057 [example of usage](../../IAO/12/IAO_0000112.md) this blood coagulation has participant this blood clot + * http://purl.obolibrary.org/obo/RO_0000057 [example of usage](../../IAO/12/IAO_0000112.md) this investigation has participant this investigator + * http://purl.obolibrary.org/obo/RO_0000057 [example of usage](../../IAO/12/IAO_0000112.md) this process has participant this input material (or this output material) + * http://purl.obolibrary.org/obo/RO_0000058 [example of usage](../../IAO/12/IAO_0000112.md) 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). + * http://purl.obolibrary.org/obo/RO_0000058 [example of usage](../../IAO/12/IAO_0000112.md) 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). + * http://purl.obolibrary.org/obo/RO_0000059 [example of usage](../../IAO/12/IAO_0000112.md) 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). + * http://purl.obolibrary.org/obo/RO_0000059 [example of usage](../../IAO/12/IAO_0000112.md) 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). + * http://purl.obolibrary.org/obo/RO_0000079 [example of usage](../../IAO/12/IAO_0000112.md) this catalysis function is a function of this enzyme + * http://purl.obolibrary.org/obo/RO_0000080 [example of usage](../../IAO/12/IAO_0000112.md) this red color is a quality of this apple + * http://purl.obolibrary.org/obo/RO_0000081 [example of usage](../../IAO/12/IAO_0000112.md) this investigator role is a role of this person + * http://purl.obolibrary.org/obo/RO_0000085 [example of usage](../../IAO/12/IAO_0000112.md) this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + * http://purl.obolibrary.org/obo/RO_0000086 [example of usage](../../IAO/12/IAO_0000112.md) this apple has quality this red color + * http://purl.obolibrary.org/obo/RO_0000087 [example of usage](../../IAO/12/IAO_0000112.md) this person has role this investigator role (more colloquially: this person has this role of investigator) + * http://purl.obolibrary.org/obo/RO_0001000 [example of usage](../../IAO/12/IAO_0000112.md) this cell derives from this parent cell (cell division) + * http://purl.obolibrary.org/obo/RO_0001000 [example of usage](../../IAO/12/IAO_0000112.md) this nucleus derives from this parent nucleus (nuclear division) + * http://purl.obolibrary.org/obo/RO_0001001 [example of usage](../../IAO/12/IAO_0000112.md) this parent cell derives into this cell (cell division) + * http://purl.obolibrary.org/obo/RO_0001001 [example of usage](../../IAO/12/IAO_0000112.md) this parent nucleus derives into this nucleus (nuclear division) + * http://purl.obolibrary.org/obo/RO_0001015 [example of usage](../../IAO/12/IAO_0000112.md) my head is the location of my brain + * http://purl.obolibrary.org/obo/RO_0001015 [example of usage](../../IAO/12/IAO_0000112.md) this cage is the location of this rat + * http://purl.obolibrary.org/obo/RO_0001025 [example of usage](../../IAO/12/IAO_0000112.md) my brain is located in my head + * http://purl.obolibrary.org/obo/RO_0001025 [example of usage](../../IAO/12/IAO_0000112.md) this rat is located in this cage + * http://purl.obolibrary.org/obo/RO_0002000 [example of usage](../../IAO/12/IAO_0000112.md) the surface of my skin is a 2D boundary of my body + * http://purl.obolibrary.org/obo/RO_0002002 [example of usage](../../IAO/12/IAO_0000112.md) my body has 2D boundary the surface of my skin + * http://purl.obolibrary.org/obo/RO_0002104 [example of usage](../../IAO/12/IAO_0000112.md) Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] + * http://purl.obolibrary.org/obo/RO_0002160 [example of usage](../../IAO/12/IAO_0000112.md) lactation SubClassOf 'only in taxon' some 'Mammalia' + * http://purl.obolibrary.org/obo/RO_0002161 [example of usage](../../IAO/12/IAO_0000112.md) tooth SubClassOf 'never in taxon' value 'Aves' + * http://purl.obolibrary.org/obo/RO_0002170 [example of usage](../../IAO/12/IAO_0000112.md) a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + * http://purl.obolibrary.org/obo/RO_0002176 [example of usage](../../IAO/12/IAO_0000112.md) The M8 connects Glasgow and Edinburgh + * http://purl.obolibrary.org/obo/RO_0002176 [example of usage](../../IAO/12/IAO_0000112.md) a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + * http://purl.obolibrary.org/obo/RO_0002205 [example of usage](../../IAO/12/IAO_0000112.md) every HOTAIR lncRNA is the gene product of some HOXC gene + * http://purl.obolibrary.org/obo/RO_0002205 [example of usage](../../IAO/12/IAO_0000112.md) every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene + * http://purl.obolibrary.org/obo/RO_0002206 [example of usage](../../IAO/12/IAO_0000112.md) 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' + * http://purl.obolibrary.org/obo/RO_0002214 [example of usage](../../IAO/12/IAO_0000112.md) 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) + * http://purl.obolibrary.org/obo/RO_0002214 [example of usage](../../IAO/12/IAO_0000112.md) heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') + * http://purl.obolibrary.org/obo/RO_0002215 [example of usage](../../IAO/12/IAO_0000112.md) mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + * http://purl.obolibrary.org/obo/RO_0002215 [example of usage](../../IAO/12/IAO_0000112.md) osteoclast SubClassOf 'capable of' some 'bone resorption' + * http://purl.obolibrary.org/obo/RO_0002218 [example of usage](../../IAO/12/IAO_0000112.md) 'heart development' has active participant some Shh protein + * http://purl.obolibrary.org/obo/RO_0002224 [example of usage](../../IAO/12/IAO_0000112.md) Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + * http://purl.obolibrary.org/obo/RO_0002254 [example of usage](../../IAO/12/IAO_0000112.md) Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] + * http://purl.obolibrary.org/obo/RO_0002287 [example of usage](../../IAO/12/IAO_0000112.md) 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue + * http://purl.obolibrary.org/obo/RO_0002296 [example of usage](../../IAO/12/IAO_0000112.md) every flower development (GO:0009908) results in development of some flower (PO:0009046) + * http://purl.obolibrary.org/obo/RO_0002297 [example of usage](../../IAO/12/IAO_0000112.md) an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. + * http://purl.obolibrary.org/obo/RO_0002297 [example of usage](../../IAO/12/IAO_0000112.md) every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + * http://purl.obolibrary.org/obo/RO_0002298 [example of usage](../../IAO/12/IAO_0000112.md) an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. + * http://purl.obolibrary.org/obo/RO_0002298 [example of usage](../../IAO/12/IAO_0000112.md) tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) + * http://purl.obolibrary.org/obo/RO_0002299 [example of usage](../../IAO/12/IAO_0000112.md) an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process + * http://purl.obolibrary.org/obo/RO_0002299 [example of usage](../../IAO/12/IAO_0000112.md) bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) + * http://purl.obolibrary.org/obo/RO_0002300 [example of usage](../../IAO/12/IAO_0000112.md) foramen ovale closure SubClassOf results in disappearance of foramen ovale + * http://purl.obolibrary.org/obo/RO_0002301 [example of usage](../../IAO/12/IAO_0000112.md) every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) + * http://purl.obolibrary.org/obo/RO_0002303 [example of usage](../../IAO/12/IAO_0000112.md) Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'marine environment' (ENVO_00000569) -- http://eol.org/pages/1795/overview + * http://purl.obolibrary.org/obo/RO_0002315 [example of usage](../../IAO/12/IAO_0000112.md) an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + * http://purl.obolibrary.org/obo/RO_0002325 [example of usage](../../IAO/12/IAO_0000112.md) Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) + * http://purl.obolibrary.org/obo/RO_0002326 [example of usage](../../IAO/12/IAO_0000112.md) ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. + * http://purl.obolibrary.org/obo/RO_0002326 [example of usage](../../IAO/12/IAO_0000112.md) Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. + * http://purl.obolibrary.org/obo/RO_0002326 [example of usage](../../IAO/12/IAO_0000112.md) eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex + * http://purl.obolibrary.org/obo/RO_0002327 [example of usage](../../IAO/12/IAO_0000112.md) a particular instances of akt-2 enables some instance of protein kinase activity + * http://purl.obolibrary.org/obo/RO_0002332 [example of usage](../../IAO/12/IAO_0000112.md) every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid + * http://purl.obolibrary.org/obo/RO_0002343 [example of usage](../../IAO/12/IAO_0000112.md) 'pollen tube growth' results_in growth_of some 'pollen tube' + * http://purl.obolibrary.org/obo/RO_0002344 [example of usage](../../IAO/12/IAO_0000112.md) 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) + * http://purl.obolibrary.org/obo/RO_0002348 [example of usage](../../IAO/12/IAO_0000112.md) an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. + * http://purl.obolibrary.org/obo/RO_0002350 [example of usage](../../IAO/12/IAO_0000112.md) An organism that is a member of a population of organisms + * http://purl.obolibrary.org/obo/RO_0002374 [example of usage](../../IAO/12/IAO_0000112.md) false + * http://purl.obolibrary.org/obo/RO_0002376 [example of usage](../../IAO/12/IAO_0000112.md) Deschutes River tributary_of Columbia River + * http://purl.obolibrary.org/obo/RO_0002376 [example of usage](../../IAO/12/IAO_0000112.md) inferior epigastric vein tributary_of external iliac vein + * http://purl.obolibrary.org/obo/RO_0002377 [example of usage](../../IAO/12/IAO_0000112.md) Deschutes River distributary_of Little Lava Lake + * http://purl.obolibrary.org/obo/RO_0002379 [example of usage](../../IAO/12/IAO_0000112.md) A lump of clay and a statue + * http://purl.obolibrary.org/obo/RO_0002400 [example of usage](../../IAO/12/IAO_0000112.md) 'protein catabolic process' SubClassOf has_direct_input some protein + * http://purl.obolibrary.org/obo/RO_0002402 [example of usage](../../IAO/12/IAO_0000112.md) translation SubClassOf has_direct_output some protein + * http://purl.obolibrary.org/obo/RO_0002439 [example of usage](../../IAO/12/IAO_0000112.md) Baleen whale preys on krill + * http://purl.obolibrary.org/obo/RO_0002444 [example of usage](../../IAO/12/IAO_0000112.md) Pediculus humanus capitis parasite of human + * http://purl.obolibrary.org/obo/RO_0002446 [example of usage](../../IAO/12/IAO_0000112.md) Porifiera attaches to substrate + * http://purl.obolibrary.org/obo/RO_0002451 [example of usage](../../IAO/12/IAO_0000112.md) all dengue disease transmitted by some mosquito + * http://purl.obolibrary.org/obo/RO_0002455 [example of usage](../../IAO/12/IAO_0000112.md) Bees pollinate Flowers + * http://purl.obolibrary.org/obo/RO_0002459 [example of usage](../../IAO/12/IAO_0000112.md) Anopheles is a vector for Plasmodium + * http://purl.obolibrary.org/obo/RO_0002473 [example of usage](../../IAO/12/IAO_0000112.md) 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' + * http://purl.obolibrary.org/obo/RO_0002475 [example of usage](../../IAO/12/IAO_0000112.md) 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' + * http://purl.obolibrary.org/obo/RO_0002476 [example of usage](../../IAO/12/IAO_0000112.md) ABal nucleus child nucleus of ABa nucleus (in C elegans) + * http://purl.obolibrary.org/obo/RO_0002504 [example of usage](../../IAO/12/IAO_0000112.md) brain always_present_in_taxon 'Vertebrata' + * http://purl.obolibrary.org/obo/RO_0002504 [example of usage](../../IAO/12/IAO_0000112.md) forelimb always_present_in_taxon Euarchontoglires + * http://purl.obolibrary.org/obo/RO_0002505 [example of usage](../../IAO/12/IAO_0000112.md) 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate + * http://purl.obolibrary.org/obo/RO_0002507 [example of usage](../../IAO/12/IAO_0000112.md) A coral reef environment is determined by a particular coral reef + * http://purl.obolibrary.org/obo/RO_0002515 [example of usage](../../IAO/12/IAO_0000112.md) Every UTR is adjacent to a CDS of the same transcript + * http://purl.obolibrary.org/obo/RO_0002515 [example of usage](../../IAO/12/IAO_0000112.md) Two consecutive DNA residues are sequentially adjacent + * http://purl.obolibrary.org/obo/RO_0002515 [example of usage](../../IAO/12/IAO_0000112.md) Two exons on a processed transcript that were previously connected by an intron are adjacent + * http://purl.obolibrary.org/obo/RO_0002516 [example of usage](../../IAO/12/IAO_0000112.md) Every CDS has as a start sequence the start codon for that transcript + * http://purl.obolibrary.org/obo/RO_0002518 [example of usage](../../IAO/12/IAO_0000112.md) Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) + * http://purl.obolibrary.org/obo/RO_0002521 [example of usage](../../IAO/12/IAO_0000112.md) Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. + * http://purl.obolibrary.org/obo/RO_0002522 [example of usage](../../IAO/12/IAO_0000112.md) The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) + * http://purl.obolibrary.org/obo/RO_0002530 [example of usage](../../IAO/12/IAO_0000112.md) A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript + * http://purl.obolibrary.org/obo/RO_0002531 [example of usage](../../IAO/12/IAO_0000112.md) A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript + * http://purl.obolibrary.org/obo/RO_0002551 [example of usage](../../IAO/12/IAO_0000112.md) Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' + * http://purl.obolibrary.org/obo/RO_0002584 [example of usage](../../IAO/12/IAO_0000112.md) gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + * http://purl.obolibrary.org/obo/RO_0002596 [example of usage](../../IAO/12/IAO_0000112.md) pyrethroid -> growth + * http://purl.obolibrary.org/obo/RO_0002598 [example of usage](../../IAO/12/IAO_0000112.md) renin -> arteriolar smooth muscle contraction + * http://purl.obolibrary.org/obo/RO_0002599 [example of usage](../../IAO/12/IAO_0000112.md) pazopanib -> pathological angiogenesis + * http://purl.obolibrary.org/obo/RO_0002600 [example of usage](../../IAO/12/IAO_0000112.md) benzene -> cancer [CHEBI] + * http://purl.obolibrary.org/obo/RO_0002604 [example of usage](../../IAO/12/IAO_0000112.md) 'anterior end of organism' is-opposite-of 'posterior end of organism' + * http://purl.obolibrary.org/obo/RO_0002604 [example of usage](../../IAO/12/IAO_0000112.md) 'increase in temperature' is-opposite-of 'decrease in temperature' + +## External Comments + diff --git a/src/ontology/md/IAO/12/IAO_0000412.md b/src/ontology/md/IAO/12/IAO_0000412.md new file mode 100644 index 00000000..b6f4020e --- /dev/null +++ b/src/ontology/md/IAO/12/IAO_0000412.md @@ -0,0 +1,54 @@ + +## Class : imported from + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000412 + * *Label* = imported from + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = imported from + +## Usage + + * - + * http://purl.obolibrary.org/obo/CARO_0000003 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/caro.owl + * http://purl.obolibrary.org/obo/CARO_0000006 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/caro.owl + * http://purl.obolibrary.org/obo/CARO_0000014 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/caro.owl + * http://purl.obolibrary.org/obo/CARO_0001000 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/caro.owl + * http://purl.obolibrary.org/obo/CARO_0001001 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/caro.owl + * http://purl.obolibrary.org/obo/CARO_0010000 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/caro.owl + * http://purl.obolibrary.org/obo/CL_0000000 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/cl.owl + * http://purl.obolibrary.org/obo/CL_0000540 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/cl.owl + * http://purl.obolibrary.org/obo/GO_0005634 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0016020 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0030424 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0030425 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0042734 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0042995 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0043005 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0044456 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0044464 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0045202 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + * http://purl.obolibrary.org/obo/GO_0045211 [imported from](../../IAO/12/IAO_0000412.md) http://purl.obolibrary.org/obo/go.owl + +## External Comments + diff --git a/src/ontology/md/IAO/14/IAO_0000114.md b/src/ontology/md/IAO/14/IAO_0000114.md new file mode 100644 index 00000000..ae6b688a --- /dev/null +++ b/src/ontology/md/IAO/14/IAO_0000114.md @@ -0,0 +1,167 @@ + +## Class : has curation status + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000114 + * *Label* = has curation status + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has curation status + +## Usage + + * - + * http://purl.obolibrary.org/obo/IAO_0000078 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/IAO_0000112 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000122 + * http://purl.obolibrary.org/obo/IAO_0000115 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000122 + * http://purl.obolibrary.org/obo/IAO_0000116 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000122 + * http://purl.obolibrary.org/obo/IAO_0000117 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000122 + * http://purl.obolibrary.org/obo/IAO_0000118 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/IAO_0000119 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000122 + * http://purl.obolibrary.org/obo/IAO_0000122 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/IAO_0000125 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/IAO_0000225 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/IAO_0000232 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000122 + * http://purl.obolibrary.org/obo/IAO_0000412 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/IAO_0000428 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/IAO_0000589 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/IAO_0100001 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0000300 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0000301 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0000302 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0001000 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0001001 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002001 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002100 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002101 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002102 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002103 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002104 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002105 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002106 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002107 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002108 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002109 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002110 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002111 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002112 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002113 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002120 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002121 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002130 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002131 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002132 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002134 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002150 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002151 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002156 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002157 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002158 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002159 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002160 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002162 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002163 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002180 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002200 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002201 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002202 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002203 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002204 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002205 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002206 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002207 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002210 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002211 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002212 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002213 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002214 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002215 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002216 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002217 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002218 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002219 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002220 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002221 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002222 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002223 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002224 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002225 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002226 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002229 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002230 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002231 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002232 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002233 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002234 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002254 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002255 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002256 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002257 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002258 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002285 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002286 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002287 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002291 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002292 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002293 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002295 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002296 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002297 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002298 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002299 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002300 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002301 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0002303 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002374 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002375 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002376 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002377 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002378 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002380 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002381 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002382 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002383 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002384 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002385 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002386 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002387 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002388 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002400 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002401 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002402 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002403 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002404 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002405 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002406 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002407 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002408 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002409 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002410 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002411 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002412 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002413 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002414 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0002464 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000428 + * http://purl.obolibrary.org/obo/RO_0003000 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + * http://purl.obolibrary.org/obo/RO_0003001 [has curation status](../../IAO/14/IAO_0000114.md) http://purl.obolibrary.org/obo/IAO_0000125 + +## External Comments + diff --git a/src/ontology/md/IAO/15/IAO_0000115.md b/src/ontology/md/IAO/15/IAO_0000115.md new file mode 100644 index 00000000..5392dc4e --- /dev/null +++ b/src/ontology/md/IAO/15/IAO_0000115.md @@ -0,0 +1,480 @@ + +## Class : definition + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000115 + * *Label* = definition + * *Label* = definition + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000122 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = definition + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = definition + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000002 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/BFO_0000003 [definition](../../IAO/15/IAO_0000115.md) An entity that has temporal parts and that happens, unfolds or develops through time. + * http://purl.obolibrary.org/obo/BFO_0000004 [definition](../../IAO/15/IAO_0000115.md) A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + * http://purl.obolibrary.org/obo/BFO_0000005 [definition](../../IAO/15/IAO_0000115.md) A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. + * http://purl.obolibrary.org/obo/BFO_0000015 [definition](../../IAO/15/IAO_0000115.md) An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + * http://purl.obolibrary.org/obo/BFO_0000017 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/BFO_0000020 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/BFO_0000023 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/BFO_0000031 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/BFO_0000040 [definition](../../IAO/15/IAO_0000115.md) An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + * http://purl.obolibrary.org/obo/BFO_0000050 [definition](../../IAO/15/IAO_0000115.md) a core relation that holds between a part and its whole + * http://purl.obolibrary.org/obo/BFO_0000051 [definition](../../IAO/15/IAO_0000115.md) a core relation that holds between a whole and its part + * http://purl.obolibrary.org/obo/BFO_0000062 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/BFO_0000063 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/BFO_0000066 [definition](../../IAO/15/IAO_0000115.md) 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 + * http://purl.obolibrary.org/obo/BFO_0000067 [definition](../../IAO/15/IAO_0000115.md) [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 + * http://purl.obolibrary.org/obo/IAO_0000426 [definition](../../IAO/15/IAO_0000115.md) An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + * http://purl.obolibrary.org/obo/RO_0000052 [definition](../../IAO/15/IAO_0000115.md) 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 + * http://purl.obolibrary.org/obo/RO_0000053 [definition](../../IAO/15/IAO_0000115.md) 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 + * http://purl.obolibrary.org/obo/RO_0000056 [definition](../../IAO/15/IAO_0000115.md) a relation between a continuant and a process, in which the continuant is somehow involved in the process + * http://purl.obolibrary.org/obo/RO_0000057 [definition](../../IAO/15/IAO_0000115.md) a relation between a process and a continuant, in which the continuant is somehow involved in the process + * http://purl.obolibrary.org/obo/RO_0000058 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0000059 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0000079 [definition](../../IAO/15/IAO_0000115.md) a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + * http://purl.obolibrary.org/obo/RO_0000080 [definition](../../IAO/15/IAO_0000115.md) a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + * http://purl.obolibrary.org/obo/RO_0000081 [definition](../../IAO/15/IAO_0000115.md) a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + * http://purl.obolibrary.org/obo/RO_0000085 [definition](../../IAO/15/IAO_0000115.md) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + * http://purl.obolibrary.org/obo/RO_0000086 [definition](../../IAO/15/IAO_0000115.md) a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + * http://purl.obolibrary.org/obo/RO_0000087 [definition](../../IAO/15/IAO_0000115.md) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + * http://purl.obolibrary.org/obo/RO_0000300 [definition](../../IAO/15/IAO_0000115.md) A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. + * http://purl.obolibrary.org/obo/RO_0000301 [definition](../../IAO/15/IAO_0000115.md) A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. + * http://purl.obolibrary.org/obo/RO_0000302 [definition](../../IAO/15/IAO_0000115.md) A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. + * http://purl.obolibrary.org/obo/RO_0001000 [definition](../../IAO/15/IAO_0000115.md) 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 + * http://purl.obolibrary.org/obo/RO_0001001 [definition](../../IAO/15/IAO_0000115.md) 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 + * http://purl.obolibrary.org/obo/RO_0001015 [definition](../../IAO/15/IAO_0000115.md) a relation between two independent continuants, the location and the target, in which the target is entirely within the location + * http://purl.obolibrary.org/obo/RO_0001025 [definition](../../IAO/15/IAO_0000115.md) a relation between two independent continuants, the target and the location, in which the target is entirely within the location + * http://purl.obolibrary.org/obo/RO_0001900 [definition](../../IAO/15/IAO_0000115.md) An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + * http://purl.obolibrary.org/obo/RO_0001901 [definition](../../IAO/15/IAO_0000115.md) + +## Elucidation + +This is used when the statement/axiom is assumed to hold true 'eternally' + +## How to interpret (informal) + +First the "atemporal" FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + + + * http://purl.obolibrary.org/obo/RO_0001902 [definition](../../IAO/15/IAO_0000115.md) + +## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + + + + * http://purl.obolibrary.org/obo/RO_0002000 [definition](../../IAO/15/IAO_0000115.md) a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + * http://purl.obolibrary.org/obo/RO_0002002 [definition](../../IAO/15/IAO_0000115.md) a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + * http://purl.obolibrary.org/obo/RO_0002003 [definition](../../IAO/15/IAO_0000115.md) A relation that holds between two neurons that are electrically coupled via gap junctions. + * http://purl.obolibrary.org/obo/RO_0002004 [definition](../../IAO/15/IAO_0000115.md) The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + * http://purl.obolibrary.org/obo/RO_0002007 [definition](../../IAO/15/IAO_0000115.md) X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + * http://purl.obolibrary.org/obo/RO_0002008 [definition](../../IAO/15/IAO_0000115.md) A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + * http://purl.obolibrary.org/obo/RO_0002009 [definition](../../IAO/15/IAO_0000115.md) A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. + * http://purl.obolibrary.org/obo/RO_0002010 [definition](../../IAO/15/IAO_0000115.md) x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + * http://purl.obolibrary.org/obo/RO_0002011 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds between a process that regulates a transport process and the entity transported by that process. + * http://purl.obolibrary.org/obo/RO_0002100 [definition](../../IAO/15/IAO_0000115.md) Relation between a neuron and an anatomical structure that its soma is part of. + * http://purl.obolibrary.org/obo/RO_0002101 [definition](../../IAO/15/IAO_0000115.md) relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. + + * http://purl.obolibrary.org/obo/RO_0002102 [definition](../../IAO/15/IAO_0000115.md) Relation between a neuron and some structure its axon forms (chemical) synapses in. + * http://purl.obolibrary.org/obo/RO_0002103 [definition](../../IAO/15/IAO_0000115.md) Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. + * http://purl.obolibrary.org/obo/RO_0002104 [definition](../../IAO/15/IAO_0000115.md) Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. + * http://purl.obolibrary.org/obo/RO_0002105 [definition](../../IAO/15/IAO_0000115.md) A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. + * http://purl.obolibrary.org/obo/RO_0002106 [definition](../../IAO/15/IAO_0000115.md) A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. + * http://purl.obolibrary.org/obo/RO_0002107 [definition](../../IAO/15/IAO_0000115.md) A relation between a motor neuron and a muscle that it synapses to via a type II bouton. + * http://purl.obolibrary.org/obo/RO_0002108 [definition](../../IAO/15/IAO_0000115.md) Relation between a muscle and a motor neuron that synapses to it via a type II bouton. + * http://purl.obolibrary.org/obo/RO_0002109 [definition](../../IAO/15/IAO_0000115.md) Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. + * http://purl.obolibrary.org/obo/RO_0002110 [definition](../../IAO/15/IAO_0000115.md) Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + * http://purl.obolibrary.org/obo/RO_0002112 [definition](../../IAO/15/IAO_0000115.md) Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. + * http://purl.obolibrary.org/obo/RO_0002113 [definition](../../IAO/15/IAO_0000115.md) Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + * http://purl.obolibrary.org/obo/RO_0002114 [definition](../../IAO/15/IAO_0000115.md) A relation between a motor neuron and a muscle that it synapses to via a type III bouton. + * http://purl.obolibrary.org/obo/RO_0002115 [definition](../../IAO/15/IAO_0000115.md) Relation between a muscle and a motor neuron that synapses to it via a type III bouton. + + * http://purl.obolibrary.org/obo/RO_0002120 [definition](../../IAO/15/IAO_0000115.md) Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. + + * http://purl.obolibrary.org/obo/RO_0002121 [definition](../../IAO/15/IAO_0000115.md) Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. + + + * http://purl.obolibrary.org/obo/RO_0002130 [definition](../../IAO/15/IAO_0000115.md) A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. + * http://purl.obolibrary.org/obo/RO_0002131 [definition](../../IAO/15/IAO_0000115.md) 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/RO_0002132 [definition](../../IAO/15/IAO_0000115.md) The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. + * http://purl.obolibrary.org/obo/RO_0002134 [definition](../../IAO/15/IAO_0000115.md) Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. +T innervates some R +Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + * http://purl.obolibrary.org/obo/RO_0002150 [definition](../../IAO/15/IAO_0000115.md) X continuous_with Y if and only if X and Y share a fiat boundary. + * http://purl.obolibrary.org/obo/RO_0002151 [definition](../../IAO/15/IAO_0000115.md) x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x + * http://purl.obolibrary.org/obo/RO_0002156 [definition](../../IAO/15/IAO_0000115.md) d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + * http://purl.obolibrary.org/obo/RO_0002158 [definition](../../IAO/15/IAO_0000115.md) two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + * http://purl.obolibrary.org/obo/RO_0002160 [definition](../../IAO/15/IAO_0000115.md) x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + * http://purl.obolibrary.org/obo/RO_0002161 [definition](../../IAO/15/IAO_0000115.md) x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. + * http://purl.obolibrary.org/obo/RO_0002162 [definition](../../IAO/15/IAO_0000115.md) x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + * http://purl.obolibrary.org/obo/RO_0002163 [definition](../../IAO/15/IAO_0000115.md) A is spatially_disjoint_from B if and only if they have no parts in common + * http://purl.obolibrary.org/obo/RO_0002170 [definition](../../IAO/15/IAO_0000115.md) a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b + * http://purl.obolibrary.org/obo/RO_0002171 [definition](../../IAO/15/IAO_0000115.md) A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. + * http://purl.obolibrary.org/obo/RO_0002172 [definition](../../IAO/15/IAO_0000115.md) An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. + * http://purl.obolibrary.org/obo/RO_0002173 [definition](../../IAO/15/IAO_0000115.md) S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] + * http://purl.obolibrary.org/obo/RO_0002174 [definition](../../IAO/15/IAO_0000115.md) S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. + * http://purl.obolibrary.org/obo/RO_0002175 [definition](../../IAO/15/IAO_0000115.md) S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S + * http://purl.obolibrary.org/obo/RO_0002176 [definition](../../IAO/15/IAO_0000115.md) c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. + * http://purl.obolibrary.org/obo/RO_0002177 [definition](../../IAO/15/IAO_0000115.md) a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + * http://purl.obolibrary.org/obo/RO_0002178 [definition](../../IAO/15/IAO_0000115.md) Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + * http://purl.obolibrary.org/obo/RO_0002179 [definition](../../IAO/15/IAO_0000115.md) Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. + * http://purl.obolibrary.org/obo/RO_0002180 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0002200 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + * http://purl.obolibrary.org/obo/RO_0002202 [definition](../../IAO/15/IAO_0000115.md) x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + * http://purl.obolibrary.org/obo/RO_0002204 [definition](../../IAO/15/IAO_0000115.md) definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" + * http://purl.obolibrary.org/obo/RO_0002205 [definition](../../IAO/15/IAO_0000115.md) x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y + * http://purl.obolibrary.org/obo/RO_0002206 [definition](../../IAO/15/IAO_0000115.md) x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process + * http://purl.obolibrary.org/obo/RO_0002207 [definition](../../IAO/15/IAO_0000115.md) Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y + * http://purl.obolibrary.org/obo/RO_0002211 [definition](../../IAO/15/IAO_0000115.md) x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + * http://purl.obolibrary.org/obo/RO_0002212 [definition](../../IAO/15/IAO_0000115.md) x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + * http://purl.obolibrary.org/obo/RO_0002213 [definition](../../IAO/15/IAO_0000115.md) x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + * http://purl.obolibrary.org/obo/RO_0002214 [definition](../../IAO/15/IAO_0000115.md) x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. + * http://purl.obolibrary.org/obo/RO_0002215 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0002216 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0002217 [definition](../../IAO/15/IAO_0000115.md) x actively participates in y if and only if x participates in y and x realizes some active role + * http://purl.obolibrary.org/obo/RO_0002218 [definition](../../IAO/15/IAO_0000115.md) x has participant y if and only if x realizes some active role that inheres in y + * http://purl.obolibrary.org/obo/RO_0002219 [definition](../../IAO/15/IAO_0000115.md) x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x + * http://purl.obolibrary.org/obo/RO_0002220 [definition](../../IAO/15/IAO_0000115.md) x adjacent to y if and only if x and y share a boundary + * http://purl.obolibrary.org/obo/RO_0002223 [definition](../../IAO/15/IAO_0000115.md) inverse of starts with + * http://purl.obolibrary.org/obo/RO_0002224 [definition](../../IAO/15/IAO_0000115.md) x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + * http://purl.obolibrary.org/obo/RO_0002225 [definition](../../IAO/15/IAO_0000115.md) x develops from part of y if and only if there exists some z such that x develops from z and z is part of y + * http://purl.obolibrary.org/obo/RO_0002226 [definition](../../IAO/15/IAO_0000115.md) x develops_in y if x is located in y whilst x is developing + * http://purl.obolibrary.org/obo/RO_0002229 [definition](../../IAO/15/IAO_0000115.md) inverse of ends with + * http://purl.obolibrary.org/obo/RO_0002230 [definition](../../IAO/15/IAO_0000115.md) x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + * http://purl.obolibrary.org/obo/RO_0002231 [definition](../../IAO/15/IAO_0000115.md) x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + * http://purl.obolibrary.org/obo/RO_0002232 [definition](../../IAO/15/IAO_0000115.md) x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + * http://purl.obolibrary.org/obo/RO_0002233 [definition](../../IAO/15/IAO_0000115.md) p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + * http://purl.obolibrary.org/obo/RO_0002234 [definition](../../IAO/15/IAO_0000115.md) p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + * http://purl.obolibrary.org/obo/RO_0002254 [definition](../../IAO/15/IAO_0000115.md) x has developmental contribution from y iff x has some part z such that z develops from y + * http://purl.obolibrary.org/obo/RO_0002256 [definition](../../IAO/15/IAO_0000115.md) t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T + * http://purl.obolibrary.org/obo/RO_0002257 [definition](../../IAO/15/IAO_0000115.md) Inverse of developmentally induced by + * http://purl.obolibrary.org/obo/RO_0002258 [definition](../../IAO/15/IAO_0000115.md) Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + * http://purl.obolibrary.org/obo/RO_0002285 [definition](../../IAO/15/IAO_0000115.md) x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else + * http://purl.obolibrary.org/obo/RO_0002286 [definition](../../IAO/15/IAO_0000115.md) Inverse of developmentally preceded by + * http://purl.obolibrary.org/obo/RO_0002291 [definition](../../IAO/15/IAO_0000115.md) x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x + * http://purl.obolibrary.org/obo/RO_0002292 [definition](../../IAO/15/IAO_0000115.md) Inverse of 'expressed in' + * http://purl.obolibrary.org/obo/RO_0002293 [definition](../../IAO/15/IAO_0000115.md) inverse of ubiquiotously expressed in + * http://purl.obolibrary.org/obo/RO_0002295 [definition](../../IAO/15/IAO_0000115.md) p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + * http://purl.obolibrary.org/obo/RO_0002296 [definition](../../IAO/15/IAO_0000115.md) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. + * http://purl.obolibrary.org/obo/RO_0002298 [definition](../../IAO/15/IAO_0000115.md) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + * http://purl.obolibrary.org/obo/RO_0002299 [definition](../../IAO/15/IAO_0000115.md) The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + * http://purl.obolibrary.org/obo/RO_0002303 [definition](../../IAO/15/IAO_0000115.md) x 'has habitat' y if and only if: x is an organism, y is a habitat, and x is specially adapted (either naturally or via artifical selection) to living in y. Here 'living in' encompasses the majority of the animal's lifespan. + * http://purl.obolibrary.org/obo/RO_0002313 [definition](../../IAO/15/IAO_0000115.md) Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c + * http://purl.obolibrary.org/obo/RO_0002314 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0002315 [definition](../../IAO/15/IAO_0000115.md) The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity + * http://purl.obolibrary.org/obo/RO_0002320 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds via some environmental process + * http://purl.obolibrary.org/obo/RO_0002321 [definition](../../IAO/15/IAO_0000115.md) A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + * http://purl.obolibrary.org/obo/RO_0002323 [definition](../../IAO/15/IAO_0000115.md) A mereological relationship or a topological relationship + * http://purl.obolibrary.org/obo/RO_0002324 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds between entities participating in some developmental process (GO:0032502) + * http://purl.obolibrary.org/obo/RO_0002325 [definition](../../IAO/15/IAO_0000115.md) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. + * http://purl.obolibrary.org/obo/RO_0002329 [definition](../../IAO/15/IAO_0000115.md) this relation holds between c and p when c is part of some c', and c' is capable of p. + * http://purl.obolibrary.org/obo/RO_0002330 [definition](../../IAO/15/IAO_0000115.md) holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + * http://purl.obolibrary.org/obo/RO_0002331 [definition](../../IAO/15/IAO_0000115.md) c involved_in p if and only if c enables some process p', and p' is part of p + * http://purl.obolibrary.org/obo/RO_0002332 [definition](../../IAO/15/IAO_0000115.md) p regulates levels of c if p regulates some amount (PATO:0000070) of c + * http://purl.obolibrary.org/obo/RO_0002333 [definition](../../IAO/15/IAO_0000115.md) inverse of enables + * http://purl.obolibrary.org/obo/RO_0002334 [definition](../../IAO/15/IAO_0000115.md) inverse of regulates + * http://purl.obolibrary.org/obo/RO_0002337 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds via some process of localization + * http://purl.obolibrary.org/obo/RO_0002338 [definition](../../IAO/15/IAO_0000115.md) This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. + * http://purl.obolibrary.org/obo/RO_0002339 [definition](../../IAO/15/IAO_0000115.md) This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. + * http://purl.obolibrary.org/obo/RO_0002340 [definition](../../IAO/15/IAO_0000115.md) Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. + * http://purl.obolibrary.org/obo/RO_0002341 [definition](../../IAO/15/IAO_0000115.md) Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l + * http://purl.obolibrary.org/obo/RO_0002342 [definition](../../IAO/15/IAO_0000115.md) Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. + * http://purl.obolibrary.org/obo/RO_0002348 [definition](../../IAO/15/IAO_0000115.md) p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. + * http://purl.obolibrary.org/obo/RO_0002349 [definition](../../IAO/15/IAO_0000115.md) p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. + * http://purl.obolibrary.org/obo/RO_0002350 [definition](../../IAO/15/IAO_0000115.md) is member of is a mereological relation between a item and a collection. + * http://purl.obolibrary.org/obo/RO_0002351 [definition](../../IAO/15/IAO_0000115.md) has member is a mereological relation between a collection and an item. + * http://purl.obolibrary.org/obo/RO_0002355 [definition](../../IAO/15/IAO_0000115.md) A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. + * http://purl.obolibrary.org/obo/RO_0002356 [definition](../../IAO/15/IAO_0000115.md) The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. + * http://purl.obolibrary.org/obo/RO_0002357 [definition](../../IAO/15/IAO_0000115.md) p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. + * http://purl.obolibrary.org/obo/RO_0002371 [definition](../../IAO/15/IAO_0000115.md) a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a + * http://purl.obolibrary.org/obo/RO_0002372 [definition](../../IAO/15/IAO_0000115.md) m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + * http://purl.obolibrary.org/obo/RO_0002373 [definition](../../IAO/15/IAO_0000115.md) m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + * http://purl.obolibrary.org/obo/RO_0002374 [definition](../../IAO/15/IAO_0000115.md) x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + * http://purl.obolibrary.org/obo/RO_0002376 [definition](../../IAO/15/IAO_0000115.md) x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. + * http://purl.obolibrary.org/obo/RO_0002377 [definition](../../IAO/15/IAO_0000115.md) x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x + * http://purl.obolibrary.org/obo/RO_0002378 [definition](../../IAO/15/IAO_0000115.md) x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. + * http://purl.obolibrary.org/obo/RO_0002379 [definition](../../IAO/15/IAO_0000115.md) x spatially_coextensive_with y if and inly if x and y have the same location + * http://purl.obolibrary.org/obo/RO_0002380 [definition](../../IAO/15/IAO_0000115.md) x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y + * http://purl.obolibrary.org/obo/RO_0002381 [definition](../../IAO/15/IAO_0000115.md) x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. + * http://purl.obolibrary.org/obo/RO_0002382 [definition](../../IAO/15/IAO_0000115.md) x proper_distributary_of y iff x distributary_of y and x does not flow back into y + * http://purl.obolibrary.org/obo/RO_0002383 [definition](../../IAO/15/IAO_0000115.md) x proper_tributary_of y iff x tributary_of y and x does not originate from y + * http://purl.obolibrary.org/obo/RO_0002384 [definition](../../IAO/15/IAO_0000115.md) x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + * http://purl.obolibrary.org/obo/RO_0002385 [definition](../../IAO/15/IAO_0000115.md) x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + * http://purl.obolibrary.org/obo/RO_0002386 [definition](../../IAO/15/IAO_0000115.md) x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y + * http://purl.obolibrary.org/obo/RO_0002387 [definition](../../IAO/15/IAO_0000115.md) x has the potential to develop into y iff x develops into y or if x is capable of developing into y + * http://purl.obolibrary.org/obo/RO_0002388 [definition](../../IAO/15/IAO_0000115.md) x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + * http://purl.obolibrary.org/obo/RO_0002400 [definition](../../IAO/15/IAO_0000115.md) p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + * http://purl.obolibrary.org/obo/RO_0002402 [definition](../../IAO/15/IAO_0000115.md) p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. + * http://purl.obolibrary.org/obo/RO_0002404 [definition](../../IAO/15/IAO_0000115.md) inverse of upstream of + * http://purl.obolibrary.org/obo/RO_0002406 [definition](../../IAO/15/IAO_0000115.md) p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q + * http://purl.obolibrary.org/obo/RO_0002407 [definition](../../IAO/15/IAO_0000115.md) p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q + * http://purl.obolibrary.org/obo/RO_0002410 [definition](../../IAO/15/IAO_0000115.md) This relation groups causal relations between material entities and causal relations between processes + * http://purl.obolibrary.org/obo/RO_0002411 [definition](../../IAO/15/IAO_0000115.md) p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + * http://purl.obolibrary.org/obo/RO_0002412 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0002413 [definition](../../IAO/15/IAO_0000115.md) p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + * http://purl.obolibrary.org/obo/RO_0002414 [definition](../../IAO/15/IAO_0000115.md) transitive form of directly_provides_input_for + * http://purl.obolibrary.org/obo/RO_0002416 [definition](../../IAO/15/IAO_0000115.md) An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. + * http://purl.obolibrary.org/obo/RO_0002418 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0002419 [definition](../../IAO/15/IAO_0000115.md) An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. + * http://purl.obolibrary.org/obo/RO_0002420 [definition](../../IAO/15/IAO_0000115.md) A logical macro assertion whose domain is an IRI for a class + * http://purl.obolibrary.org/obo/RO_0002421 [definition](../../IAO/15/IAO_0000115.md) A logical macro assertion whose domain is an IRI for a property + * http://purl.obolibrary.org/obo/RO_0002428 [definition](../../IAO/15/IAO_0000115.md) c involved in regulation of p if c is involved in some 'p' and p' regulates some p + * http://purl.obolibrary.org/obo/RO_0002431 [definition](../../IAO/15/IAO_0000115.md) 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 + * http://purl.obolibrary.org/obo/RO_0002432 [definition](../../IAO/15/IAO_0000115.md) c executes activity in d if and only if c enables p and p occurs_in d + * http://purl.obolibrary.org/obo/RO_0002433 [definition](../../IAO/15/IAO_0000115.md) p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. + * http://purl.obolibrary.org/obo/RO_0002434 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + * http://purl.obolibrary.org/obo/RO_0002436 [definition](../../IAO/15/IAO_0000115.md) An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. + * http://purl.obolibrary.org/obo/RO_0002437 [definition](../../IAO/15/IAO_0000115.md) An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. + * http://purl.obolibrary.org/obo/RO_0002438 [definition](../../IAO/15/IAO_0000115.md) An interaction relationship in which the partners are related via a feeding relationship. + * http://purl.obolibrary.org/obo/RO_0002439 [definition](../../IAO/15/IAO_0000115.md) An interaction relationship involving a predation process, where the subject consumes all or part of the target + * http://purl.obolibrary.org/obo/RO_0002440 [definition](../../IAO/15/IAO_0000115.md) A biotic interaction in which the two organisms live together in more or less intimate association. + * http://purl.obolibrary.org/obo/RO_0002441 [definition](../../IAO/15/IAO_0000115.md) An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + * http://purl.obolibrary.org/obo/RO_0002442 [definition](../../IAO/15/IAO_0000115.md) An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + * http://purl.obolibrary.org/obo/RO_0002443 [definition](../../IAO/15/IAO_0000115.md) An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + * http://purl.obolibrary.org/obo/RO_0002446 [definition](../../IAO/15/IAO_0000115.md) A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. + * http://purl.obolibrary.org/obo/RO_0002448 [definition](../../IAO/15/IAO_0000115.md) Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b + * http://purl.obolibrary.org/obo/RO_0002449 [definition](../../IAO/15/IAO_0000115.md) Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. + * http://purl.obolibrary.org/obo/RO_0002450 [definition](../../IAO/15/IAO_0000115.md) Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. + * http://purl.obolibrary.org/obo/RO_0002451 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds between a disease and organism + * http://purl.obolibrary.org/obo/RO_0002452 [definition](../../IAO/15/IAO_0000115.md) A relation that holds between a disease or an organism and a phenotype + * http://purl.obolibrary.org/obo/RO_0002472 [definition](../../IAO/15/IAO_0000115.md) A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and +the a supports either the existence of b, or the truth value of b. + * http://purl.obolibrary.org/obo/RO_0002473 [definition](../../IAO/15/IAO_0000115.md) x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. + * http://purl.obolibrary.org/obo/RO_0002474 [definition](../../IAO/15/IAO_0000115.md) An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. + * http://purl.obolibrary.org/obo/RO_0002475 [definition](../../IAO/15/IAO_0000115.md) A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. + * http://purl.obolibrary.org/obo/RO_0002476 [definition](../../IAO/15/IAO_0000115.md) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d + * http://purl.obolibrary.org/obo/RO_0002477 [definition](../../IAO/15/IAO_0000115.md) A child nucleus relationship in which the cells are part of a hermaphroditic organism + * http://purl.obolibrary.org/obo/RO_0002478 [definition](../../IAO/15/IAO_0000115.md) A child nucleus relationship in which the cells are part of a male organism + * http://purl.obolibrary.org/obo/RO_0002479 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0002480 [definition](../../IAO/15/IAO_0000115.md) An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y + * http://purl.obolibrary.org/obo/RO_0002484 [definition](../../IAO/15/IAO_0000115.md) Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) + * http://purl.obolibrary.org/obo/RO_0002488 [definition](../../IAO/15/IAO_0000115.md) x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + * http://purl.obolibrary.org/obo/RO_0002489 [definition](../../IAO/15/IAO_0000115.md) x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + * http://purl.obolibrary.org/obo/RO_0002490 [definition](../../IAO/15/IAO_0000115.md) x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + * http://purl.obolibrary.org/obo/RO_0002491 [definition](../../IAO/15/IAO_0000115.md) x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + * http://purl.obolibrary.org/obo/RO_0002492 [definition](../../IAO/15/IAO_0000115.md) x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + * http://purl.obolibrary.org/obo/RO_0002493 [definition](../../IAO/15/IAO_0000115.md) x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). + * http://purl.obolibrary.org/obo/RO_0002494 [definition](../../IAO/15/IAO_0000115.md) x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships + * http://purl.obolibrary.org/obo/RO_0002495 [definition](../../IAO/15/IAO_0000115.md) x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t + * http://purl.obolibrary.org/obo/RO_0002496 [definition](../../IAO/15/IAO_0000115.md) x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + * http://purl.obolibrary.org/obo/RO_0002497 [definition](../../IAO/15/IAO_0000115.md) x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. + * http://purl.obolibrary.org/obo/RO_0002501 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0002503 [definition](../../IAO/15/IAO_0000115.md) q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + * http://purl.obolibrary.org/obo/RO_0002504 [definition](../../IAO/15/IAO_0000115.md) S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S + * http://purl.obolibrary.org/obo/RO_0002505 [definition](../../IAO/15/IAO_0000115.md) p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c + * http://purl.obolibrary.org/obo/RO_0002507 [definition](../../IAO/15/IAO_0000115.md) s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. + * http://purl.obolibrary.org/obo/RO_0002509 [definition](../../IAO/15/IAO_0000115.md) s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. + * http://purl.obolibrary.org/obo/RO_0002510 [definition](../../IAO/15/IAO_0000115.md) x is transcribed from y if and only if x is synthesized from template y + * http://purl.obolibrary.org/obo/RO_0002512 [definition](../../IAO/15/IAO_0000115.md) x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y + * http://purl.obolibrary.org/obo/RO_0002513 [definition](../../IAO/15/IAO_0000115.md) inverse of ribosomal translation of + * http://purl.obolibrary.org/obo/RO_0002514 [definition](../../IAO/15/IAO_0000115.md) A relation that holds between two entities that have the property of being sequences or having sequences. + * http://purl.obolibrary.org/obo/RO_0002515 [definition](../../IAO/15/IAO_0000115.md) x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y + * http://purl.obolibrary.org/obo/RO_0002516 [definition](../../IAO/15/IAO_0000115.md) x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence + * http://purl.obolibrary.org/obo/RO_0002517 [definition](../../IAO/15/IAO_0000115.md) inverse of has start sequence + * http://purl.obolibrary.org/obo/RO_0002518 [definition](../../IAO/15/IAO_0000115.md) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence + * http://purl.obolibrary.org/obo/RO_0002519 [definition](../../IAO/15/IAO_0000115.md) inverse of has end sequence + * http://purl.obolibrary.org/obo/RO_0002520 [definition](../../IAO/15/IAO_0000115.md) x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. + * http://purl.obolibrary.org/obo/RO_0002521 [definition](../../IAO/15/IAO_0000115.md) x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering + * http://purl.obolibrary.org/obo/RO_0002522 [definition](../../IAO/15/IAO_0000115.md) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + * http://purl.obolibrary.org/obo/RO_0002523 [definition](../../IAO/15/IAO_0000115.md) inverse of bounds sequence of + * http://purl.obolibrary.org/obo/RO_0002524 [definition](../../IAO/15/IAO_0000115.md) x has subsequence y iff all of the sequence parts of x are sequence parts of y + * http://purl.obolibrary.org/obo/RO_0002525 [definition](../../IAO/15/IAO_0000115.md) inverse of has subsequence + * http://purl.obolibrary.org/obo/RO_0002526 [definition](../../IAO/15/IAO_0000115.md) x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. + * http://purl.obolibrary.org/obo/RO_0002527 [definition](../../IAO/15/IAO_0000115.md) x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + * http://purl.obolibrary.org/obo/RO_0002528 [definition](../../IAO/15/IAO_0000115.md) inverse of downstream of sequence of + * http://purl.obolibrary.org/obo/RO_0002529 [definition](../../IAO/15/IAO_0000115.md) x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + * http://purl.obolibrary.org/obo/RO_0002530 [definition](../../IAO/15/IAO_0000115.md) x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y + * http://purl.obolibrary.org/obo/RO_0002531 [definition](../../IAO/15/IAO_0000115.md) inverse of immediately downstream of + * http://purl.obolibrary.org/obo/RO_0002532 [definition](../../IAO/15/IAO_0000115.md) Any entity that is ordered in discrete units along a linear axis. + * http://purl.obolibrary.org/obo/RO_0002533 [definition](../../IAO/15/IAO_0000115.md) Any individual unit of a collection of like units arranged in a linear order + * http://purl.obolibrary.org/obo/RO_0002534 [definition](../../IAO/15/IAO_0000115.md) Any entity that can be divided into parts such that each part is an atomical unit of a sequence + * http://purl.obolibrary.org/obo/RO_0002539 [definition](../../IAO/15/IAO_0000115.md) Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. + * http://purl.obolibrary.org/obo/RO_0002540 [definition](../../IAO/15/IAO_0000115.md) Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. + * http://purl.obolibrary.org/obo/RO_0002541 [definition](../../IAO/15/IAO_0000115.md) Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. + * http://purl.obolibrary.org/obo/RO_0002542 [definition](../../IAO/15/IAO_0000115.md) Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 + * http://purl.obolibrary.org/obo/RO_0002543 [definition](../../IAO/15/IAO_0000115.md) Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. + * http://purl.obolibrary.org/obo/RO_0002544 [definition](../../IAO/15/IAO_0000115.md) Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 + * http://purl.obolibrary.org/obo/RO_0002545 [definition](../../IAO/15/IAO_0000115.md) Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. + * http://purl.obolibrary.org/obo/RO_0002546 [definition](../../IAO/15/IAO_0000115.md) A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process + * http://purl.obolibrary.org/obo/RO_0002547 [definition](../../IAO/15/IAO_0000115.md) Count of number of days intervening between the start of the stage and the time of coitum. + * http://purl.obolibrary.org/obo/RO_0002548 [definition](../../IAO/15/IAO_0000115.md) Count of number of days intervening between the end of the stage and the time of coitum. + * http://purl.obolibrary.org/obo/RO_0002551 [definition](../../IAO/15/IAO_0000115.md) A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. + * http://purl.obolibrary.org/obo/RO_0002552 [definition](../../IAO/15/IAO_0000115.md) p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. + * http://purl.obolibrary.org/obo/RO_0002553 [definition](../../IAO/15/IAO_0000115.md) x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y + * http://purl.obolibrary.org/obo/RO_0002560 [definition](../../IAO/15/IAO_0000115.md) If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p + * http://purl.obolibrary.org/obo/RO_0002561 [definition](../../IAO/15/IAO_0000115.md) If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p + * http://purl.obolibrary.org/obo/RO_0002562 [definition](../../IAO/15/IAO_0000115.md) R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process + * http://purl.obolibrary.org/obo/RO_0002565 [definition](../../IAO/15/IAO_0000115.md) Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c + * http://purl.obolibrary.org/obo/RO_0002566 [definition](../../IAO/15/IAO_0000115.md) 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 + * http://purl.obolibrary.org/obo/RO_0002567 [definition](../../IAO/15/IAO_0000115.md) A relation that holds between elements of a musculoskeletal system or its analogs. + * http://purl.obolibrary.org/obo/RO_0002568 [definition](../../IAO/15/IAO_0000115.md) m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. + * http://purl.obolibrary.org/obo/RO_0002570 [definition](../../IAO/15/IAO_0000115.md) x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. + * http://purl.obolibrary.org/obo/RO_0002571 [definition](../../IAO/15/IAO_0000115.md) x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + * http://purl.obolibrary.org/obo/RO_0002572 [definition](../../IAO/15/IAO_0000115.md) s is luminal space of x iff s is lumen_of x and s is an immaterial entity + * http://purl.obolibrary.org/obo/RO_0002573 [definition](../../IAO/15/IAO_0000115.md) A relation that holds between an attribute or a qualifier and another attribute. + * http://purl.obolibrary.org/obo/RO_0002575 [definition](../../IAO/15/IAO_0000115.md) relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y + * http://purl.obolibrary.org/obo/RO_0002577 [definition](../../IAO/15/IAO_0000115.md) A material entity consisting of multiple components that are causally integrated. + * http://purl.obolibrary.org/obo/RO_0002578 [definition](../../IAO/15/IAO_0000115.md) p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + * http://purl.obolibrary.org/obo/RO_0002579 [definition](../../IAO/15/IAO_0000115.md) relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y + * http://purl.obolibrary.org/obo/RO_0002581 [definition](../../IAO/15/IAO_0000115.md) 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 + * http://purl.obolibrary.org/obo/RO_0002582 [definition](../../IAO/15/IAO_0000115.md) 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. + * http://purl.obolibrary.org/obo/RO_0002583 [definition](../../IAO/15/IAO_0000115.md) x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + * http://purl.obolibrary.org/obo/RO_0002584 [definition](../../IAO/15/IAO_0000115.md) 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 + * http://purl.obolibrary.org/obo/RO_0002586 [definition](../../IAO/15/IAO_0000115.md) p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + * http://purl.obolibrary.org/obo/RO_0002589 [definition](../../IAO/15/IAO_0000115.md) p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + * http://purl.obolibrary.org/obo/RO_0002592 [definition](../../IAO/15/IAO_0000115.md) p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c + * http://purl.obolibrary.org/obo/RO_0002593 [definition](../../IAO/15/IAO_0000115.md) x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + * http://purl.obolibrary.org/obo/RO_0002594 [definition](../../IAO/15/IAO_0000115.md) An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. + * http://purl.obolibrary.org/obo/RO_0002596 [definition](../../IAO/15/IAO_0000115.md) Holds between c and p if and only if c is capable of some activity a, and a regulates p. + * http://purl.obolibrary.org/obo/RO_0002597 [definition](../../IAO/15/IAO_0000115.md) Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + * http://purl.obolibrary.org/obo/RO_0002598 [definition](../../IAO/15/IAO_0000115.md) Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + * http://purl.obolibrary.org/obo/RO_0002599 [definition](../../IAO/15/IAO_0000115.md) Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. + * http://purl.obolibrary.org/obo/RO_0002600 [definition](../../IAO/15/IAO_0000115.md) Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + * http://purl.obolibrary.org/obo/RO_0002601 [definition](../../IAO/15/IAO_0000115.md) A shortcut relationship that holds between two entities based on their identity criteria + * http://purl.obolibrary.org/obo/RO_0002602 [definition](../../IAO/15/IAO_0000115.md) A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. + * http://purl.obolibrary.org/obo/RO_0002603 [definition](../../IAO/15/IAO_0000115.md) x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y + * http://purl.obolibrary.org/obo/RO_0002604 [definition](../../IAO/15/IAO_0000115.md) x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + * http://purl.obolibrary.org/obo/RO_0002605 [definition](../../IAO/15/IAO_0000115.md) x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + * http://purl.obolibrary.org/obo/RO_0002606 [definition](../../IAO/15/IAO_0000115.md) c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. + * http://purl.obolibrary.org/obo/RO_0002607 [definition](../../IAO/15/IAO_0000115.md) c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. + * http://purl.obolibrary.org/obo/RO_0002609 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + * http://purl.obolibrary.org/obo/RO_0002610 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + * http://purl.obolibrary.org/obo/RO_0003000 [definition](../../IAO/15/IAO_0000115.md) a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + * http://purl.obolibrary.org/obo/RO_0003002 [definition](../../IAO/15/IAO_0000115.md) Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. + * http://purl.obolibrary.org/obo/RO_0003003 [definition](../../IAO/15/IAO_0000115.md) Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. + * http://purl.obolibrary.org/obo/RO_0003301 [definition](../../IAO/15/IAO_0000115.md) Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + * http://purl.obolibrary.org/obo/RO_HOM0000000 [definition](../../IAO/15/IAO_0000115.md) Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + * http://purl.obolibrary.org/obo/RO_HOM0000001 [definition](../../IAO/15/IAO_0000115.md) Similarity that results from common evolutionary origin. + * http://purl.obolibrary.org/obo/RO_HOM0000002 [definition](../../IAO/15/IAO_0000115.md) Similarity that results from independent evolution. + * http://purl.obolibrary.org/obo/RO_HOM0000003 [definition](../../IAO/15/IAO_0000115.md) Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + * http://purl.obolibrary.org/obo/RO_HOM0000004 [definition](../../IAO/15/IAO_0000115.md) Homoplasy that involves different underlying mechanisms or structures. + * http://purl.obolibrary.org/obo/RO_HOM0000005 [definition](../../IAO/15/IAO_0000115.md) Homoplasy that involves homologous underlying mechanisms or structures. + * http://purl.obolibrary.org/obo/RO_HOM0000006 [definition](../../IAO/15/IAO_0000115.md) Homology that is defined by similarity with regard to selected structural parameters. + * http://purl.obolibrary.org/obo/RO_HOM0000007 [definition](../../IAO/15/IAO_0000115.md) Homology that is defined by common descent. + * http://purl.obolibrary.org/obo/RO_HOM0000008 [definition](../../IAO/15/IAO_0000115.md) Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + * http://purl.obolibrary.org/obo/RO_HOM0000009 [definition](../../IAO/15/IAO_0000115.md) Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + * http://purl.obolibrary.org/obo/RO_HOM0000010 [definition](../../IAO/15/IAO_0000115.md) Structural homology that is detected by similarity in content and organization between chromosomes. + * http://purl.obolibrary.org/obo/RO_HOM0000011 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves genes that diverged after a duplication event. + * http://purl.obolibrary.org/obo/RO_HOM0000012 [definition](../../IAO/15/IAO_0000115.md) Paralogy that involves sets of syntenic blocks. + * http://purl.obolibrary.org/obo/RO_HOM0000013 [definition](../../IAO/15/IAO_0000115.md) Syntenic homology that involves chromosomes of different species. + * http://purl.obolibrary.org/obo/RO_HOM0000014 [definition](../../IAO/15/IAO_0000115.md) Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + * http://purl.obolibrary.org/obo/RO_HOM0000015 [definition](../../IAO/15/IAO_0000115.md) Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + * http://purl.obolibrary.org/obo/RO_HOM0000016 [definition](../../IAO/15/IAO_0000115.md) Structural homology that involves a pseudogenic feature and its functional ancestor. + * http://purl.obolibrary.org/obo/RO_HOM0000017 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves genes that diverged after a speciation event. + * http://purl.obolibrary.org/obo/RO_HOM0000018 [definition](../../IAO/15/IAO_0000115.md) Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + * http://purl.obolibrary.org/obo/RO_HOM0000019 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves two members sharing no other homologs in the lineages considered. + * http://purl.obolibrary.org/obo/RO_HOM0000020 [definition](../../IAO/15/IAO_0000115.md) Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + * http://purl.obolibrary.org/obo/RO_HOM0000022 [definition](../../IAO/15/IAO_0000115.md) Paralogy that results from a whole genome duplication event. + * http://purl.obolibrary.org/obo/RO_HOM0000023 [definition](../../IAO/15/IAO_0000115.md) Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + * http://purl.obolibrary.org/obo/RO_HOM0000024 [definition](../../IAO/15/IAO_0000115.md) Paralogy that results from a duplication preceding a given speciation event. + * http://purl.obolibrary.org/obo/RO_HOM0000025 [definition](../../IAO/15/IAO_0000115.md) 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + * http://purl.obolibrary.org/obo/RO_HOM0000026 [definition](../../IAO/15/IAO_0000115.md) 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + * http://purl.obolibrary.org/obo/RO_HOM0000027 [definition](../../IAO/15/IAO_0000115.md) Iterative homology that involves structures arranged along the main body axis. + * http://purl.obolibrary.org/obo/RO_HOM0000028 [definition](../../IAO/15/IAO_0000115.md) Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + * http://purl.obolibrary.org/obo/RO_HOM0000029 [definition](../../IAO/15/IAO_0000115.md) Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + * http://purl.obolibrary.org/obo/RO_HOM0000030 [definition](../../IAO/15/IAO_0000115.md) Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + * http://purl.obolibrary.org/obo/RO_HOM0000031 [definition](../../IAO/15/IAO_0000115.md) Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + * http://purl.obolibrary.org/obo/RO_HOM0000032 [definition](../../IAO/15/IAO_0000115.md) Paedomorphosis that is produced by a retardation of somatic development. + * http://purl.obolibrary.org/obo/RO_HOM0000033 [definition](../../IAO/15/IAO_0000115.md) Convergence that results from co-evolution usually involving an evolutionary arms race. + * http://purl.obolibrary.org/obo/RO_HOM0000034 [definition](../../IAO/15/IAO_0000115.md) Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + * http://purl.obolibrary.org/obo/RO_HOM0000036 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves two members of a larger set of homologs. + * http://purl.obolibrary.org/obo/RO_HOM0000037 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + * http://purl.obolibrary.org/obo/RO_HOM0000042 [definition](../../IAO/15/IAO_0000115.md) Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + * http://purl.obolibrary.org/obo/RO_HOM0000043 [definition](../../IAO/15/IAO_0000115.md) Historical homology that is based on distant shared ancestry. + * http://purl.obolibrary.org/obo/RO_HOM0000044 [definition](../../IAO/15/IAO_0000115.md) Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + * http://purl.obolibrary.org/obo/RO_HOM0000045 [definition](../../IAO/15/IAO_0000115.md) Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + * http://purl.obolibrary.org/obo/RO_HOM0000046 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + * http://purl.obolibrary.org/obo/RO_HOM0000047 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + * http://purl.obolibrary.org/obo/RO_HOM0000048 [definition](../../IAO/15/IAO_0000115.md) Orthology that involves two genes that experienced duplications more recent than the species split that created them. + * http://purl.obolibrary.org/obo/RO_HOM0000049 [definition](../../IAO/15/IAO_0000115.md) Paralogy that involves genes from the same species. + * http://purl.obolibrary.org/obo/RO_HOM0000050 [definition](../../IAO/15/IAO_0000115.md) Paralogy that involves genes from different species. + * http://purl.obolibrary.org/obo/RO_HOM0000051 [definition](../../IAO/15/IAO_0000115.md) Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + * http://purl.obolibrary.org/obo/RO_HOM0000052 [definition](../../IAO/15/IAO_0000115.md) Peramorphosis that is produced by a delay in the offset of development. + * http://purl.obolibrary.org/obo/RO_HOM0000053 [definition](../../IAO/15/IAO_0000115.md) Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + * http://purl.obolibrary.org/obo/RO_HOM0000054 [definition](../../IAO/15/IAO_0000115.md) Orthology that involves functional equivalent genes with retention of the ancestral function. + * http://purl.obolibrary.org/obo/RO_HOM0000055 [definition](../../IAO/15/IAO_0000115.md) Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + * http://purl.obolibrary.org/obo/RO_HOM0000057 [definition](../../IAO/15/IAO_0000115.md) Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + * http://purl.obolibrary.org/obo/RO_HOM0000058 [definition](../../IAO/15/IAO_0000115.md) Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + * http://purl.obolibrary.org/obo/RO_HOM0000060 [definition](../../IAO/15/IAO_0000115.md) Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + * http://purl.obolibrary.org/obo/RO_HOM0000061 [definition](../../IAO/15/IAO_0000115.md) Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + * http://purl.obolibrary.org/obo/RO_HOM0000062 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves functional equivalent genes with retention of the ancestral function. + * http://purl.obolibrary.org/obo/RO_HOM0000063 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves orthologous pairs of interacting molecules in different organisms. + * http://purl.obolibrary.org/obo/RO_HOM0000065 [definition](../../IAO/15/IAO_0000115.md) Similarity that is characterized by interchangeability in function. + * http://purl.obolibrary.org/obo/RO_HOM0000066 [definition](../../IAO/15/IAO_0000115.md) Biological homology that involves parts of the same organism. + * http://purl.obolibrary.org/obo/RO_HOM0000068 [definition](../../IAO/15/IAO_0000115.md) Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + * http://purl.obolibrary.org/obo/RO_HOM0000069 [definition](../../IAO/15/IAO_0000115.md) Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + * http://purl.obolibrary.org/obo/RO_HOM0000071 [definition](../../IAO/15/IAO_0000115.md) Structural homology that involves structures with the same or similar relative positions. + * http://purl.obolibrary.org/obo/RO_HOM0000072 [definition](../../IAO/15/IAO_0000115.md) Biological homology that involves an ectopic structure and the normally positioned structure. + * http://purl.obolibrary.org/obo/RO_HOM0000073 [definition](../../IAO/15/IAO_0000115.md) Synology that results from allopolyploidy. + * http://purl.obolibrary.org/obo/RO_HOM0000074 [definition](../../IAO/15/IAO_0000115.md) Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + * http://purl.obolibrary.org/obo/RO_HOM0000075 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + +## External Comments + diff --git a/src/ontology/md/IAO/16/IAO_0000116.md b/src/ontology/md/IAO/16/IAO_0000116.md new file mode 100644 index 00000000..10b82f89 --- /dev/null +++ b/src/ontology/md/IAO/16/IAO_0000116.md @@ -0,0 +1,150 @@ + +## Class : editor note + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000116 + * *Label* = editor note + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000122 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = editor note + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000050 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/BFO_0000050 [editor note](../../IAO/16/IAO_0000116.md) 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 + * http://purl.obolibrary.org/obo/BFO_0000050 [editor note](../../IAO/16/IAO_0000116.md) 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'. + * http://purl.obolibrary.org/obo/BFO_0000051 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/BFO_0000051 [editor note](../../IAO/16/IAO_0000116.md) 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 + * http://purl.obolibrary.org/obo/BFO_0000051 [editor note](../../IAO/16/IAO_0000116.md) 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'. + * http://purl.obolibrary.org/obo/BFO_0000062 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0000052 [editor note](../../IAO/16/IAO_0000116.md) A dependent inheres in its bearer at all times for which the dependent exists. + * http://purl.obolibrary.org/obo/RO_0000053 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0000057 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0000079 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0000080 [editor note](../../IAO/16/IAO_0000116.md) A quality inheres in its bearer at all times for which the quality exists. + * http://purl.obolibrary.org/obo/RO_0000081 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0000085 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0000086 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0000087 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0001000 [editor note](../../IAO/16/IAO_0000116.md) This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + * http://purl.obolibrary.org/obo/RO_0001001 [editor note](../../IAO/16/IAO_0000116.md) 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'. + * http://purl.obolibrary.org/obo/RO_0001015 [editor note](../../IAO/16/IAO_0000116.md) 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 + * http://purl.obolibrary.org/obo/RO_0001018 [editor note](../../IAO/16/IAO_0000116.md) Containment is location not involving parthood, and arises only where some immaterial continuant is involved. + * http://purl.obolibrary.org/obo/RO_0001018 [editor note](../../IAO/16/IAO_0000116.md) 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): + * http://purl.obolibrary.org/obo/RO_0001018 [editor note](../../IAO/16/IAO_0000116.md) Intended meaning: +domain: material entity +range: spatial region or site (immaterial continuant) + + * http://purl.obolibrary.org/obo/RO_0001025 [editor note](../../IAO/16/IAO_0000116.md) 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 + * http://purl.obolibrary.org/obo/RO_0001025 [editor note](../../IAO/16/IAO_0000116.md) 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 + * http://purl.obolibrary.org/obo/RO_0002000 [editor note](../../IAO/16/IAO_0000116.md) A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + * http://purl.obolibrary.org/obo/RO_0002000 [editor note](../../IAO/16/IAO_0000116.md) Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + * http://purl.obolibrary.org/obo/RO_0002002 [editor note](../../IAO/16/IAO_0000116.md) A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + * http://purl.obolibrary.org/obo/RO_0002002 [editor note](../../IAO/16/IAO_0000116.md) Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + * http://purl.obolibrary.org/obo/RO_0002008 [editor note](../../IAO/16/IAO_0000116.md) Note from NCEAS meeting: consider changing primary label + * http://purl.obolibrary.org/obo/RO_0002151 [editor note](../../IAO/16/IAO_0000116.md) We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom + * http://purl.obolibrary.org/obo/RO_0002160 [editor note](../../IAO/16/IAO_0000116.md) The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. + + 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria + * http://purl.obolibrary.org/obo/RO_0002163 [editor note](../../IAO/16/IAO_0000116.md) There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. + * http://purl.obolibrary.org/obo/RO_0002178 [editor note](../../IAO/16/IAO_0000116.md) Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure + * http://purl.obolibrary.org/obo/RO_0002179 [editor note](../../IAO/16/IAO_0000116.md) Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure + * http://purl.obolibrary.org/obo/RO_0002180 [editor note](../../IAO/16/IAO_0000116.md) The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + * http://purl.obolibrary.org/obo/RO_0002204 [editor note](../../IAO/16/IAO_0000116.md) We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. + * http://purl.obolibrary.org/obo/RO_0002211 [editor note](../../IAO/16/IAO_0000116.md) 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 + * http://purl.obolibrary.org/obo/RO_0002214 [editor note](../../IAO/16/IAO_0000116.md) Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + * http://purl.obolibrary.org/obo/RO_0002214 [editor note](../../IAO/16/IAO_0000116.md) This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. + * http://purl.obolibrary.org/obo/RO_0002218 [editor note](../../IAO/16/IAO_0000116.md) This may be obsoleted and replaced by the original 'has agent' relation + * http://purl.obolibrary.org/obo/RO_0002220 [editor note](../../IAO/16/IAO_0000116.md) This relation acts as a join point with BSPO + * http://purl.obolibrary.org/obo/RO_0002258 [editor note](../../IAO/16/IAO_0000116.md) false + * http://purl.obolibrary.org/obo/RO_0002285 [editor note](../../IAO/16/IAO_0000116.md) This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage + * http://purl.obolibrary.org/obo/RO_0002291 [editor note](../../IAO/16/IAO_0000116.md) Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. + * http://purl.obolibrary.org/obo/RO_0002295 [editor note](../../IAO/16/IAO_0000116.md) This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. + * http://purl.obolibrary.org/obo/RO_0002314 [editor note](../../IAO/16/IAO_0000116.md) Because part_of is transitive, inheres in is a sub-relation of inheres in part of + * http://purl.obolibrary.org/obo/RO_0002322 [editor note](../../IAO/16/IAO_0000116.md) An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. + * http://purl.obolibrary.org/obo/RO_0002326 [editor note](../../IAO/16/IAO_0000116.md) We would like to say + +if and only if + exists c', p' + c part_of c' and c' capable_of p + and + c capable_of p' and p' part_of p +then + c contributes_to p + +However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. + * http://purl.obolibrary.org/obo/RO_0002410 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0002413 [editor note](../../IAO/16/IAO_0000116.md) This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit + * http://purl.obolibrary.org/obo/RO_0002418 [editor note](../../IAO/16/IAO_0000116.md) We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + * http://purl.obolibrary.org/obo/RO_0002420 [editor note](../../IAO/16/IAO_0000116.md) The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL + * http://purl.obolibrary.org/obo/RO_0002424 [editor note](../../IAO/16/IAO_0000116.md) false + * http://purl.obolibrary.org/obo/RO_0002434 [editor note](../../IAO/16/IAO_0000116.md) Considering relabeling as 'pairwise interacts with' + * http://purl.obolibrary.org/obo/RO_0002434 [editor note](../../IAO/16/IAO_0000116.md) 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. + * http://purl.obolibrary.org/obo/RO_0002435 [editor note](../../IAO/16/IAO_0000116.md) An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) + * http://purl.obolibrary.org/obo/RO_0002447 [editor note](../../IAO/16/IAO_0000116.md) Axiomatization to GO to be added later + * http://purl.obolibrary.org/obo/RO_0002451 [editor note](../../IAO/16/IAO_0000116.md) Add domain and range constraints + * http://purl.obolibrary.org/obo/RO_0002455 [editor note](../../IAO/16/IAO_0000116.md) This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. + * http://purl.obolibrary.org/obo/RO_0002480 [editor note](../../IAO/16/IAO_0000116.md) Axiomatization to GO to be added later + * http://purl.obolibrary.org/obo/RO_0002485 [editor note](../../IAO/16/IAO_0000116.md) See notes for inverse relation + * http://purl.obolibrary.org/obo/RO_0002486 [editor note](../../IAO/16/IAO_0000116.md) This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. + * http://purl.obolibrary.org/obo/RO_0002503 [editor note](../../IAO/16/IAO_0000116.md) This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + * http://purl.obolibrary.org/obo/RO_0002504 [editor note](../../IAO/16/IAO_0000116.md) This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. + * http://purl.obolibrary.org/obo/RO_0002506 [editor note](../../IAO/16/IAO_0000116.md) 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 + * http://purl.obolibrary.org/obo/RO_0002507 [editor note](../../IAO/16/IAO_0000116.md) The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future + * http://purl.obolibrary.org/obo/RO_0002520 [editor note](../../IAO/16/IAO_0000116.md) In the SO paper, this was defined as an instance-type relation + * http://purl.obolibrary.org/obo/RO_0002575 [editor note](../../IAO/16/IAO_0000116.md) The general property hierarchy is: + + "directly P" SubPropertyOf "P" + Transitive(P) + +Where we have an annotation assertion + + "directly P" "is direct form of" "P" + * http://purl.obolibrary.org/obo/RO_0002577 [editor note](../../IAO/16/IAO_0000116.md) May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 + * http://purl.obolibrary.org/obo/RO_0002585 [editor note](../../IAO/16/IAO_0000116.md) p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. + * http://purl.obolibrary.org/obo/RO_0002595 [editor note](../../IAO/16/IAO_0000116.md) Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * http://purl.obolibrary.org/obo/RO_0002607 [editor note](../../IAO/16/IAO_0000116.md) May be ceded to OBI + * http://purl.obolibrary.org/obo/RO_0003002 [editor note](../../IAO/16/IAO_0000116.md) Logical axioms to be added after the relevant branch of GO is MIREOTed in + * http://purl.obolibrary.org/obo/RO_0003003 [editor note](../../IAO/16/IAO_0000116.md) Logical axioms to be added after the relevant branch of GO is MIREOTed in + * http://purl.obolibrary.org/obo/RO_0003301 [editor note](../../IAO/16/IAO_0000116.md) To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + +## External Comments + diff --git a/src/ontology/md/IAO/17/IAO_0000117.md b/src/ontology/md/IAO/17/IAO_0000117.md new file mode 100644 index 00000000..d51c52ba --- /dev/null +++ b/src/ontology/md/IAO/17/IAO_0000117.md @@ -0,0 +1,367 @@ + +## Class : term editor + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000117 + * *Label* = term editor + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000122 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = term editor + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0000300 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0000301 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0000302 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002001 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002002 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002003 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002004 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002005 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002006 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002007 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002008 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002009 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002010 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002011 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002081 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002082 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002083 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002084 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002085 [term editor](../../IAO/17/IAO_0000117.md) David Osumi-Sutherland + * http://purl.obolibrary.org/obo/RO_0002086 [term 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editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002374 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002375 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002376 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002377 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002378 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002379 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002380 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002381 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002382 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002383 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002384 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002385 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002386 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002387 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002388 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002400 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002401 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002402 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002403 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002404 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002405 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002406 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002407 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002408 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002409 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002410 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002411 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002412 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002413 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002414 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002418 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002424 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002425 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002426 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002427 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002428 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002429 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002430 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002431 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002432 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002433 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002434 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002435 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002436 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002437 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002438 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002439 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002440 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002441 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002442 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002443 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002444 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002445 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002446 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002447 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002448 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002449 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002450 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002451 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002452 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002453 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002454 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002455 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002456 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002457 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002458 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002459 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002460 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002461 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002462 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002463 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002464 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002465 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002466 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002467 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002468 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002469 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002470 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002471 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002472 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002473 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002476 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002477 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002478 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002479 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002480 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002481 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002482 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002485 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002486 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002487 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002488 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002489 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002490 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002491 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002492 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002493 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002494 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002495 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002496 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002497 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002501 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002502 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002503 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002505 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002506 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002507 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002508 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002509 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002510 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002511 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002512 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002513 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002514 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002515 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002516 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002517 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002518 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002519 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002520 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002521 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002522 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002523 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002524 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002525 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002526 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002527 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002528 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002529 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002530 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002531 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002532 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002533 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002534 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002551 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002552 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002553 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002554 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002555 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002556 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002557 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002558 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002559 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002563 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002564 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002565 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002566 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002567 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002568 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002569 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002570 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002571 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002572 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002573 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002574 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002576 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002577 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002578 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002584 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002595 [term editor](../../IAO/17/IAO_0000117.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0003000 [term editor](../../IAO/17/IAO_0000117.md) Melissa Haendel + * http://purl.obolibrary.org/obo/RO_0003001 [term editor](../../IAO/17/IAO_0000117.md) Melissa Haendel + * http://purl.obolibrary.org/obo/RO_0003301 [term editor](../../IAO/17/IAO_0000117.md) Matthew Brush + +## External Comments + diff --git a/src/ontology/md/IAO/18/IAO_0000118.md b/src/ontology/md/IAO/18/IAO_0000118.md new file mode 100644 index 00000000..bae061bc --- /dev/null +++ b/src/ontology/md/IAO/18/IAO_0000118.md @@ -0,0 +1,163 @@ + +## Class : alternative term + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000118 + * *Label* = alternative term + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = alternative term + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000050 [alternative term](../../IAO/18/IAO_0000118.md) part_of + * http://purl.obolibrary.org/obo/BFO_0000051 [alternative term](../../IAO/18/IAO_0000118.md) has_part + * http://purl.obolibrary.org/obo/BFO_0000054 [alternative term](../../IAO/18/IAO_0000118.md) is realized by + * http://purl.obolibrary.org/obo/BFO_0000054 [alternative term](../../IAO/18/IAO_0000118.md) realized_in + * http://purl.obolibrary.org/obo/BFO_0000062 [alternative term](../../IAO/18/IAO_0000118.md) is preceded by + * http://purl.obolibrary.org/obo/BFO_0000062 [alternative term](../../IAO/18/IAO_0000118.md) preceded_by + * http://purl.obolibrary.org/obo/BFO_0000066 [alternative term](../../IAO/18/IAO_0000118.md) occurs_in + * http://purl.obolibrary.org/obo/BFO_0000066 [alternative term](../../IAO/18/IAO_0000118.md) unfolds in + * http://purl.obolibrary.org/obo/BFO_0000066 [alternative term](../../IAO/18/IAO_0000118.md) unfolds_in + * http://purl.obolibrary.org/obo/RO_0000052 [alternative term](../../IAO/18/IAO_0000118.md) inheres_in + * http://purl.obolibrary.org/obo/RO_0000053 [alternative term](../../IAO/18/IAO_0000118.md) bearer_of + * http://purl.obolibrary.org/obo/RO_0000053 [alternative term](../../IAO/18/IAO_0000118.md) is bearer of + * http://purl.obolibrary.org/obo/RO_0000056 [alternative term](../../IAO/18/IAO_0000118.md) participates_in + * http://purl.obolibrary.org/obo/RO_0000057 [alternative term](../../IAO/18/IAO_0000118.md) has_participant + * http://purl.obolibrary.org/obo/RO_0000079 [alternative term](../../IAO/18/IAO_0000118.md) function_of + * http://purl.obolibrary.org/obo/RO_0000079 [alternative term](../../IAO/18/IAO_0000118.md) is function of + * http://purl.obolibrary.org/obo/RO_0000080 [alternative term](../../IAO/18/IAO_0000118.md) is quality of + * http://purl.obolibrary.org/obo/RO_0000080 [alternative term](../../IAO/18/IAO_0000118.md) quality_of + * http://purl.obolibrary.org/obo/RO_0000081 [alternative term](../../IAO/18/IAO_0000118.md) is role of + * http://purl.obolibrary.org/obo/RO_0000081 [alternative term](../../IAO/18/IAO_0000118.md) role_of + * http://purl.obolibrary.org/obo/RO_0000085 [alternative term](../../IAO/18/IAO_0000118.md) has_function + * http://purl.obolibrary.org/obo/RO_0000086 [alternative term](../../IAO/18/IAO_0000118.md) has_quality + * http://purl.obolibrary.org/obo/RO_0000087 [alternative term](../../IAO/18/IAO_0000118.md) has_role + * http://purl.obolibrary.org/obo/RO_0001000 [alternative term](../../IAO/18/IAO_0000118.md) derives_from + * http://purl.obolibrary.org/obo/RO_0001001 [alternative term](../../IAO/18/IAO_0000118.md) derives_into + * http://purl.obolibrary.org/obo/RO_0001015 [alternative term](../../IAO/18/IAO_0000118.md) location_of + * http://purl.obolibrary.org/obo/RO_0001018 [alternative term](../../IAO/18/IAO_0000118.md) contained_in + * http://purl.obolibrary.org/obo/RO_0001025 [alternative term](../../IAO/18/IAO_0000118.md) located_in + * http://purl.obolibrary.org/obo/RO_0002000 [alternative term](../../IAO/18/IAO_0000118.md) 2D_boundary_of + * http://purl.obolibrary.org/obo/RO_0002000 [alternative term](../../IAO/18/IAO_0000118.md) boundary of + * http://purl.obolibrary.org/obo/RO_0002000 [alternative term](../../IAO/18/IAO_0000118.md) is 2D boundary of + * http://purl.obolibrary.org/obo/RO_0002000 [alternative term](../../IAO/18/IAO_0000118.md) is boundary of + * http://purl.obolibrary.org/obo/RO_0002002 [alternative term](../../IAO/18/IAO_0000118.md) has boundary + * http://purl.obolibrary.org/obo/RO_0002002 [alternative term](../../IAO/18/IAO_0000118.md) has_2D_boundary + * http://purl.obolibrary.org/obo/RO_0002081 [alternative term](../../IAO/18/IAO_0000118.md) <= + * http://purl.obolibrary.org/obo/RO_0002085 [alternative term](../../IAO/18/IAO_0000118.md) di + * http://purl.obolibrary.org/obo/RO_0002087 [alternative term](../../IAO/18/IAO_0000118.md) starts_at_end_of + * http://purl.obolibrary.org/obo/RO_0002090 [alternative term](../../IAO/18/IAO_0000118.md) ends_at_start_of + * http://purl.obolibrary.org/obo/RO_0002090 [alternative term](../../IAO/18/IAO_0000118.md) meets + * http://purl.obolibrary.org/obo/RO_0002091 [alternative term](../../IAO/18/IAO_0000118.md) io + * http://purl.obolibrary.org/obo/RO_0002092 [alternative term](../../IAO/18/IAO_0000118.md) d + * http://purl.obolibrary.org/obo/RO_0002092 [alternative term](../../IAO/18/IAO_0000118.md) during + * http://purl.obolibrary.org/obo/RO_0002093 [alternative term](../../IAO/18/IAO_0000118.md) o + * http://purl.obolibrary.org/obo/RO_0002093 [alternative term](../../IAO/18/IAO_0000118.md) overlaps + * http://purl.obolibrary.org/obo/RO_0002101 [alternative term](../../IAO/18/IAO_0000118.md) fasciculates with + * http://purl.obolibrary.org/obo/RO_0002110 [alternative term](../../IAO/18/IAO_0000118.md) synapsed in + * http://purl.obolibrary.org/obo/RO_0002111 [alternative term](../../IAO/18/IAO_0000118.md) has neurotransmitter + * http://purl.obolibrary.org/obo/RO_0002113 [alternative term](../../IAO/18/IAO_0000118.md) synapses in + * http://purl.obolibrary.org/obo/RO_0002130 [alternative term](../../IAO/18/IAO_0000118.md) has synapse in + * http://purl.obolibrary.org/obo/RO_0002132 [alternative term](../../IAO/18/IAO_0000118.md) has fasciculating component + * http://purl.obolibrary.org/obo/RO_0002150 [alternative term](../../IAO/18/IAO_0000118.md) connected to + * http://purl.obolibrary.org/obo/RO_0002151 [alternative term](../../IAO/18/IAO_0000118.md) proper overlaps + * http://purl.obolibrary.org/obo/RO_0002156 [alternative term](../../IAO/18/IAO_0000118.md) ancestral_stucture_of + * http://purl.obolibrary.org/obo/RO_0002156 [alternative term](../../IAO/18/IAO_0000118.md) evolutionarily_descended_from + * http://purl.obolibrary.org/obo/RO_0002171 [alternative term](../../IAO/18/IAO_0000118.md) non-overlapping with + * http://purl.obolibrary.org/obo/RO_0002171 [alternative term](../../IAO/18/IAO_0000118.md) shares no parts with + * http://purl.obolibrary.org/obo/RO_0002210 [alternative term](../../IAO/18/IAO_0000118.md) developmental precursor of + * http://purl.obolibrary.org/obo/RO_0002215 [alternative term](../../IAO/18/IAO_0000118.md) has function realized in + * http://purl.obolibrary.org/obo/RO_0002216 [alternative term](../../IAO/18/IAO_0000118.md) has function in + * http://purl.obolibrary.org/obo/RO_0002217 [alternative term](../../IAO/18/IAO_0000118.md) agent in + * http://purl.obolibrary.org/obo/RO_0002218 [alternative term](../../IAO/18/IAO_0000118.md) has agent + * http://purl.obolibrary.org/obo/RO_0002224 [alternative term](../../IAO/18/IAO_0000118.md) started by + * http://purl.obolibrary.org/obo/RO_0002230 [alternative term](../../IAO/18/IAO_0000118.md) finished by + * http://purl.obolibrary.org/obo/RO_0002231 [alternative term](../../IAO/18/IAO_0000118.md) starts with process that occurs in + * http://purl.obolibrary.org/obo/RO_0002232 [alternative term](../../IAO/18/IAO_0000118.md) ends with process that occurs in + * http://purl.obolibrary.org/obo/RO_0002233 [alternative term](../../IAO/18/IAO_0000118.md) consumes + * http://purl.obolibrary.org/obo/RO_0002234 [alternative term](../../IAO/18/IAO_0000118.md) produces + * http://purl.obolibrary.org/obo/RO_0002256 [alternative term](../../IAO/18/IAO_0000118.md) induced by + * http://purl.obolibrary.org/obo/RO_0002285 [alternative term](../../IAO/18/IAO_0000118.md) replaces + * http://purl.obolibrary.org/obo/RO_0002303 [alternative term](../../IAO/18/IAO_0000118.md) adapted for living in + * http://purl.obolibrary.org/obo/RO_0002313 [alternative term](../../IAO/18/IAO_0000118.md) regulates location of + * http://purl.obolibrary.org/obo/RO_0002313 [alternative term](../../IAO/18/IAO_0000118.md) transports + * http://purl.obolibrary.org/obo/RO_0002322 [alternative term](../../IAO/18/IAO_0000118.md) adapted for + * http://purl.obolibrary.org/obo/RO_0002327 [alternative term](../../IAO/18/IAO_0000118.md) catalyzes + * http://purl.obolibrary.org/obo/RO_0002327 [alternative term](../../IAO/18/IAO_0000118.md) executes + * http://purl.obolibrary.org/obo/RO_0002327 [alternative term](../../IAO/18/IAO_0000118.md) has + * http://purl.obolibrary.org/obo/RO_0002329 [alternative term](../../IAO/18/IAO_0000118.md) false + * http://purl.obolibrary.org/obo/RO_0002331 [alternative term](../../IAO/18/IAO_0000118.md) actively involved in + * http://purl.obolibrary.org/obo/RO_0002331 [alternative term](../../IAO/18/IAO_0000118.md) enables part of + * http://purl.obolibrary.org/obo/RO_0002350 [alternative term](../../IAO/18/IAO_0000118.md) is member of + * http://purl.obolibrary.org/obo/RO_0002350 [alternative term](../../IAO/18/IAO_0000118.md) member part of + * http://purl.obolibrary.org/obo/RO_0002376 [alternative term](../../IAO/18/IAO_0000118.md) drains into + * http://purl.obolibrary.org/obo/RO_0002376 [alternative term](../../IAO/18/IAO_0000118.md) drains to + * http://purl.obolibrary.org/obo/RO_0002376 [alternative term](../../IAO/18/IAO_0000118.md) tributary channel of + * http://purl.obolibrary.org/obo/RO_0002377 [alternative term](../../IAO/18/IAO_0000118.md) branch of + * http://purl.obolibrary.org/obo/RO_0002377 [alternative term](../../IAO/18/IAO_0000118.md) distributary channel of + * http://purl.obolibrary.org/obo/RO_0002378 [alternative term](../../IAO/18/IAO_0000118.md) anastomoses with + * http://purl.obolibrary.org/obo/RO_0002400 [alternative term](../../IAO/18/IAO_0000118.md) directly consumes + * http://purl.obolibrary.org/obo/RO_0002402 [alternative term](../../IAO/18/IAO_0000118.md) directly produces + * http://purl.obolibrary.org/obo/RO_0002406 [alternative term](../../IAO/18/IAO_0000118.md) directly positively regulates + * http://purl.obolibrary.org/obo/RO_0002407 [alternative term](../../IAO/18/IAO_0000118.md) indirectly positively regulates + * http://purl.obolibrary.org/obo/RO_0002408 [alternative term](../../IAO/18/IAO_0000118.md) directly negatively regulates + * http://purl.obolibrary.org/obo/RO_0002409 [alternative term](../../IAO/18/IAO_0000118.md) indirectly negatively regulates + * http://purl.obolibrary.org/obo/RO_0002418 [alternative term](../../IAO/18/IAO_0000118.md) influences (processual) + * http://purl.obolibrary.org/obo/RO_0002431 [alternative term](../../IAO/18/IAO_0000118.md) involved in or involved in regulation of + * http://purl.obolibrary.org/obo/RO_0002432 [alternative term](../../IAO/18/IAO_0000118.md) executes activity in + * http://purl.obolibrary.org/obo/RO_0002436 [alternative term](../../IAO/18/IAO_0000118.md) binds + * http://purl.obolibrary.org/obo/RO_0002436 [alternative term](../../IAO/18/IAO_0000118.md) molecularly binds with + * http://purl.obolibrary.org/obo/RO_0002437 [alternative term](../../IAO/18/IAO_0000118.md) interacts with on organism level + * http://purl.obolibrary.org/obo/RO_0002439 [alternative term](../../IAO/18/IAO_0000118.md) is subject of predation interaction with + * http://purl.obolibrary.org/obo/RO_0002439 [alternative term](../../IAO/18/IAO_0000118.md) preys upon + * http://purl.obolibrary.org/obo/RO_0002444 [alternative term](../../IAO/18/IAO_0000118.md) parasitizes + * http://purl.obolibrary.org/obo/RO_0002445 [alternative term](../../IAO/18/IAO_0000118.md) has parasite + * http://purl.obolibrary.org/obo/RO_0002445 [alternative term](../../IAO/18/IAO_0000118.md) parasitised by + * http://purl.obolibrary.org/obo/RO_0002447 [alternative term](../../IAO/18/IAO_0000118.md) An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + * http://purl.obolibrary.org/obo/RO_0002449 [alternative term](../../IAO/18/IAO_0000118.md) inhibits + * http://purl.obolibrary.org/obo/RO_0002450 [alternative term](../../IAO/18/IAO_0000118.md) activates + * http://purl.obolibrary.org/obo/RO_0002455 [alternative term](../../IAO/18/IAO_0000118.md) is subject of pollination interaction with + * http://purl.obolibrary.org/obo/RO_0002456 [alternative term](../../IAO/18/IAO_0000118.md) has polinator + * http://purl.obolibrary.org/obo/RO_0002456 [alternative term](../../IAO/18/IAO_0000118.md) is target of pollination interaction with + * http://purl.obolibrary.org/obo/RO_0002458 [alternative term](../../IAO/18/IAO_0000118.md) has predator + * http://purl.obolibrary.org/obo/RO_0002458 [alternative term](../../IAO/18/IAO_0000118.md) is target of predation interaction with + * http://purl.obolibrary.org/obo/RO_0002470 [alternative term](../../IAO/18/IAO_0000118.md) is subject of eating interaction with + * http://purl.obolibrary.org/obo/RO_0002471 [alternative term](../../IAO/18/IAO_0000118.md) is target of eating interaction with + * http://purl.obolibrary.org/obo/RO_0002475 [alternative term](../../IAO/18/IAO_0000118.md) shares no connection with + * http://purl.obolibrary.org/obo/RO_0002504 [alternative term](../../IAO/18/IAO_0000118.md) never lost in + * http://purl.obolibrary.org/obo/RO_0002505 [alternative term](../../IAO/18/IAO_0000118.md) has intermediate product + * http://purl.obolibrary.org/obo/RO_0002516 [alternative term](../../IAO/18/IAO_0000118.md) started by + * http://purl.obolibrary.org/obo/RO_0002517 [alternative term](../../IAO/18/IAO_0000118.md) starts + * http://purl.obolibrary.org/obo/RO_0002518 [alternative term](../../IAO/18/IAO_0000118.md) ended by + * http://purl.obolibrary.org/obo/RO_0002519 [alternative term](../../IAO/18/IAO_0000118.md) ends + * http://purl.obolibrary.org/obo/RO_0002524 [alternative term](../../IAO/18/IAO_0000118.md) contains + * http://purl.obolibrary.org/obo/RO_0002525 [alternative term](../../IAO/18/IAO_0000118.md) contained by + * http://purl.obolibrary.org/obo/RO_0002527 [alternative term](../../IAO/18/IAO_0000118.md) disconnected from + * http://purl.obolibrary.org/obo/RO_0002551 [alternative term](../../IAO/18/IAO_0000118.md) has supporting framework + * http://purl.obolibrary.org/obo/RO_0002599 [alternative term](../../IAO/18/IAO_0000118.md) treats + * http://purl.obolibrary.org/obo/RO_0002600 [alternative term](../../IAO/18/IAO_0000118.md) causes disease + * http://purl.obolibrary.org/obo/RO_0002606 [alternative term](../../IAO/18/IAO_0000118.md) treats + +## External Comments + diff --git a/src/ontology/md/IAO/19/IAO_0000119.md b/src/ontology/md/IAO/19/IAO_0000119.md new file mode 100644 index 00000000..4c4aa472 --- /dev/null +++ b/src/ontology/md/IAO/19/IAO_0000119.md @@ -0,0 +1,110 @@ + +## Class : definition source + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000119 + * *Label* = definition source + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000122 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = definition source + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002104 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/19243617 + * http://purl.obolibrary.org/obo/RO_0002160 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/17921072 + * http://purl.obolibrary.org/obo/RO_0002160 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20973947 + * http://purl.obolibrary.org/obo/RO_0002161 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/17921072 + * http://purl.obolibrary.org/obo/RO_0002161 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20973947 + * http://purl.obolibrary.org/obo/RO_0002162 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/17921072 + * http://purl.obolibrary.org/obo/RO_0002162 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20973947 + * http://purl.obolibrary.org/obo/RO_0002163 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * http://purl.obolibrary.org/obo/RO_0002170 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * http://purl.obolibrary.org/obo/RO_0002171 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * http://purl.obolibrary.org/obo/RO_0002174 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * http://purl.obolibrary.org/obo/RO_0002175 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * http://purl.obolibrary.org/obo/RO_0002176 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * http://purl.obolibrary.org/obo/RO_0002178 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * http://purl.obolibrary.org/obo/RO_0002179 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * http://purl.obolibrary.org/obo/RO_0002207 [definition source](../../IAO/19/IAO_0000119.md) FBbt + * http://purl.obolibrary.org/obo/RO_0002211 [definition source](../../IAO/19/IAO_0000119.md) GO + * http://purl.obolibrary.org/obo/RO_0002215 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20123131 + * http://purl.obolibrary.org/obo/RO_0002215 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/21208450 + * http://purl.obolibrary.org/obo/RO_0002222 [definition source](../../IAO/19/IAO_0000119.md) https://en.wikipedia.org/wiki/Allen%27s_interval_algebra + * http://purl.obolibrary.org/obo/RO_0002223 [definition source](../../IAO/19/IAO_0000119.md) Allen + * http://purl.obolibrary.org/obo/RO_0002226 [definition source](../../IAO/19/IAO_0000119.md) EHDAA2 + * http://purl.obolibrary.org/obo/RO_0002226 [definition source](../../IAO/19/IAO_0000119.md) Jonathan Bard, EHDAA2 + * http://purl.obolibrary.org/obo/RO_0002256 [definition source](../../IAO/19/IAO_0000119.md) Developmental Biology, Gilbert, 8th edition, figure 6.5(F) + * http://purl.obolibrary.org/obo/RO_0002256 [definition source](../../IAO/19/IAO_0000119.md) GO:0001759 + * http://purl.obolibrary.org/obo/RO_0002256 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * http://purl.obolibrary.org/obo/RO_0002296 [definition source](../../IAO/19/IAO_0000119.md) http://www.geneontology.org/GO.doc.development.shtml + * http://purl.obolibrary.org/obo/RO_0002297 [definition source](../../IAO/19/IAO_0000119.md) GOC:mtg_berkeley_2013 + * http://purl.obolibrary.org/obo/RO_0002298 [definition source](../../IAO/19/IAO_0000119.md) GOC:mtg_berkeley_2013 + * http://purl.obolibrary.org/obo/RO_0002299 [definition source](../../IAO/19/IAO_0000119.md) GOC:mtg_berkeley_2013 + * http://purl.obolibrary.org/obo/RO_0002314 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * http://purl.obolibrary.org/obo/RO_0002315 [definition source](../../IAO/19/IAO_0000119.md) GOC:mtg_berkeley_2013 + * http://purl.obolibrary.org/obo/RO_0002325 [definition source](../../IAO/19/IAO_0000119.md) http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with + * http://purl.obolibrary.org/obo/RO_0002326 [definition source](../../IAO/19/IAO_0000119.md) http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to + * http://purl.obolibrary.org/obo/RO_0002348 [definition source](../../IAO/19/IAO_0000119.md) http://www.geneontology.org/GO.doc.development.shtml#fate + * http://purl.obolibrary.org/obo/RO_0002349 [definition source](../../IAO/19/IAO_0000119.md) http://www.geneontology.org/GO.doc.development.shtml#fate + * http://purl.obolibrary.org/obo/RO_0002350 [definition source](../../IAO/19/IAO_0000119.md) SIO + * http://purl.obolibrary.org/obo/RO_0002351 [definition source](../../IAO/19/IAO_0000119.md) SIO + * http://purl.obolibrary.org/obo/RO_0002356 [definition source](../../IAO/19/IAO_0000119.md) http://www.geneontology.org/GO.doc.development.shtml#fate + * http://purl.obolibrary.org/obo/RO_0002372 [definition source](../../IAO/19/IAO_0000119.md) Wikipedia:Insertion_(anatomy) + * http://purl.obolibrary.org/obo/RO_0002373 [definition source](../../IAO/19/IAO_0000119.md) Wikipedia:Insertion_(anatomy) + * http://purl.obolibrary.org/obo/RO_0002374 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * http://purl.obolibrary.org/obo/RO_0002376 [definition source](../../IAO/19/IAO_0000119.md) http://en.wikipedia.org/wiki/Tributary + * http://purl.obolibrary.org/obo/RO_0002376 [definition source](../../IAO/19/IAO_0000119.md) http://www.medindia.net/glossary/venous_tributary.htm + * http://purl.obolibrary.org/obo/RO_0002377 [definition source](../../IAO/19/IAO_0000119.md) http://en.wikipedia.org/wiki/Distributary + * http://purl.obolibrary.org/obo/RO_0002440 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/19278549 + * http://purl.obolibrary.org/obo/RO_0002441 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/19278549 + * http://purl.obolibrary.org/obo/RO_0002442 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/19278549 + * http://purl.obolibrary.org/obo/RO_0002443 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/19278549 + * http://purl.obolibrary.org/obo/RO_0002459 [definition source](../../IAO/19/IAO_0000119.md) a is a vector for b if a carries and transmits an infectious pathogen b into another living organism + * http://purl.obolibrary.org/obo/RO_0002473 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * http://purl.obolibrary.org/obo/RO_0002501 [definition source](../../IAO/19/IAO_0000119.md) https://docs.google.com/document/d/1WxocTXZaGVhEV1n7NB86pCF3SUcBJh8bq4vQrVCkjSU/edit# + * http://purl.obolibrary.org/obo/RO_0002503 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * http://purl.obolibrary.org/obo/RO_0002507 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/24330602 + * http://purl.obolibrary.org/obo/RO_0002510 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002511 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002512 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002513 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002514 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002515 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002516 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002517 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002518 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002519 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002520 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002524 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * http://purl.obolibrary.org/obo/RO_0002553 [definition source](../../IAO/19/IAO_0000119.md) http://eol.org/schema/terms/hyperparasitoidOf + * http://purl.obolibrary.org/obo/RO_0002553 [definition source](../../IAO/19/IAO_0000119.md) https://en.wikipedia.org/wiki/Hyperparasite + * http://purl.obolibrary.org/obo/RO_0002555 [definition source](../../IAO/19/IAO_0000119.md) http://en.wikipedia.org/wiki/Allelopathy + * http://purl.obolibrary.org/obo/RO_0002558 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/25052702 + * http://purl.obolibrary.org/obo/RO_0002568 [definition source](../../IAO/19/IAO_0000119.md) Wikipedia:Antagonist_(muscle) + * http://purl.obolibrary.org/obo/RO_0002570 [definition source](../../IAO/19/IAO_0000119.md) UBERON:cjm + * http://purl.obolibrary.org/obo/RO_0002571 [definition source](../../IAO/19/IAO_0000119.md) GOC:cjm + * http://purl.obolibrary.org/obo/RO_0002573 [definition source](../../IAO/19/IAO_0000119.md) http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * http://purl.obolibrary.org/obo/RO_0002577 [definition source](../../IAO/19/IAO_0000119.md) http://www.jbiomedsem.com/content/4/1/43 + +## External Comments + diff --git a/src/ontology/md/IAO/24/IAO_0000424.md b/src/ontology/md/IAO/24/IAO_0000424.md new file mode 100644 index 00000000..b3a89e0e --- /dev/null +++ b/src/ontology/md/IAO/24/IAO_0000424.md @@ -0,0 +1,66 @@ + +## Class : expand expression to + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000424 + * *Label* = expand expression to + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = expand expression to + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002100 [expand expression to](../../IAO/24/IAO_0000424.md) some ( + and some ?Y) + * http://purl.obolibrary.org/obo/RO_0002102 [expand expression to](../../IAO/24/IAO_0000424.md) some ( + and some ( + and some ( + and some ?Y))) + * http://purl.obolibrary.org/obo/RO_0002103 [expand expression to](../../IAO/24/IAO_0000424.md) some ( that part_of some ( that has_part some ( that some Y?))) + * http://purl.obolibrary.org/obo/RO_0002104 [expand expression to](../../IAO/24/IAO_0000424.md) some ( and some ?Y) + * http://purl.obolibrary.org/obo/RO_0002105 [expand expression to](../../IAO/24/IAO_0000424.md) BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + * http://purl.obolibrary.org/obo/RO_0002106 [expand expression to](../../IAO/24/IAO_0000424.md) BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + * http://purl.obolibrary.org/obo/RO_0002107 [expand expression to](../../IAO/24/IAO_0000424.md) BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + * http://purl.obolibrary.org/obo/RO_0002108 [expand expression to](../../IAO/24/IAO_0000424.md) BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + * http://purl.obolibrary.org/obo/RO_0002109 [expand expression to](../../IAO/24/IAO_0000424.md) BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + * http://purl.obolibrary.org/obo/RO_0002110 [expand expression to](../../IAO/24/IAO_0000424.md) http://purl.obolibrary.org/obo/BFO_0000051 some ( + http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( + http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) + * http://purl.obolibrary.org/obo/RO_0002112 [expand expression to](../../IAO/24/IAO_0000424.md) BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + * http://purl.obolibrary.org/obo/RO_0002113 [expand expression to](../../IAO/24/IAO_0000424.md) some ( that some ( that some Y?) + * http://purl.obolibrary.org/obo/RO_0002114 [expand expression to](../../IAO/24/IAO_0000424.md) BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + * http://purl.obolibrary.org/obo/RO_0002115 [expand expression to](../../IAO/24/IAO_0000424.md) BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + * http://purl.obolibrary.org/obo/RO_0002120 [expand expression to](../../IAO/24/IAO_0000424.md) some ( that part_of some ( that some ( that some Y?))) + * http://purl.obolibrary.org/obo/RO_0002121 [expand expression to](../../IAO/24/IAO_0000424.md) some ( + and some ( + http://purl.obolibrary.org/obo/GO_0042734 and some ( + and some ?Y))) + * http://purl.obolibrary.org/obo/RO_0002130 [expand expression to](../../IAO/24/IAO_0000424.md) some ( that some Y?) + * http://purl.obolibrary.org/obo/RO_0002131 [expand expression to](../../IAO/24/IAO_0000424.md) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + * http://purl.obolibrary.org/obo/RO_0002134 [expand expression to](../../IAO/24/IAO_0000424.md) some ( that ( some ( that some Y?))) + * http://purl.obolibrary.org/obo/RO_0002163 [expand expression to](../../IAO/24/IAO_0000424.md) BFO_0000051 exactly 0 (BFO_0000050 some ?Y) + * http://purl.obolibrary.org/obo/RO_0002215 [expand expression to](../../IAO/24/IAO_0000424.md) RO_0000053 some (RO_0000054 only ?Y) + * http://purl.obolibrary.org/obo/RO_0002216 [expand expression to](../../IAO/24/IAO_0000424.md) RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + +## External Comments + diff --git a/src/ontology/md/IAO/25/IAO_0000425.md b/src/ontology/md/IAO/25/IAO_0000425.md new file mode 100644 index 00000000..58f5bf54 --- /dev/null +++ b/src/ontology/md/IAO/25/IAO_0000425.md @@ -0,0 +1,37 @@ + +## Class : expand assertion to + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000425 + * *Label* = expand assertion to + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = expand assertion to + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002161 [expand assertion to](../../IAO/25/IAO_0000425.md) ?X DisjointWith RO_0002162 some ?Y + * http://purl.obolibrary.org/obo/RO_0002171 [expand assertion to](../../IAO/25/IAO_0000425.md) Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) + * http://purl.obolibrary.org/obo/RO_0002475 [expand assertion to](../../IAO/25/IAO_0000425.md) Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) + +## External Comments + diff --git a/src/ontology/md/IAO/26/IAO_0000426.md b/src/ontology/md/IAO/26/IAO_0000426.md new file mode 100644 index 00000000..33ab0168 --- /dev/null +++ b/src/ontology/md/IAO/26/IAO_0000426.md @@ -0,0 +1,158 @@ + +## Class : first order logic expression + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000426 + * *Label* = first order logic expression + * *Definition* = An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on an object property](../../RO/22/RO_0002422.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = first order logic expression + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * http://purl.obolibrary.org/obo/RO_0000300 [first order logic expression](../../IAO/26/IAO_0000426.md) (forall (?x ?y) + (iff + (neural_circuit_path ?x ?y) + (and + ("neuron ; CL_0000540" ?x) + ("neuron ; CL_0000540" ?y) + (or + (synapsed_by ?x ?y) + (synapsed_to ?x ?y))))) + +(forall (...s ?x ?y ?z) + (iff + (neural_circuit_path ...s ?x ?y ?z) + (and + (neural_circuit_path ...s ?x ?y) + ("neuron ; CL_0000540" ?z) + (or + (synapsed_by ?y ?z) + (synapsed_to ?y ?z))))) + +(forall (?x ?y) + (iff + (in_neural_circuit_with ?x ?y) + (exists (...s) + (neural_circuit_path ?x ...s ?y)))) + * http://purl.obolibrary.org/obo/RO_0000301 [first order logic expression](../../IAO/26/IAO_0000426.md) (forall (?x ?y) + (iff + (upstream_neural_circuit_path ?x ?y) + (and + ("neuron ; CL_0000540" ?x) + ("neuron ; CL_0000540" ?y) + (synapsed_to ?x ?y)))) + + +(forall (...s ?x ?y ?z) + (iff + (upstream_neural_circuit_path ...s ?x ?y ?z ) + (and + (upstream_neural_circuit_path ...s ?x ?y) + ("neuron ; CL_0000540" ?z) + (synapsed_to ?y ?z)))) + +(forall (?x ?y) + (iff + (upstream_in_neural_circuit_with ?x ?y) + (exists (...s) + (upstream_neural_circuit_path ?x ...s ?y)))) + * http://purl.obolibrary.org/obo/RO_0000302 [first order logic expression](../../IAO/26/IAO_0000426.md) (forall (?x ?y) + (iff + (downstream_neural_circuit_path ?x ?y) + (and + ("neuron ; CL_0000540" ?x) + ("neuron ; CL_0000540" ?y) + (synapsed_by ?x ?y)))) + + +(forall (...s ?x ?y ?z) + (iff + (downstream_neural_circuit_path ...s ?x ?y ?z ) + (and + (downstream_neural_circuit_path ...s ?x ?y) + ("neuron ; CL_0000540" ?z) + (synapsed_by ?y ?z)))) + +(forall (?x ?y) + (iff + (downstream_in_neural_circuit_with ?x ?y) + (exists (...s) + (downstream_neural_circuit_path ?x ...s ?y)))) + + * http://purl.obolibrary.org/obo/RO_0002101 [first order logic expression](../../IAO/26/IAO_0000426.md) (forall (?x ?y) + (iff + (fasciculates_with ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron ; CL_0000540" ?x) + ("neuron projection bundle ; CARO_0001001" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500' " ?npbs) + (part_of ?npbs ?y) + (part_of ?nps ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + * http://purl.obolibrary.org/obo/RO_0002132 [first order logic expression](../../IAO/26/IAO_0000426.md) (forall (?x ?y) + (iff + (has_fasciculating_neuron_projection ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron projection bundle ; CARO_0001001" ?x) + ("neuron projection ; GO0043005" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500" ?npbs) + (part_of ?nps ?y) + (part_of ?npbs ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + + * http://purl.obolibrary.org/obo/RO_0002151 [first order logic expression](../../IAO/26/IAO_0000426.md) (forall (?x ?y) + (iff + (proper_overlaps ?x ?y) + (and + (overlaps ?x ?y) + (not (part_of ?x ?y)) + (not (part_of ?y ?x))))) + +## External Comments + diff --git a/src/ontology/md/IAO/32/IAO_0000232.md b/src/ontology/md/IAO/32/IAO_0000232.md new file mode 100644 index 00000000..e2295389 --- /dev/null +++ b/src/ontology/md/IAO/32/IAO_0000232.md @@ -0,0 +1,89 @@ + +## Class : curator note + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000232 + * *Label* = curator note + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000122 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = curator note + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0001000 [curator note](../../IAO/32/IAO_0000232.md) This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + * http://purl.obolibrary.org/obo/RO_0002150 [curator note](../../IAO/32/IAO_0000232.md) The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) + * http://purl.obolibrary.org/obo/RO_0002158 [curator note](../../IAO/32/IAO_0000232.md) Consider obsoleting and merging with child relation, 'in homology relationship with' + * http://purl.obolibrary.org/obo/RO_0002163 [curator note](../../IAO/32/IAO_0000232.md) Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy + * http://purl.obolibrary.org/obo/RO_0002180 [curator note](../../IAO/32/IAO_0000232.md) 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. + * http://purl.obolibrary.org/obo/RO_0002211 [curator note](../../IAO/32/IAO_0000232.md) Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. + * http://purl.obolibrary.org/obo/RO_0002215 [curator note](../../IAO/32/IAO_0000232.md) 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)". + * http://purl.obolibrary.org/obo/RO_0002222 [curator note](../../IAO/32/IAO_0000232.md) 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. + * http://purl.obolibrary.org/obo/RO_0002256 [curator note](../../IAO/32/IAO_0000232.md) We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] + * http://purl.obolibrary.org/obo/RO_0002258 [curator note](../../IAO/32/IAO_0000232.md) In general you should not use this relation to make assertions - use one of the more specific relations below this one + * http://purl.obolibrary.org/obo/RO_0002300 [curator note](../../IAO/32/IAO_0000232.md) May be merged into parent relation + * http://purl.obolibrary.org/obo/RO_0002301 [curator note](../../IAO/32/IAO_0000232.md) May be merged into parent relation + * http://purl.obolibrary.org/obo/RO_0002320 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + * http://purl.obolibrary.org/obo/RO_0002321 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + * http://purl.obolibrary.org/obo/RO_0002323 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + * http://purl.obolibrary.org/obo/RO_0002324 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development + * http://purl.obolibrary.org/obo/RO_0002325 [curator note](../../IAO/32/IAO_0000232.md) In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] + * http://purl.obolibrary.org/obo/RO_0002326 [curator note](../../IAO/32/IAO_0000232.md) In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + * http://purl.obolibrary.org/obo/RO_0002327 [curator note](../../IAO/32/IAO_0000232.md) This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + * http://purl.obolibrary.org/obo/RO_0002328 [curator note](../../IAO/32/IAO_0000232.md) This is a grouping relation that collects relations used for the purpose of connecting structure and function + * http://purl.obolibrary.org/obo/RO_0002330 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism + * http://purl.obolibrary.org/obo/RO_0002375 [curator note](../../IAO/32/IAO_0000232.md) This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) + * http://purl.obolibrary.org/obo/RO_0002376 [curator note](../../IAO/32/IAO_0000232.md) This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) + * http://purl.obolibrary.org/obo/RO_0002379 [curator note](../../IAO/32/IAO_0000232.md) This relation is added for formal completeness. It is unlikely to be used in many practical scenarios + * http://purl.obolibrary.org/obo/RO_0002400 [curator note](../../IAO/32/IAO_0000232.md) This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' + * http://purl.obolibrary.org/obo/RO_0002410 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * http://purl.obolibrary.org/obo/RO_0002414 [curator note](../../IAO/32/IAO_0000232.md) This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') + * http://purl.obolibrary.org/obo/RO_0002434 [curator note](../../IAO/32/IAO_0000232.md) 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. + * http://purl.obolibrary.org/obo/RO_0002440 [curator note](../../IAO/32/IAO_0000232.md) We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism + * http://purl.obolibrary.org/obo/RO_0002443 [curator note](../../IAO/32/IAO_0000232.md) This relation groups a pair of inverse relations, parasite of and parasitized by + * http://purl.obolibrary.org/obo/RO_0002453 [curator note](../../IAO/32/IAO_0000232.md) The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) + * http://purl.obolibrary.org/obo/RO_0002457 [curator note](../../IAO/32/IAO_0000232.md) Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. + * http://purl.obolibrary.org/obo/RO_0002461 [curator note](../../IAO/32/IAO_0000232.md) Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + * http://purl.obolibrary.org/obo/RO_0002462 [curator note](../../IAO/32/IAO_0000232.md) Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + * http://purl.obolibrary.org/obo/RO_0002463 [curator note](../../IAO/32/IAO_0000232.md) Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + * http://purl.obolibrary.org/obo/RO_0002464 [curator note](../../IAO/32/IAO_0000232.md) This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + * http://purl.obolibrary.org/obo/RO_0002476 [curator note](../../IAO/32/IAO_0000232.md) This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. + * http://purl.obolibrary.org/obo/RO_0002487 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. + * http://purl.obolibrary.org/obo/RO_0002501 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * http://purl.obolibrary.org/obo/RO_0002506 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * http://purl.obolibrary.org/obo/RO_0002514 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + * http://purl.obolibrary.org/obo/RO_0002514 [curator note](../../IAO/32/IAO_0000232.md) The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. + * http://purl.obolibrary.org/obo/RO_0002533 [curator note](../../IAO/32/IAO_0000232.md) An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. + * http://purl.obolibrary.org/obo/RO_0002534 [curator note](../../IAO/32/IAO_0000232.md) Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. + * http://purl.obolibrary.org/obo/RO_0002535 [curator note](../../IAO/32/IAO_0000232.md) This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. + * http://purl.obolibrary.org/obo/RO_0002547 [curator note](../../IAO/32/IAO_0000232.md) For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + * http://purl.obolibrary.org/obo/RO_0002551 [curator note](../../IAO/32/IAO_0000232.md) The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). + * http://purl.obolibrary.org/obo/RO_0002565 [curator note](../../IAO/32/IAO_0000232.md) + * http://purl.obolibrary.org/obo/RO_0002570 [curator note](../../IAO/32/IAO_0000232.md) This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. + * http://purl.obolibrary.org/obo/RO_0002573 [curator note](../../IAO/32/IAO_0000232.md) This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + * http://purl.obolibrary.org/obo/RO_0002599 [curator note](../../IAO/32/IAO_0000232.md) The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. + * http://purl.obolibrary.org/obo/RO_0002603 [curator note](../../IAO/32/IAO_0000232.md) The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + * http://purl.obolibrary.org/obo/RO_0002609 [curator note](../../IAO/32/IAO_0000232.md) Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * http://purl.obolibrary.org/obo/RO_0002610 [curator note](../../IAO/32/IAO_0000232.md) Groups both positive and negative correlation + +## External Comments + diff --git a/src/ontology/md/IAO/89/IAO_0000589.md b/src/ontology/md/IAO/89/IAO_0000589.md new file mode 100644 index 00000000..f52a7d3e --- /dev/null +++ b/src/ontology/md/IAO/89/IAO_0000589.md @@ -0,0 +1,52 @@ + +## Class : OBO foundry unique label + + * *IRI* = http://purl.obolibrary.org/obo/IAO_0000589 + * *Label* = OBO foundry unique label + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = OBO foundry unique label + +## Usage + + * http://purl.obolibrary.org/obo/CARO_0000014 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) cell part (CARO) + * http://purl.obolibrary.org/obo/GO_0003674 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) molecular process + * http://purl.obolibrary.org/obo/PATO_0000001 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) quality (PATO) + * http://purl.obolibrary.org/obo/RO_0002211 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) regulates (processual) + * http://purl.obolibrary.org/obo/RO_0002212 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) negatively regulates (process to process) + * http://purl.obolibrary.org/obo/RO_0002213 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) positively regulates (process to process) + * http://purl.obolibrary.org/obo/RO_0002332 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) regulates levels of (process to entity) + * http://purl.obolibrary.org/obo/RO_0002334 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) regulated by (processual) + * http://purl.obolibrary.org/obo/RO_0002406 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) directly activates (process to process) + * http://purl.obolibrary.org/obo/RO_0002408 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) directly inhibits (process to process) + * http://purl.obolibrary.org/obo/RO_0002413 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) directly provides input for (process to process) + * http://purl.obolibrary.org/obo/RO_0002414 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) transitively provides input for (process to process) + * http://purl.obolibrary.org/obo/RO_0002507 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) determined by (system to material entity) + * http://purl.obolibrary.org/obo/RO_0002508 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) determines (material entity to system) + * http://purl.obolibrary.org/obo/RO_0002559 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) causally influenced by (material entity to material entity) + * http://purl.obolibrary.org/obo/RO_0002566 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) causally influences (material entity to material entity) + * http://purl.obolibrary.org/obo/RO_0002578 [OBO foundry unique label](../../IAO/89/IAO_0000589.md) directly regulates (processual) + * http://www.w3.org/2000/01/rdf-schema#isDefinedBy [OBO foundry unique label](../../IAO/89/IAO_0000589.md) is defined by + +## External Comments + diff --git a/src/ontology/md/PATO/01/PATO_0000001.md b/src/ontology/md/PATO/01/PATO_0000001.md new file mode 100644 index 00000000..07d5d627 --- /dev/null +++ b/src/ontology/md/PATO/01/PATO_0000001.md @@ -0,0 +1,39 @@ + +## Class : quality + + * *IRI* = http://purl.obolibrary.org/obo/PATO_0000001 + * *Label* = quality + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = quality (PATO) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = quality + +## Usage + + * - + * [has modifier](../../RO/73/RO_0002573.md) Domain [quality](../../PATO/01/PATO_0000001.md) + * [physical object quality](../../PATO/41/PATO_0001241.md) SubClassOf [quality](../../PATO/01/PATO_0000001.md) + * [quality](../../PATO/01/PATO_0000001.md) SubClassOf [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + +## External Comments + diff --git a/src/ontology/md/PATO/02/PATO_0000402.md b/src/ontology/md/PATO/02/PATO_0000402.md new file mode 100644 index 00000000..85411b68 --- /dev/null +++ b/src/ontology/md/PATO/02/PATO_0000402.md @@ -0,0 +1,37 @@ + +## Class : branched + + * *IRI* = http://purl.obolibrary.org/obo/PATO_0000402 + * *Label* = branched + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [branchiness](../../PATO/09/PATO_0002009.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = branched + +## Usage + + * - + * [branched](../../PATO/02/PATO_0000402.md) SubClassOf [branchiness](../../PATO/09/PATO_0002009.md) + * [branching part of](../../RO/80/RO_0002380.md) Range [bearer of](../../RO/53/RO_0000053.md) some [branched](../../PATO/02/PATO_0000402.md) + +## External Comments + diff --git a/src/ontology/md/PATO/09/PATO_0002009.md b/src/ontology/md/PATO/09/PATO_0002009.md new file mode 100644 index 00000000..701b0f01 --- /dev/null +++ b/src/ontology/md/PATO/09/PATO_0002009.md @@ -0,0 +1,37 @@ + +## Class : branchiness + + * *IRI* = http://purl.obolibrary.org/obo/PATO_0002009 + * *Label* = branchiness + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [shape](../../PATO/52/PATO_0000052.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = branchiness + +## Usage + + * - + * [branched](../../PATO/02/PATO_0000402.md) SubClassOf [branchiness](../../PATO/09/PATO_0002009.md) + * [branchiness](../../PATO/09/PATO_0002009.md) SubClassOf [shape](../../PATO/52/PATO_0000052.md) + +## External Comments + diff --git a/src/ontology/md/PATO/24/PATO_0002124.md b/src/ontology/md/PATO/24/PATO_0002124.md new file mode 100644 index 00000000..da969432 --- /dev/null +++ b/src/ontology/md/PATO/24/PATO_0002124.md @@ -0,0 +1,37 @@ + +## Class : laminar + + * *IRI* = http://purl.obolibrary.org/obo/PATO_0002124 + * *Label* = laminar + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [structure](../../PATO/41/PATO_0000141.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = laminar + +## Usage + + * - + * [bounding layer of](../../RO/07/RO_0002007.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [laminar](../../PATO/24/PATO_0002124.md) and [material entity](../../BFO/40/BFO_0000040.md) + * [laminar](../../PATO/24/PATO_0002124.md) SubClassOf [structure](../../PATO/41/PATO_0000141.md) + +## External Comments + diff --git a/src/ontology/md/PATO/41/PATO_0000141.md b/src/ontology/md/PATO/41/PATO_0000141.md new file mode 100644 index 00000000..0644cff6 --- /dev/null +++ b/src/ontology/md/PATO/41/PATO_0000141.md @@ -0,0 +1,37 @@ + +## Class : structure + + * *IRI* = http://purl.obolibrary.org/obo/PATO_0000141 + * *Label* = structure + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [morphology](../../PATO/51/PATO_0000051.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = structure + +## Usage + + * - + * [laminar](../../PATO/24/PATO_0002124.md) SubClassOf [structure](../../PATO/41/PATO_0000141.md) + * [structure](../../PATO/41/PATO_0000141.md) SubClassOf [morphology](../../PATO/51/PATO_0000051.md) + +## External Comments + diff --git a/src/ontology/md/PATO/41/PATO_0001241.md b/src/ontology/md/PATO/41/PATO_0001241.md new file mode 100644 index 00000000..d089e153 --- /dev/null +++ b/src/ontology/md/PATO/41/PATO_0001241.md @@ -0,0 +1,37 @@ + +## Class : physical object quality + + * *IRI* = http://purl.obolibrary.org/obo/PATO_0001241 + * *Label* = physical object quality + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [quality](../../PATO/01/PATO_0000001.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = physical object quality + +## Usage + + * - + * [morphology](../../PATO/51/PATO_0000051.md) SubClassOf [physical object quality](../../PATO/41/PATO_0001241.md) + * [physical object quality](../../PATO/41/PATO_0001241.md) SubClassOf [quality](../../PATO/01/PATO_0000001.md) + +## External Comments + diff --git a/src/ontology/md/PATO/51/PATO_0000051.md b/src/ontology/md/PATO/51/PATO_0000051.md new file mode 100644 index 00000000..0a9af929 --- /dev/null +++ b/src/ontology/md/PATO/51/PATO_0000051.md @@ -0,0 +1,40 @@ + +## Class : morphology + + * *IRI* = http://purl.obolibrary.org/obo/PATO_0000051 + * *Label* = morphology + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [quality](../../BFO/19/BFO_0000019.md) + * [physical object quality](../../PATO/41/PATO_0001241.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = morphology + +## Usage + + * - + * [morphology](../../PATO/51/PATO_0000051.md) SubClassOf [physical object quality](../../PATO/41/PATO_0001241.md) + * [morphology](../../PATO/51/PATO_0000051.md) SubClassOf [quality](../../BFO/19/BFO_0000019.md) + * [shape](../../PATO/52/PATO_0000052.md) SubClassOf [morphology](../../PATO/51/PATO_0000051.md) + * [structure](../../PATO/41/PATO_0000141.md) SubClassOf [morphology](../../PATO/51/PATO_0000051.md) + +## External Comments + diff --git a/src/ontology/md/PATO/52/PATO_0000052.md b/src/ontology/md/PATO/52/PATO_0000052.md new file mode 100644 index 00000000..e3b6d0c0 --- /dev/null +++ b/src/ontology/md/PATO/52/PATO_0000052.md @@ -0,0 +1,38 @@ + +## Class : shape + + * *IRI* = http://purl.obolibrary.org/obo/PATO_0000052 + * *Label* = shape + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [morphology](../../PATO/51/PATO_0000051.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = shape + +## Usage + + * - + * [branchiness](../../PATO/09/PATO_0002009.md) SubClassOf [shape](../../PATO/52/PATO_0000052.md) + * [linear](../../PATO/99/PATO_0001199.md) SubClassOf [shape](../../PATO/52/PATO_0000052.md) + * [shape](../../PATO/52/PATO_0000052.md) SubClassOf [morphology](../../PATO/51/PATO_0000051.md) + +## External Comments + diff --git a/src/ontology/md/PATO/99/PATO_0001199.md b/src/ontology/md/PATO/99/PATO_0001199.md new file mode 100644 index 00000000..c3cf64b4 --- /dev/null +++ b/src/ontology/md/PATO/99/PATO_0001199.md @@ -0,0 +1,38 @@ + +## Class : linear + + * *IRI* = http://purl.obolibrary.org/obo/PATO_0001199 + * *Label* = linear + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [shape](../../PATO/52/PATO_0000052.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = linear + +## Usage + + * - + * [coincident with](../../RO/08/RO_0002008.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [coincident with](../../RO/08/RO_0002008.md) Range [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [linear](../../PATO/99/PATO_0001199.md) SubClassOf [shape](../../PATO/52/PATO_0000052.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0000300.md b/src/ontology/md/RO/00/RO_0000300.md new file mode 100644 index 00000000..5fc1aaef --- /dev/null +++ b/src/ontology/md/RO/00/RO_0000300.md @@ -0,0 +1,70 @@ + +## Class : in neural circuit with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000300 + * *Label* = in neural circuit with + * *Definition* = A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [in neural circuit with](../../RO/00/RO_0000300.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[first order logic expression](../../IAO/26/IAO_0000426.md)* = (forall (?x ?y) + (iff + (neural_circuit_path ?x ?y) + (and + ("neuron ; CL_0000540" ?x) + ("neuron ; CL_0000540" ?y) + (or + (synapsed_by ?x ?y) + (synapsed_to ?x ?y))))) + +(forall (...s ?x ?y ?z) + (iff + (neural_circuit_path ...s ?x ?y ?z) + (and + (neural_circuit_path ...s ?x ?y) + ("neuron ; CL_0000540" ?z) + (or + (synapsed_by ?y ?z) + (synapsed_to ?y ?z))))) + +(forall (?x ?y) + (iff + (in_neural_circuit_with ?x ?y) + (exists (...s) + (neural_circuit_path ?x ...s ?y)))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in neural circuit with + +## Usage + + * - + * TransitiveObjectProperty [in neural circuit with](../../RO/00/RO_0000300.md) + * [downstream in neural circuit with](../../RO/02/RO_0000302.md) SubPropertyOf [in neural circuit with](../../RO/00/RO_0000300.md) + * [electrically_synapsed_to](../../RO/03/RO_0002003.md) SubPropertyOf [in neural circuit with](../../RO/00/RO_0000300.md) + * [upstream in neural circuit with](../../RO/01/RO_0000301.md) SubPropertyOf [in neural circuit with](../../RO/00/RO_0000300.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0001000.md b/src/ontology/md/RO/00/RO_0001000.md new file mode 100644 index 00000000..a9620eec --- /dev/null +++ b/src/ontology/md/RO/00/RO_0001000.md @@ -0,0 +1,46 @@ + +## Class : derives from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0001000 + * *Label* = derives from + * *Definition* = a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [derives into](../../RO/01/RO_0001001.md) InverseOf [derives from](../../RO/00/RO_0001000.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this cell derives from this parent cell (cell division) + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this nucleus derives from this parent nucleus (nuclear division) + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + * *[editor note](../../IAO/16/IAO_0000116.md)* = This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = derives_from + * *[curator note](../../IAO/32/IAO_0000232.md)* = This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = derives from + +## Usage + + * - + * [derives into](../../RO/01/RO_0001001.md) InverseOf [derives from](../../RO/00/RO_0001000.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0001900.md b/src/ontology/md/RO/00/RO_0001900.md new file mode 100644 index 00000000..b85c5127 --- /dev/null +++ b/src/ontology/md/RO/00/RO_0001900.md @@ -0,0 +1,86 @@ + +## Class : temporal interpretation + + * *IRI* = http://purl.obolibrary.org/obo/RO_0001900 + * *Label* = temporal interpretation + * *Definition* = An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on an object property](../../RO/22/RO_0002422.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = temporal interpretation + * *[page](../../ge/page.md)* = https://code.google.com/p/obo-relations/wiki/ROAndTime + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * http://purl.obolibrary.org/obo/BFO_0000050 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/BFO_0000051 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0000052 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0000053 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0000300 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0000301 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0000302 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0001015 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0001018 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0001019 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0001025 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002000 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002001 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002002 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002100 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002101 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002102 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002103 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002104 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002105 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002106 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002107 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002108 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002109 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002110 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002112 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002113 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002114 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002115 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002120 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002121 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002130 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002131 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002132 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002134 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002150 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002151 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002163 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002180 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002219 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002220 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002221 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002314 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002323 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002350 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002351 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + * http://purl.obolibrary.org/obo/RO_0002473 [temporal interpretation](../../RO/00/RO_0001900.md) http://purl.obolibrary.org/obo/RO_0001901 + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0002000.md b/src/ontology/md/RO/00/RO_0002000.md new file mode 100644 index 00000000..c8cd7182 --- /dev/null +++ b/src/ontology/md/RO/00/RO_0002000.md @@ -0,0 +1,49 @@ + +## Class : 2D boundary of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002000 + * *Label* = 2D boundary of + * *Definition* = a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [2D boundary of](../../RO/00/RO_0002000.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) InverseOf [2D boundary of](../../RO/00/RO_0002000.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = the surface of my skin is a 2D boundary of my body + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + * *[editor note](../../IAO/16/IAO_0000116.md)* = A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = 2D_boundary_of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = boundary of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is 2D boundary of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is boundary of + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = 2D boundary of + +## Usage + + * - + * [2D boundary of](../../RO/00/RO_0002000.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) InverseOf [2D boundary of](../../RO/00/RO_0002000.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0002100.md b/src/ontology/md/RO/00/RO_0002100.md new file mode 100644 index 00000000..d3f606f2 --- /dev/null +++ b/src/ontology/md/RO/00/RO_0002100.md @@ -0,0 +1,47 @@ + +## Class : has soma location + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002100 + * *Label* = has soma location + * *Definition* = Relation between a neuron and an anatomical structure that its soma is part of. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [has soma location](../../RO/00/RO_0002100.md) Domain [neuron](../../CL/40/CL_0000540.md) + * [has soma location](../../RO/00/RO_0002100.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a neuron and an anatomical structure that its soma is part of. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = some ( + and some ?Y) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has soma location + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has soma location](../../RO/00/RO_0002100.md) Domain [neuron](../../CL/40/CL_0000540.md) + * [has soma location](../../RO/00/RO_0002100.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0002200.md b/src/ontology/md/RO/00/RO_0002200.md new file mode 100644 index 00000000..984761c1 --- /dev/null +++ b/src/ontology/md/RO/00/RO_0002200.md @@ -0,0 +1,48 @@ + +## Class : has phenotype + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002200 + * *Label* = has phenotype + * *Definition* = A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## SubProperties + + +## Other Logical Axioms + + * [has phenotype](../../RO/00/RO_0002200.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [has phenotype](../../RO/00/RO_0002200.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + * [phenotype of](../../RO/01/RO_0002201.md) InverseOf [has phenotype](../../RO/00/RO_0002200.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has phenotype + +## Usage + + * - + * [has phenotype](../../RO/00/RO_0002200.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [has phenotype](../../RO/00/RO_0002200.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + * [has symptom](../../RO/52/RO_0002452.md) SubPropertyOf [has phenotype](../../RO/00/RO_0002200.md) + * [phenotype of](../../RO/01/RO_0002201.md) InverseOf [has phenotype](../../RO/00/RO_0002200.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0002300.md b/src/ontology/md/RO/00/RO_0002300.md new file mode 100644 index 00000000..af102197 --- /dev/null +++ b/src/ontology/md/RO/00/RO_0002300.md @@ -0,0 +1,42 @@ + +## Class : results in disappearance of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002300 + * *Label* = results in disappearance of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in ending of](../../RO/52/RO_0002552.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in disappearance of](../../RO/00/RO_0002300.md) SubPropertyOf [results in ending of](../../RO/52/RO_0002552.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = foramen ovale closure SubClassOf results in disappearance of foramen ovale + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = May be merged into parent relation + * *[shorthand](../../nd/oboInOwl#shorthand.md)* = results_in_disappearance_of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in disappearance of + +## Usage + + * - + * [results in disappearance of](../../RO/00/RO_0002300.md) SubPropertyOf [results in ending of](../../RO/52/RO_0002552.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0002400.md b/src/ontology/md/RO/00/RO_0002400.md new file mode 100644 index 00000000..1ddf8178 --- /dev/null +++ b/src/ontology/md/RO/00/RO_0002400.md @@ -0,0 +1,48 @@ + +## Class : has direct input + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002400 + * *Label* = has direct input + * *Definition* = p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has input](../../RO/33/RO_0002233.md) + +## SubProperties + + +## Other Logical Axioms + + * [has direct input](../../RO/00/RO_0002400.md) SubPropertyOf [has input](../../RO/33/RO_0002233.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'protein catabolic process' SubClassOf has_direct_input some protein + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = directly consumes + * *[curator note](../../IAO/32/IAO_0000232.md)* = This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has direct input + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has direct input](../../RO/00/RO_0002400.md) SubPropertyOf [has input](../../RO/33/RO_0002233.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0002600.md b/src/ontology/md/RO/00/RO_0002600.md new file mode 100644 index 00000000..f620c540 --- /dev/null +++ b/src/ontology/md/RO/00/RO_0002600.md @@ -0,0 +1,41 @@ + +## Class : capable of upregulating or causing pathological process + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002600 + * *Label* = capable of upregulating or causing pathological process + * *Definition* = Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [capable of positively regulating](../../RO/98/RO_0002598.md) + +## SubProperties + + +## Other Logical Axioms + + * [capable of upregulating or causing pathological process](../../RO/00/RO_0002600.md) SubPropertyOf [capable of positively regulating](../../RO/98/RO_0002598.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = benzene -> cancer [CHEBI] + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = causes disease + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = capable of upregulating or causing pathological process + +## Usage + + * - + * [capable of upregulating or causing pathological process](../../RO/00/RO_0002600.md) SubPropertyOf [capable of positively regulating](../../RO/98/RO_0002598.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_0003000.md b/src/ontology/md/RO/00/RO_0003000.md new file mode 100644 index 00000000..0aee2526 --- /dev/null +++ b/src/ontology/md/RO/00/RO_0003000.md @@ -0,0 +1,49 @@ + +## Class : produces + + * *IRI* = http://purl.obolibrary.org/obo/RO_0003000 + * *Label* = produces + * *Definition* = a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + * *Comment* = Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [produces](../../RO/00/RO_0003000.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [produces](../../RO/00/RO_0003000.md) InverseOf [produced by](../../RO/01/RO_0003001.md) + * [produces](../../RO/00/RO_0003000.md) Range [material entity](../../BFO/40/BFO_0000040.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Melissa Haendel + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = produces + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [produces](../../RO/00/RO_0003000.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [produces](../../RO/00/RO_0003000.md) InverseOf [produced by](../../RO/01/RO_0003001.md) + * [produces](../../RO/00/RO_0003000.md) Range [material entity](../../BFO/40/BFO_0000040.md) + +## External Comments + diff --git a/src/ontology/md/RO/00/RO_HOM0000000.md b/src/ontology/md/RO/00/RO_HOM0000000.md new file mode 100644 index 00000000..686a3740 --- /dev/null +++ b/src/ontology/md/RO/00/RO_HOM0000000.md @@ -0,0 +1,57 @@ + +## Class : in similarity relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000000 + * *Label* = in similarity relationship with + * *Definition* = Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = BGEE:curator, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000000 ] + +## Synonyms + + * sameness + * similar to + * correspondence [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814479 ] + * resemblance + +## Cross-references + + * ECO:0000041 + * SO:similar_to + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = ECO:0000041 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:similar_to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = sameness + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = similar to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = correspondence + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = resemblance + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in similarity relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000000 + +## Usage + + * - + * SymmetricObjectProperty [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + * [in functional equivalence relationship with](../../RO/65/RO_HOM0000065.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + * [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + * [in homology relationship with](../../RO/01/RO_HOM0000001.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + * [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0000301.md b/src/ontology/md/RO/01/RO_0000301.md new file mode 100644 index 00000000..b6c80145 --- /dev/null +++ b/src/ontology/md/RO/01/RO_0000301.md @@ -0,0 +1,68 @@ + +## Class : upstream in neural circuit with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000301 + * *Label* = upstream in neural circuit with + * *Definition* = A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in neural circuit with](../../RO/00/RO_0000300.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [upstream in neural circuit with](../../RO/01/RO_0000301.md) + * [upstream in neural circuit with](../../RO/01/RO_0000301.md) SubPropertyOf [in neural circuit with](../../RO/00/RO_0000300.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[first order logic expression](../../IAO/26/IAO_0000426.md)* = (forall (?x ?y) + (iff + (upstream_neural_circuit_path ?x ?y) + (and + ("neuron ; CL_0000540" ?x) + ("neuron ; CL_0000540" ?y) + (synapsed_to ?x ?y)))) + + +(forall (...s ?x ?y ?z) + (iff + (upstream_neural_circuit_path ...s ?x ?y ?z ) + (and + (upstream_neural_circuit_path ...s ?x ?y) + ("neuron ; CL_0000540" ?z) + (synapsed_to ?y ?z)))) + +(forall (?x ?y) + (iff + (upstream_in_neural_circuit_with ?x ?y) + (exists (...s) + (upstream_neural_circuit_path ?x ...s ?y)))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = upstream in neural circuit with + +## Usage + + * - + * TransitiveObjectProperty [upstream in neural circuit with](../../RO/01/RO_0000301.md) + * [synapsed by](../../RO/03/RO_0002103.md) SubPropertyOf [upstream in neural circuit with](../../RO/01/RO_0000301.md) + * [upstream in neural circuit with](../../RO/01/RO_0000301.md) SubPropertyOf [in neural circuit with](../../RO/00/RO_0000300.md) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0001001.md b/src/ontology/md/RO/01/RO_0001001.md new file mode 100644 index 00000000..a8f4f521 --- /dev/null +++ b/src/ontology/md/RO/01/RO_0001001.md @@ -0,0 +1,45 @@ + +## Class : derives into + + * *IRI* = http://purl.obolibrary.org/obo/RO_0001001 + * *Label* = derives into + * *Definition* = a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [derives into](../../RO/01/RO_0001001.md) InverseOf [derives from](../../RO/00/RO_0001000.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this parent cell derives into this cell (cell division) + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this parent nucleus derives into this nucleus (nuclear division) + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + * *[editor note](../../IAO/16/IAO_0000116.md)* = This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = derives_into + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = derives into + +## Usage + + * - + * [derives into](../../RO/01/RO_0001001.md) InverseOf [derives from](../../RO/00/RO_0001000.md) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0002001.md b/src/ontology/md/RO/01/RO_0002001.md new file mode 100644 index 00000000..e2f0a5f6 --- /dev/null +++ b/src/ontology/md/RO/01/RO_0002001.md @@ -0,0 +1,39 @@ + +## Class : aligned with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002001 + * *Label* = aligned with + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [aligned with](../../RO/01/RO_0002001.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = aligned with + +## Usage + + * - + * TransitiveObjectProperty [aligned with](../../RO/01/RO_0002001.md) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0002101.md b/src/ontology/md/RO/01/RO_0002101.md new file mode 100644 index 00000000..2213e72d --- /dev/null +++ b/src/ontology/md/RO/01/RO_0002101.md @@ -0,0 +1,72 @@ + +## Class : fasciculates with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002101 + * *Label* = fasciculates with + * *Definition* = relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. + + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [fasciculates with](../../RO/01/RO_0002101.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [fasciculates with](../../RO/01/RO_0002101.md) Range [neuron projection bundle](../../CARO/01/CARO_0001001.md) + * [fasciculates with](../../RO/01/RO_0002101.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) InverseOf [fasciculates with](../../RO/01/RO_0002101.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = fasciculates with + * *[first order logic expression](../../IAO/26/IAO_0000426.md)* = (forall (?x ?y) + (iff + (fasciculates_with ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron ; CL_0000540" ?x) + ("neuron projection bundle ; CARO_0001001" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500' " ?npbs) + (part_of ?npbs ?y) + (part_of ?nps ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = fasciculates with + +## Usage + + * - + * [fasciculates with](../../RO/01/RO_0002101.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [fasciculates with](../../RO/01/RO_0002101.md) Range [neuron projection bundle](../../CARO/01/CARO_0001001.md) + * [fasciculates with](../../RO/01/RO_0002101.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) InverseOf [fasciculates with](../../RO/01/RO_0002101.md) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0002201.md b/src/ontology/md/RO/01/RO_0002201.md new file mode 100644 index 00000000..81e05323 --- /dev/null +++ b/src/ontology/md/RO/01/RO_0002201.md @@ -0,0 +1,45 @@ + +## Class : phenotype of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002201 + * *Label* = phenotype of + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## SubProperties + + +## Other Logical Axioms + + * FunctionalObjectProperty [phenotype of](../../RO/01/RO_0002201.md) + * [phenotype of](../../RO/01/RO_0002201.md) InverseOf [has phenotype](../../RO/00/RO_0002200.md) + * [phenotype of](../../RO/01/RO_0002201.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = phenotype of + +## Usage + + * - + * FunctionalObjectProperty [phenotype of](../../RO/01/RO_0002201.md) + * [phenotype of](../../RO/01/RO_0002201.md) InverseOf [has phenotype](../../RO/00/RO_0002200.md) + * [phenotype of](../../RO/01/RO_0002201.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0002301.md b/src/ontology/md/RO/01/RO_0002301.md new file mode 100644 index 00000000..11eedae2 --- /dev/null +++ b/src/ontology/md/RO/01/RO_0002301.md @@ -0,0 +1,41 @@ + +## Class : results in developmental regression of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002301 + * *Label* = results in developmental regression of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in ending of](../../RO/52/RO_0002552.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in developmental regression of](../../RO/01/RO_0002301.md) SubPropertyOf [results in ending of](../../RO/52/RO_0002552.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = May be merged into parent relation + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in developmental regression of + +## Usage + + * - + * [results in developmental regression of](../../RO/01/RO_0002301.md) SubPropertyOf [results in ending of](../../RO/52/RO_0002552.md) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0002401.md b/src/ontology/md/RO/01/RO_0002401.md new file mode 100644 index 00000000..6bcef7d5 --- /dev/null +++ b/src/ontology/md/RO/01/RO_0002401.md @@ -0,0 +1,41 @@ + +## Class : obsolete has indirect input + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002401 + * *Label* = obsolete has indirect input + * *Comment* = Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = obsolete has indirect input + * *[owl#deprecated](../../ed/owl#deprecated.md)* = true + +## Usage + + * - + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0002501.md b/src/ontology/md/RO/01/RO_0002501.md new file mode 100644 index 00000000..81689418 --- /dev/null +++ b/src/ontology/md/RO/01/RO_0002501.md @@ -0,0 +1,48 @@ + +## Class : causal relation between processes + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002501 + * *Label* = causal relation between processes + * *Definition* = p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causally related to](../../RO/10/RO_0002410.md) + +## SubProperties + + +## Other Logical Axioms + + * [causal relation between processes](../../RO/01/RO_0002501.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [causal relation between processes](../../RO/01/RO_0002501.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [causal relation between processes](../../RO/01/RO_0002501.md) SubPropertyOf [causally related to](../../RO/10/RO_0002410.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = https://docs.google.com/document/d/1WxocTXZaGVhEV1n7NB86pCF3SUcBJh8bq4vQrVCkjSU/edit# + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causal relation between processes + +## Usage + + * - + * [causal relation between processes](../../RO/01/RO_0002501.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [causal relation between processes](../../RO/01/RO_0002501.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [causal relation between processes](../../RO/01/RO_0002501.md) SubPropertyOf [causally related to](../../RO/10/RO_0002410.md) + * [causally downstream of or within](../../RO/27/RO_0002427.md) SubPropertyOf [causal relation between processes](../../RO/01/RO_0002501.md) + * [causally upstream of or within](../../RO/18/RO_0002418.md) SubPropertyOf [causal relation between processes](../../RO/01/RO_0002501.md) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0002601.md b/src/ontology/md/RO/01/RO_0002601.md new file mode 100644 index 00000000..0a168d81 --- /dev/null +++ b/src/ontology/md/RO/01/RO_0002601.md @@ -0,0 +1,40 @@ + +## Class : logical macro assertion involving identity + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002601 + * *Label* = logical macro assertion involving identity + * *Definition* = A shortcut relationship that holds between two entities based on their identity criteria + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion](../../RO/16/RO_0002416.md) + +## SubProperties + + * [in approximate one to one relationship with](../../RO/02/RO_0002602.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A shortcut relationship that holds between two entities based on their identity criteria + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = logical macro assertion involving identity + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0003001.md b/src/ontology/md/RO/01/RO_0003001.md new file mode 100644 index 00000000..6a09f23b --- /dev/null +++ b/src/ontology/md/RO/01/RO_0003001.md @@ -0,0 +1,44 @@ + +## Class : produced by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0003001 + * *Label* = produced by + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [produced by](../../RO/01/RO_0003001.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [produced by](../../RO/01/RO_0003001.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [produces](../../RO/00/RO_0003000.md) InverseOf [produced by](../../RO/01/RO_0003001.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Melissa Haendel + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = produced by + +## Usage + + * - + * [produced by](../../RO/01/RO_0003001.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [produced by](../../RO/01/RO_0003001.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [produces](../../RO/00/RO_0003000.md) InverseOf [produced by](../../RO/01/RO_0003001.md) + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_0003301.md b/src/ontology/md/RO/01/RO_0003301.md new file mode 100644 index 00000000..16aba468 --- /dev/null +++ b/src/ontology/md/RO/01/RO_0003301.md @@ -0,0 +1,40 @@ + +## Class : is model of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0003301 + * *Label* = is model of + * *Definition* = Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + * *Comment* = The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + * *[editor note](../../IAO/16/IAO_0000116.md)* = To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + * *[term editor](../../IAO/17/IAO_0000117.md)* = Matthew Brush + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is model of + +## Usage + + * - + +## External Comments + diff --git a/src/ontology/md/RO/01/RO_HOM0000001.md b/src/ontology/md/RO/01/RO_HOM0000001.md new file mode 100644 index 00000000..2ae50b29 --- /dev/null +++ b/src/ontology/md/RO/01/RO_HOM0000001.md @@ -0,0 +1,56 @@ + +## Class : in homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000001 + * *Label* = in homology relationship with + * *Definition* = Similarity that results from common evolutionary origin. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1002/bies.950180611, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1002/jmor.1051730307, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814480, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000001 ] + * *Comment* = This broad definition encompasses all the working definitions proposed so far in the literature. + +## Synonyms + + * homologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [shares ancestor with](../../RO/58/RO_0002158.md) + * [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in homology relationship with](../../RO/01/RO_HOM0000001.md) + * [in homology relationship with](../../RO/01/RO_HOM0000001.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + * [in homology relationship with](../../RO/01/RO_HOM0000001.md) SubPropertyOf [shares ancestor with](../../RO/58/RO_0002158.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Similarity that results from common evolutionary origin. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = homologous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = This broad definition encompasses all the working definitions proposed so far in the literature. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000001 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in homology relationship with](../../RO/01/RO_HOM0000001.md) + * [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) SubPropertyOf [in homology relationship with](../../RO/01/RO_HOM0000001.md) + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) SubPropertyOf [in homology relationship with](../../RO/01/RO_HOM0000001.md) + * [in homology relationship with](../../RO/01/RO_HOM0000001.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + * [in homology relationship with](../../RO/01/RO_HOM0000001.md) SubPropertyOf [shares ancestor with](../../RO/58/RO_0002158.md) + * [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) SubPropertyOf [in homology relationship with](../../RO/01/RO_HOM0000001.md) + +## External Comments + diff --git a/src/ontology/md/RO/02/RO_0000302.md b/src/ontology/md/RO/02/RO_0000302.md new file mode 100644 index 00000000..8493d4d0 --- /dev/null +++ b/src/ontology/md/RO/02/RO_0000302.md @@ -0,0 +1,69 @@ + +## Class : downstream in neural circuit with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000302 + * *Label* = downstream in neural circuit with + * *Definition* = A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in neural circuit with](../../RO/00/RO_0000300.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [downstream in neural circuit with](../../RO/02/RO_0000302.md) + * [downstream in neural circuit with](../../RO/02/RO_0000302.md) SubPropertyOf [in neural circuit with](../../RO/00/RO_0000300.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[first order logic expression](../../IAO/26/IAO_0000426.md)* = (forall (?x ?y) + (iff + (downstream_neural_circuit_path ?x ?y) + (and + ("neuron ; CL_0000540" ?x) + ("neuron ; CL_0000540" ?y) + (synapsed_by ?x ?y)))) + + +(forall (...s ?x ?y ?z) + (iff + (downstream_neural_circuit_path ...s ?x ?y ?z ) + (and + (downstream_neural_circuit_path ...s ?x ?y) + ("neuron ; CL_0000540" ?z) + (synapsed_by ?y ?z)))) + +(forall (?x ?y) + (iff + (downstream_in_neural_circuit_with ?x ?y) + (exists (...s) + (downstream_neural_circuit_path ?x ...s ?y)))) + + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = downstream in neural circuit with + +## Usage + + * - + * TransitiveObjectProperty [downstream in neural circuit with](../../RO/02/RO_0000302.md) + * [downstream in neural circuit with](../../RO/02/RO_0000302.md) SubPropertyOf [in neural circuit with](../../RO/00/RO_0000300.md) + * [synapsed to](../../RO/20/RO_0002120.md) SubPropertyOf [downstream in neural circuit with](../../RO/02/RO_0000302.md) + +## External Comments + diff --git a/src/ontology/md/RO/02/RO_0002002.md b/src/ontology/md/RO/02/RO_0002002.md new file mode 100644 index 00000000..8bcd59d2 --- /dev/null +++ b/src/ontology/md/RO/02/RO_0002002.md @@ -0,0 +1,52 @@ + +## Class : has 2D boundary + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002002 + * *Label* = has 2D boundary + * *Definition* = a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [has 2D boundary](../../RO/02/RO_0002002.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) InverseOf [2D boundary of](../../RO/00/RO_0002000.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) Range [immaterial entity](../../BFO/41/BFO_0000141.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = my body has 2D boundary the surface of my skin + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + * *[editor note](../../IAO/16/IAO_0000116.md)* = A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has boundary + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has_2D_boundary + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has 2D boundary + +## Usage + + * - + * [has 2D boundary](../../RO/02/RO_0002002.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) InverseOf [2D boundary of](../../RO/00/RO_0002000.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) Range [immaterial entity](../../BFO/41/BFO_0000141.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## External Comments + diff --git a/src/ontology/md/RO/02/RO_0002102.md b/src/ontology/md/RO/02/RO_0002102.md new file mode 100644 index 00000000..091f68d4 --- /dev/null +++ b/src/ontology/md/RO/02/RO_0002102.md @@ -0,0 +1,54 @@ + +## Class : axon synapses in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002102 + * *Label* = axon synapses in + * *Definition* = Relation between a neuron and some structure its axon forms (chemical) synapses in. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has presynaptic terminal in](../../RO/13/RO_0002113.md) + +## SubProperties + + +## Other Logical Axioms + + * [axon synapses in](../../RO/02/RO_0002102.md) Domain [neuron](../../CL/40/CL_0000540.md) + * [axon synapses in](../../RO/02/RO_0002102.md) SubPropertyOf [has presynaptic terminal in](../../RO/13/RO_0002113.md) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) InverseOf [axon synapses in](../../RO/02/RO_0002102.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a neuron and some structure its axon forms (chemical) synapses in. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = some ( + and some ( + and some ( + and some ?Y))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = axon synapses in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [axon synapses in](../../RO/02/RO_0002102.md) Domain [neuron](../../CL/40/CL_0000540.md) + * [axon synapses in](../../RO/02/RO_0002102.md) SubPropertyOf [has presynaptic terminal in](../../RO/13/RO_0002113.md) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) InverseOf [axon synapses in](../../RO/02/RO_0002102.md) + +## External Comments + diff --git a/src/ontology/md/RO/02/RO_0002202.md b/src/ontology/md/RO/02/RO_0002202.md new file mode 100644 index 00000000..b0bbce4f --- /dev/null +++ b/src/ontology/md/RO/02/RO_0002202.md @@ -0,0 +1,59 @@ + +## Class : develops from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002202 + * *Label* = develops from + * *Definition* = x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + * *Comment* = This is the transitive form of the develops from relation + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally preceded by](../../RO/58/RO_0002258.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [develops from](../../RO/02/RO_0002202.md) + * [develops from](../../RO/02/RO_0002202.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [develops from](../../RO/02/RO_0002202.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [develops from](../../RO/02/RO_0002202.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [develops into](../../RO/03/RO_0002203.md) InverseOf [develops from](../../RO/02/RO_0002202.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = Melissa Haendel + * *[term editor](../../IAO/17/IAO_0000117.md)* = Terry Meehan + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = This is the transitive form of the develops from relation + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = develops from + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [develops from](../../RO/02/RO_0002202.md) + * [develops from part of](../../RO/25/RO_0002225.md) SubPropertyOf [develops from](../../RO/02/RO_0002202.md) + * [develops from](../../RO/02/RO_0002202.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [develops from](../../RO/02/RO_0002202.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [develops from](../../RO/02/RO_0002202.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [develops into](../../RO/03/RO_0002203.md) InverseOf [develops from](../../RO/02/RO_0002202.md) + * [directly develops from](../../RO/07/RO_0002207.md) SubPropertyOf [develops from](../../RO/02/RO_0002202.md) + * [transformation of](../../RO/94/RO_0002494.md) SubPropertyOf [develops from](../../RO/02/RO_0002202.md) + +## External Comments + diff --git a/src/ontology/md/RO/02/RO_0002402.md b/src/ontology/md/RO/02/RO_0002402.md new file mode 100644 index 00000000..6d787191 --- /dev/null +++ b/src/ontology/md/RO/02/RO_0002402.md @@ -0,0 +1,43 @@ + +## Class : obsolete has direct output + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002402 + * *Label* = obsolete has direct output + * *Definition* = p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = translation SubClassOf has_direct_output some protein + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = directly produces + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = obsolete has direct output + * *[owl#deprecated](../../ed/owl#deprecated.md)* = true + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + +## External Comments + diff --git a/src/ontology/md/RO/02/RO_0002502.md b/src/ontology/md/RO/02/RO_0002502.md new file mode 100644 index 00000000..c2345c84 --- /dev/null +++ b/src/ontology/md/RO/02/RO_0002502.md @@ -0,0 +1,38 @@ + +## Class : depends on + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002502 + * *Label* = depends on + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = depends on + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/BFO_0000169 + +## Usage + + * - + * [inheres in part of](../../RO/14/RO_0002314.md) SubPropertyOf [depends on](../../RO/02/RO_0002502.md) + * [towards](../../RO/03/RO_0002503.md) SubPropertyOf [depends on](../../RO/02/RO_0002502.md) + +## External Comments + diff --git a/src/ontology/md/RO/02/RO_0002602.md b/src/ontology/md/RO/02/RO_0002602.md new file mode 100644 index 00000000..32388db1 --- /dev/null +++ b/src/ontology/md/RO/02/RO_0002602.md @@ -0,0 +1,42 @@ + +## Class : in approximate one to one relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002602 + * *Label* = in approximate one to one relationship with + * *Definition* = A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion involving identity](../../RO/01/RO_0002601.md) + +## SubProperties + + * [is approximately equivalent to](../../RO/03/RO_0002603.md) + * [is opposite of](../../RO/04/RO_0002604.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in approximate one to one relationship with + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/02/RO_0003002.md b/src/ontology/md/RO/02/RO_0003002.md new file mode 100644 index 00000000..710c618d --- /dev/null +++ b/src/ontology/md/RO/02/RO_0003002.md @@ -0,0 +1,40 @@ + +## Class : represses expression of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0003002 + * *Label* = represses expression of + * *Definition* = Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [molecularly decreases activity of](../../RO/49/RO_0002449.md) + +## SubProperties + + +## Other Logical Axioms + + * [represses expression of](../../RO/02/RO_0003002.md) SubPropertyOf [molecularly decreases activity of](../../RO/49/RO_0002449.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between protein a (a transcription factor) and DNA element b if and only if a diminishes the process of transcription of b. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Logical axioms to be added after the relevant branch of GO is MIREOTed in + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = represses expression of + +## Usage + + * - + * [represses expression of](../../RO/02/RO_0003002.md) SubPropertyOf [molecularly decreases activity of](../../RO/49/RO_0002449.md) + +## External Comments + diff --git a/src/ontology/md/RO/02/RO_HOM0000002.md b/src/ontology/md/RO/02/RO_HOM0000002.md new file mode 100644 index 00000000..d1a5a4cd --- /dev/null +++ b/src/ontology/md/RO/02/RO_HOM0000002.md @@ -0,0 +1,53 @@ + +## Class : in homoplasy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000002 + * *Label* = in homoplasy relationship with + * *Definition* = Similarity that results from independent evolution. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/j.jhevol.2006.11.010, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000002 ] + +## Synonyms + + * homoplasous to + * analogy + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + * [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Similarity that results from independent evolution. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = homoplasous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = analogy + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in homoplasy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000002 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + * [in convergence relationship with](../../RO/04/RO_HOM0000004.md) SubPropertyOf [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + * [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + * [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) SubPropertyOf [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + * [in reversal relationship with](../../RO/09/RO_HOM0000009.md) SubPropertyOf [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + +## External Comments + diff --git a/src/ontology/md/RO/03/RO_0002003.md b/src/ontology/md/RO/03/RO_0002003.md new file mode 100644 index 00000000..f091f470 --- /dev/null +++ b/src/ontology/md/RO/03/RO_0002003.md @@ -0,0 +1,41 @@ + +## Class : electrically_synapsed_to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002003 + * *Label* = electrically_synapsed_to + * *Definition* = A relation that holds between two neurons that are electrically coupled via gap junctions. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in neural circuit with](../../RO/00/RO_0000300.md) + +## SubProperties + + +## Other Logical Axioms + + * [electrically_synapsed_to](../../RO/03/RO_0002003.md) SubPropertyOf [in neural circuit with](../../RO/00/RO_0000300.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that holds between two neurons that are electrically coupled via gap junctions. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = electrically_synapsed_to + +## Usage + + * - + * [electrically_synapsed_to](../../RO/03/RO_0002003.md) SubPropertyOf [in neural circuit with](../../RO/00/RO_0000300.md) + +## External Comments + diff --git a/src/ontology/md/RO/03/RO_0002103.md b/src/ontology/md/RO/03/RO_0002103.md new file mode 100644 index 00000000..286fb5ba --- /dev/null +++ b/src/ontology/md/RO/03/RO_0002103.md @@ -0,0 +1,53 @@ + +## Class : synapsed by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002103 + * *Label* = synapsed by + * *Definition* = Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [upstream in neural circuit with](../../RO/01/RO_0000301.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed by](../../RO/03/RO_0002103.md) InverseOf [synapsed to](../../RO/20/RO_0002120.md) + * [synapsed by](../../RO/03/RO_0002103.md) Range [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [synapsed by](../../RO/03/RO_0002103.md) SubPropertyOf [upstream in neural circuit with](../../RO/01/RO_0000301.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = some ( that part_of some ( that has_part some ( that some Y?))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed by + +## Usage + + * - + * [synapsed by](../../RO/03/RO_0002103.md) InverseOf [synapsed to](../../RO/20/RO_0002120.md) + * [synapsed by](../../RO/03/RO_0002103.md) Range [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [synapsed by](../../RO/03/RO_0002103.md) SubPropertyOf [upstream in neural circuit with](../../RO/01/RO_0000301.md) + * [synapsed_by_via_type_III_bouton](../../RO/15/RO_0002115.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_by_via_type_II_bouton](../../RO/08/RO_0002108.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_by_via_type_Ib_bouton](../../RO/09/RO_0002109.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_by_via_type_Is_bouton](../../RO/12/RO_0002112.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + +## External Comments + diff --git a/src/ontology/md/RO/03/RO_0002203.md b/src/ontology/md/RO/03/RO_0002203.md new file mode 100644 index 00000000..c28fe9ad --- /dev/null +++ b/src/ontology/md/RO/03/RO_0002203.md @@ -0,0 +1,53 @@ + +## Class : develops into + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002203 + * *Label* = develops into + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has potential to directly develop into](../../RO/88/RO_0002388.md) + * [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [has potential to develop into](../../RO/87/RO_0002387.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [develops into](../../RO/03/RO_0002203.md) + * [develops into](../../RO/03/RO_0002203.md) InverseOf [develops from](../../RO/02/RO_0002202.md) + * [develops into](../../RO/03/RO_0002203.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [develops into](../../RO/03/RO_0002203.md) SubPropertyOf [has potential to develop into](../../RO/87/RO_0002387.md) + * [develops into](../../RO/03/RO_0002203.md) SubPropertyOf [has potential to directly develop into](../../RO/88/RO_0002388.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = Terry Meehan + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = develops into + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [develops into](../../RO/03/RO_0002203.md) + * [develops into](../../RO/03/RO_0002203.md) InverseOf [develops from](../../RO/02/RO_0002202.md) + * [develops into](../../RO/03/RO_0002203.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [develops into](../../RO/03/RO_0002203.md) SubPropertyOf [has potential to develop into](../../RO/87/RO_0002387.md) + * [develops into](../../RO/03/RO_0002203.md) SubPropertyOf [has potential to directly develop into](../../RO/88/RO_0002388.md) + * [directly develops into](../../RO/10/RO_0002210.md) SubPropertyOf [develops into](../../RO/03/RO_0002203.md) + +## External Comments + diff --git a/src/ontology/md/RO/03/RO_0002303.md b/src/ontology/md/RO/03/RO_0002303.md new file mode 100644 index 00000000..ad878007 --- /dev/null +++ b/src/ontology/md/RO/03/RO_0002303.md @@ -0,0 +1,49 @@ + +## Class : has habitat + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002303 + * *Label* = has habitat + * *Definition* = x 'has habitat' y if and only if: x is an organism, y is a habitat, and x is specially adapted (either naturally or via artifical selection) to living in y. Here 'living in' encompasses the majority of the animal's lifespan. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [ecologically related to](../../RO/21/RO_0002321.md) + +## SubProperties + + +## Other Logical Axioms + + * [has habitat](../../RO/03/RO_0002303.md) Domain [material anatomical entity](../../CARO/06/CARO_0000006.md) + * [has habitat](../../RO/03/RO_0002303.md) Range [environmental system](../../ENVO/54/ENVO_01000254.md) + * [has habitat](../../RO/03/RO_0002303.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'marine environment' (ENVO_00000569) -- http://eol.org/pages/1795/overview + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x 'has habitat' y if and only if: x is an organism, y is a habitat, and x is specially adapted (either naturally or via artifical selection) to living in y. Here 'living in' encompasses the majority of the animal's lifespan. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = adapted for living in + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has habitat + +## Usage + + * - + * [has habitat](../../RO/03/RO_0002303.md) Domain [material anatomical entity](../../CARO/06/CARO_0000006.md) + * [has habitat](../../RO/03/RO_0002303.md) Range [environmental system](../../ENVO/54/ENVO_01000254.md) + * [has habitat](../../RO/03/RO_0002303.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + +## External Comments + diff --git a/src/ontology/md/RO/03/RO_0002403.md b/src/ontology/md/RO/03/RO_0002403.md new file mode 100644 index 00000000..75911028 --- /dev/null +++ b/src/ontology/md/RO/03/RO_0002403.md @@ -0,0 +1,45 @@ + +## Class : obsolete has indirect output + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002403 + * *Label* = obsolete has indirect output + * *Comment* = Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has output](../../RO/34/RO_0002234.md) + +## SubProperties + + +## Other Logical Axioms + + * [obsolete has indirect output](../../RO/03/RO_0002403.md) SubPropertyOf [has output](../../RO/34/RO_0002234.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = obsolete has indirect output + * *[owl#deprecated](../../ed/owl#deprecated.md)* = true + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [obsolete has indirect output](../../RO/03/RO_0002403.md) SubPropertyOf [has output](../../RO/34/RO_0002234.md) + +## External Comments + diff --git a/src/ontology/md/RO/03/RO_0002503.md b/src/ontology/md/RO/03/RO_0002503.md new file mode 100644 index 00000000..ae1046a1 --- /dev/null +++ b/src/ontology/md/RO/03/RO_0002503.md @@ -0,0 +1,42 @@ + +## Class : towards + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002503 + * *Label* = towards + * *Definition* = q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [depends on](../../RO/02/RO_0002502.md) + +## SubProperties + + +## Other Logical Axioms + + * [towards](../../RO/03/RO_0002503.md) SubPropertyOf [depends on](../../RO/02/RO_0002502.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + * *[editor note](../../IAO/16/IAO_0000116.md)* = This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = towards + +## Usage + + * - + * [towards](../../RO/03/RO_0002503.md) SubPropertyOf [depends on](../../RO/02/RO_0002502.md) + +## External Comments + diff --git a/src/ontology/md/RO/03/RO_0002603.md b/src/ontology/md/RO/03/RO_0002603.md new file mode 100644 index 00000000..ca6286e6 --- /dev/null +++ b/src/ontology/md/RO/03/RO_0002603.md @@ -0,0 +1,41 @@ + +## Class : is approximately equivalent to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002603 + * *Label* = is approximately equivalent to + * *Definition* = x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in approximate one to one relationship with](../../RO/02/RO_0002602.md) + +## SubProperties + + * [is indistinguishable from](../../RO/05/RO_0002605.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y + * *[curator note](../../IAO/32/IAO_0000232.md)* = The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is approximately equivalent to + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/03/RO_0003003.md b/src/ontology/md/RO/03/RO_0003003.md new file mode 100644 index 00000000..c596336f --- /dev/null +++ b/src/ontology/md/RO/03/RO_0003003.md @@ -0,0 +1,40 @@ + +## Class : increases expression of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0003003 + * *Label* = increases expression of + * *Definition* = Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [molecularly increases activity of](../../RO/50/RO_0002450.md) + +## SubProperties + + +## Other Logical Axioms + + * [increases expression of](../../RO/03/RO_0003003.md) SubPropertyOf [molecularly increases activity of](../../RO/50/RO_0002450.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Logical axioms to be added after the relevant branch of GO is MIREOTed in + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = increases expression of + +## Usage + + * - + * [increases expression of](../../RO/03/RO_0003003.md) SubPropertyOf [molecularly increases activity of](../../RO/50/RO_0002450.md) + +## External Comments + diff --git a/src/ontology/md/RO/03/RO_HOM0000003.md b/src/ontology/md/RO/03/RO_HOM0000003.md new file mode 100644 index 00000000..15004c30 --- /dev/null +++ b/src/ontology/md/RO/03/RO_HOM0000003.md @@ -0,0 +1,56 @@ + +## Class : in homocracy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000003 + * *Label* = in homocracy relationship with + * *Definition* = Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814484, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/s00427-003-0301-4, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1186/1742-9994-2-15, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000003 ] + * *Comment* = Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + +## Synonyms + + * homocracous to + +## Cross-references + + * ECO:0000075 + +## Subsets + + +## SuperProperties + + * [evolutionarily related to](../../RO/20/RO_0002320.md) + * [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + * [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = ECO:0000075 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = homocracous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in homocracy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000003 + +## Usage + + * - + * SymmetricObjectProperty [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + * [in deep homology relationship with](../../RO/44/RO_HOM0000044.md) SubPropertyOf [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + * [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + * [in paramorphism relationship with](../../RO/74/RO_HOM0000074.md) SubPropertyOf [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + * [in syngeny relationship with](../../RO/58/RO_HOM0000058.md) SubPropertyOf [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + +## External Comments + diff --git a/src/ontology/md/RO/04/RO_0002004.md b/src/ontology/md/RO/04/RO_0002004.md new file mode 100644 index 00000000..6d2f0f4e --- /dev/null +++ b/src/ontology/md/RO/04/RO_0002004.md @@ -0,0 +1,40 @@ + +## Class : tracheates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002004 + * *Label* = tracheates + * *Definition* = The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [contained in](../../RO/18/RO_0001018.md) + +## SubProperties + + +## Other Logical Axioms + + * [tracheates](../../RO/04/RO_0002004.md) SubPropertyOf [contained in](../../RO/18/RO_0001018.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = tracheates + +## Usage + + * - + * [tracheates](../../RO/04/RO_0002004.md) SubPropertyOf [contained in](../../RO/18/RO_0001018.md) + +## External Comments + diff --git a/src/ontology/md/RO/04/RO_0002104.md b/src/ontology/md/RO/04/RO_0002104.md new file mode 100644 index 00000000..61de84e8 --- /dev/null +++ b/src/ontology/md/RO/04/RO_0002104.md @@ -0,0 +1,47 @@ + +## Class : has plasma membrane part + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002104 + * *Label* = has plasma membrane part + * *Definition* = Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has part](../../BFO/51/BFO_0000051.md) + +## SubProperties + + +## Other Logical Axioms + + * [has plasma membrane part](../../RO/04/RO_0002104.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Alexander Diehl + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = Lindsay Cowell + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/19243617 + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = some ( and some ?Y) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has plasma membrane part + +## Usage + + * - + * [has plasma membrane part](../../RO/04/RO_0002104.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + +## External Comments + diff --git a/src/ontology/md/RO/04/RO_0002204.md b/src/ontology/md/RO/04/RO_0002204.md new file mode 100644 index 00000000..a709c695 --- /dev/null +++ b/src/ontology/md/RO/04/RO_0002204.md @@ -0,0 +1,49 @@ + +## Class : gene product of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002204 + * *Label* = gene product of + * *Definition* = definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [genomically related to](../../RO/30/RO_0002330.md) + +## SubProperties + + +## Other Logical Axioms + + * [gene product of](../../RO/04/RO_0002204.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [gene product of](../../RO/04/RO_0002204.md) Range [continuant](../../BFO/02/BFO_0000002.md) + * [gene product of](../../RO/04/RO_0002204.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [has gene product](../../RO/05/RO_0002205.md) InverseOf [gene product of](../../RO/04/RO_0002204.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" + * *[editor note](../../IAO/16/IAO_0000116.md)* = We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = gene product of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [gene product of](../../RO/04/RO_0002204.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [gene product of](../../RO/04/RO_0002204.md) Range [continuant](../../BFO/02/BFO_0000002.md) + * [gene product of](../../RO/04/RO_0002204.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [has gene product](../../RO/05/RO_0002205.md) InverseOf [gene product of](../../RO/04/RO_0002204.md) + +## External Comments + diff --git a/src/ontology/md/RO/04/RO_0002404.md b/src/ontology/md/RO/04/RO_0002404.md new file mode 100644 index 00000000..80dbc479 --- /dev/null +++ b/src/ontology/md/RO/04/RO_0002404.md @@ -0,0 +1,47 @@ + +## Class : causally downstream of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002404 + * *Label* = causally downstream of + * *Definition* = inverse of upstream of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [preceded by](../../BFO/62/BFO_0000062.md) + * [causally downstream of or within](../../RO/27/RO_0002427.md) + +## SubProperties + + +## Other Logical Axioms + + * [causally downstream of](../../RO/04/RO_0002404.md) InverseOf [causally upstream of](../../RO/11/RO_0002411.md) + * [causally downstream of](../../RO/04/RO_0002404.md) SubPropertyOf [causally downstream of or within](../../RO/27/RO_0002427.md) + * [causally downstream of](../../RO/04/RO_0002404.md) SubPropertyOf [preceded by](../../BFO/62/BFO_0000062.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of upstream of + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causally downstream of + +## Usage + + * - + * [causally downstream of](../../RO/04/RO_0002404.md) InverseOf [causally upstream of](../../RO/11/RO_0002411.md) + * [causally downstream of](../../RO/04/RO_0002404.md) SubPropertyOf [causally downstream of or within](../../RO/27/RO_0002427.md) + * [causally downstream of](../../RO/04/RO_0002404.md) SubPropertyOf [preceded by](../../BFO/62/BFO_0000062.md) + * [immediately causally downstream of](../../RO/05/RO_0002405.md) SubPropertyOf [causally downstream of](../../RO/04/RO_0002404.md) + +## External Comments + diff --git a/src/ontology/md/RO/04/RO_0002504.md b/src/ontology/md/RO/04/RO_0002504.md new file mode 100644 index 00000000..07361079 --- /dev/null +++ b/src/ontology/md/RO/04/RO_0002504.md @@ -0,0 +1,42 @@ + +## Class : always present in taxon + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002504 + * *Label* = always present in taxon + * *Definition* = S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [present in taxon](../../RO/75/RO_0002175.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = brain always_present_in_taxon 'Vertebrata' + * *[example of usage](../../IAO/12/IAO_0000112.md)* = forelimb always_present_in_taxon Euarchontoglires + * *[definition](../../IAO/15/IAO_0000115.md)* = S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S + * *[editor note](../../IAO/16/IAO_0000116.md)* = This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = never lost in + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = always present in taxon + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/04/RO_0002604.md b/src/ontology/md/RO/04/RO_0002604.md new file mode 100644 index 00000000..d1425dcf --- /dev/null +++ b/src/ontology/md/RO/04/RO_0002604.md @@ -0,0 +1,40 @@ + +## Class : is opposite of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002604 + * *Label* = is opposite of + * *Definition* = x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in approximate one to one relationship with](../../RO/02/RO_0002602.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'anterior end of organism' is-opposite-of 'posterior end of organism' + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'increase in temperature' is-opposite-of 'decrease in temperature' + * *[definition](../../IAO/15/IAO_0000115.md)* = x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is opposite of + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/04/RO_HOM0000004.md b/src/ontology/md/RO/04/RO_HOM0000004.md new file mode 100644 index 00000000..d8f2c8d0 --- /dev/null +++ b/src/ontology/md/RO/04/RO_HOM0000004.md @@ -0,0 +1,49 @@ + +## Class : in convergence relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000004 + * *Label* = in convergence relationship with + * *Definition* = Homoplasy that involves different underlying mechanisms or structures. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/j.jhevol.2006.11.010, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000004 ] + * *Comment* = Convergence usually implies a notion of adaptation. + +## Synonyms + + * analogy + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in convergence relationship with](../../RO/04/RO_HOM0000004.md) + * [in convergence relationship with](../../RO/04/RO_HOM0000004.md) SubPropertyOf [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Homoplasy that involves different underlying mechanisms or structures. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = analogy + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Convergence usually implies a notion of adaptation. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in convergence relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000004 + +## Usage + + * - + * SymmetricObjectProperty [in convergence relationship with](../../RO/04/RO_HOM0000004.md) + * [in convergence relationship with](../../RO/04/RO_HOM0000004.md) SubPropertyOf [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + * [in mimicry relationship with](../../RO/33/RO_HOM0000033.md) SubPropertyOf [in convergence relationship with](../../RO/04/RO_HOM0000004.md) + +## External Comments + diff --git a/src/ontology/md/RO/05/RO_0002005.md b/src/ontology/md/RO/05/RO_0002005.md new file mode 100644 index 00000000..1199564c --- /dev/null +++ b/src/ontology/md/RO/05/RO_0002005.md @@ -0,0 +1,38 @@ + +## Class : innervated_by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002005 + * *Label* = innervated_by + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [innervated_by](../../RO/05/RO_0002005.md) InverseOf [innervates](../../RO/34/RO_0002134.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = innervated_by + +## Usage + + * - + * [innervated_by](../../RO/05/RO_0002005.md) InverseOf [innervates](../../RO/34/RO_0002134.md) + +## External Comments + diff --git a/src/ontology/md/RO/05/RO_0002105.md b/src/ontology/md/RO/05/RO_0002105.md new file mode 100644 index 00000000..12d615d5 --- /dev/null +++ b/src/ontology/md/RO/05/RO_0002105.md @@ -0,0 +1,49 @@ + +## Class : synapsed_via_type_Ib_bouton_to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002105 + * *Label* = synapsed_via_type_Ib_bouton_to + * *Definition* = A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. + * *Comment* = Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [synapsed to](../../RO/20/RO_0002120.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed_via_type_Ib_bouton_to](../../RO/05/RO_0002105.md) InverseOf [synapsed_by_via_type_Ib_bouton](../../RO/09/RO_0002109.md) + * [synapsed_via_type_Ib_bouton_to](../../RO/05/RO_0002105.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = Marta Costa + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed_via_type_Ib_bouton_to + +## Usage + + * - + * [synapsed_via_type_Ib_bouton_to](../../RO/05/RO_0002105.md) InverseOf [synapsed_by_via_type_Ib_bouton](../../RO/09/RO_0002109.md) + * [synapsed_via_type_Ib_bouton_to](../../RO/05/RO_0002105.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + +## External Comments + diff --git a/src/ontology/md/RO/05/RO_0002205.md b/src/ontology/md/RO/05/RO_0002205.md new file mode 100644 index 00000000..17cb8dae --- /dev/null +++ b/src/ontology/md/RO/05/RO_0002205.md @@ -0,0 +1,50 @@ + +## Class : has gene product + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002205 + * *Label* = has gene product + * *Definition* = x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [genomically related to](../../RO/30/RO_0002330.md) + +## SubProperties + + +## Other Logical Axioms + + * [has gene product](../../RO/05/RO_0002205.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [has gene product](../../RO/05/RO_0002205.md) InverseOf [gene product of](../../RO/04/RO_0002204.md) + * [has gene product](../../RO/05/RO_0002205.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has gene product](../../RO/05/RO_0002205.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = every HOTAIR lncRNA is the gene product of some HOXC gene + * *[example of usage](../../IAO/12/IAO_0000112.md)* = every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has gene product + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has gene product](../../RO/05/RO_0002205.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [has gene product](../../RO/05/RO_0002205.md) InverseOf [gene product of](../../RO/04/RO_0002204.md) + * [has gene product](../../RO/05/RO_0002205.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has gene product](../../RO/05/RO_0002205.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## External Comments + diff --git a/src/ontology/md/RO/05/RO_0002405.md b/src/ontology/md/RO/05/RO_0002405.md new file mode 100644 index 00000000..82348095 --- /dev/null +++ b/src/ontology/md/RO/05/RO_0002405.md @@ -0,0 +1,44 @@ + +## Class : immediately causally downstream of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002405 + * *Label* = immediately causally downstream of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causally downstream of](../../RO/04/RO_0002404.md) + * [immediately preceded by](../../RO/87/RO_0002087.md) + +## SubProperties + + +## Other Logical Axioms + + * [immediately causally downstream of](../../RO/05/RO_0002405.md) InverseOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [immediately causally downstream of](../../RO/05/RO_0002405.md) SubPropertyOf [causally downstream of](../../RO/04/RO_0002404.md) + * [immediately causally downstream of](../../RO/05/RO_0002405.md) SubPropertyOf [immediately preceded by](../../RO/87/RO_0002087.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = immediately causally downstream of + +## Usage + + * - + * [immediately causally downstream of](../../RO/05/RO_0002405.md) InverseOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [immediately causally downstream of](../../RO/05/RO_0002405.md) SubPropertyOf [causally downstream of](../../RO/04/RO_0002404.md) + * [immediately causally downstream of](../../RO/05/RO_0002405.md) SubPropertyOf [immediately preceded by](../../RO/87/RO_0002087.md) + +## External Comments + diff --git a/src/ontology/md/RO/05/RO_0002505.md b/src/ontology/md/RO/05/RO_0002505.md new file mode 100644 index 00000000..d682af2a --- /dev/null +++ b/src/ontology/md/RO/05/RO_0002505.md @@ -0,0 +1,44 @@ + +## Class : has intermediate + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002505 + * *Label* = has intermediate + * *Definition* = p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [has intermediate](../../RO/05/RO_0002505.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate + * *[definition](../../IAO/15/IAO_0000115.md)* = p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has intermediate product + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has intermediate + +## Usage + + * - + * [has intermediate](../../RO/05/RO_0002505.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + +## External Comments + diff --git a/src/ontology/md/RO/05/RO_0002605.md b/src/ontology/md/RO/05/RO_0002605.md new file mode 100644 index 00000000..0284624e --- /dev/null +++ b/src/ontology/md/RO/05/RO_0002605.md @@ -0,0 +1,38 @@ + +## Class : is indistinguishable from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002605 + * *Label* = is indistinguishable from + * *Definition* = x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is approximately equivalent to](../../RO/03/RO_0002603.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is indistinguishable from + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/05/RO_HOM0000005.md b/src/ontology/md/RO/05/RO_HOM0000005.md new file mode 100644 index 00000000..3f8a4b63 --- /dev/null +++ b/src/ontology/md/RO/05/RO_HOM0000005.md @@ -0,0 +1,50 @@ + +## Class : in parallelism relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000005 + * *Label* = in parallelism relationship with + * *Definition* = Homoplasy that involves homologous underlying mechanisms or structures. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/j.jhevol.2006.11.010, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000005 ] + * *Comment* = Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + +## Synonyms + + * parallel evolution + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + * [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) SubPropertyOf [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Homoplasy that involves homologous underlying mechanisms or structures. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = parallel evolution + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in parallelism relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000005 + +## Usage + + * - + * SymmetricObjectProperty [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + * [in deep homology relationship with](../../RO/44/RO_HOM0000044.md) SubPropertyOf [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + * [in latent homology relationship with](../../RO/57/RO_HOM0000057.md) SubPropertyOf [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + * [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) SubPropertyOf [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + +## External Comments + diff --git a/src/ontology/md/RO/06/RO_0002006.md b/src/ontology/md/RO/06/RO_0002006.md new file mode 100644 index 00000000..2cc8f261 --- /dev/null +++ b/src/ontology/md/RO/06/RO_0002006.md @@ -0,0 +1,40 @@ + +## Class : has synaptic terminal of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002006 + * *Label* = has synaptic terminal of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [has synaptic terminal of](../../RO/06/RO_0002006.md) InverseOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + * [has synaptic terminal of](../../RO/06/RO_0002006.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has synaptic terminal of + +## Usage + + * - + * [has synaptic terminal of](../../RO/06/RO_0002006.md) InverseOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + * [has synaptic terminal of](../../RO/06/RO_0002006.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## External Comments + diff --git a/src/ontology/md/RO/06/RO_0002106.md b/src/ontology/md/RO/06/RO_0002106.md new file mode 100644 index 00000000..5d94c60a --- /dev/null +++ b/src/ontology/md/RO/06/RO_0002106.md @@ -0,0 +1,49 @@ + +## Class : synapsed_via_type_Is_bouton_to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002106 + * *Label* = synapsed_via_type_Is_bouton_to + * *Definition* = A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. + * *Comment* = Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [synapsed to](../../RO/20/RO_0002120.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed_via_type_Is_bouton_to](../../RO/06/RO_0002106.md) InverseOf [synapsed_by_via_type_Is_bouton](../../RO/12/RO_0002112.md) + * [synapsed_via_type_Is_bouton_to](../../RO/06/RO_0002106.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = Marta Costa + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed_via_type_Is_bouton_to + +## Usage + + * - + * [synapsed_via_type_Is_bouton_to](../../RO/06/RO_0002106.md) InverseOf [synapsed_by_via_type_Is_bouton](../../RO/12/RO_0002112.md) + * [synapsed_via_type_Is_bouton_to](../../RO/06/RO_0002106.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + +## External Comments + diff --git a/src/ontology/md/RO/06/RO_0002206.md b/src/ontology/md/RO/06/RO_0002206.md new file mode 100644 index 00000000..ae8f7886 --- /dev/null +++ b/src/ontology/md/RO/06/RO_0002206.md @@ -0,0 +1,51 @@ + +## Class : expressed in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002206 + * *Label* = expressed in + * *Definition* = x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [genomically related to](../../RO/30/RO_0002330.md) + +## SubProperties + + +## Other Logical Axioms + + * [expressed in](../../RO/06/RO_0002206.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [expressed in](../../RO/06/RO_0002206.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [expressed in](../../RO/06/RO_0002206.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [expresses](../../RO/92/RO_0002292.md) InverseOf [expressed in](../../RO/06/RO_0002206.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = expressed in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [expressed in](../../RO/06/RO_0002206.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [expressed in](../../RO/06/RO_0002206.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [expressed in](../../RO/06/RO_0002206.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [expresses](../../RO/92/RO_0002292.md) InverseOf [expressed in](../../RO/06/RO_0002206.md) + * [ubiquitously expressed in](../../RO/91/RO_0002291.md) SubPropertyOf [expressed in](../../RO/06/RO_0002206.md) + +## External Comments + diff --git a/src/ontology/md/RO/06/RO_0002406.md b/src/ontology/md/RO/06/RO_0002406.md new file mode 100644 index 00000000..198c31a7 --- /dev/null +++ b/src/ontology/md/RO/06/RO_0002406.md @@ -0,0 +1,53 @@ + +## Class : directly activates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002406 + * *Label* = directly activates + * *Definition* = p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [positively regulates](../../RO/13/RO_0002213.md) + * [directly regulates](../../RO/78/RO_0002578.md) + * [immediately causally upstream of](../../RO/12/RO_0002412.md) + +## SubProperties + + +## Other Logical Axioms + + * [directly activates](../../RO/06/RO_0002406.md) SubPropertyOf [directly regulates](../../RO/78/RO_0002578.md) + * [directly activates](../../RO/06/RO_0002406.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly activates](../../RO/06/RO_0002406.md) SubPropertyOf [positively regulates](../../RO/13/RO_0002213.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = directly positively regulates + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = directly activates (process to process) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = directly activates + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [directly activates](../../RO/06/RO_0002406.md) SubPropertyOf [directly regulates](../../RO/78/RO_0002578.md) + * [directly activates](../../RO/06/RO_0002406.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly activates](../../RO/06/RO_0002406.md) SubPropertyOf [positively regulates](../../RO/13/RO_0002213.md) + +## External Comments + diff --git a/src/ontology/md/RO/06/RO_0002506.md b/src/ontology/md/RO/06/RO_0002506.md new file mode 100644 index 00000000..45d29c5e --- /dev/null +++ b/src/ontology/md/RO/06/RO_0002506.md @@ -0,0 +1,47 @@ + +## Class : causal relation between material entities + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002506 + * *Label* = causal relation between material entities + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causally related to](../../RO/10/RO_0002410.md) + +## SubProperties + + +## Other Logical Axioms + + * [causal relation between material entities](../../RO/06/RO_0002506.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [causal relation between material entities](../../RO/06/RO_0002506.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [causal relation between material entities](../../RO/06/RO_0002506.md) SubPropertyOf [causally related to](../../RO/10/RO_0002410.md) + +## Other Annotations + + * *[editor note](../../IAO/16/IAO_0000116.md)* = The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causal relation between material entities + +## Usage + + * - + * [causal relation between material entities](../../RO/06/RO_0002506.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [causal relation between material entities](../../RO/06/RO_0002506.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [causal relation between material entities](../../RO/06/RO_0002506.md) SubPropertyOf [causally related to](../../RO/10/RO_0002410.md) + * [causally influenced by](../../RO/59/RO_0002559.md) SubPropertyOf [causal relation between material entities](../../RO/06/RO_0002506.md) + * [causally influences](../../RO/66/RO_0002566.md) SubPropertyOf [causal relation between material entities](../../RO/06/RO_0002506.md) + * [determined by part of](../../RO/09/RO_0002509.md) SubPropertyOf [causal relation between material entities](../../RO/06/RO_0002506.md) + +## External Comments + diff --git a/src/ontology/md/RO/06/RO_0002606.md b/src/ontology/md/RO/06/RO_0002606.md new file mode 100644 index 00000000..b551a86b --- /dev/null +++ b/src/ontology/md/RO/06/RO_0002606.md @@ -0,0 +1,41 @@ + +## Class : is substance that treats + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002606 + * *Label* = is substance that treats + * *Definition* = c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [capable of inhibiting or preventing pathological process](../../RO/99/RO_0002599.md) + +## SubProperties + + +## Other Logical Axioms + + * [is substance that treats](../../RO/06/RO_0002606.md) SubPropertyOf [capable of inhibiting or preventing pathological process](../../RO/99/RO_0002599.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = treats + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is substance that treats + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = https://code.google.com/p/obo-relations/issues/detail?id=46 + +## Usage + + * - + * [is substance that treats](../../RO/06/RO_0002606.md) SubPropertyOf [capable of inhibiting or preventing pathological process](../../RO/99/RO_0002599.md) + +## External Comments + diff --git a/src/ontology/md/RO/06/RO_HOM0000006.md b/src/ontology/md/RO/06/RO_HOM0000006.md new file mode 100644 index 00000000..90eef1c9 --- /dev/null +++ b/src/ontology/md/RO/06/RO_HOM0000006.md @@ -0,0 +1,57 @@ + +## Class : in structural homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000006 + * *Label* = in structural homology relationship with + * *Definition* = Homology that is defined by similarity with regard to selected structural parameters. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:0123195837, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/j.jhevol.2006.11.014, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.es.20.110189.000411, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000006 ] + +## Synonyms + + * structural homologous to + * idealistic homology + +## Cross-references + + * ECO:0000071 + * MI:2163 + +## Subsets + + +## SuperProperties + + * [in homology relationship with](../../RO/01/RO_HOM0000001.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + * [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) SubPropertyOf [in homology relationship with](../../RO/01/RO_HOM0000001.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Homology that is defined by similarity with regard to selected structural parameters. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = ECO:0000071 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = MI:2163 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = structural homologous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = idealistic homology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in structural homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000006 + +## Usage + + * - + * SymmetricObjectProperty [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + * [in homotopy relationship with](../../RO/71/RO_HOM0000071.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + * [in non functional homology relationship with](../../RO/16/RO_HOM0000016.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + * [in partial homology relationship with](../../RO/14/RO_HOM0000014.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + * [in protein structural homology relationship with](../../RO/15/RO_HOM0000015.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + * [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) SubPropertyOf [in homology relationship with](../../RO/01/RO_HOM0000001.md) + * [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## External Comments + diff --git a/src/ontology/md/RO/07/RO_0002007.md b/src/ontology/md/RO/07/RO_0002007.md new file mode 100644 index 00000000..8834f1f9 --- /dev/null +++ b/src/ontology/md/RO/07/RO_0002007.md @@ -0,0 +1,64 @@ + +## Class : bounding layer of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002007 + * *Label* = bounding layer of + * *Definition* = X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + * *Comment* = A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [part of](../../BFO/50/BFO_0000050.md) + +## SubProperties + + +## Other Logical Axioms + + * [bounding layer of](../../RO/07/RO_0002007.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [laminar](../../PATO/24/PATO_0002124.md) and [material entity](../../BFO/40/BFO_0000040.md) + * [bounding layer of](../../RO/07/RO_0002007.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [bounding layer of](../../RO/07/RO_0002007.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = bounding layer of + +## Usage + + * - + * [bounding layer of](../../RO/07/RO_0002007.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [laminar](../../PATO/24/PATO_0002124.md) and [material entity](../../BFO/40/BFO_0000040.md) + * [bounding layer of](../../RO/07/RO_0002007.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [bounding layer of](../../RO/07/RO_0002007.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## External Comments + diff --git a/src/ontology/md/RO/07/RO_0002107.md b/src/ontology/md/RO/07/RO_0002107.md new file mode 100644 index 00000000..3a3db0e4 --- /dev/null +++ b/src/ontology/md/RO/07/RO_0002107.md @@ -0,0 +1,48 @@ + +## Class : synapsed_via_type_II_bouton_to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002107 + * *Label* = synapsed_via_type_II_bouton_to + * *Definition* = A relation between a motor neuron and a muscle that it synapses to via a type II bouton. + * *Comment* = Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [synapsed to](../../RO/20/RO_0002120.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed_via_type_II_bouton_to](../../RO/07/RO_0002107.md) InverseOf [synapsed_by_via_type_II_bouton](../../RO/08/RO_0002108.md) + * [synapsed_via_type_II_bouton_to](../../RO/07/RO_0002107.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation between a motor neuron and a muscle that it synapses to via a type II bouton. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = Marta Costa + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed_via_type_II_bouton_to + +## Usage + + * - + * [synapsed_via_type_II_bouton_to](../../RO/07/RO_0002107.md) InverseOf [synapsed_by_via_type_II_bouton](../../RO/08/RO_0002108.md) + * [synapsed_via_type_II_bouton_to](../../RO/07/RO_0002107.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + +## External Comments + diff --git a/src/ontology/md/RO/07/RO_0002207.md b/src/ontology/md/RO/07/RO_0002207.md new file mode 100644 index 00000000..650d0430 --- /dev/null +++ b/src/ontology/md/RO/07/RO_0002207.md @@ -0,0 +1,58 @@ + +## Class : directly develops from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002207 + * *Label* = directly develops from + * *Definition* = Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y + * *Comment* = TODO - add child relations from DOS + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [develops from](../../RO/02/RO_0002202.md) + +## SubProperties + + +## Other Logical Axioms + + * [directly develops from](../../RO/07/RO_0002207.md) Domain [cell](../../CL/00/CL_0000000.md)or[multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + * [directly develops from](../../RO/07/RO_0002207.md) Range [cell](../../CL/00/CL_0000000.md)or[multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + * [directly develops from](../../RO/07/RO_0002207.md) SubPropertyOf [develops from](../../RO/02/RO_0002202.md) + * [directly develops into](../../RO/10/RO_0002210.md) InverseOf [directly develops from](../../RO/07/RO_0002207.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = has developmental precursor + * *[definition source](../../IAO/19/IAO_0000119.md)* = FBbt + * *[is direct form of](../../RO/75/RO_0002575.md)* = http://purl.obolibrary.org/obo/RO_0002202 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = TODO - add child relations from DOS + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = directly develops from + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [cell](../../CL/00/CL_0000000.md) SubClassOf [directly develops from](../../RO/07/RO_0002207.md) only [cell](../../CL/00/CL_0000000.md) + * [directly develops from](../../RO/07/RO_0002207.md) Domain [cell](../../CL/00/CL_0000000.md)or[multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + * [directly develops from](../../RO/07/RO_0002207.md) Range [cell](../../CL/00/CL_0000000.md)or[multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + * [directly develops from](../../RO/07/RO_0002207.md) SubPropertyOf [develops from](../../RO/02/RO_0002202.md) + * [directly develops into](../../RO/10/RO_0002210.md) InverseOf [directly develops from](../../RO/07/RO_0002207.md) + * [immediate transformation of](../../RO/95/RO_0002495.md) SubPropertyOf [directly develops from](../../RO/07/RO_0002207.md) + * [multicellular anatomical structure](../../CARO/00/CARO_0010000.md) SubClassOf [directly develops from](../../RO/07/RO_0002207.md) only [multicellular anatomical structure](../../CARO/00/CARO_0010000.md) + +## External Comments + diff --git a/src/ontology/md/RO/07/RO_0002407.md b/src/ontology/md/RO/07/RO_0002407.md new file mode 100644 index 00000000..a7e769d7 --- /dev/null +++ b/src/ontology/md/RO/07/RO_0002407.md @@ -0,0 +1,48 @@ + +## Class : indirectly activates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002407 + * *Label* = indirectly activates + * *Definition* = p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [positively regulates](../../RO/13/RO_0002213.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [indirectly activates](../../RO/07/RO_0002407.md) + * [indirectly activates](../../RO/07/RO_0002407.md) SubPropertyOf [positively regulates](../../RO/13/RO_0002213.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = indirectly positively regulates + * *[is indirect form of](../../RO/79/RO_0002579.md)* = http://purl.obolibrary.org/obo/RO_0002213 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = indirectly activates + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [indirectly activates](../../RO/07/RO_0002407.md) + * [indirectly activates](../../RO/07/RO_0002407.md) SubPropertyOf [positively regulates](../../RO/13/RO_0002213.md) + +## External Comments + diff --git a/src/ontology/md/RO/07/RO_0002507.md b/src/ontology/md/RO/07/RO_0002507.md new file mode 100644 index 00000000..664606df --- /dev/null +++ b/src/ontology/md/RO/07/RO_0002507.md @@ -0,0 +1,61 @@ + +## Class : determined by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002507 + * *Label* = determined by + * *Definition* = s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [causally influenced by](../../RO/59/RO_0002559.md) + * [part of](../../BFO/50/BFO_0000050.md) + * [determined by part of](../../RO/09/RO_0002509.md) + +## SubProperties + + +## Other Logical Axioms + + * [determined by](../../RO/07/RO_0002507.md) Domain [system](../../RO/77/RO_0002577.md) + * [determined by](../../RO/07/RO_0002507.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [determined by](../../RO/07/RO_0002507.md) SubPropertyOf [causally influenced by](../../RO/59/RO_0002559.md) + * [determined by](../../RO/07/RO_0002507.md) SubPropertyOf [determined by part of](../../RO/09/RO_0002509.md) + * [determined by](../../RO/07/RO_0002507.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [determines](../../RO/08/RO_0002508.md) InverseOf [determined by](../../RO/07/RO_0002507.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = A coral reef environment is determined by a particular coral reef + * *[definition](../../IAO/15/IAO_0000115.md)* = s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. + * *[editor note](../../IAO/16/IAO_0000116.md)* = The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/24330602 + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = determined by (system to material entity) + * *[creator](../../or/creator.md)* = Chris Mungall + * *[creator](../../or/creator.md)* = Pier Buttigieg + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = determined by + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * [determined by](../../RO/07/RO_0002507.md) Domain [system](../../RO/77/RO_0002577.md) + * [determined by](../../RO/07/RO_0002507.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [determined by](../../RO/07/RO_0002507.md) SubPropertyOf [causally influenced by](../../RO/59/RO_0002559.md) + * [determined by](../../RO/07/RO_0002507.md) SubPropertyOf [determined by part of](../../RO/09/RO_0002509.md) + * [determined by](../../RO/07/RO_0002507.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [determines](../../RO/08/RO_0002508.md) InverseOf [determined by](../../RO/07/RO_0002507.md) + +## External Comments + diff --git a/src/ontology/md/RO/07/RO_0002607.md b/src/ontology/md/RO/07/RO_0002607.md new file mode 100644 index 00000000..0b4eea80 --- /dev/null +++ b/src/ontology/md/RO/07/RO_0002607.md @@ -0,0 +1,40 @@ + +## Class : is marker for + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002607 + * *Label* = is marker for + * *Definition* = c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [correlated with](../../RO/10/RO_0002610.md) + +## SubProperties + + +## Other Logical Axioms + + * [is marker for](../../RO/07/RO_0002607.md) SubPropertyOf [correlated with](../../RO/10/RO_0002610.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. + * *[editor note](../../IAO/16/IAO_0000116.md)* = May be ceded to OBI + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is marker for + +## Usage + + * - + * [is marker for](../../RO/07/RO_0002607.md) SubPropertyOf [correlated with](../../RO/10/RO_0002610.md) + +## External Comments + diff --git a/src/ontology/md/RO/07/RO_HOM0000007.md b/src/ontology/md/RO/07/RO_HOM0000007.md new file mode 100644 index 00000000..6233d0df --- /dev/null +++ b/src/ontology/md/RO/07/RO_HOM0000007.md @@ -0,0 +1,83 @@ + +## Class : in historical homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000007 + * *Label* = in historical homology relationship with + * *Definition* = Homology that is defined by common descent. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:0123195837, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/S0169-5347(97)01125-7, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000007 ] + +## Synonyms + + * cladistic homology + * historical homologous to + * phylogenetic homology + * taxic homology + * homology + * true homology + +## Cross-references + + * ECO:0000080 + * RO_proposed_relation:homologous_to + * SO:0000330 + * SO:0000853 + * SO:0000857 + * SO:homologous_to + * TAO:homologous_to + +## Subsets + + +## SuperProperties + + * [in homology relationship with](../../RO/01/RO_HOM0000001.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) SubPropertyOf [in homology relationship with](../../RO/01/RO_HOM0000001.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Homology that is defined by common descent. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_broad_synonym](../../ym/oboInOwl#hasBroadSynonym.md)* = homology + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = ECO:0000080 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = RO_proposed_relation:homologous_to + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:0000330 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:0000853 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:0000857 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:homologous_to + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = TAO:homologous_to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = cladistic homology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = historical homologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = phylogenetic homology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = taxic homology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = true homology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in historical homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000007 + +## Usage + + * - + * SymmetricObjectProperty [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in 1 to many homology relationship with](../../RO/37/RO_HOM0000037.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in apomorphy relationship with](../../RO/42/RO_HOM0000042.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in chromosomal homology relationship with](../../RO/47/RO_HOM0000047.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in hemiplasy relationship with](../../RO/45/RO_HOM0000045.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) SubPropertyOf [in homology relationship with](../../RO/01/RO_HOM0000001.md) + * [in interology relationship with](../../RO/63/RO_HOM0000063.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in many to many homology relationship with](../../RO/36/RO_HOM0000036.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in orthology relationship with](../../RO/17/RO_HOM0000017.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in plesiomorphy relationship with](../../RO/43/RO_HOM0000043.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in regulogy relationship with](../../RO/75/RO_HOM0000075.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in xenology relationship with](../../RO/18/RO_HOM0000018.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## External Comments + diff --git a/src/ontology/md/RO/08/RO_0002008.md b/src/ontology/md/RO/08/RO_0002008.md new file mode 100644 index 00000000..d2f97a5f --- /dev/null +++ b/src/ontology/md/RO/08/RO_0002008.md @@ -0,0 +1,49 @@ + +## Class : coincident with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002008 + * *Label* = coincident with + * *Definition* = A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + * *Comment* = Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [coincident with](../../RO/08/RO_0002008.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [coincident with](../../RO/08/RO_0002008.md) Range [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [coincident with](../../RO/08/RO_0002008.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Note from NCEAS meeting: consider changing primary label + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = coincident with + +## Usage + + * - + * [coincident with](../../RO/08/RO_0002008.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [coincident with](../../RO/08/RO_0002008.md) Range [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [coincident with](../../RO/08/RO_0002008.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## External Comments + diff --git a/src/ontology/md/RO/08/RO_0002108.md b/src/ontology/md/RO/08/RO_0002108.md new file mode 100644 index 00000000..628bdec1 --- /dev/null +++ b/src/ontology/md/RO/08/RO_0002108.md @@ -0,0 +1,50 @@ + +## Class : synapsed_by_via_type_II_bouton + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002108 + * *Label* = synapsed_by_via_type_II_bouton + * *Definition* = Relation between a muscle and a motor neuron that synapses to it via a type II bouton. + * *Comment* = Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [synapsed by](../../RO/03/RO_0002103.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed_by_via_type_II_bouton](../../RO/08/RO_0002108.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_via_type_II_bouton_to](../../RO/07/RO_0002107.md) InverseOf [synapsed_by_via_type_II_bouton](../../RO/08/RO_0002108.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a muscle and a motor neuron that synapses to it via a type II bouton. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = Marta Costa + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed_by_via_type_II_bouton + +## Usage + + * - + * [synapsed_by_via_type_II_bouton](../../RO/08/RO_0002108.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_via_type_II_bouton_to](../../RO/07/RO_0002107.md) InverseOf [synapsed_by_via_type_II_bouton](../../RO/08/RO_0002108.md) + +## External Comments + diff --git a/src/ontology/md/RO/08/RO_0002408.md b/src/ontology/md/RO/08/RO_0002408.md new file mode 100644 index 00000000..162bb79f --- /dev/null +++ b/src/ontology/md/RO/08/RO_0002408.md @@ -0,0 +1,51 @@ + +## Class : directly inhibits + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002408 + * *Label* = directly inhibits + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [negatively regulates](../../RO/12/RO_0002212.md) + * [directly regulates](../../RO/78/RO_0002578.md) + * [immediately causally upstream of](../../RO/12/RO_0002412.md) + +## SubProperties + + +## Other Logical Axioms + + * [directly inhibits](../../RO/08/RO_0002408.md) SubPropertyOf [directly regulates](../../RO/78/RO_0002578.md) + * [directly inhibits](../../RO/08/RO_0002408.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly inhibits](../../RO/08/RO_0002408.md) SubPropertyOf [negatively regulates](../../RO/12/RO_0002212.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = directly negatively regulates + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = directly inhibits (process to process) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = directly inhibits + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [directly inhibits](../../RO/08/RO_0002408.md) SubPropertyOf [directly regulates](../../RO/78/RO_0002578.md) + * [directly inhibits](../../RO/08/RO_0002408.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly inhibits](../../RO/08/RO_0002408.md) SubPropertyOf [negatively regulates](../../RO/12/RO_0002212.md) + +## External Comments + diff --git a/src/ontology/md/RO/08/RO_0002508.md b/src/ontology/md/RO/08/RO_0002508.md new file mode 100644 index 00000000..8ab348f5 --- /dev/null +++ b/src/ontology/md/RO/08/RO_0002508.md @@ -0,0 +1,43 @@ + +## Class : determines + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002508 + * *Label* = determines + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [causally influences](../../RO/66/RO_0002566.md) + +## SubProperties + + +## Other Logical Axioms + + * [determines](../../RO/08/RO_0002508.md) InverseOf [determined by](../../RO/07/RO_0002507.md) + * [determines](../../RO/08/RO_0002508.md) SubPropertyOf [causally influences](../../RO/66/RO_0002566.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = determines (material entity to system) + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = determines + +## Usage + + * - + * [determines](../../RO/08/RO_0002508.md) InverseOf [determined by](../../RO/07/RO_0002507.md) + * [determines](../../RO/08/RO_0002508.md) SubPropertyOf [causally influences](../../RO/66/RO_0002566.md) + +## External Comments + diff --git a/src/ontology/md/RO/08/RO_HOM0000008.md b/src/ontology/md/RO/08/RO_HOM0000008.md new file mode 100644 index 00000000..9b20ac93 --- /dev/null +++ b/src/ontology/md/RO/08/RO_HOM0000008.md @@ -0,0 +1,55 @@ + +## Class : in biological homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000008 + * *Label* = in biological homology relationship with + * *Definition* = Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/S0169-5347(97)01125-7, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.es.20.110189.000411, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000008 ] + * *Comment* = Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + +## Synonyms + + * biological homologous to + * transformational homology + +## Cross-references + + * ECO:0000067 + +## Subsets + + +## SuperProperties + + * [in homology relationship with](../../RO/01/RO_HOM0000001.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + * [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) SubPropertyOf [in homology relationship with](../../RO/01/RO_HOM0000001.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = ECO:0000067 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = biological homologous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = transformational homology + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in biological homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000008 + +## Usage + + * - + * SymmetricObjectProperty [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + * [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) SubPropertyOf [in homology relationship with](../../RO/01/RO_HOM0000001.md) + * [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) SubPropertyOf [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + * [in homeosis relationship with](../../RO/72/RO_HOM0000072.md) SubPropertyOf [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + * [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) SubPropertyOf [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + +## External Comments + diff --git a/src/ontology/md/RO/09/RO_0002009.md b/src/ontology/md/RO/09/RO_0002009.md new file mode 100644 index 00000000..fc7c9601 --- /dev/null +++ b/src/ontology/md/RO/09/RO_0002009.md @@ -0,0 +1,48 @@ + +## Class : cell expresses + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002009 + * *Label* = cell expresses + * *Definition* = A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [expresses](../../RO/92/RO_0002292.md) + +## SubProperties + + +## Other Logical Axioms + + * [cell expresses](../../RO/09/RO_0002009.md) Domain [cell](../../CL/00/CL_0000000.md) + * [cell expresses](../../RO/09/RO_0002009.md) SubPropertyOf [expresses](../../RO/92/RO_0002292.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[description](../../on/description.md)* = x 'cell expresses' y iff: +cell(x) +AND gene(y) +AND exists some 'transcription, DNA templated (GO_0006351)'(t) +AND t occurs_in x +AND t has_input y + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = cell expresses + +## Usage + + * - + * [cell expresses](../../RO/09/RO_0002009.md) Domain [cell](../../CL/00/CL_0000000.md) + * [cell expresses](../../RO/09/RO_0002009.md) SubPropertyOf [expresses](../../RO/92/RO_0002292.md) + +## External Comments + diff --git a/src/ontology/md/RO/09/RO_0002109.md b/src/ontology/md/RO/09/RO_0002109.md new file mode 100644 index 00000000..e3cf4dc3 --- /dev/null +++ b/src/ontology/md/RO/09/RO_0002109.md @@ -0,0 +1,49 @@ + +## Class : synapsed_by_via_type_Ib_bouton + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002109 + * *Label* = synapsed_by_via_type_Ib_bouton + * *Definition* = Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. + * *Comment* = Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [synapsed by](../../RO/03/RO_0002103.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed_by_via_type_Ib_bouton](../../RO/09/RO_0002109.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_via_type_Ib_bouton_to](../../RO/05/RO_0002105.md) InverseOf [synapsed_by_via_type_Ib_bouton](../../RO/09/RO_0002109.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = Marta Costa + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed_by_via_type_Ib_bouton + +## Usage + + * - + * [synapsed_by_via_type_Ib_bouton](../../RO/09/RO_0002109.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_via_type_Ib_bouton_to](../../RO/05/RO_0002105.md) InverseOf [synapsed_by_via_type_Ib_bouton](../../RO/09/RO_0002109.md) + +## External Comments + diff --git a/src/ontology/md/RO/09/RO_0002409.md b/src/ontology/md/RO/09/RO_0002409.md new file mode 100644 index 00000000..3eae2904 --- /dev/null +++ b/src/ontology/md/RO/09/RO_0002409.md @@ -0,0 +1,46 @@ + +## Class : indirectly inhibits + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002409 + * *Label* = indirectly inhibits + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [negatively regulates](../../RO/12/RO_0002212.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [indirectly inhibits](../../RO/09/RO_0002409.md) + * [indirectly inhibits](../../RO/09/RO_0002409.md) SubPropertyOf [negatively regulates](../../RO/12/RO_0002212.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = indirectly negatively regulates + * *[is indirect form of](../../RO/79/RO_0002579.md)* = http://purl.obolibrary.org/obo/RO_0002212 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = indirectly inhibits + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [indirectly inhibits](../../RO/09/RO_0002409.md) + * [indirectly inhibits](../../RO/09/RO_0002409.md) SubPropertyOf [negatively regulates](../../RO/12/RO_0002212.md) + +## External Comments + diff --git a/src/ontology/md/RO/09/RO_0002509.md b/src/ontology/md/RO/09/RO_0002509.md new file mode 100644 index 00000000..050e7df1 --- /dev/null +++ b/src/ontology/md/RO/09/RO_0002509.md @@ -0,0 +1,51 @@ + +## Class : determined by part of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002509 + * *Label* = determined by part of + * *Definition* = s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [causal relation between material entities](../../RO/06/RO_0002506.md) + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [determined by part of](../../RO/09/RO_0002509.md) Domain [system](../../RO/77/RO_0002577.md) + * [determined by part of](../../RO/09/RO_0002509.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [determined by part of](../../RO/09/RO_0002509.md) SubPropertyOf [causal relation between material entities](../../RO/06/RO_0002506.md) + * [determined by part of](../../RO/09/RO_0002509.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = determined by part of + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * [determined by part of](../../RO/09/RO_0002509.md) Domain [system](../../RO/77/RO_0002577.md) + * [determined by part of](../../RO/09/RO_0002509.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [determined by part of](../../RO/09/RO_0002509.md) SubPropertyOf [causal relation between material entities](../../RO/06/RO_0002506.md) + * [determined by part of](../../RO/09/RO_0002509.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [determined by](../../RO/07/RO_0002507.md) SubPropertyOf [determined by part of](../../RO/09/RO_0002509.md) + +## External Comments + diff --git a/src/ontology/md/RO/09/RO_0002609.md b/src/ontology/md/RO/09/RO_0002609.md new file mode 100644 index 00000000..195a29d6 --- /dev/null +++ b/src/ontology/md/RO/09/RO_0002609.md @@ -0,0 +1,39 @@ + +## Class : related via dependence to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002609 + * *Label* = related via dependence to + * *Definition* = A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = related via dependence to + +## Usage + + * - + * [causally related to](../../RO/10/RO_0002410.md) SubPropertyOf [related via dependence to](../../RO/09/RO_0002609.md) + * [correlated with](../../RO/10/RO_0002610.md) SubPropertyOf [related via dependence to](../../RO/09/RO_0002609.md) + +## External Comments + diff --git a/src/ontology/md/RO/09/RO_HOM0000009.md b/src/ontology/md/RO/09/RO_HOM0000009.md new file mode 100644 index 00000000..1afc29db --- /dev/null +++ b/src/ontology/md/RO/09/RO_HOM0000009.md @@ -0,0 +1,50 @@ + +## Class : in reversal relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000009 + * *Label* = in reversal relationship with + * *Definition* = Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/j.jhevol.2006.11.010, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000009 ] + +## Synonyms + + * atavism + * rudiment + * reversion + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in reversal relationship with](../../RO/09/RO_HOM0000009.md) + * [in reversal relationship with](../../RO/09/RO_HOM0000009.md) SubPropertyOf [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = atavism + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = rudiment + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = reversion + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in reversal relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000009 + +## Usage + + * - + * SymmetricObjectProperty [in reversal relationship with](../../RO/09/RO_HOM0000009.md) + * [in reversal relationship with](../../RO/09/RO_HOM0000009.md) SubPropertyOf [in homoplasy relationship with](../../RO/02/RO_HOM0000002.md) + +## External Comments + diff --git a/src/ontology/md/RO/10/RO_0002010.md b/src/ontology/md/RO/10/RO_0002010.md new file mode 100644 index 00000000..7edf595c --- /dev/null +++ b/src/ontology/md/RO/10/RO_0002010.md @@ -0,0 +1,44 @@ + +## Class : regulates in other organism + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002010 + * *Label* = regulates in other organism + * *Definition* = x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causally upstream of or within](../../RO/18/RO_0002418.md) + +## SubProperties + + +## Other Logical Axioms + + * [regulates in other organism](../../RO/10/RO_0002010.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulates in other organism](../../RO/10/RO_0002010.md) Range [process](../../BFO/15/BFO_0000015.md) + * [regulates in other organism](../../RO/10/RO_0002010.md) SubPropertyOf [causally upstream of or within](../../RO/18/RO_0002418.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = regulates in other organism + +## Usage + + * - + * [regulates in other organism](../../RO/10/RO_0002010.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulates in other organism](../../RO/10/RO_0002010.md) Range [process](../../BFO/15/BFO_0000015.md) + * [regulates in other organism](../../RO/10/RO_0002010.md) SubPropertyOf [causally upstream of or within](../../RO/18/RO_0002418.md) + +## External Comments + diff --git a/src/ontology/md/RO/10/RO_0002110.md b/src/ontology/md/RO/10/RO_0002110.md new file mode 100644 index 00000000..b9ea3efa --- /dev/null +++ b/src/ontology/md/RO/10/RO_0002110.md @@ -0,0 +1,54 @@ + +## Class : has postsynaptic terminal in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002110 + * *Label* = has postsynaptic terminal in + * *Definition* = Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has synaptic terminal in](../../RO/30/RO_0002130.md) + +## SubProperties + + +## Other Logical Axioms + + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) InverseOf [axon synapses in](../../RO/02/RO_0002102.md) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) SubPropertyOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = synapsed in + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = http://purl.obolibrary.org/obo/BFO_0000051 some ( + http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( + http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has postsynaptic terminal in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [dendrite synapsed in](../../RO/21/RO_0002121.md) SubPropertyOf [has postsynaptic terminal in](../../RO/10/RO_0002110.md) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) InverseOf [axon synapses in](../../RO/02/RO_0002102.md) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) SubPropertyOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + +## External Comments + diff --git a/src/ontology/md/RO/10/RO_0002210.md b/src/ontology/md/RO/10/RO_0002210.md new file mode 100644 index 00000000..3e47e2c2 --- /dev/null +++ b/src/ontology/md/RO/10/RO_0002210.md @@ -0,0 +1,42 @@ + +## Class : directly develops into + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002210 + * *Label* = directly develops into + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [develops into](../../RO/03/RO_0002203.md) + +## SubProperties + + +## Other Logical Axioms + + * [directly develops into](../../RO/10/RO_0002210.md) InverseOf [directly develops from](../../RO/07/RO_0002207.md) + * [directly develops into](../../RO/10/RO_0002210.md) SubPropertyOf [develops into](../../RO/03/RO_0002203.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[alternative term](../../IAO/18/IAO_0000118.md)* = developmental precursor of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = directly develops into + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [directly develops into](../../RO/10/RO_0002210.md) InverseOf [directly develops from](../../RO/07/RO_0002207.md) + * [directly develops into](../../RO/10/RO_0002210.md) SubPropertyOf [develops into](../../RO/03/RO_0002203.md) + +## External Comments + diff --git a/src/ontology/md/RO/10/RO_0002410.md b/src/ontology/md/RO/10/RO_0002410.md new file mode 100644 index 00000000..1e9b0134 --- /dev/null +++ b/src/ontology/md/RO/10/RO_0002410.md @@ -0,0 +1,60 @@ + +## Class : causally related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002410 + * *Label* = causally related to + * *Definition* = This relation groups causal relations between material entities and causal relations between processes + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [related via dependence to](../../RO/09/RO_0002609.md) + +## SubProperties + + +## Other Logical Axioms + + * [causally related to](../../RO/10/RO_0002410.md) SubPropertyOf [related via dependence to](../../RO/09/RO_0002609.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = This relation groups causal relations between material entities and causal relations between processes + * *[editor note](../../IAO/16/IAO_0000116.md)* = 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. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causally related to + +## Usage + + * - + * [causal relation between material entities](../../RO/06/RO_0002506.md) SubPropertyOf [causally related to](../../RO/10/RO_0002410.md) + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) SubPropertyOf [causally related to](../../RO/10/RO_0002410.md) + * [causal relation between processes](../../RO/01/RO_0002501.md) SubPropertyOf [causally related to](../../RO/10/RO_0002410.md) + * [causally related to](../../RO/10/RO_0002410.md) SubPropertyOf [related via dependence to](../../RO/09/RO_0002609.md) + +## External Comments + diff --git a/src/ontology/md/RO/10/RO_0002510.md b/src/ontology/md/RO/10/RO_0002510.md new file mode 100644 index 00000000..3328f629 --- /dev/null +++ b/src/ontology/md/RO/10/RO_0002510.md @@ -0,0 +1,44 @@ + +## Class : transcribed from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002510 + * *Label* = transcribed from + * *Definition* = x is transcribed from y if and only if x is synthesized from template y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [genomically related to](../../RO/30/RO_0002330.md) + +## SubProperties + + +## Other Logical Axioms + + * [transcribed from](../../RO/10/RO_0002510.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [transcribed to](../../RO/11/RO_0002511.md) InverseOf [transcribed from](../../RO/10/RO_0002510.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x is transcribed from y if and only if x is synthesized from template y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = transcribed from + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [transcribed from](../../RO/10/RO_0002510.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [transcribed to](../../RO/11/RO_0002511.md) InverseOf [transcribed from](../../RO/10/RO_0002510.md) + +## External Comments + diff --git a/src/ontology/md/RO/10/RO_0002610.md b/src/ontology/md/RO/10/RO_0002610.md new file mode 100644 index 00000000..3493bb94 --- /dev/null +++ b/src/ontology/md/RO/10/RO_0002610.md @@ -0,0 +1,41 @@ + +## Class : correlated with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002610 + * *Label* = correlated with + * *Definition* = A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [related via dependence to](../../RO/09/RO_0002609.md) + +## SubProperties + + +## Other Logical Axioms + + * [correlated with](../../RO/10/RO_0002610.md) SubPropertyOf [related via dependence to](../../RO/09/RO_0002609.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + * *[curator note](../../IAO/32/IAO_0000232.md)* = Groups both positive and negative correlation + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = correlated with + +## Usage + + * - + * [correlated with](../../RO/10/RO_0002610.md) SubPropertyOf [related via dependence to](../../RO/09/RO_0002609.md) + * [is marker for](../../RO/07/RO_0002607.md) SubPropertyOf [correlated with](../../RO/10/RO_0002610.md) + +## External Comments + diff --git a/src/ontology/md/RO/10/RO_HOM0000010.md b/src/ontology/md/RO/10/RO_HOM0000010.md new file mode 100644 index 00000000..bd2aa8bc --- /dev/null +++ b/src/ontology/md/RO/10/RO_HOM0000010.md @@ -0,0 +1,56 @@ + +## Class : in syntenic homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000010 + * *Label* = in syntenic homology relationship with + * *Definition* = Structural homology that is detected by similarity in content and organization between chromosomes. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = MeSH:Synteny, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000010 ] + +## Synonyms + + * syntenic homologous to + * synteny + +## Cross-references + + * MeSH:Synteny + * SO:0000860 + * SO:0005858 + +## Subsets + + +## SuperProperties + + * [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + * [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Structural homology that is detected by similarity in content and organization between chromosomes. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = MeSH:Synteny + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:0000860 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:0005858 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = syntenic homologous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = synteny + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in syntenic homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000010 + +## Usage + + * - + * SymmetricObjectProperty [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + * [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + * [in syntenic orthology relationship with](../../RO/13/RO_HOM0000013.md) SubPropertyOf [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + * [in syntenic paralogy relationship with](../../RO/12/RO_HOM0000012.md) SubPropertyOf [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + +## External Comments + diff --git a/src/ontology/md/RO/11/RO_0002011.md b/src/ontology/md/RO/11/RO_0002011.md new file mode 100644 index 00000000..0bc7699d --- /dev/null +++ b/src/ontology/md/RO/11/RO_0002011.md @@ -0,0 +1,40 @@ + +## Class : regulates transport of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002011 + * *Label* = regulates transport of + * *Definition* = A relationship that holds between a process that regulates a transport process and the entity transported by that process. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = GOC:dos ] + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that holds between a process that regulates a transport process and the entity transported by that process. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = regulates transport of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + +## External Comments + diff --git a/src/ontology/md/RO/11/RO_0002111.md b/src/ontology/md/RO/11/RO_0002111.md new file mode 100644 index 00000000..4a1c789f --- /dev/null +++ b/src/ontology/md/RO/11/RO_0002111.md @@ -0,0 +1,39 @@ + +## Class : releases neurotransmitter + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002111 + * *Label* = releases neurotransmitter + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## SubProperties + + +## Other Logical Axioms + + * [releases neurotransmitter](../../RO/11/RO_0002111.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has neurotransmitter + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = releases neurotransmitter + +## Usage + + * - + * [releases neurotransmitter](../../RO/11/RO_0002111.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## External Comments + diff --git a/src/ontology/md/RO/11/RO_0002211.md b/src/ontology/md/RO/11/RO_0002211.md new file mode 100644 index 00000000..5fe4bd80 --- /dev/null +++ b/src/ontology/md/RO/11/RO_0002211.md @@ -0,0 +1,65 @@ + +## Class : regulates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002211 + * *Label* = regulates + * *Definition* = x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causally upstream of or within](../../RO/18/RO_0002418.md) + +## SubProperties + + +## Other Logical Axioms + + * [regulated by](../../RO/34/RO_0002334.md) InverseOf [regulates](../../RO/11/RO_0002211.md) + * [regulates](../../RO/11/RO_0002211.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulates](../../RO/11/RO_0002211.md) Range [process](../../BFO/15/BFO_0000015.md) + * [regulates](../../RO/11/RO_0002211.md) SubPropertyOf [causally upstream of or within](../../RO/18/RO_0002418.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y + * *[editor note](../../IAO/16/IAO_0000116.md)* = 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 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Hill + * *[term editor](../../IAO/17/IAO_0000117.md)* = Tanya Berardini + * *[definition source](../../IAO/19/IAO_0000119.md)* = GO + * *[curator note](../../IAO/32/IAO_0000232.md)* = Regulation does not preclude parthood; the regulatory process may be upstream, or may be within the regulated process. + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = regulates (processual) + * *[elucidation](../../IAO/00/IAO_0000600.md)* = false + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = regulates + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [directly regulates](../../RO/78/RO_0002578.md) SubPropertyOf [regulates](../../RO/11/RO_0002211.md) + * [negatively regulates](../../RO/12/RO_0002212.md) SubPropertyOf [regulates](../../RO/11/RO_0002211.md) + * [positively regulates](../../RO/13/RO_0002213.md) SubPropertyOf [regulates](../../RO/11/RO_0002211.md) + * [regulated by](../../RO/34/RO_0002334.md) InverseOf [regulates](../../RO/11/RO_0002211.md) + * [regulates](../../RO/11/RO_0002211.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulates](../../RO/11/RO_0002211.md) Range [process](../../BFO/15/BFO_0000015.md) + * [regulates](../../RO/11/RO_0002211.md) SubPropertyOf [causally upstream of or within](../../RO/18/RO_0002418.md) + +## External Comments + diff --git a/src/ontology/md/RO/11/RO_0002411.md b/src/ontology/md/RO/11/RO_0002411.md new file mode 100644 index 00000000..07c02968 --- /dev/null +++ b/src/ontology/md/RO/11/RO_0002411.md @@ -0,0 +1,51 @@ + +## Class : causally upstream of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002411 + * *Label* = causally upstream of + * *Definition* = p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causally upstream of or within](../../RO/18/RO_0002418.md) + * [precedes](../../BFO/63/BFO_0000063.md) + +## SubProperties + + +## Other Logical Axioms + + * [causally downstream of](../../RO/04/RO_0002404.md) InverseOf [causally upstream of](../../RO/11/RO_0002411.md) + * [causally upstream of](../../RO/11/RO_0002411.md) SubPropertyOf [causally upstream of or within](../../RO/18/RO_0002418.md) + * [causally upstream of](../../RO/11/RO_0002411.md) SubPropertyOf [precedes](../../BFO/63/BFO_0000063.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causally upstream of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [causally downstream of](../../RO/04/RO_0002404.md) InverseOf [causally upstream of](../../RO/11/RO_0002411.md) + * [causally upstream of](../../RO/11/RO_0002411.md) SubPropertyOf [causally upstream of or within](../../RO/18/RO_0002418.md) + * [causally upstream of](../../RO/11/RO_0002411.md) SubPropertyOf [precedes](../../BFO/63/BFO_0000063.md) + * [immediately causally upstream of](../../RO/12/RO_0002412.md) SubPropertyOf [causally upstream of](../../RO/11/RO_0002411.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) SubPropertyOf [causally upstream of](../../RO/11/RO_0002411.md) + +## External Comments + diff --git a/src/ontology/md/RO/11/RO_0002511.md b/src/ontology/md/RO/11/RO_0002511.md new file mode 100644 index 00000000..78dd8f74 --- /dev/null +++ b/src/ontology/md/RO/11/RO_0002511.md @@ -0,0 +1,42 @@ + +## Class : transcribed to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002511 + * *Label* = transcribed to + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [genomically related to](../../RO/30/RO_0002330.md) + +## SubProperties + + +## Other Logical Axioms + + * [transcribed to](../../RO/11/RO_0002511.md) InverseOf [transcribed from](../../RO/10/RO_0002510.md) + * [transcribed to](../../RO/11/RO_0002511.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = transcribed to + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [transcribed to](../../RO/11/RO_0002511.md) InverseOf [transcribed from](../../RO/10/RO_0002510.md) + * [transcribed to](../../RO/11/RO_0002511.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## External Comments + diff --git a/src/ontology/md/RO/11/RO_HOM0000011.md b/src/ontology/md/RO/11/RO_HOM0000011.md new file mode 100644 index 00000000..e5aecf2b --- /dev/null +++ b/src/ontology/md/RO/11/RO_HOM0000011.md @@ -0,0 +1,62 @@ + +## Class : in paralogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000011 + * *Label* = in paralogy relationship with + * *Definition* = Historical homology that involves genes that diverged after a duplication event. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/S0168-9525(00)02005-9, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000011, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ncbi.nlm.nih.gov/pubmed/5449325 ] + +## Synonyms + + * paralogous to + +## Cross-references + + * SO:0000854 + * SO:0000859 + * SO:paralogous_to + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves genes that diverged after a duplication event. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:0000854 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:0000859 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:paralogous_to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = paralogous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in paralogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000011 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in between-species paralogy relationship with](../../RO/50/RO_HOM0000050.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in in-paralogy relationship with](../../RO/23/RO_HOM0000023.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in ohnology relationship with](../../RO/22/RO_HOM0000022.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in out-paralogy relationship with](../../RO/24/RO_HOM0000024.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in plerology relationship with](../../RO/69/RO_HOM0000069.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in syntenic paralogy relationship with](../../RO/12/RO_HOM0000012.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in tandem paralogy relationship with](../../RO/55/RO_HOM0000055.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in within-species paralogy relationship with](../../RO/49/RO_HOM0000049.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## External Comments + diff --git a/src/ontology/md/RO/12/RO_0002112.md b/src/ontology/md/RO/12/RO_0002112.md new file mode 100644 index 00000000..3c80196d --- /dev/null +++ b/src/ontology/md/RO/12/RO_0002112.md @@ -0,0 +1,49 @@ + +## Class : synapsed_by_via_type_Is_bouton + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002112 + * *Label* = synapsed_by_via_type_Is_bouton + * *Definition* = Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. + * *Comment* = Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [synapsed by](../../RO/03/RO_0002103.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed_by_via_type_Is_bouton](../../RO/12/RO_0002112.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_via_type_Is_bouton_to](../../RO/06/RO_0002106.md) InverseOf [synapsed_by_via_type_Is_bouton](../../RO/12/RO_0002112.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = Marta Costa + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed_by_via_type_Is_bouton + +## Usage + + * - + * [synapsed_by_via_type_Is_bouton](../../RO/12/RO_0002112.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_via_type_Is_bouton_to](../../RO/06/RO_0002106.md) InverseOf [synapsed_by_via_type_Is_bouton](../../RO/12/RO_0002112.md) + +## External Comments + diff --git a/src/ontology/md/RO/12/RO_0002212.md b/src/ontology/md/RO/12/RO_0002212.md new file mode 100644 index 00000000..87b2f71e --- /dev/null +++ b/src/ontology/md/RO/12/RO_0002212.md @@ -0,0 +1,50 @@ + +## Class : negatively regulates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002212 + * *Label* = negatively regulates + * *Definition* = x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [regulates](../../RO/11/RO_0002211.md) + +## SubProperties + + +## Other Logical Axioms + + * [negatively regulated by](../../RO/35/RO_0002335.md) InverseOf [negatively regulates](../../RO/12/RO_0002212.md) + * [negatively regulates](../../RO/12/RO_0002212.md) SubPropertyOf [regulates](../../RO/11/RO_0002211.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = negatively regulates (process to process) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = negatively regulates + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [directly inhibits](../../RO/08/RO_0002408.md) SubPropertyOf [negatively regulates](../../RO/12/RO_0002212.md) + * [indirectly inhibits](../../RO/09/RO_0002409.md) SubPropertyOf [negatively regulates](../../RO/12/RO_0002212.md) + * [negatively regulated by](../../RO/35/RO_0002335.md) InverseOf [negatively regulates](../../RO/12/RO_0002212.md) + * [negatively regulates](../../RO/12/RO_0002212.md) SubPropertyOf [regulates](../../RO/11/RO_0002211.md) + +## External Comments + diff --git a/src/ontology/md/RO/12/RO_0002312.md b/src/ontology/md/RO/12/RO_0002312.md new file mode 100644 index 00000000..fbe0c358 --- /dev/null +++ b/src/ontology/md/RO/12/RO_0002312.md @@ -0,0 +1,38 @@ + +## Class : evolutionary variant of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002312 + * *Label* = evolutionary variant of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [evolutionarily related to](../../RO/20/RO_0002320.md) + +## SubProperties + + +## Other Logical Axioms + + * [evolutionary variant of](../../RO/12/RO_0002312.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = evolutionary variant of + +## Usage + + * - + * [evolutionary variant of](../../RO/12/RO_0002312.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## External Comments + diff --git a/src/ontology/md/RO/12/RO_0002412.md b/src/ontology/md/RO/12/RO_0002412.md new file mode 100644 index 00000000..db4fe454 --- /dev/null +++ b/src/ontology/md/RO/12/RO_0002412.md @@ -0,0 +1,51 @@ + +## Class : immediately causally upstream of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002412 + * *Label* = immediately causally upstream of + * *Definition* = p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [immediately precedes](../../RO/90/RO_0002090.md) + * [causally upstream of](../../RO/11/RO_0002411.md) + +## SubProperties + + +## Other Logical Axioms + + * [immediately causally downstream of](../../RO/05/RO_0002405.md) InverseOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [immediately causally upstream of](../../RO/12/RO_0002412.md) SubPropertyOf [causally upstream of](../../RO/11/RO_0002411.md) + * [immediately causally upstream of](../../RO/12/RO_0002412.md) SubPropertyOf [immediately precedes](../../RO/90/RO_0002090.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[is direct form of](../../RO/75/RO_0002575.md)* = http://purl.obolibrary.org/obo/RO_0002411 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = immediately causally upstream of + +## Usage + + * - + * [directly activates](../../RO/06/RO_0002406.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly inhibits](../../RO/08/RO_0002408.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly provides input for](../../RO/13/RO_0002413.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly regulates](../../RO/78/RO_0002578.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [immediately causally downstream of](../../RO/05/RO_0002405.md) InverseOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [immediately causally upstream of](../../RO/12/RO_0002412.md) SubPropertyOf [causally upstream of](../../RO/11/RO_0002411.md) + * [immediately causally upstream of](../../RO/12/RO_0002412.md) SubPropertyOf [immediately precedes](../../RO/90/RO_0002090.md) + +## External Comments + diff --git a/src/ontology/md/RO/12/RO_0002512.md b/src/ontology/md/RO/12/RO_0002512.md new file mode 100644 index 00000000..d8cb1e21 --- /dev/null +++ b/src/ontology/md/RO/12/RO_0002512.md @@ -0,0 +1,42 @@ + +## Class : ribosomal translation of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002512 + * *Label* = ribosomal translation of + * *Definition* = x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [genomically related to](../../RO/30/RO_0002330.md) + +## SubProperties + + +## Other Logical Axioms + + * [ribosomal translation of](../../RO/12/RO_0002512.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ribosomal translation of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [ribosomal translation of](../../RO/12/RO_0002512.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## External Comments + diff --git a/src/ontology/md/RO/12/RO_HOM0000012.md b/src/ontology/md/RO/12/RO_HOM0000012.md new file mode 100644 index 00000000..2a1fcc49 --- /dev/null +++ b/src/ontology/md/RO/12/RO_HOM0000012.md @@ -0,0 +1,53 @@ + +## Class : in syntenic paralogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000012 + * *Label* = in syntenic paralogy relationship with + * *Definition* = Paralogy that involves sets of syntenic blocks. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1186/1471-213X-7-100, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000012 ] + +## Synonyms + + * syntenic paralogous to + * duplicon + * paralogon + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in syntenic paralogy relationship with](../../RO/12/RO_HOM0000012.md) + * [in syntenic paralogy relationship with](../../RO/12/RO_HOM0000012.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in syntenic paralogy relationship with](../../RO/12/RO_HOM0000012.md) SubPropertyOf [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paralogy that involves sets of syntenic blocks. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = syntenic paralogous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = duplicon + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = paralogon + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in syntenic paralogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000012 + +## Usage + + * - + * SymmetricObjectProperty [in syntenic paralogy relationship with](../../RO/12/RO_HOM0000012.md) + * [in syntenic paralogy relationship with](../../RO/12/RO_HOM0000012.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + * [in syntenic paralogy relationship with](../../RO/12/RO_HOM0000012.md) SubPropertyOf [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + +## External Comments + diff --git a/src/ontology/md/RO/13/RO_0002113.md b/src/ontology/md/RO/13/RO_0002113.md new file mode 100644 index 00000000..887d61b3 --- /dev/null +++ b/src/ontology/md/RO/13/RO_0002113.md @@ -0,0 +1,48 @@ + +## Class : has presynaptic terminal in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002113 + * *Label* = has presynaptic terminal in + * *Definition* = Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has synaptic terminal in](../../RO/30/RO_0002130.md) + +## SubProperties + + +## Other Logical Axioms + + * [has presynaptic terminal in](../../RO/13/RO_0002113.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has presynaptic terminal in](../../RO/13/RO_0002113.md) SubPropertyOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = synapses in + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = some ( that some ( that some Y?) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has presynaptic terminal in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [axon synapses in](../../RO/02/RO_0002102.md) SubPropertyOf [has presynaptic terminal in](../../RO/13/RO_0002113.md) + * [has presynaptic terminal in](../../RO/13/RO_0002113.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has presynaptic terminal in](../../RO/13/RO_0002113.md) SubPropertyOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + +## External Comments + diff --git a/src/ontology/md/RO/13/RO_0002213.md b/src/ontology/md/RO/13/RO_0002213.md new file mode 100644 index 00000000..f33fb09f --- /dev/null +++ b/src/ontology/md/RO/13/RO_0002213.md @@ -0,0 +1,50 @@ + +## Class : positively regulates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002213 + * *Label* = positively regulates + * *Definition* = x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [regulates](../../RO/11/RO_0002211.md) + +## SubProperties + + +## Other Logical Axioms + + * [positively regulated by](../../RO/36/RO_0002336.md) InverseOf [positively regulates](../../RO/13/RO_0002213.md) + * [positively regulates](../../RO/13/RO_0002213.md) SubPropertyOf [regulates](../../RO/11/RO_0002211.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = positively regulates (process to process) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = positively regulates + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [directly activates](../../RO/06/RO_0002406.md) SubPropertyOf [positively regulates](../../RO/13/RO_0002213.md) + * [indirectly activates](../../RO/07/RO_0002407.md) SubPropertyOf [positively regulates](../../RO/13/RO_0002213.md) + * [positively regulated by](../../RO/36/RO_0002336.md) InverseOf [positively regulates](../../RO/13/RO_0002213.md) + * [positively regulates](../../RO/13/RO_0002213.md) SubPropertyOf [regulates](../../RO/11/RO_0002211.md) + +## External Comments + diff --git a/src/ontology/md/RO/13/RO_0002313.md b/src/ontology/md/RO/13/RO_0002313.md new file mode 100644 index 00000000..a0e64403 --- /dev/null +++ b/src/ontology/md/RO/13/RO_0002313.md @@ -0,0 +1,49 @@ + +## Class : transports or maintains localization of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002313 + * *Label* = transports or maintains localization of + * *Definition* = Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [related via localization to](../../RO/37/RO_0002337.md) + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [transports or maintains localization of](../../RO/13/RO_0002313.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [transports or maintains localization of](../../RO/13/RO_0002313.md) SubPropertyOf [related via localization to](../../RO/37/RO_0002337.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = regulates location of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = transports + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = transports or maintains localization of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [exports](../../RO/45/RO_0002345.md) SubPropertyOf [transports or maintains localization of](../../RO/13/RO_0002313.md) + * [imports](../../RO/40/RO_0002340.md) SubPropertyOf [transports or maintains localization of](../../RO/13/RO_0002313.md) + * [transports or maintains localization of](../../RO/13/RO_0002313.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [transports or maintains localization of](../../RO/13/RO_0002313.md) SubPropertyOf [related via localization to](../../RO/37/RO_0002337.md) + +## External Comments + diff --git a/src/ontology/md/RO/13/RO_0002413.md b/src/ontology/md/RO/13/RO_0002413.md new file mode 100644 index 00000000..fa2f23a8 --- /dev/null +++ b/src/ontology/md/RO/13/RO_0002413.md @@ -0,0 +1,47 @@ + +## Class : directly provides input for + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002413 + * *Label* = directly provides input for + * *Definition* = p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) + +## SubProperties + + +## Other Logical Axioms + + * [directly provides input for](../../RO/13/RO_0002413.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly provides input for](../../RO/13/RO_0002413.md) SubPropertyOf [transitively provides input for](../../RO/14/RO_0002414.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c + * *[editor note](../../IAO/16/IAO_0000116.md)* = This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = directly provides input for (process to process) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = directly provides input for + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [directly provides input for](../../RO/13/RO_0002413.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly provides input for](../../RO/13/RO_0002413.md) SubPropertyOf [transitively provides input for](../../RO/14/RO_0002414.md) + +## External Comments + diff --git a/src/ontology/md/RO/13/RO_0002513.md b/src/ontology/md/RO/13/RO_0002513.md new file mode 100644 index 00000000..edc9d352 --- /dev/null +++ b/src/ontology/md/RO/13/RO_0002513.md @@ -0,0 +1,42 @@ + +## Class : ribosomally translates to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002513 + * *Label* = ribosomally translates to + * *Definition* = inverse of ribosomal translation of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [genomically related to](../../RO/30/RO_0002330.md) + +## SubProperties + + +## Other Logical Axioms + + * [ribosomally translates to](../../RO/13/RO_0002513.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of ribosomal translation of + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ribosomally translates to + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [ribosomally translates to](../../RO/13/RO_0002513.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## External Comments + diff --git a/src/ontology/md/RO/13/RO_HOM0000013.md b/src/ontology/md/RO/13/RO_HOM0000013.md new file mode 100644 index 00000000..563f97b3 --- /dev/null +++ b/src/ontology/md/RO/13/RO_HOM0000013.md @@ -0,0 +1,46 @@ + +## Class : in syntenic orthology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000013 + * *Label* = in syntenic orthology relationship with + * *Definition* = Syntenic homology that involves chromosomes of different species. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1101/gr.6380007, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000013 ] + +## Synonyms + + * syntenic orthologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in syntenic orthology relationship with](../../RO/13/RO_HOM0000013.md) + * [in syntenic orthology relationship with](../../RO/13/RO_HOM0000013.md) SubPropertyOf [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Syntenic homology that involves chromosomes of different species. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = syntenic orthologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in syntenic orthology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000013 + +## Usage + + * - + * SymmetricObjectProperty [in syntenic orthology relationship with](../../RO/13/RO_HOM0000013.md) + * [in syntenic orthology relationship with](../../RO/13/RO_HOM0000013.md) SubPropertyOf [in syntenic homology relationship with](../../RO/10/RO_HOM0000010.md) + +## External Comments + diff --git a/src/ontology/md/RO/14/RO_0002114.md b/src/ontology/md/RO/14/RO_0002114.md new file mode 100644 index 00000000..e3efcb00 --- /dev/null +++ b/src/ontology/md/RO/14/RO_0002114.md @@ -0,0 +1,46 @@ + +## Class : synapsed_via_type_III_bouton_to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002114 + * *Label* = synapsed_via_type_III_bouton_to + * *Definition* = A relation between a motor neuron and a muscle that it synapses to via a type III bouton. + * *Comment* = Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [synapsed to](../../RO/20/RO_0002120.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed_via_type_III_bouton_to](../../RO/14/RO_0002114.md) InverseOf [synapsed_by_via_type_III_bouton](../../RO/15/RO_0002115.md) + * [synapsed_via_type_III_bouton_to](../../RO/14/RO_0002114.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation between a motor neuron and a muscle that it synapses to via a type III bouton. + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed_via_type_III_bouton_to + +## Usage + + * - + * [synapsed_via_type_III_bouton_to](../../RO/14/RO_0002114.md) InverseOf [synapsed_by_via_type_III_bouton](../../RO/15/RO_0002115.md) + * [synapsed_via_type_III_bouton_to](../../RO/14/RO_0002114.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + +## External Comments + diff --git a/src/ontology/md/RO/14/RO_0002214.md b/src/ontology/md/RO/14/RO_0002214.md new file mode 100644 index 00000000..db8c6d97 --- /dev/null +++ b/src/ontology/md/RO/14/RO_0002214.md @@ -0,0 +1,44 @@ + +## Class : has prototype + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002214 + * *Label* = has prototype + * *Definition* = x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) + * *[example of usage](../../IAO/12/IAO_0000112.md)* = heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + * *[editor note](../../IAO/16/IAO_0000116.md)* = This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has prototype + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + +## External Comments + diff --git a/src/ontology/md/RO/14/RO_0002314.md b/src/ontology/md/RO/14/RO_0002314.md new file mode 100644 index 00000000..23abc823 --- /dev/null +++ b/src/ontology/md/RO/14/RO_0002314.md @@ -0,0 +1,45 @@ + +## Class : inheres in part of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002314 + * *Label* = inheres in part of + * *Definition* = q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [depends on](../../RO/02/RO_0002502.md) + +## SubProperties + + +## Other Logical Axioms + + * [inheres in part of](../../RO/14/RO_0002314.md) SubPropertyOf [depends on](../../RO/02/RO_0002502.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Because part_of is transitive, inheres in is a sub-relation of inheres in part of + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = inheres in part of + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * [inheres in part of](../../RO/14/RO_0002314.md) SubPropertyOf [depends on](../../RO/02/RO_0002502.md) + * [inheres in](../../RO/52/RO_0000052.md) SubPropertyOf [inheres in part of](../../RO/14/RO_0002314.md) + +## External Comments + diff --git a/src/ontology/md/RO/14/RO_0002414.md b/src/ontology/md/RO/14/RO_0002414.md new file mode 100644 index 00000000..353980f1 --- /dev/null +++ b/src/ontology/md/RO/14/RO_0002414.md @@ -0,0 +1,50 @@ + +## Class : transitively provides input for + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002414 + * *Label* = transitively provides input for + * *Definition* = transitive form of directly_provides_input_for + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causally upstream of](../../RO/11/RO_0002411.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [transitively provides input for](../../RO/14/RO_0002414.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) Range [process](../../BFO/15/BFO_0000015.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) SubPropertyOf [causally upstream of](../../RO/11/RO_0002411.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = transitive form of directly_provides_input_for + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = transitively provides input for (process to process) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = transitively provides input for + +## Usage + + * - + * TransitiveObjectProperty [transitively provides input for](../../RO/14/RO_0002414.md) + * [directly provides input for](../../RO/13/RO_0002413.md) SubPropertyOf [transitively provides input for](../../RO/14/RO_0002414.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) Range [process](../../BFO/15/BFO_0000015.md) + * [transitively provides input for](../../RO/14/RO_0002414.md) SubPropertyOf [causally upstream of](../../RO/11/RO_0002411.md) + +## External Comments + diff --git a/src/ontology/md/RO/14/RO_0002514.md b/src/ontology/md/RO/14/RO_0002514.md new file mode 100644 index 00000000..8a417224 --- /dev/null +++ b/src/ontology/md/RO/14/RO_0002514.md @@ -0,0 +1,50 @@ + +## Class : sequentially related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002514 + * *Label* = sequentially related to + * *Definition* = A relation that holds between two entities that have the property of being sequences or having sequences. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [sequentially related to](../../RO/14/RO_0002514.md) Domain [sequentially ordered entity](../../RO/32/RO_0002532.md) + * [sequentially related to](../../RO/14/RO_0002514.md) Range [sequentially ordered entity](../../RO/32/RO_0002532.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that holds between two entities that have the property of being sequences or having sequences. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + * *[curator note](../../IAO/32/IAO_0000232.md)* = The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = sequentially related to + +## Usage + + * - + * [bounds sequence of](../../RO/22/RO_0002522.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + * [does not overlap sequence of](../../RO/27/RO_0002527.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + * [is bound by sequence of](../../RO/23/RO_0002523.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + * [is sequentially aligned with](../../RO/21/RO_0002521.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + * [overlaps sequence of](../../RO/26/RO_0002526.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + * [sequentially related to](../../RO/14/RO_0002514.md) Domain [sequentially ordered entity](../../RO/32/RO_0002532.md) + * [sequentially related to](../../RO/14/RO_0002514.md) Range [sequentially ordered entity](../../RO/32/RO_0002532.md) + +## External Comments + diff --git a/src/ontology/md/RO/14/RO_HOM0000014.md b/src/ontology/md/RO/14/RO_HOM0000014.md new file mode 100644 index 00000000..1ca4ae1c --- /dev/null +++ b/src/ontology/md/RO/14/RO_HOM0000014.md @@ -0,0 +1,58 @@ + +## Class : in partial homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000014 + * *Label* = in partial homology relationship with + * *Definition* = Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:0123195837, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:978-0471984931, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000014 ] + +## Synonyms + + * fractional homology + * partial homologous to + * segmental homology + * mixed homology + * modular homology + * partial correspondence + * percent homology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in partial homology relationship with](../../RO/14/RO_HOM0000014.md) + * [in partial homology relationship with](../../RO/14/RO_HOM0000014.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = fractional homology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = partial homologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = segmental homology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = mixed homology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = modular homology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = partial correspondence + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = percent homology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in partial homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000014 + +## Usage + + * - + * SymmetricObjectProperty [in partial homology relationship with](../../RO/14/RO_HOM0000014.md) + * [in partial homology relationship with](../../RO/14/RO_HOM0000014.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## External Comments + diff --git a/src/ontology/md/RO/15/RO_0001015.md b/src/ontology/md/RO/15/RO_0001015.md new file mode 100644 index 00000000..ee81a5fb --- /dev/null +++ b/src/ontology/md/RO/15/RO_0001015.md @@ -0,0 +1,46 @@ + +## Class : location of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0001015 + * *Label* = location of + * *Definition* = a relation between two independent continuants, the location and the target, in which the target is entirely within the location + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [location of](../../RO/15/RO_0001015.md) + * [located in](../../RO/25/RO_0001025.md) InverseOf [location of](../../RO/15/RO_0001015.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = is location of + * *[example of usage](../../IAO/12/IAO_0000112.md)* = my head is the location of my brain + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this cage is the location of this rat + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between two independent continuants, the location and the target, in which the target is entirely within the location + * *[editor note](../../IAO/16/IAO_0000116.md)* = Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + * *[alternative term](../../IAO/18/IAO_0000118.md)* = location_of + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = location of + +## Usage + + * - + * TransitiveObjectProperty [location of](../../RO/15/RO_0001015.md) + * [located in](../../RO/25/RO_0001025.md) InverseOf [location of](../../RO/15/RO_0001015.md) + +## External Comments + diff --git a/src/ontology/md/RO/15/RO_0002115.md b/src/ontology/md/RO/15/RO_0002115.md new file mode 100644 index 00000000..f7ce4090 --- /dev/null +++ b/src/ontology/md/RO/15/RO_0002115.md @@ -0,0 +1,48 @@ + +## Class : synapsed_by_via_type_III_bouton + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002115 + * *Label* = synapsed_by_via_type_III_bouton + * *Definition* = Relation between a muscle and a motor neuron that synapses to it via a type III bouton. + + * *Comment* = Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [synapsed by](../../RO/03/RO_0002103.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed_by_via_type_III_bouton](../../RO/15/RO_0002115.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_via_type_III_bouton_to](../../RO/14/RO_0002114.md) InverseOf [synapsed_by_via_type_III_bouton](../../RO/15/RO_0002115.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a muscle and a motor neuron that synapses to it via a type III bouton. + + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed_by_via_type_III_bouton + +## Usage + + * - + * [synapsed_by_via_type_III_bouton](../../RO/15/RO_0002115.md) SubPropertyOf [synapsed by](../../RO/03/RO_0002103.md) + * [synapsed_via_type_III_bouton_to](../../RO/14/RO_0002114.md) InverseOf [synapsed_by_via_type_III_bouton](../../RO/15/RO_0002115.md) + +## External Comments + diff --git a/src/ontology/md/RO/15/RO_0002215.md b/src/ontology/md/RO/15/RO_0002215.md new file mode 100644 index 00000000..0a803486 --- /dev/null +++ b/src/ontology/md/RO/15/RO_0002215.md @@ -0,0 +1,70 @@ + +## Class : capable of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002215 + * *Label* = capable of + * *Definition* = A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [functionally related to](../../RO/28/RO_0002328.md) + +## SubProperties + + +## Other Logical Axioms + + * [capable of](../../RO/15/RO_0002215.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [capable of](../../RO/15/RO_0002215.md) Range [process](../../BFO/15/BFO_0000015.md) + * [capable of](../../RO/15/RO_0002215.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [capable of](../../RO/15/RO_0002215.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + * *[example of usage](../../IAO/12/IAO_0000112.md)* = osteoclast SubClassOf 'capable of' some 'bone resorption' + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has function realized in + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20123131 + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/21208450 + * *[curator note](../../IAO/32/IAO_0000232.md)* = 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)". + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = RO_0000053 some (RO_0000054 only ?Y) + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = capable of + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [capable of](../../RO/15/RO_0002215.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [capable of](../../RO/15/RO_0002215.md) Range [process](../../BFO/15/BFO_0000015.md) + * [capable of](../../RO/15/RO_0002215.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [capable of](../../RO/15/RO_0002215.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [causally influences](../../RO/66/RO_0002566.md) some [material entity](../../BFO/40/BFO_0000040.md) SubClassOf [capable of](../../RO/15/RO_0002215.md) some [participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md)or[participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md) + * [enabled by](../../RO/33/RO_0002333.md) SubPropertyOf InverseOf() + * [enables](../../RO/27/RO_0002327.md) SubPropertyOf [capable of](../../RO/15/RO_0002215.md) + +## External Comments + diff --git a/src/ontology/md/RO/15/RO_0002315.md b/src/ontology/md/RO/15/RO_0002315.md new file mode 100644 index 00000000..6ae46971 --- /dev/null +++ b/src/ontology/md/RO/15/RO_0002315.md @@ -0,0 +1,48 @@ + +## Class : results in acquisition of features of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002315 + * *Label* = results in acquisition of features of + * *Definition* = The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in acquisition of features of](../../RO/15/RO_0002315.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in acquisition of features of](../../RO/15/RO_0002315.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in acquisition of features of](../../RO/15/RO_0002315.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + * *[definition](../../IAO/15/IAO_0000115.md)* = The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = GOC:mtg_berkeley_2013 + * *[shorthand](../../nd/oboInOwl#shorthand.md)* = results_in_acquisition_of_features_of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in acquisition of features of + +## Usage + + * - + * [results in acquisition of features of](../../RO/15/RO_0002315.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in acquisition of features of](../../RO/15/RO_0002315.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in acquisition of features of](../../RO/15/RO_0002315.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/15/RO_0002515.md b/src/ontology/md/RO/15/RO_0002515.md new file mode 100644 index 00000000..89a06413 --- /dev/null +++ b/src/ontology/md/RO/15/RO_0002515.md @@ -0,0 +1,47 @@ + +## Class : sequentially adjacent to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002515 + * *Label* = sequentially adjacent to + * *Definition* = x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [does not overlap sequence of](../../RO/27/RO_0002527.md) + +## SubProperties + + +## Other Logical Axioms + + * [sequentially adjacent to](../../RO/15/RO_0002515.md) SubPropertyOf [does not overlap sequence of](../../RO/27/RO_0002527.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Every UTR is adjacent to a CDS of the same transcript + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Two consecutive DNA residues are sequentially adjacent + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Two exons on a processed transcript that were previously connected by an intron are adjacent + * *[definition](../../IAO/15/IAO_0000115.md)* = x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = sequentially adjacent to + +## Usage + + * - + * [is immediately downstream of sequence of](../../RO/30/RO_0002530.md) SubPropertyOf [sequentially adjacent to](../../RO/15/RO_0002515.md) + * [is immediately upstream of sequence of](../../RO/31/RO_0002531.md) SubPropertyOf [sequentially adjacent to](../../RO/15/RO_0002515.md) + * [sequentially adjacent to](../../RO/15/RO_0002515.md) SubPropertyOf [does not overlap sequence of](../../RO/27/RO_0002527.md) + +## External Comments + diff --git a/src/ontology/md/RO/15/RO_HOM0000015.md b/src/ontology/md/RO/15/RO_HOM0000015.md new file mode 100644 index 00000000..3726b2b2 --- /dev/null +++ b/src/ontology/md/RO/15/RO_HOM0000015.md @@ -0,0 +1,48 @@ + +## Class : in protein structural homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000015 + * *Label* = in protein structural homology relationship with + * *Definition* = Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/0022-2836(76)90195-9, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000015 ] + +## Synonyms + + * protein structural homologous to + +## Cross-references + + * MeSH:Structural_Homology,_Protein + +## Subsets + + +## SuperProperties + + * [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in protein structural homology relationship with](../../RO/15/RO_HOM0000015.md) + * [in protein structural homology relationship with](../../RO/15/RO_HOM0000015.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = MeSH:Structural_Homology,_Protein + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = protein structural homologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in protein structural homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000015 + +## Usage + + * - + * SymmetricObjectProperty [in protein structural homology relationship with](../../RO/15/RO_HOM0000015.md) + * [in protein structural homology relationship with](../../RO/15/RO_HOM0000015.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## External Comments + diff --git a/src/ontology/md/RO/16/RO_0002216.md b/src/ontology/md/RO/16/RO_0002216.md new file mode 100644 index 00000000..76750a43 --- /dev/null +++ b/src/ontology/md/RO/16/RO_0002216.md @@ -0,0 +1,48 @@ + +## Class : capable of part of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002216 + * *Label* = capable of part of + * *Definition* = c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [functionally related to](../../RO/28/RO_0002328.md) + +## SubProperties + + +## Other Logical Axioms + + * [capable of part of](../../RO/16/RO_0002216.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [capable of part of](../../RO/16/RO_0002216.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has function in + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = capable of part of + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * [capable of part of](../../RO/16/RO_0002216.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [capable of part of](../../RO/16/RO_0002216.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [contributes to](../../RO/26/RO_0002326.md) SubPropertyOf [capable of part of](../../RO/16/RO_0002216.md) + +## External Comments + diff --git a/src/ontology/md/RO/16/RO_0002416.md b/src/ontology/md/RO/16/RO_0002416.md new file mode 100644 index 00000000..c9b74b05 --- /dev/null +++ b/src/ontology/md/RO/16/RO_0002416.md @@ -0,0 +1,45 @@ + +## Class : logical macro assertion + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002416 + * *Label* = logical macro assertion + * *Definition* = An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + * [logical macro assertion on a property](../../RO/21/RO_0002421.md) + * [logical macro assertion on a class](../../RO/20/RO_0002420.md) + * [logical macro assertion involving identity](../../RO/01/RO_0002601.md) + * [logical macro assertion on an axiom](../../RO/80/RO_0002580.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = logical macro assertion + * *[page](../../ge/page.md)* = https://code.google.com/p/obo-relations/wiki/ShortcutRelations + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/16/RO_0002516.md b/src/ontology/md/RO/16/RO_0002516.md new file mode 100644 index 00000000..60e09843 --- /dev/null +++ b/src/ontology/md/RO/16/RO_0002516.md @@ -0,0 +1,48 @@ + +## Class : has start sequence + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002516 + * *Label* = has start sequence + * *Definition* = x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has subsequence](../../RO/24/RO_0002524.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [has start sequence](../../RO/16/RO_0002516.md) + * [has start sequence](../../RO/16/RO_0002516.md) InverseOf [is start sequence of](../../RO/17/RO_0002517.md) + * [has start sequence](../../RO/16/RO_0002516.md) SubPropertyOf [has subsequence](../../RO/24/RO_0002524.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Every CDS has as a start sequence the start codon for that transcript + * *[definition](../../IAO/15/IAO_0000115.md)* = x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = started by + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has start sequence + +## Usage + + * - + * TransitiveObjectProperty [has start sequence](../../RO/16/RO_0002516.md) + * [has start sequence](../../RO/16/RO_0002516.md) InverseOf [is start sequence of](../../RO/17/RO_0002517.md) + * [has start sequence](../../RO/16/RO_0002516.md) SubPropertyOf [has subsequence](../../RO/24/RO_0002524.md) + +## External Comments + diff --git a/src/ontology/md/RO/16/RO_HOM0000016.md b/src/ontology/md/RO/16/RO_HOM0000016.md new file mode 100644 index 00000000..2ae8f8e0 --- /dev/null +++ b/src/ontology/md/RO/16/RO_HOM0000016.md @@ -0,0 +1,52 @@ + +## Class : in non functional homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000016 + * *Label* = in non functional homology relationship with + * *Definition* = Structural homology that involves a pseudogenic feature and its functional ancestor. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = SO:non_functional_homolog_of, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000016 ] + +## Synonyms + + * non functional homologous to + * pseudogene + +## Cross-references + + * SO:non_functional_homolog_of + +## Subsets + + +## SuperProperties + + * [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in non functional homology relationship with](../../RO/16/RO_HOM0000016.md) + * [in non functional homology relationship with](../../RO/16/RO_HOM0000016.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Structural homology that involves a pseudogenic feature and its functional ancestor. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_broad_synonym](../../ym/oboInOwl#hasBroadSynonym.md)* = pseudogene + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:non_functional_homolog_of + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = non functional homologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in non functional homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000016 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in non functional homology relationship with](../../RO/16/RO_HOM0000016.md) + * [in non functional homology relationship with](../../RO/16/RO_HOM0000016.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## External Comments + diff --git a/src/ontology/md/RO/17/RO_0002217.md b/src/ontology/md/RO/17/RO_0002217.md new file mode 100644 index 00000000..671dc0c9 --- /dev/null +++ b/src/ontology/md/RO/17/RO_0002217.md @@ -0,0 +1,46 @@ + +## Class : actively participates in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002217 + * *Label* = actively participates in + * *Definition* = x actively participates in y if and only if x participates in y and x realizes some active role + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [participates in](../../RO/56/RO_0000056.md) + +## SubProperties + + +## Other Logical Axioms + + * [actively participates in](../../RO/17/RO_0002217.md) InverseOf [has active participant](../../RO/18/RO_0002218.md) + * [actively participates in](../../RO/17/RO_0002217.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x actively participates in y if and only if x participates in y and x realizes some active role + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = agent in + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = actively participates in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [actively participates in](../../RO/17/RO_0002217.md) InverseOf [has active participant](../../RO/18/RO_0002218.md) + * [actively participates in](../../RO/17/RO_0002217.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + +## External Comments + diff --git a/src/ontology/md/RO/17/RO_0002517.md b/src/ontology/md/RO/17/RO_0002517.md new file mode 100644 index 00000000..88336fab --- /dev/null +++ b/src/ontology/md/RO/17/RO_0002517.md @@ -0,0 +1,47 @@ + +## Class : is start sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002517 + * *Label* = is start sequence of + * *Definition* = inverse of has start sequence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is subsequence of](../../RO/25/RO_0002525.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [is start sequence of](../../RO/17/RO_0002517.md) + * [has start sequence](../../RO/16/RO_0002516.md) InverseOf [is start sequence of](../../RO/17/RO_0002517.md) + * [is start sequence of](../../RO/17/RO_0002517.md) SubPropertyOf [is subsequence of](../../RO/25/RO_0002525.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of has start sequence + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = starts + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is start sequence of + +## Usage + + * - + * TransitiveObjectProperty [is start sequence of](../../RO/17/RO_0002517.md) + * [has start sequence](../../RO/16/RO_0002516.md) InverseOf [is start sequence of](../../RO/17/RO_0002517.md) + * [is start sequence of](../../RO/17/RO_0002517.md) SubPropertyOf [is subsequence of](../../RO/25/RO_0002525.md) + +## External Comments + diff --git a/src/ontology/md/RO/17/RO_HOM0000017.md b/src/ontology/md/RO/17/RO_HOM0000017.md new file mode 100644 index 00000000..eb2766ab --- /dev/null +++ b/src/ontology/md/RO/17/RO_HOM0000017.md @@ -0,0 +1,62 @@ + +## Class : in orthology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000017 + * *Label* = in orthology relationship with + * *Definition* = Historical homology that involves genes that diverged after a speciation event. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814484, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/S0168-9525(00)02005-9, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000017, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ncbi.nlm.nih.gov/pubmed/5449325 ] + * *Comment* = The term is sometimes also used for anatomical structures. + +## Synonyms + + * orthologous to + +## Cross-references + + * ECO:00000060 + * SO:0000855 + * SO:0000858 + * SO:orthologous_to + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in orthology relationship with](../../RO/17/RO_HOM0000017.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves genes that diverged after a speciation event. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = ECO:00000060 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:0000855 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:0000858 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = SO:orthologous_to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = orthologous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The term is sometimes also used for anatomical structures. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in orthology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000017 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in 1 to 1 orthology relationship with](../../RO/20/RO_HOM0000020.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in isoorthology relationship with](../../RO/54/RO_HOM0000054.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in many to many orthology relationship with](../../RO/48/RO_HOM0000048.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in orthology relationship with](../../RO/17/RO_HOM0000017.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## External Comments + diff --git a/src/ontology/md/RO/18/RO_0001018.md b/src/ontology/md/RO/18/RO_0001018.md new file mode 100644 index 00000000..f752bb63 --- /dev/null +++ b/src/ontology/md/RO/18/RO_0001018.md @@ -0,0 +1,53 @@ + +## Class : contained in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0001018 + * *Label* = contained in + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [contained in](../../RO/18/RO_0001018.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [contained in](../../RO/18/RO_0001018.md) InverseOf [contains](../../RO/19/RO_0001019.md) + * [contained in](../../RO/18/RO_0001018.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = contained in + * *[editor note](../../IAO/16/IAO_0000116.md)* = Containment is location not involving parthood, and arises only where some immaterial continuant is involved. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): + * *[editor note](../../IAO/16/IAO_0000116.md)* = Intended meaning: +domain: material entity +range: spatial region or site (immaterial continuant) + + * *[alternative term](../../IAO/18/IAO_0000118.md)* = contained_in + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = contained in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [contained in](../../RO/18/RO_0001018.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [contained in](../../RO/18/RO_0001018.md) InverseOf [contains](../../RO/19/RO_0001019.md) + * [contained in](../../RO/18/RO_0001018.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [tracheates](../../RO/04/RO_0002004.md) SubPropertyOf [contained in](../../RO/18/RO_0001018.md) + +## External Comments + diff --git a/src/ontology/md/RO/18/RO_0002218.md b/src/ontology/md/RO/18/RO_0002218.md new file mode 100644 index 00000000..b58b5e0e --- /dev/null +++ b/src/ontology/md/RO/18/RO_0002218.md @@ -0,0 +1,48 @@ + +## Class : has active participant + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002218 + * *Label* = has active participant + * *Definition* = x has participant y if and only if x realizes some active role that inheres in y + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [actively participates in](../../RO/17/RO_0002217.md) InverseOf [has active participant](../../RO/18/RO_0002218.md) + * [has active participant](../../RO/18/RO_0002218.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'heart development' has active participant some Shh protein + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has participant y if and only if x realizes some active role that inheres in y + * *[editor note](../../IAO/16/IAO_0000116.md)* = This may be obsoleted and replaced by the original 'has agent' relation + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has agent + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has active participant + +## Usage + + * - + * [actively participates in](../../RO/17/RO_0002217.md) InverseOf [has active participant](../../RO/18/RO_0002218.md) + * [has active participant](../../RO/18/RO_0002218.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + +## External Comments + diff --git a/src/ontology/md/RO/18/RO_0002418.md b/src/ontology/md/RO/18/RO_0002418.md new file mode 100644 index 00000000..df9d5056 --- /dev/null +++ b/src/ontology/md/RO/18/RO_0002418.md @@ -0,0 +1,50 @@ + +## Class : causally upstream of or within + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002418 + * *Label* = causally upstream of or within + * *Definition* = p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causal relation between processes](../../RO/01/RO_0002501.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [causally upstream of or within](../../RO/18/RO_0002418.md) + * [causally downstream of or within](../../RO/27/RO_0002427.md) InverseOf [causally upstream of or within](../../RO/18/RO_0002418.md) + * [causally upstream of or within](../../RO/18/RO_0002418.md) SubPropertyOf [causal relation between processes](../../RO/01/RO_0002501.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + * *[editor note](../../IAO/16/IAO_0000116.md)* = We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = influences (processual) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causally upstream of or within + +## Usage + + * - + * TransitiveObjectProperty [causally upstream of or within](../../RO/18/RO_0002418.md) + * [causally downstream of or within](../../RO/27/RO_0002427.md) InverseOf [causally upstream of or within](../../RO/18/RO_0002418.md) + * [causally influences](../../RO/66/RO_0002566.md) some [material entity](../../BFO/40/BFO_0000040.md) SubClassOf [capable of](../../RO/15/RO_0002215.md) some [participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md)or[participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md) + * [causally upstream of or within](../../RO/18/RO_0002418.md) SubPropertyOf [causal relation between processes](../../RO/01/RO_0002501.md) + * [causally upstream of](../../RO/11/RO_0002411.md) SubPropertyOf [causally upstream of or within](../../RO/18/RO_0002418.md) + * [regulates in other organism](../../RO/10/RO_0002010.md) SubPropertyOf [causally upstream of or within](../../RO/18/RO_0002418.md) + * [regulates](../../RO/11/RO_0002211.md) SubPropertyOf [causally upstream of or within](../../RO/18/RO_0002418.md) + +## External Comments + diff --git a/src/ontology/md/RO/18/RO_0002518.md b/src/ontology/md/RO/18/RO_0002518.md new file mode 100644 index 00000000..ea92735e --- /dev/null +++ b/src/ontology/md/RO/18/RO_0002518.md @@ -0,0 +1,48 @@ + +## Class : has end sequence + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002518 + * *Label* = has end sequence + * *Definition* = x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has subsequence](../../RO/24/RO_0002524.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [has end sequence](../../RO/18/RO_0002518.md) + * [has end sequence](../../RO/18/RO_0002518.md) InverseOf [is end sequence of](../../RO/19/RO_0002519.md) + * [has end sequence](../../RO/18/RO_0002518.md) SubPropertyOf [has subsequence](../../RO/24/RO_0002524.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) + * *[definition](../../IAO/15/IAO_0000115.md)* = x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = ended by + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has end sequence + +## Usage + + * - + * TransitiveObjectProperty [has end sequence](../../RO/18/RO_0002518.md) + * [has end sequence](../../RO/18/RO_0002518.md) InverseOf [is end sequence of](../../RO/19/RO_0002519.md) + * [has end sequence](../../RO/18/RO_0002518.md) SubPropertyOf [has subsequence](../../RO/24/RO_0002524.md) + +## External Comments + diff --git a/src/ontology/md/RO/18/RO_HOM0000018.md b/src/ontology/md/RO/18/RO_HOM0000018.md new file mode 100644 index 00000000..18d629dd --- /dev/null +++ b/src/ontology/md/RO/18/RO_HOM0000018.md @@ -0,0 +1,51 @@ + +## Class : in xenology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000018 + * *Label* = in xenology relationship with + * *Definition* = Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/S0168-9525(00)02005-9, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000018 ] + * *Comment* = The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + +## Synonyms + + * xenologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + * [in xenology relationship with](../../RO/18/RO_HOM0000018.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = xenologous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in xenology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000018 + +## Usage + + * - + * SymmetricObjectProperty [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + * [in paraxenology relationship with](../../RO/68/RO_HOM0000068.md) SubPropertyOf [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + * [in pseudoparalogy relationship with](../../RO/61/RO_HOM0000061.md) SubPropertyOf [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + * [in synology relationship with](../../RO/53/RO_HOM0000053.md) SubPropertyOf [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + * [in xenology relationship with](../../RO/18/RO_HOM0000018.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## External Comments + diff --git a/src/ontology/md/RO/19/RO_0001019.md b/src/ontology/md/RO/19/RO_0001019.md new file mode 100644 index 00000000..6e57bfd2 --- /dev/null +++ b/src/ontology/md/RO/19/RO_0001019.md @@ -0,0 +1,40 @@ + +## Class : contains + + * *IRI* = http://purl.obolibrary.org/obo/RO_0001019 + * *Label* = contains + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [contained in](../../RO/18/RO_0001018.md) InverseOf [contains](../../RO/19/RO_0001019.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = contains + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = contains + +## Usage + + * - + * [contained in](../../RO/18/RO_0001018.md) InverseOf [contains](../../RO/19/RO_0001019.md) + +## External Comments + diff --git a/src/ontology/md/RO/19/RO_0002219.md b/src/ontology/md/RO/19/RO_0002219.md new file mode 100644 index 00000000..67252f3a --- /dev/null +++ b/src/ontology/md/RO/19/RO_0002219.md @@ -0,0 +1,44 @@ + +## Class : surrounded by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002219 + * *Label* = surrounded by + * *Definition* = x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [adjacent to](../../RO/20/RO_0002220.md) + +## SubProperties + + +## Other Logical Axioms + + * [surrounded by](../../RO/19/RO_0002219.md) SubPropertyOf [adjacent to](../../RO/20/RO_0002220.md) + * [surrounds](../../RO/21/RO_0002221.md) InverseOf [surrounded by](../../RO/19/RO_0002219.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = surrounded by + +## Usage + + * - + * [surrounded by](../../RO/19/RO_0002219.md) SubPropertyOf [adjacent to](../../RO/20/RO_0002220.md) + * [surrounds](../../RO/21/RO_0002221.md) InverseOf [surrounded by](../../RO/19/RO_0002219.md) + +## External Comments + diff --git a/src/ontology/md/RO/19/RO_0002419.md b/src/ontology/md/RO/19/RO_0002419.md new file mode 100644 index 00000000..961c3c5f --- /dev/null +++ b/src/ontology/md/RO/19/RO_0002419.md @@ -0,0 +1,39 @@ + +## Class : annotation property cardinality + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002419 + * *Label* = annotation property cardinality + * *Definition* = An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on an annotation property](../../RO/23/RO_0002423.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = annotation property cardinality + +## Usage + + * - + * AnnotationPropertyRange( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/19/RO_0002519.md b/src/ontology/md/RO/19/RO_0002519.md new file mode 100644 index 00000000..fb6b3596 --- /dev/null +++ b/src/ontology/md/RO/19/RO_0002519.md @@ -0,0 +1,47 @@ + +## Class : is end sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002519 + * *Label* = is end sequence of + * *Definition* = inverse of has end sequence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is subsequence of](../../RO/25/RO_0002525.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [is end sequence of](../../RO/19/RO_0002519.md) + * [has end sequence](../../RO/18/RO_0002518.md) InverseOf [is end sequence of](../../RO/19/RO_0002519.md) + * [is end sequence of](../../RO/19/RO_0002519.md) SubPropertyOf [is subsequence of](../../RO/25/RO_0002525.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of has end sequence + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = ends + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is end sequence of + +## Usage + + * - + * TransitiveObjectProperty [is end sequence of](../../RO/19/RO_0002519.md) + * [has end sequence](../../RO/18/RO_0002518.md) InverseOf [is end sequence of](../../RO/19/RO_0002519.md) + * [is end sequence of](../../RO/19/RO_0002519.md) SubPropertyOf [is subsequence of](../../RO/25/RO_0002525.md) + +## External Comments + diff --git a/src/ontology/md/RO/19/RO_HOM0000019.md b/src/ontology/md/RO/19/RO_HOM0000019.md new file mode 100644 index 00000000..64b3d49e --- /dev/null +++ b/src/ontology/md/RO/19/RO_HOM0000019.md @@ -0,0 +1,52 @@ + +## Class : in 1 to 1 homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000019 + * *Label* = in 1 to 1 homology relationship with + * *Definition* = Historical homology that involves two members sharing no other homologs in the lineages considered. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = BGEE:curator, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000019 ] + +## Synonyms + + * 1 to 1 homologous to + * 1:1 homology + * one-to-one homology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + * [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves two members sharing no other homologs in the lineages considered. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = 1 to 1 homologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = 1:1 homology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = one-to-one homology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in 1 to 1 homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000019 + +## Usage + + * - + * SymmetricObjectProperty [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + * [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in 1 to 1 orthology relationship with](../../RO/20/RO_HOM0000020.md) SubPropertyOf [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + * [in apparent orthology relationship with](../../RO/60/RO_HOM0000060.md) SubPropertyOf [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + +## External Comments + diff --git a/src/ontology/md/RO/20/RO_0002120.md b/src/ontology/md/RO/20/RO_0002120.md new file mode 100644 index 00000000..a135a656 --- /dev/null +++ b/src/ontology/md/RO/20/RO_0002120.md @@ -0,0 +1,69 @@ + +## Class : synapsed to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002120 + * *Label* = synapsed to + * *Definition* = Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. + + * *Comment* = N1 synapsed_to some N2 +Expands to: +N1 SubclassOf ( + has_part some ( + ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( + ‘synapse ; GO:0045202’ that has_part some ( + ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [downstream in neural circuit with](../../RO/02/RO_0000302.md) + +## SubProperties + + +## Other Logical Axioms + + * [synapsed by](../../RO/03/RO_0002103.md) InverseOf [synapsed to](../../RO/20/RO_0002120.md) + * [synapsed to](../../RO/20/RO_0002120.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [synapsed to](../../RO/20/RO_0002120.md) SubPropertyOf [downstream in neural circuit with](../../RO/02/RO_0000302.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = some ( that part_of some ( that some ( that some Y?))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = N1 synapsed_to some N2 +Expands to: +N1 SubclassOf ( + has_part some ( + ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( + ‘synapse ; GO:0045202’ that has_part some ( + ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = synapsed to + +## Usage + + * - + * [synapsed by](../../RO/03/RO_0002103.md) InverseOf [synapsed to](../../RO/20/RO_0002120.md) + * [synapsed to](../../RO/20/RO_0002120.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [synapsed to](../../RO/20/RO_0002120.md) SubPropertyOf [downstream in neural circuit with](../../RO/02/RO_0000302.md) + * [synapsed_via_type_III_bouton_to](../../RO/14/RO_0002114.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + * [synapsed_via_type_II_bouton_to](../../RO/07/RO_0002107.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + * [synapsed_via_type_Ib_bouton_to](../../RO/05/RO_0002105.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + * [synapsed_via_type_Is_bouton_to](../../RO/06/RO_0002106.md) SubPropertyOf [synapsed to](../../RO/20/RO_0002120.md) + +## External Comments + diff --git a/src/ontology/md/RO/20/RO_0002220.md b/src/ontology/md/RO/20/RO_0002220.md new file mode 100644 index 00000000..ac333081 --- /dev/null +++ b/src/ontology/md/RO/20/RO_0002220.md @@ -0,0 +1,49 @@ + +## Class : adjacent to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002220 + * *Label* = adjacent to + * *Definition* = x adjacent to y if and only if x and y share a boundary + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [spatially disjoint from](../../RO/63/RO_0002163.md) + +## SubProperties + + +## Other Logical Axioms + + * [adjacent to](../../RO/20/RO_0002220.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [adjacent to](../../RO/20/RO_0002220.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [adjacent to](../../RO/20/RO_0002220.md) SubPropertyOf [spatially disjoint from](../../RO/63/RO_0002163.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x adjacent to y if and only if x and y share a boundary + * *[editor note](../../IAO/16/IAO_0000116.md)* = This relation acts as a join point with BSPO + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = adjacent to + +## Usage + + * - + * [adjacent to](../../RO/20/RO_0002220.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [adjacent to](../../RO/20/RO_0002220.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [adjacent to](../../RO/20/RO_0002220.md) SubPropertyOf [spatially disjoint from](../../RO/63/RO_0002163.md) + * [surrounded by](../../RO/19/RO_0002219.md) SubPropertyOf [adjacent to](../../RO/20/RO_0002220.md) + * [surrounds](../../RO/21/RO_0002221.md) SubPropertyOf [adjacent to](../../RO/20/RO_0002220.md) + +## External Comments + diff --git a/src/ontology/md/RO/20/RO_0002320.md b/src/ontology/md/RO/20/RO_0002320.md new file mode 100644 index 00000000..fdb4a97f --- /dev/null +++ b/src/ontology/md/RO/20/RO_0002320.md @@ -0,0 +1,46 @@ + +## Class : evolutionarily related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002320 + * *Label* = evolutionarily related to + * *Definition* = A relationship that holds via some environmental process + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that holds via some environmental process + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = evolutionarily related to + +## Usage + + * - + * [derived by descent from](../../RO/56/RO_0002156.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [evolutionary variant of](../../RO/12/RO_0002312.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [has derived by descendant](../../RO/57/RO_0002157.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [has fused element](../../RO/74/RO_0002374.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [in taxon](../../RO/62/RO_0002162.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [serially homologous to](../../RO/59/RO_0002159.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [shares ancestor with](../../RO/58/RO_0002158.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## External Comments + diff --git a/src/ontology/md/RO/20/RO_0002420.md b/src/ontology/md/RO/20/RO_0002420.md new file mode 100644 index 00000000..082a59ec --- /dev/null +++ b/src/ontology/md/RO/20/RO_0002420.md @@ -0,0 +1,47 @@ + +## Class : logical macro assertion on a class + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002420 + * *Label* = logical macro assertion on a class + * *Definition* = A logical macro assertion whose domain is an IRI for a class + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion](../../RO/16/RO_0002416.md) + +## SubProperties + + * [has no connections with](../../RO/75/RO_0002475.md) + * [temporal logical macro assertion on a class](../../RO/35/RO_0002535.md) + * [mutually spatially disjoint with](../../RO/71/RO_0002171.md) + * [taxonomic class assertion](../../RO/72/RO_0002172.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A logical macro assertion whose domain is an IRI for a class + * *[editor note](../../IAO/16/IAO_0000116.md)* = The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = logical macro assertion on a class + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/20/RO_0002520.md b/src/ontology/md/RO/20/RO_0002520.md new file mode 100644 index 00000000..ac1de625 --- /dev/null +++ b/src/ontology/md/RO/20/RO_0002520.md @@ -0,0 +1,43 @@ + +## Class : is consecutive sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002520 + * *Label* = is consecutive sequence of + * *Definition* = x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has subsequence](../../RO/24/RO_0002524.md) + +## SubProperties + + +## Other Logical Axioms + + * [is consecutive sequence of](../../RO/20/RO_0002520.md) SubPropertyOf [has subsequence](../../RO/24/RO_0002524.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. + * *[editor note](../../IAO/16/IAO_0000116.md)* = In the SO paper, this was defined as an instance-type relation + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is consecutive sequence of + +## Usage + + * - + * [is consecutive sequence of](../../RO/20/RO_0002520.md) SubPropertyOf [has subsequence](../../RO/24/RO_0002524.md) + +## External Comments + diff --git a/src/ontology/md/RO/20/RO_HOM0000020.md b/src/ontology/md/RO/20/RO_HOM0000020.md new file mode 100644 index 00000000..f67ceb7b --- /dev/null +++ b/src/ontology/md/RO/20/RO_HOM0000020.md @@ -0,0 +1,53 @@ + +## Class : in 1 to 1 orthology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000020 + * *Label* = in 1 to 1 orthology relationship with + * *Definition* = Orthology that involves two genes that did not experience any duplication after the speciation event that created them. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814484, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000020, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ensembl.org/info/docs/compara/homology_method.html ] + +## Synonyms + + * 1 to 1 orthologous to + * 1:1 orthology + * one-to-one orthology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + * [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in 1 to 1 orthology relationship with](../../RO/20/RO_HOM0000020.md) + * [in 1 to 1 orthology relationship with](../../RO/20/RO_HOM0000020.md) SubPropertyOf [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + * [in 1 to 1 orthology relationship with](../../RO/20/RO_HOM0000020.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = 1 to 1 orthologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = 1:1 orthology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = one-to-one orthology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in 1 to 1 orthology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000020 + +## Usage + + * - + * SymmetricObjectProperty [in 1 to 1 orthology relationship with](../../RO/20/RO_HOM0000020.md) + * [in 1 to 1 orthology relationship with](../../RO/20/RO_HOM0000020.md) SubPropertyOf [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + * [in 1 to 1 orthology relationship with](../../RO/20/RO_HOM0000020.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + +## External Comments + diff --git a/src/ontology/md/RO/21/RO_0002121.md b/src/ontology/md/RO/21/RO_0002121.md new file mode 100644 index 00000000..2efe1bf0 --- /dev/null +++ b/src/ontology/md/RO/21/RO_0002121.md @@ -0,0 +1,55 @@ + +## Class : dendrite synapsed in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002121 + * *Label* = dendrite synapsed in + * *Definition* = Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. + + + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) + +## SubProperties + + +## Other Logical Axioms + + * [dendrite synapsed in](../../RO/21/RO_0002121.md) Domain [neuron](../../CL/40/CL_0000540.md) + * [dendrite synapsed in](../../RO/21/RO_0002121.md) SubPropertyOf [has postsynaptic terminal in](../../RO/10/RO_0002110.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. + + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = some ( + and some ( + http://purl.obolibrary.org/obo/GO_0042734 and some ( + and some ?Y))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = dendrite synapsed in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [dendrite synapsed in](../../RO/21/RO_0002121.md) Domain [neuron](../../CL/40/CL_0000540.md) + * [dendrite synapsed in](../../RO/21/RO_0002121.md) SubPropertyOf [has postsynaptic terminal in](../../RO/10/RO_0002110.md) + +## External Comments + diff --git a/src/ontology/md/RO/21/RO_0002221.md b/src/ontology/md/RO/21/RO_0002221.md new file mode 100644 index 00000000..ba43190e --- /dev/null +++ b/src/ontology/md/RO/21/RO_0002221.md @@ -0,0 +1,42 @@ + +## Class : surrounds + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002221 + * *Label* = surrounds + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [adjacent to](../../RO/20/RO_0002220.md) + +## SubProperties + + +## Other Logical Axioms + + * [surrounds](../../RO/21/RO_0002221.md) InverseOf [surrounded by](../../RO/19/RO_0002219.md) + * [surrounds](../../RO/21/RO_0002221.md) SubPropertyOf [adjacent to](../../RO/20/RO_0002220.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = surrounds + +## Usage + + * - + * [surrounds](../../RO/21/RO_0002221.md) InverseOf [surrounded by](../../RO/19/RO_0002219.md) + * [surrounds](../../RO/21/RO_0002221.md) SubPropertyOf [adjacent to](../../RO/20/RO_0002220.md) + +## External Comments + diff --git a/src/ontology/md/RO/21/RO_0002321.md b/src/ontology/md/RO/21/RO_0002321.md new file mode 100644 index 00000000..8ed2c41e --- /dev/null +++ b/src/ontology/md/RO/21/RO_0002321.md @@ -0,0 +1,44 @@ + +## Class : ecologically related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002321 + * *Label* = ecologically related to + * *Definition* = A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ecologically related to + +## Usage + + * - + * [biotically interacts with](../../RO/37/RO_0002437.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + * [confers advantage in](../../RO/22/RO_0002322.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + * [has habitat](../../RO/03/RO_0002303.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + * [transmitted by](../../RO/51/RO_0002451.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + +## External Comments + diff --git a/src/ontology/md/RO/21/RO_0002421.md b/src/ontology/md/RO/21/RO_0002421.md new file mode 100644 index 00000000..a9cb9769 --- /dev/null +++ b/src/ontology/md/RO/21/RO_0002421.md @@ -0,0 +1,42 @@ + +## Class : logical macro assertion on a property + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002421 + * *Label* = logical macro assertion on a property + * *Definition* = A logical macro assertion whose domain is an IRI for a property + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion](../../RO/16/RO_0002416.md) + +## SubProperties + + * [logical macro assertion on an object property](../../RO/22/RO_0002422.md) + * [logical macro assertion on an annotation property](../../RO/23/RO_0002423.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A logical macro assertion whose domain is an IRI for a property + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = logical macro assertion on a property + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/21/RO_0002521.md b/src/ontology/md/RO/21/RO_0002521.md new file mode 100644 index 00000000..c8772497 --- /dev/null +++ b/src/ontology/md/RO/21/RO_0002521.md @@ -0,0 +1,44 @@ + +## Class : is sequentially aligned with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002521 + * *Label* = is sequentially aligned with + * *Definition* = x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [sequentially related to](../../RO/14/RO_0002514.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [is sequentially aligned with](../../RO/21/RO_0002521.md) + * [is sequentially aligned with](../../RO/21/RO_0002521.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. + * *[definition](../../IAO/15/IAO_0000115.md)* = x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is sequentially aligned with + +## Usage + + * - + * SymmetricObjectProperty [is sequentially aligned with](../../RO/21/RO_0002521.md) + * [is sequentially aligned with](../../RO/21/RO_0002521.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + +## External Comments + diff --git a/src/ontology/md/RO/22/RO_0002222.md b/src/ontology/md/RO/22/RO_0002222.md new file mode 100644 index 00000000..8c532207 --- /dev/null +++ b/src/ontology/md/RO/22/RO_0002222.md @@ -0,0 +1,59 @@ + +## Class : temporally related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002222 + * *Label* = temporally related to + * *Comment* = A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [temporally related to](../../RO/22/RO_0002222.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [temporally related to](../../RO/22/RO_0002222.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = https://en.wikipedia.org/wiki/Allen%27s_interval_algebra + * *[curator note](../../IAO/32/IAO_0000232.md)* = 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. + * *[source](../../ce/source.md)* = https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = temporally related to + +## Usage + + * - + * [before or simultaneous with](../../RO/81/RO_0002081.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [during which ends](../../RO/84/RO_0002084.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [during which starts](../../RO/88/RO_0002088.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [ends after](../../RO/86/RO_0002086.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [ends during](../../RO/93/RO_0002093.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [ends with](../../RO/30/RO_0002230.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [ends](../../RO/29/RO_0002229.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [precedes](../../BFO/63/BFO_0000063.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [starts before](../../RO/89/RO_0002089.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [starts during](../../RO/91/RO_0002091.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [starts with](../../RO/24/RO_0002224.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [starts](../../RO/23/RO_0002223.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [temporally related to](../../RO/22/RO_0002222.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [temporally related to](../../RO/22/RO_0002222.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + +## External Comments + diff --git a/src/ontology/md/RO/22/RO_0002322.md b/src/ontology/md/RO/22/RO_0002322.md new file mode 100644 index 00000000..19e133c1 --- /dev/null +++ b/src/ontology/md/RO/22/RO_0002322.md @@ -0,0 +1,42 @@ + +## Class : confers advantage in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002322 + * *Label* = confers advantage in + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [ecologically related to](../../RO/21/RO_0002321.md) + +## SubProperties + + +## Other Logical Axioms + + * [confers advantage in](../../RO/22/RO_0002322.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + +## Other Annotations + + * *[editor note](../../IAO/16/IAO_0000116.md)* = An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = adapted for + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = confers advantage in + +## Usage + + * - + * [confers advantage in](../../RO/22/RO_0002322.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + +## External Comments + diff --git a/src/ontology/md/RO/22/RO_0002422.md b/src/ontology/md/RO/22/RO_0002422.md new file mode 100644 index 00000000..c36219cb --- /dev/null +++ b/src/ontology/md/RO/22/RO_0002422.md @@ -0,0 +1,48 @@ + +## Class : logical macro assertion on an object property + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002422 + * *Label* = logical macro assertion on an object property + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on a property](../../RO/21/RO_0002421.md) + +## SubProperties + + * [dispositional interpretation](../../RO/74/RO_0002474.md) + * [is direct form of](../../RO/75/RO_0002575.md) + * [temporal interpretation](../../RO/00/RO_0001900.md) + * [first order logic expression](../../IAO/26/IAO_0000426.md) + * [is relational form of a class](../../RO/94/RO_0002594.md) + * [is indirect form of](../../RO/79/RO_0002579.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = logical macro assertion on an object property + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/22/RO_0002522.md b/src/ontology/md/RO/22/RO_0002522.md new file mode 100644 index 00000000..328a8217 --- /dev/null +++ b/src/ontology/md/RO/22/RO_0002522.md @@ -0,0 +1,47 @@ + +## Class : bounds sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002522 + * *Label* = bounds sequence of + * *Definition* = x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [sequentially related to](../../RO/14/RO_0002514.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [bounds sequence of](../../RO/22/RO_0002522.md) + * [bounds sequence of](../../RO/22/RO_0002522.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + * [is bound by sequence of](../../RO/23/RO_0002523.md) InverseOf [bounds sequence of](../../RO/22/RO_0002522.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) + * *[definition](../../IAO/15/IAO_0000115.md)* = x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = bounds sequence of + +## Usage + + * - + * TransitiveObjectProperty [bounds sequence of](../../RO/22/RO_0002522.md) + * [bounds sequence of](../../RO/22/RO_0002522.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + * [has subsequence](../../RO/24/RO_0002524.md) SubPropertyOf [bounds sequence of](../../RO/22/RO_0002522.md) + * [is bound by sequence of](../../RO/23/RO_0002523.md) InverseOf [bounds sequence of](../../RO/22/RO_0002522.md) + +## External Comments + diff --git a/src/ontology/md/RO/22/RO_HOM0000022.md b/src/ontology/md/RO/22/RO_HOM0000022.md new file mode 100644 index 00000000..6afc18ef --- /dev/null +++ b/src/ontology/md/RO/22/RO_HOM0000022.md @@ -0,0 +1,49 @@ + +## Class : in ohnology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000022 + * *Label* = in ohnology relationship with + * *Definition* = Paralogy that results from a whole genome duplication event. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1038/75560, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000022 ] + +## Synonyms + + * ohnologous to + * homoeology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in ohnology relationship with](../../RO/22/RO_HOM0000022.md) + * [in ohnology relationship with](../../RO/22/RO_HOM0000022.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paralogy that results from a whole genome duplication event. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = ohnologous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = homoeology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in ohnology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000022 + +## Usage + + * - + * SymmetricObjectProperty [in ohnology relationship with](../../RO/22/RO_HOM0000022.md) + * [in homoeology relationship with](../../RO/73/RO_HOM0000073.md) SubPropertyOf [in ohnology relationship with](../../RO/22/RO_HOM0000022.md) + * [in ohnology relationship with](../../RO/22/RO_HOM0000022.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## External Comments + diff --git a/src/ontology/md/RO/23/RO_0002223.md b/src/ontology/md/RO/23/RO_0002223.md new file mode 100644 index 00000000..3fda827c --- /dev/null +++ b/src/ontology/md/RO/23/RO_0002223.md @@ -0,0 +1,49 @@ + +## Class : starts + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002223 + * *Label* = starts + * *Definition* = inverse of starts with + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [part of](../../BFO/50/BFO_0000050.md) + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * [starts with](../../RO/24/RO_0002224.md) InverseOf [starts](../../RO/23/RO_0002223.md) + * [starts](../../RO/23/RO_0002223.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [starts](../../RO/23/RO_0002223.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of starts with + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = Allen + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = starts + +## Usage + + * - + * [starts with](../../RO/24/RO_0002224.md) InverseOf [starts](../../RO/23/RO_0002223.md) + * [starts](../../RO/23/RO_0002223.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [starts](../../RO/23/RO_0002223.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## External Comments + diff --git a/src/ontology/md/RO/23/RO_0002323.md b/src/ontology/md/RO/23/RO_0002323.md new file mode 100644 index 00000000..8bca9fc6 --- /dev/null +++ b/src/ontology/md/RO/23/RO_0002323.md @@ -0,0 +1,50 @@ + +## Class : mereotopologically related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002323 + * *Label* = mereotopologically related to + * *Definition* = A mereological relationship or a topological relationship + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A mereological relationship or a topological relationship + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = mereotopologically related to + +## Usage + + * - + * [2D boundary of](../../RO/00/RO_0002000.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [attached to part of](../../RO/77/RO_0002177.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [coincident with](../../RO/08/RO_0002008.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [colocalizes with](../../RO/25/RO_0002325.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [connected to](../../RO/70/RO_0002170.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [connects](../../RO/76/RO_0002176.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [continuous with](../../RO/50/RO_0002150.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [has 2D boundary](../../RO/02/RO_0002002.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [overlaps](../../RO/31/RO_0002131.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [spatially disjoint from](../../RO/63/RO_0002163.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## External Comments + diff --git a/src/ontology/md/RO/23/RO_0002423.md b/src/ontology/md/RO/23/RO_0002423.md new file mode 100644 index 00000000..81657bf1 --- /dev/null +++ b/src/ontology/md/RO/23/RO_0002423.md @@ -0,0 +1,41 @@ + +## Class : logical macro assertion on an annotation property + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002423 + * *Label* = logical macro assertion on an annotation property + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on a property](../../RO/21/RO_0002421.md) + +## SubProperties + + * [measurement property has unit](../../RO/36/RO_0002536.md) + * [annotation property cardinality](../../RO/19/RO_0002419.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = logical macro assertion on an annotation property + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * http://purl.obolibrary.org/obo/RO_0002575 [logical macro assertion on an annotation property](../../RO/23/RO_0002423.md) If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' + +## External Comments + diff --git a/src/ontology/md/RO/23/RO_0002523.md b/src/ontology/md/RO/23/RO_0002523.md new file mode 100644 index 00000000..3f5ca775 --- /dev/null +++ b/src/ontology/md/RO/23/RO_0002523.md @@ -0,0 +1,46 @@ + +## Class : is bound by sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002523 + * *Label* = is bound by sequence of + * *Definition* = inverse of bounds sequence of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [sequentially related to](../../RO/14/RO_0002514.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [is bound by sequence of](../../RO/23/RO_0002523.md) + * [is bound by sequence of](../../RO/23/RO_0002523.md) InverseOf [bounds sequence of](../../RO/22/RO_0002522.md) + * [is bound by sequence of](../../RO/23/RO_0002523.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of bounds sequence of + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is bound by sequence of + +## Usage + + * - + * TransitiveObjectProperty [is bound by sequence of](../../RO/23/RO_0002523.md) + * [is bound by sequence of](../../RO/23/RO_0002523.md) InverseOf [bounds sequence of](../../RO/22/RO_0002522.md) + * [is bound by sequence of](../../RO/23/RO_0002523.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + * [is subsequence of](../../RO/25/RO_0002525.md) SubPropertyOf [is bound by sequence of](../../RO/23/RO_0002523.md) + +## External Comments + diff --git a/src/ontology/md/RO/23/RO_HOM0000023.md b/src/ontology/md/RO/23/RO_HOM0000023.md new file mode 100644 index 00000000..7943aab3 --- /dev/null +++ b/src/ontology/md/RO/23/RO_HOM0000023.md @@ -0,0 +1,52 @@ + +## Class : in in-paralogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000023 + * *Label* = in in-paralogy relationship with + * *Definition* = Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000023 ] + +## Synonyms + + * in-paralogous to + * inparalogy + * symparalogy + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in in-paralogy relationship with](../../RO/23/RO_HOM0000023.md) + * [in in-paralogy relationship with](../../RO/23/RO_HOM0000023.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = in-paralogous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = inparalogy + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = symparalogy + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in in-paralogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000023 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in in-paralogy relationship with](../../RO/23/RO_HOM0000023.md) + * [in in-paralogy relationship with](../../RO/23/RO_HOM0000023.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## External Comments + diff --git a/src/ontology/md/RO/24/RO_0002224.md b/src/ontology/md/RO/24/RO_0002224.md new file mode 100644 index 00000000..aa95adf6 --- /dev/null +++ b/src/ontology/md/RO/24/RO_0002224.md @@ -0,0 +1,56 @@ + +## Class : starts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002224 + * *Label* = starts with + * *Definition* = x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has part](../../BFO/51/BFO_0000051.md) + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [starts with](../../RO/24/RO_0002224.md) + * [starts with](../../RO/24/RO_0002224.md) InverseOf [starts](../../RO/23/RO_0002223.md) + * [starts with](../../RO/24/RO_0002224.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [starts with](../../RO/24/RO_0002224.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = started by + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = starts with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [starts with](../../RO/24/RO_0002224.md) + * [starts with](../../RO/24/RO_0002224.md) InverseOf [starts](../../RO/23/RO_0002223.md) + * [starts with](../../RO/24/RO_0002224.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [starts with](../../RO/24/RO_0002224.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## External Comments + diff --git a/src/ontology/md/RO/24/RO_0002324.md b/src/ontology/md/RO/24/RO_0002324.md new file mode 100644 index 00000000..fcb55de0 --- /dev/null +++ b/src/ontology/md/RO/24/RO_0002324.md @@ -0,0 +1,41 @@ + +## Class : developmentally related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002324 + * *Label* = developmentally related to + * *Definition* = A relationship that holds between entities participating in some developmental process (GO:0032502) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that holds between entities participating in some developmental process (GO:0032502) + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = developmentally related to + +## Usage + + * - + * [developmentally preceded by](../../RO/58/RO_0002258.md) SubPropertyOf [developmentally related to](../../RO/24/RO_0002324.md) + * [has developmental potential involving](../../RO/84/RO_0002384.md) SubPropertyOf [developmentally related to](../../RO/24/RO_0002324.md) + * [results in developmental progression of](../../RO/95/RO_0002295.md) SubPropertyOf [developmentally related to](../../RO/24/RO_0002324.md) + +## External Comments + diff --git a/src/ontology/md/RO/24/RO_0002424.md b/src/ontology/md/RO/24/RO_0002424.md new file mode 100644 index 00000000..8ce16574 --- /dev/null +++ b/src/ontology/md/RO/24/RO_0002424.md @@ -0,0 +1,41 @@ + +## Class : differs in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002424 + * *Label* = differs in + * *Comment* = This is an exploratory relation + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[editor note](../../IAO/16/IAO_0000116.md)* = false + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = This is an exploratory relation + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = differs in + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions + +## Usage + + * - + * [differs in attribute of](../../RO/25/RO_0002425.md) SubPropertyOf [differs in](../../RO/24/RO_0002424.md) + * [differs in attribute](../../RO/26/RO_0002426.md) SubPropertyOf [differs in](../../RO/24/RO_0002424.md) + +## External Comments + diff --git a/src/ontology/md/RO/24/RO_0002524.md b/src/ontology/md/RO/24/RO_0002524.md new file mode 100644 index 00000000..19b09ddc --- /dev/null +++ b/src/ontology/md/RO/24/RO_0002524.md @@ -0,0 +1,58 @@ + +## Class : has subsequence + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002524 + * *Label* = has subsequence + * *Definition* = x has subsequence y iff all of the sequence parts of x are sequence parts of y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps sequence of](../../RO/26/RO_0002526.md) + * [bounds sequence of](../../RO/22/RO_0002522.md) + * [has part](../../BFO/51/BFO_0000051.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [has subsequence](../../RO/24/RO_0002524.md) + * [has subsequence](../../RO/24/RO_0002524.md) SubPropertyOf [bounds sequence of](../../RO/22/RO_0002522.md) + * [has subsequence](../../RO/24/RO_0002524.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [has subsequence](../../RO/24/RO_0002524.md) SubPropertyOf [overlaps sequence of](../../RO/26/RO_0002526.md) + * [is subsequence of](../../RO/25/RO_0002525.md) InverseOf [has subsequence](../../RO/24/RO_0002524.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x has subsequence y iff all of the sequence parts of x are sequence parts of y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = contains + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20226267 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has subsequence + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [has subsequence](../../RO/24/RO_0002524.md) + * [has end sequence](../../RO/18/RO_0002518.md) SubPropertyOf [has subsequence](../../RO/24/RO_0002524.md) + * [has start sequence](../../RO/16/RO_0002516.md) SubPropertyOf [has subsequence](../../RO/24/RO_0002524.md) + * [has subsequence](../../RO/24/RO_0002524.md) SubPropertyOf [bounds sequence of](../../RO/22/RO_0002522.md) + * [has subsequence](../../RO/24/RO_0002524.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [has subsequence](../../RO/24/RO_0002524.md) SubPropertyOf [overlaps sequence of](../../RO/26/RO_0002526.md) + * [is consecutive sequence of](../../RO/20/RO_0002520.md) SubPropertyOf [has subsequence](../../RO/24/RO_0002524.md) + * [is subsequence of](../../RO/25/RO_0002525.md) InverseOf [has subsequence](../../RO/24/RO_0002524.md) + * [sequentially ordered entity](../../RO/32/RO_0002532.md) SubClassOf [has subsequence](../../RO/24/RO_0002524.md) some [sequence atomic unit](../../RO/33/RO_0002533.md) + +## External Comments + diff --git a/src/ontology/md/RO/24/RO_HOM0000024.md b/src/ontology/md/RO/24/RO_HOM0000024.md new file mode 100644 index 00000000..9d0927ca --- /dev/null +++ b/src/ontology/md/RO/24/RO_HOM0000024.md @@ -0,0 +1,52 @@ + +## Class : in out-paralogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000024 + * *Label* = in out-paralogy relationship with + * *Definition* = Paralogy that results from a duplication preceding a given speciation event. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000024 ] + +## Synonyms + + * alloparalogy + * out-paralogous to + * outparalogy + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in out-paralogy relationship with](../../RO/24/RO_HOM0000024.md) + * [in out-paralogy relationship with](../../RO/24/RO_HOM0000024.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paralogy that results from a duplication preceding a given speciation event. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = alloparalogy + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = out-paralogous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = outparalogy + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in out-paralogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000024 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in out-paralogy relationship with](../../RO/24/RO_HOM0000024.md) + * [in out-paralogy relationship with](../../RO/24/RO_HOM0000024.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## External Comments + diff --git a/src/ontology/md/RO/25/RO_0001025.md b/src/ontology/md/RO/25/RO_0001025.md new file mode 100644 index 00000000..757e61d0 --- /dev/null +++ b/src/ontology/md/RO/25/RO_0001025.md @@ -0,0 +1,51 @@ + +## Class : located in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0001025 + * *Label* = located in + * *Definition* = a relation between two independent continuants, the target and the location, in which the target is entirely within the location + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [located in](../../RO/25/RO_0001025.md) + * [located in](../../RO/25/RO_0001025.md) InverseOf [location of](../../RO/15/RO_0001015.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = located in + * *[example of usage](../../IAO/12/IAO_0000112.md)* = my brain is located in my head + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this rat is located in this cage + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between two independent continuants, the target and the location, in which the target is entirely within the location + * *[editor note](../../IAO/16/IAO_0000116.md)* = Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + * *[editor note](../../IAO/16/IAO_0000116.md)* = Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + * *[alternative term](../../IAO/18/IAO_0000118.md)* = located_in + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[source](../../ce/source.md)* = http://www.obofoundry.org/ro/#OBO_REL:located_in + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = located in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [located in](../../RO/25/RO_0001025.md) + * [located in](../../RO/25/RO_0001025.md) InverseOf [location of](../../RO/15/RO_0001015.md) + +## External Comments + diff --git a/src/ontology/md/RO/25/RO_0002225.md b/src/ontology/md/RO/25/RO_0002225.md new file mode 100644 index 00000000..fe6d60fd --- /dev/null +++ b/src/ontology/md/RO/25/RO_0002225.md @@ -0,0 +1,43 @@ + +## Class : develops from part of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002225 + * *Label* = develops from part of + * *Definition* = x develops from part of y if and only if there exists some z such that x develops from z and z is part of y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [develops from](../../RO/02/RO_0002202.md) + +## SubProperties + + +## Other Logical Axioms + + * [develops from part of](../../RO/25/RO_0002225.md) SubPropertyOf [develops from](../../RO/02/RO_0002202.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x develops from part of y if and only if there exists some z such that x develops from z and z is part of y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = develops from part of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [develops from part of](../../RO/25/RO_0002225.md) SubPropertyOf [develops from](../../RO/02/RO_0002202.md) + +## External Comments + diff --git a/src/ontology/md/RO/25/RO_0002325.md b/src/ontology/md/RO/25/RO_0002325.md new file mode 100644 index 00000000..fbf3e7ae --- /dev/null +++ b/src/ontology/md/RO/25/RO_0002325.md @@ -0,0 +1,48 @@ + +## Class : colocalizes with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002325 + * *Label* = colocalizes with + * *Definition* = a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [colocalizes with](../../RO/25/RO_0002325.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [colocalizes with](../../RO/25/RO_0002325.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [colocalizes with](../../RO/25/RO_0002325.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) + * *[definition](../../IAO/15/IAO_0000115.md)* = a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with + * *[curator note](../../IAO/32/IAO_0000232.md)* = In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] + * *[creator](../../or/creator.md)* = Gene Ontology Consortium + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = colocalizes with + +## Usage + + * - + * [colocalizes with](../../RO/25/RO_0002325.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [colocalizes with](../../RO/25/RO_0002325.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [colocalizes with](../../RO/25/RO_0002325.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## External Comments + diff --git a/src/ontology/md/RO/25/RO_0002425.md b/src/ontology/md/RO/25/RO_0002425.md new file mode 100644 index 00000000..976b0e5d --- /dev/null +++ b/src/ontology/md/RO/25/RO_0002425.md @@ -0,0 +1,40 @@ + +## Class : differs in attribute of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002425 + * *Label* = differs in attribute of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [differs in](../../RO/24/RO_0002424.md) + +## SubProperties + + +## Other Logical Axioms + + * [differs in attribute of](../../RO/25/RO_0002425.md) Range [independent continuant](../../BFO/04/BFO_0000004.md)or[process](../../BFO/15/BFO_0000015.md) + * [differs in attribute of](../../RO/25/RO_0002425.md) SubPropertyOf [differs in](../../RO/24/RO_0002424.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = differs in attribute of + +## Usage + + * - + * [differs in attribute of](../../RO/25/RO_0002425.md) Range [independent continuant](../../BFO/04/BFO_0000004.md)or[process](../../BFO/15/BFO_0000015.md) + * [differs in attribute of](../../RO/25/RO_0002425.md) SubPropertyOf [differs in](../../RO/24/RO_0002424.md) + +## External Comments + diff --git a/src/ontology/md/RO/25/RO_0002525.md b/src/ontology/md/RO/25/RO_0002525.md new file mode 100644 index 00000000..5998fd77 --- /dev/null +++ b/src/ontology/md/RO/25/RO_0002525.md @@ -0,0 +1,55 @@ + +## Class : is subsequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002525 + * *Label* = is subsequence of + * *Definition* = inverse of has subsequence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps sequence of](../../RO/26/RO_0002526.md) + * [is bound by sequence of](../../RO/23/RO_0002523.md) + * [part of](../../BFO/50/BFO_0000050.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [is subsequence of](../../RO/25/RO_0002525.md) + * [is subsequence of](../../RO/25/RO_0002525.md) InverseOf [has subsequence](../../RO/24/RO_0002524.md) + * [is subsequence of](../../RO/25/RO_0002525.md) SubPropertyOf [is bound by sequence of](../../RO/23/RO_0002523.md) + * [is subsequence of](../../RO/25/RO_0002525.md) SubPropertyOf [overlaps sequence of](../../RO/26/RO_0002526.md) + * [is subsequence of](../../RO/25/RO_0002525.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of has subsequence + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = contained by + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is subsequence of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [is subsequence of](../../RO/25/RO_0002525.md) + * [is end sequence of](../../RO/19/RO_0002519.md) SubPropertyOf [is subsequence of](../../RO/25/RO_0002525.md) + * [is start sequence of](../../RO/17/RO_0002517.md) SubPropertyOf [is subsequence of](../../RO/25/RO_0002525.md) + * [is subsequence of](../../RO/25/RO_0002525.md) InverseOf [has subsequence](../../RO/24/RO_0002524.md) + * [is subsequence of](../../RO/25/RO_0002525.md) SubPropertyOf [is bound by sequence of](../../RO/23/RO_0002523.md) + * [is subsequence of](../../RO/25/RO_0002525.md) SubPropertyOf [overlaps sequence of](../../RO/26/RO_0002526.md) + * [is subsequence of](../../RO/25/RO_0002525.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## External Comments + diff --git a/src/ontology/md/RO/25/RO_HOM0000025.md b/src/ontology/md/RO/25/RO_HOM0000025.md new file mode 100644 index 00000000..a46e340c --- /dev/null +++ b/src/ontology/md/RO/25/RO_HOM0000025.md @@ -0,0 +1,46 @@ + +## Class : in pro-orthology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000025 + * *Label* = in pro-orthology relationship with + * *Definition* = 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1006/scdb.1999.0338, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1038/nrg2099, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000025 ] + +## Synonyms + + * pro-orthologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in pro-orthology relationship with](../../RO/25/RO_HOM0000025.md) + * [in pro-orthology relationship with](../../RO/25/RO_HOM0000025.md) SubPropertyOf [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = pro-orthologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in pro-orthology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000025 + +## Usage + + * - + * SymmetricObjectProperty [in pro-orthology relationship with](../../RO/25/RO_HOM0000025.md) + * [in pro-orthology relationship with](../../RO/25/RO_HOM0000025.md) SubPropertyOf [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + +## External Comments + diff --git a/src/ontology/md/RO/26/RO_0002226.md b/src/ontology/md/RO/26/RO_0002226.md new file mode 100644 index 00000000..f9950213 --- /dev/null +++ b/src/ontology/md/RO/26/RO_0002226.md @@ -0,0 +1,46 @@ + +## Class : develops in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002226 + * *Label* = develops in + * *Definition* = x develops_in y if x is located in y whilst x is developing + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally preceded by](../../RO/58/RO_0002258.md) + +## SubProperties + + +## Other Logical Axioms + + * [develops in](../../RO/26/RO_0002226.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [develops in](../../RO/26/RO_0002226.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x develops_in y if x is located in y whilst x is developing + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = EHDAA2 + * *[definition source](../../IAO/19/IAO_0000119.md)* = Jonathan Bard, EHDAA2 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = develops in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [develops in](../../RO/26/RO_0002226.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [develops in](../../RO/26/RO_0002226.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## External Comments + diff --git a/src/ontology/md/RO/26/RO_0002326.md b/src/ontology/md/RO/26/RO_0002326.md new file mode 100644 index 00000000..dd6ffff5 --- /dev/null +++ b/src/ontology/md/RO/26/RO_0002326.md @@ -0,0 +1,57 @@ + +## Class : contributes to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002326 + * *Label* = contributes to + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [capable of part of](../../RO/16/RO_0002216.md) + * [part of structure that is capable of](../../RO/29/RO_0002329.md) + +## SubProperties + + +## Other Logical Axioms + + * [contributes to](../../RO/26/RO_0002326.md) SubPropertyOf [capable of part of](../../RO/16/RO_0002216.md) + * [contributes to](../../RO/26/RO_0002326.md) SubPropertyOf [part of structure that is capable of](../../RO/29/RO_0002329.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. + * *[example of usage](../../IAO/12/IAO_0000112.md)* = eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex + * *[editor note](../../IAO/16/IAO_0000116.md)* = We would like to say + +if and only if + exists c', p' + c part_of c' and c' capable_of p + and + c capable_of p' and p' part_of p +then + c contributes_to p + +However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.geneontology.org/GO.annotation.conventions.shtml#contributes_to + * *[curator note](../../IAO/32/IAO_0000232.md)* = In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = contributes to + +## Usage + + * - + * [contributes to](../../RO/26/RO_0002326.md) SubPropertyOf [capable of part of](../../RO/16/RO_0002216.md) + * [contributes to](../../RO/26/RO_0002326.md) SubPropertyOf [part of structure that is capable of](../../RO/29/RO_0002329.md) + +## External Comments + diff --git a/src/ontology/md/RO/26/RO_0002426.md b/src/ontology/md/RO/26/RO_0002426.md new file mode 100644 index 00000000..fa5a8e8f --- /dev/null +++ b/src/ontology/md/RO/26/RO_0002426.md @@ -0,0 +1,40 @@ + +## Class : differs in attribute + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002426 + * *Label* = differs in attribute + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [differs in](../../RO/24/RO_0002424.md) + +## SubProperties + + +## Other Logical Axioms + + * [differs in attribute](../../RO/26/RO_0002426.md) Range [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [differs in attribute](../../RO/26/RO_0002426.md) SubPropertyOf [differs in](../../RO/24/RO_0002424.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = differs in attribute + +## Usage + + * - + * [differs in attribute](../../RO/26/RO_0002426.md) Range [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [differs in attribute](../../RO/26/RO_0002426.md) SubPropertyOf [differs in](../../RO/24/RO_0002424.md) + +## External Comments + diff --git a/src/ontology/md/RO/26/RO_0002526.md b/src/ontology/md/RO/26/RO_0002526.md new file mode 100644 index 00000000..4c1f1364 --- /dev/null +++ b/src/ontology/md/RO/26/RO_0002526.md @@ -0,0 +1,49 @@ + +## Class : overlaps sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002526 + * *Label* = overlaps sequence of + * *Definition* = x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [sequentially related to](../../RO/14/RO_0002514.md) + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [overlaps sequence of](../../RO/26/RO_0002526.md) + * [overlaps sequence of](../../RO/26/RO_0002526.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [overlaps sequence of](../../RO/26/RO_0002526.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x overlaps the sequence of x if and only if x has a subsequence z and z is a subsequence of y. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = overlaps sequence of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SymmetricObjectProperty [overlaps sequence of](../../RO/26/RO_0002526.md) + * [has subsequence](../../RO/24/RO_0002524.md) SubPropertyOf [overlaps sequence of](../../RO/26/RO_0002526.md) + * [is subsequence of](../../RO/25/RO_0002525.md) SubPropertyOf [overlaps sequence of](../../RO/26/RO_0002526.md) + * [overlaps sequence of](../../RO/26/RO_0002526.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [overlaps sequence of](../../RO/26/RO_0002526.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + +## External Comments + diff --git a/src/ontology/md/RO/26/RO_HOM0000026.md b/src/ontology/md/RO/26/RO_HOM0000026.md new file mode 100644 index 00000000..03eddf5a --- /dev/null +++ b/src/ontology/md/RO/26/RO_HOM0000026.md @@ -0,0 +1,48 @@ + +## Class : in semi-orthology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000026 + * *Label* = in semi-orthology relationship with + * *Definition* = 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1006/scdb.1999.0338, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1038/nrg2099, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000026 ] + * *Comment* = The converse of pro-orthologous. + +## Synonyms + + * semi-orthologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in semi-orthology relationship with](../../RO/26/RO_HOM0000026.md) + * [in semi-orthology relationship with](../../RO/26/RO_HOM0000026.md) SubPropertyOf [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = semi-orthologous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The converse of pro-orthologous. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in semi-orthology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000026 + +## Usage + + * - + * SymmetricObjectProperty [in semi-orthology relationship with](../../RO/26/RO_HOM0000026.md) + * [in semi-orthology relationship with](../../RO/26/RO_HOM0000026.md) SubPropertyOf [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + +## External Comments + diff --git a/src/ontology/md/RO/27/RO_0002327.md b/src/ontology/md/RO/27/RO_0002327.md new file mode 100644 index 00000000..f73564f2 --- /dev/null +++ b/src/ontology/md/RO/27/RO_0002327.md @@ -0,0 +1,55 @@ + +## Class : enables + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002327 + * *Label* = enables [ [contributor](../../or/contributor.md) = http://www.arabidopsis.org/ ] + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [capable of](../../RO/15/RO_0002215.md) + +## SubProperties + + +## Other Logical Axioms + + * [enabled by](../../RO/33/RO_0002333.md) InverseOf [enables](../../RO/27/RO_0002327.md) + * [enables](../../RO/27/RO_0002327.md) SubPropertyOf [capable of](../../RO/15/RO_0002215.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = a particular instances of akt-2 enables some instance of protein kinase activity + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = catalyzes + * *[alternative term](../../IAO/18/IAO_0000118.md)* = executes + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has + * *[curator note](../../IAO/32/IAO_0000232.md)* = This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = enables + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [enabled by](../../RO/33/RO_0002333.md) InverseOf [enables](../../RO/27/RO_0002327.md) + * [enables](../../RO/27/RO_0002327.md) SubPropertyOf [capable of](../../RO/15/RO_0002215.md) + +## External Comments + diff --git a/src/ontology/md/RO/27/RO_0002427.md b/src/ontology/md/RO/27/RO_0002427.md new file mode 100644 index 00000000..05e9d1b0 --- /dev/null +++ b/src/ontology/md/RO/27/RO_0002427.md @@ -0,0 +1,44 @@ + +## Class : causally downstream of or within + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002427 + * *Label* = causally downstream of or within + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causal relation between processes](../../RO/01/RO_0002501.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [causally downstream of or within](../../RO/27/RO_0002427.md) + * [causally downstream of or within](../../RO/27/RO_0002427.md) InverseOf [causally upstream of or within](../../RO/18/RO_0002418.md) + * [causally downstream of or within](../../RO/27/RO_0002427.md) SubPropertyOf [causal relation between processes](../../RO/01/RO_0002501.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causally downstream of or within + +## Usage + + * - + * TransitiveObjectProperty [causally downstream of or within](../../RO/27/RO_0002427.md) + * [causally downstream of or within](../../RO/27/RO_0002427.md) InverseOf [causally upstream of or within](../../RO/18/RO_0002418.md) + * [causally downstream of or within](../../RO/27/RO_0002427.md) SubPropertyOf [causal relation between processes](../../RO/01/RO_0002501.md) + * [causally downstream of](../../RO/04/RO_0002404.md) SubPropertyOf [causally downstream of or within](../../RO/27/RO_0002427.md) + * [regulated by](../../RO/34/RO_0002334.md) SubPropertyOf [causally downstream of or within](../../RO/27/RO_0002427.md) + +## External Comments + diff --git a/src/ontology/md/RO/27/RO_0002527.md b/src/ontology/md/RO/27/RO_0002527.md new file mode 100644 index 00000000..5473c42f --- /dev/null +++ b/src/ontology/md/RO/27/RO_0002527.md @@ -0,0 +1,47 @@ + +## Class : does not overlap sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002527 + * *Label* = does not overlap sequence of + * *Definition* = x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [sequentially related to](../../RO/14/RO_0002514.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [does not overlap sequence of](../../RO/27/RO_0002527.md) + * [does not overlap sequence of](../../RO/27/RO_0002527.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x does not overlaps the sequence of x if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = disconnected from + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = does not overlap sequence of + +## Usage + + * - + * SymmetricObjectProperty [does not overlap sequence of](../../RO/27/RO_0002527.md) + * [does not overlap sequence of](../../RO/27/RO_0002527.md) SubPropertyOf [sequentially related to](../../RO/14/RO_0002514.md) + * [is downstream of sequence of](../../RO/29/RO_0002529.md) SubPropertyOf [does not overlap sequence of](../../RO/27/RO_0002527.md) + * [is upstream of sequence of](../../RO/28/RO_0002528.md) SubPropertyOf [does not overlap sequence of](../../RO/27/RO_0002527.md) + * [sequentially adjacent to](../../RO/15/RO_0002515.md) SubPropertyOf [does not overlap sequence of](../../RO/27/RO_0002527.md) + +## External Comments + diff --git a/src/ontology/md/RO/27/RO_HOM0000027.md b/src/ontology/md/RO/27/RO_HOM0000027.md new file mode 100644 index 00000000..6f6d9adf --- /dev/null +++ b/src/ontology/md/RO/27/RO_HOM0000027.md @@ -0,0 +1,48 @@ + +## Class : in serial homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000027 + * *Label* = in serial homology relationship with + * *Definition* = Iterative homology that involves structures arranged along the main body axis. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.es.20.110189.000411, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000027 ] + +## Synonyms + + * serial homologous to + * homonomy + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in serial homology relationship with](../../RO/27/RO_HOM0000027.md) + * [in serial homology relationship with](../../RO/27/RO_HOM0000027.md) SubPropertyOf [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Iterative homology that involves structures arranged along the main body axis. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = serial homologous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = homonomy + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in serial homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000027 + +## Usage + + * - + * SymmetricObjectProperty [in serial homology relationship with](../../RO/27/RO_HOM0000027.md) + * [in serial homology relationship with](../../RO/27/RO_HOM0000027.md) SubPropertyOf [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + +## External Comments + diff --git a/src/ontology/md/RO/28/RO_0002328.md b/src/ontology/md/RO/28/RO_0002328.md new file mode 100644 index 00000000..521af3ff --- /dev/null +++ b/src/ontology/md/RO/28/RO_0002328.md @@ -0,0 +1,47 @@ + +## Class : functionally related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002328 + * *Label* = functionally related to + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = This is a grouping relation that collects relations used for the purpose of connecting structure and function + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = functionally related to + +## Usage + + * - + * [biomechanically related to](../../RO/67/RO_0002567.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [capable of part of](../../RO/16/RO_0002216.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [capable of](../../RO/15/RO_0002215.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [enabled by](../../RO/33/RO_0002333.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [enables activity in](../../RO/32/RO_0002432.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [has part structure that is capable of](../../RO/84/RO_0002584.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [input of](../../RO/52/RO_0002352.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [involved in or regulates](../../RO/31/RO_0002431.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [output of](../../RO/53/RO_0002353.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [part of structure that is capable of](../../RO/29/RO_0002329.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [regulates levels of](../../RO/32/RO_0002332.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## External Comments + diff --git a/src/ontology/md/RO/28/RO_0002428.md b/src/ontology/md/RO/28/RO_0002428.md new file mode 100644 index 00000000..8a2c2205 --- /dev/null +++ b/src/ontology/md/RO/28/RO_0002428.md @@ -0,0 +1,44 @@ + +## Class : involved in regulation of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002428 + * *Label* = involved in regulation of + * *Definition* = c involved in regulation of p if c is involved in some 'p' and p' regulates some p + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [involved in or regulates](../../RO/31/RO_0002431.md) + +## SubProperties + + +## Other Logical Axioms + + * [involved in regulation of](../../RO/28/RO_0002428.md) SubPropertyOf [involved in or regulates](../../RO/31/RO_0002431.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = c involved in regulation of p if c is involved in some 'p' and p' regulates some p + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = involved in regulation of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [involved in negative regulation of](../../RO/30/RO_0002430.md) SubPropertyOf [involved in regulation of](../../RO/28/RO_0002428.md) + * [involved in positive regulation of](../../RO/29/RO_0002429.md) SubPropertyOf [involved in regulation of](../../RO/28/RO_0002428.md) + * [involved in regulation of](../../RO/28/RO_0002428.md) SubPropertyOf [involved in or regulates](../../RO/31/RO_0002431.md) + +## External Comments + diff --git a/src/ontology/md/RO/28/RO_0002528.md b/src/ontology/md/RO/28/RO_0002528.md new file mode 100644 index 00000000..2ae81410 --- /dev/null +++ b/src/ontology/md/RO/28/RO_0002528.md @@ -0,0 +1,44 @@ + +## Class : is upstream of sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002528 + * *Label* = is upstream of sequence of + * *Definition* = inverse of downstream of sequence of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [does not overlap sequence of](../../RO/27/RO_0002527.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [is upstream of sequence of](../../RO/28/RO_0002528.md) + * [is upstream of sequence of](../../RO/28/RO_0002528.md) SubPropertyOf [does not overlap sequence of](../../RO/27/RO_0002527.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of downstream of sequence of + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is upstream of sequence of + +## Usage + + * - + * TransitiveObjectProperty [is upstream of sequence of](../../RO/28/RO_0002528.md) + * [is immediately upstream of sequence of](../../RO/31/RO_0002531.md) SubPropertyOf [is upstream of sequence of](../../RO/28/RO_0002528.md) + * [is upstream of sequence of](../../RO/28/RO_0002528.md) SubPropertyOf [does not overlap sequence of](../../RO/27/RO_0002527.md) + +## External Comments + diff --git a/src/ontology/md/RO/28/RO_HOM0000028.md b/src/ontology/md/RO/28/RO_HOM0000028.md new file mode 100644 index 00000000..3a122c11 --- /dev/null +++ b/src/ontology/md/RO/28/RO_HOM0000028.md @@ -0,0 +1,50 @@ + +## Class : in heterochronous homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000028 + * *Label* = in heterochronous homology relationship with + * *Definition* = Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:978-0674639416, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000028 ] + +## Synonyms + + * heterochronous homologous to + * heterochrony + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + * [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) SubPropertyOf [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = heterochronous homologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = heterochrony + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in heterochronous homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000028 + +## Usage + + * - + * SymmetricObjectProperty [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + * [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) SubPropertyOf [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + * [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) SubPropertyOf [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + * [in peramorphosis relationship with](../../RO/30/RO_HOM0000030.md) SubPropertyOf [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + +## External Comments + diff --git a/src/ontology/md/RO/29/RO_0002229.md b/src/ontology/md/RO/29/RO_0002229.md new file mode 100644 index 00000000..3df4137c --- /dev/null +++ b/src/ontology/md/RO/29/RO_0002229.md @@ -0,0 +1,48 @@ + +## Class : ends + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002229 + * *Label* = ends + * *Definition* = inverse of ends with + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [part of](../../BFO/50/BFO_0000050.md) + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * [ends](../../RO/29/RO_0002229.md) InverseOf [ends with](../../RO/30/RO_0002230.md) + * [ends](../../RO/29/RO_0002229.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [ends](../../RO/29/RO_0002229.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of ends with + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ends + +## Usage + + * - + * [ends](../../RO/29/RO_0002229.md) InverseOf [ends with](../../RO/30/RO_0002230.md) + * [ends](../../RO/29/RO_0002229.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [ends](../../RO/29/RO_0002229.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## External Comments + diff --git a/src/ontology/md/RO/29/RO_0002329.md b/src/ontology/md/RO/29/RO_0002329.md new file mode 100644 index 00000000..3019ba50 --- /dev/null +++ b/src/ontology/md/RO/29/RO_0002329.md @@ -0,0 +1,43 @@ + +## Class : part of structure that is capable of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002329 + * *Label* = part of structure that is capable of + * *Definition* = this relation holds between c and p when c is part of some c', and c' is capable of p. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [functionally related to](../../RO/28/RO_0002328.md) + +## SubProperties + + +## Other Logical Axioms + + * [part of structure that is capable of](../../RO/29/RO_0002329.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = this relation holds between c and p when c is part of some c', and c' is capable of p. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = false + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = part of structure that is capable of + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * [contributes to](../../RO/26/RO_0002326.md) SubPropertyOf [part of structure that is capable of](../../RO/29/RO_0002329.md) + * [part of structure that is capable of](../../RO/29/RO_0002329.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## External Comments + diff --git a/src/ontology/md/RO/29/RO_0002429.md b/src/ontology/md/RO/29/RO_0002429.md new file mode 100644 index 00000000..ea2ed352 --- /dev/null +++ b/src/ontology/md/RO/29/RO_0002429.md @@ -0,0 +1,40 @@ + +## Class : involved in positive regulation of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002429 + * *Label* = involved in positive regulation of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [involved in regulation of](../../RO/28/RO_0002428.md) + +## SubProperties + + +## Other Logical Axioms + + * [involved in positive regulation of](../../RO/29/RO_0002429.md) SubPropertyOf [involved in regulation of](../../RO/28/RO_0002428.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = involved in positive regulation of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [involved in positive regulation of](../../RO/29/RO_0002429.md) SubPropertyOf [involved in regulation of](../../RO/28/RO_0002428.md) + +## External Comments + diff --git a/src/ontology/md/RO/29/RO_0002529.md b/src/ontology/md/RO/29/RO_0002529.md new file mode 100644 index 00000000..f0fb311e --- /dev/null +++ b/src/ontology/md/RO/29/RO_0002529.md @@ -0,0 +1,46 @@ + +## Class : is downstream of sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002529 + * *Label* = is downstream of sequence of + * *Definition* = x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [does not overlap sequence of](../../RO/27/RO_0002527.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [is downstream of sequence of](../../RO/29/RO_0002529.md) + * [is downstream of sequence of](../../RO/29/RO_0002529.md) InverseOf [is downstream of sequence of](../../RO/29/RO_0002529.md) + * [is downstream of sequence of](../../RO/29/RO_0002529.md) SubPropertyOf [does not overlap sequence of](../../RO/27/RO_0002527.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is downstream of sequence of + +## Usage + + * - + * TransitiveObjectProperty [is downstream of sequence of](../../RO/29/RO_0002529.md) + * [is downstream of sequence of](../../RO/29/RO_0002529.md) InverseOf [is downstream of sequence of](../../RO/29/RO_0002529.md) + * [is downstream of sequence of](../../RO/29/RO_0002529.md) SubPropertyOf [does not overlap sequence of](../../RO/27/RO_0002527.md) + * [is immediately downstream of sequence of](../../RO/30/RO_0002530.md) SubPropertyOf [is downstream of sequence of](../../RO/29/RO_0002529.md) + +## External Comments + diff --git a/src/ontology/md/RO/29/RO_HOM0000029.md b/src/ontology/md/RO/29/RO_HOM0000029.md new file mode 100644 index 00000000..fe221438 --- /dev/null +++ b/src/ontology/md/RO/29/RO_HOM0000029.md @@ -0,0 +1,53 @@ + +## Class : in paedomorphorsis relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000029 + * *Label* = in paedomorphorsis relationship with + * *Definition* = Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:978-0674639416, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://en.wikipedia.org/wiki/Pedomorphosis, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000029 ] + +## Synonyms + + * juvenification + * pedomorphosis + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + * [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) SubPropertyOf [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = juvenification + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = pedomorphosis + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in paedomorphorsis relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000029 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + * [in neoteny relationship with](../../RO/32/RO_HOM0000032.md) SubPropertyOf [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + * [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) SubPropertyOf [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + * [in postdisplacement relationship with](../../RO/51/RO_HOM0000051.md) SubPropertyOf [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + * [in progenesis relationship with](../../RO/31/RO_HOM0000031.md) SubPropertyOf [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## External Comments + diff --git a/src/ontology/md/RO/30/RO_0002130.md b/src/ontology/md/RO/30/RO_0002130.md new file mode 100644 index 00000000..8b7741c9 --- /dev/null +++ b/src/ontology/md/RO/30/RO_0002130.md @@ -0,0 +1,52 @@ + +## Class : has synaptic terminal in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002130 + * *Label* = has synaptic terminal in + * *Definition* = A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [has synaptic terminal in](../../RO/30/RO_0002130.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has synaptic terminal in](../../RO/30/RO_0002130.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has synaptic terminal of](../../RO/06/RO_0002006.md) InverseOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has synapse in + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = some ( that some Y?) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has synaptic terminal in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has postsynaptic terminal in](../../RO/10/RO_0002110.md) SubPropertyOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + * [has presynaptic terminal in](../../RO/13/RO_0002113.md) SubPropertyOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + * [has synaptic terminal in](../../RO/30/RO_0002130.md) Domain [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has synaptic terminal in](../../RO/30/RO_0002130.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has synaptic terminal of](../../RO/06/RO_0002006.md) InverseOf [has synaptic terminal in](../../RO/30/RO_0002130.md) + +## External Comments + diff --git a/src/ontology/md/RO/30/RO_0002230.md b/src/ontology/md/RO/30/RO_0002230.md new file mode 100644 index 00000000..0029ccfc --- /dev/null +++ b/src/ontology/md/RO/30/RO_0002230.md @@ -0,0 +1,57 @@ + +## Class : ends with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002230 + * *Label* = ends with + * *Definition* = x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has part](../../BFO/51/BFO_0000051.md) + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [ends with](../../RO/30/RO_0002230.md) + * [ends with](../../RO/30/RO_0002230.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [ends with](../../RO/30/RO_0002230.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [ends](../../RO/29/RO_0002229.md) InverseOf [ends with](../../RO/30/RO_0002230.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = finished by + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ends with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [ends with](../../RO/30/RO_0002230.md) + * [ends with](../../RO/30/RO_0002230.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [ends with](../../RO/30/RO_0002230.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [ends](../../RO/29/RO_0002229.md) InverseOf [ends with](../../RO/30/RO_0002230.md) + +## External Comments + diff --git a/src/ontology/md/RO/30/RO_0002330.md b/src/ontology/md/RO/30/RO_0002330.md new file mode 100644 index 00000000..ecaf998f --- /dev/null +++ b/src/ontology/md/RO/30/RO_0002330.md @@ -0,0 +1,50 @@ + +## Class : genomically related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002330 + * *Label* = genomically related to + * *Definition* = holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [genomically related to](../../RO/30/RO_0002330.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [genomically related to](../../RO/30/RO_0002330.md) Range [continuant](../../BFO/02/BFO_0000002.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = genomically related to + +## Usage + + * - + * [expressed in](../../RO/06/RO_0002206.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [expresses](../../RO/92/RO_0002292.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [gene product of](../../RO/04/RO_0002204.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [genomically related to](../../RO/30/RO_0002330.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [genomically related to](../../RO/30/RO_0002330.md) Range [continuant](../../BFO/02/BFO_0000002.md) + * [has gene product](../../RO/05/RO_0002205.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [ribosomal translation of](../../RO/12/RO_0002512.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [ribosomally translates to](../../RO/13/RO_0002513.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [transcribed from](../../RO/10/RO_0002510.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [transcribed to](../../RO/11/RO_0002511.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## External Comments + diff --git a/src/ontology/md/RO/30/RO_0002430.md b/src/ontology/md/RO/30/RO_0002430.md new file mode 100644 index 00000000..9e1e5236 --- /dev/null +++ b/src/ontology/md/RO/30/RO_0002430.md @@ -0,0 +1,40 @@ + +## Class : involved in negative regulation of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002430 + * *Label* = involved in negative regulation of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [involved in regulation of](../../RO/28/RO_0002428.md) + +## SubProperties + + +## Other Logical Axioms + + * [involved in negative regulation of](../../RO/30/RO_0002430.md) SubPropertyOf [involved in regulation of](../../RO/28/RO_0002428.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = involved in negative regulation of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [involved in negative regulation of](../../RO/30/RO_0002430.md) SubPropertyOf [involved in regulation of](../../RO/28/RO_0002428.md) + +## External Comments + diff --git a/src/ontology/md/RO/30/RO_0002530.md b/src/ontology/md/RO/30/RO_0002530.md new file mode 100644 index 00000000..fda6cc4b --- /dev/null +++ b/src/ontology/md/RO/30/RO_0002530.md @@ -0,0 +1,46 @@ + +## Class : is immediately downstream of sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002530 + * *Label* = is immediately downstream of sequence of + * *Definition* = x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [sequentially adjacent to](../../RO/15/RO_0002515.md) + * [is downstream of sequence of](../../RO/29/RO_0002529.md) + +## SubProperties + + +## Other Logical Axioms + + * [is immediately downstream of sequence of](../../RO/30/RO_0002530.md) SubPropertyOf [is downstream of sequence of](../../RO/29/RO_0002529.md) + * [is immediately downstream of sequence of](../../RO/30/RO_0002530.md) SubPropertyOf [sequentially adjacent to](../../RO/15/RO_0002515.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript + * *[definition](../../IAO/15/IAO_0000115.md)* = x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[is direct form of](../../RO/75/RO_0002575.md)* = http://purl.obolibrary.org/obo/RO_0002529 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is immediately downstream of sequence of + +## Usage + + * - + * [is immediately downstream of sequence of](../../RO/30/RO_0002530.md) SubPropertyOf [is downstream of sequence of](../../RO/29/RO_0002529.md) + * [is immediately downstream of sequence of](../../RO/30/RO_0002530.md) SubPropertyOf [sequentially adjacent to](../../RO/15/RO_0002515.md) + +## External Comments + diff --git a/src/ontology/md/RO/30/RO_HOM0000030.md b/src/ontology/md/RO/30/RO_HOM0000030.md new file mode 100644 index 00000000..6ac8166c --- /dev/null +++ b/src/ontology/md/RO/30/RO_HOM0000030.md @@ -0,0 +1,47 @@ + +## Class : in peramorphosis relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000030 + * *Label* = in peramorphosis relationship with + * *Definition* = Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://en.wikipedia.org/wiki/Peramorphosis, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000030 ] + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in peramorphosis relationship with](../../RO/30/RO_HOM0000030.md) + * [in peramorphosis relationship with](../../RO/30/RO_HOM0000030.md) SubPropertyOf [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in peramorphosis relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000030 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in peramorphosis relationship with](../../RO/30/RO_HOM0000030.md) + * [in hypermorphosis relationship with](../../RO/52/RO_HOM0000052.md) SubPropertyOf [in peramorphosis relationship with](../../RO/30/RO_HOM0000030.md) + * [in peramorphosis relationship with](../../RO/30/RO_HOM0000030.md) SubPropertyOf [in heterochronous homology relationship with](../../RO/28/RO_HOM0000028.md) + +## External Comments + diff --git a/src/ontology/md/RO/31/RO_0002131.md b/src/ontology/md/RO/31/RO_0002131.md new file mode 100644 index 00000000..a585fab0 --- /dev/null +++ b/src/ontology/md/RO/31/RO_0002131.md @@ -0,0 +1,61 @@ + +## Class : overlaps + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002131 + * *Label* = overlaps + * *Definition* = x overlaps y if and only if there exists some z such that x has part z and z part of y + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [overlaps](../../RO/31/RO_0002131.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x overlaps y if and only if there exists some z such that x has part z and z part of y + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = overlaps + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [conduit for](../../RO/70/RO_0002570.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [contributes to morphology of](../../RO/33/RO_0002433.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [determined by part of](../../RO/09/RO_0002509.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [fasciculates with](../../RO/01/RO_0002101.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has dendrite location](../../RO/60/RO_0002360.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has part](../../BFO/51/BFO_0000051.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has soma location](../../RO/00/RO_0002100.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has synaptic terminal in](../../RO/30/RO_0002130.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [has synaptic terminal of](../../RO/06/RO_0002006.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [overlaps sequence of](../../RO/26/RO_0002526.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [overlaps](../../RO/31/RO_0002131.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [part of](../../BFO/50/BFO_0000050.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [partially overlaps](../../RO/51/RO_0002151.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + * [spatially coextensive with](../../RO/79/RO_0002379.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## External Comments + diff --git a/src/ontology/md/RO/31/RO_0002231.md b/src/ontology/md/RO/31/RO_0002231.md new file mode 100644 index 00000000..a7b3cc48 --- /dev/null +++ b/src/ontology/md/RO/31/RO_0002231.md @@ -0,0 +1,49 @@ + +## Class : has start location + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002231 + * *Label* = has start location + * *Definition* = x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has part that occurs in](../../RO/79/RO_0002479.md) + +## SubProperties + + +## Other Logical Axioms + + * [has start location](../../RO/31/RO_0002231.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [has start location](../../RO/31/RO_0002231.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has start location](../../RO/31/RO_0002231.md) SubPropertyOf [has part that occurs in](../../RO/79/RO_0002479.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = starts with process that occurs in + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has start location + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has start location](../../RO/31/RO_0002231.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [has start location](../../RO/31/RO_0002231.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has start location](../../RO/31/RO_0002231.md) SubPropertyOf [has part that occurs in](../../RO/79/RO_0002479.md) + +## External Comments + diff --git a/src/ontology/md/RO/31/RO_0002331.md b/src/ontology/md/RO/31/RO_0002331.md new file mode 100644 index 00000000..82c4e43f --- /dev/null +++ b/src/ontology/md/RO/31/RO_0002331.md @@ -0,0 +1,47 @@ + +## Class : involved in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002331 + * *Label* = involved in + * *Definition* = c involved_in p if and only if c enables some process p', and p' is part of p + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [involved in or regulates](../../RO/31/RO_0002431.md) + +## SubProperties + + +## Other Logical Axioms + + * [involved in](../../RO/31/RO_0002331.md) SubPropertyOf [involved in or regulates](../../RO/31/RO_0002431.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = c involved_in p if and only if c enables some process p', and p' is part of p + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = actively involved in + * *[alternative term](../../IAO/18/IAO_0000118.md)* = enables part of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = involved in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [involved in](../../RO/31/RO_0002331.md) SubPropertyOf [involved in or regulates](../../RO/31/RO_0002431.md) + +## External Comments + diff --git a/src/ontology/md/RO/31/RO_0002431.md b/src/ontology/md/RO/31/RO_0002431.md new file mode 100644 index 00000000..0d170306 --- /dev/null +++ b/src/ontology/md/RO/31/RO_0002431.md @@ -0,0 +1,43 @@ + +## Class : involved in or regulates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002431 + * *Label* = involved in or regulates + * *Definition* = c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [functionally related to](../../RO/28/RO_0002328.md) + +## SubProperties + + +## Other Logical Axioms + + * [involved in or regulates](../../RO/31/RO_0002431.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = involved in or involved in regulation of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = involved in or regulates + +## Usage + + * - + * [involved in or regulates](../../RO/31/RO_0002431.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [involved in regulation of](../../RO/28/RO_0002428.md) SubPropertyOf [involved in or regulates](../../RO/31/RO_0002431.md) + * [involved in](../../RO/31/RO_0002331.md) SubPropertyOf [involved in or regulates](../../RO/31/RO_0002431.md) + +## External Comments + diff --git a/src/ontology/md/RO/31/RO_0002531.md b/src/ontology/md/RO/31/RO_0002531.md new file mode 100644 index 00000000..bb8cfe64 --- /dev/null +++ b/src/ontology/md/RO/31/RO_0002531.md @@ -0,0 +1,45 @@ + +## Class : is immediately upstream of sequence of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002531 + * *Label* = is immediately upstream of sequence of + * *Definition* = inverse of immediately downstream of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [sequentially adjacent to](../../RO/15/RO_0002515.md) + * [is upstream of sequence of](../../RO/28/RO_0002528.md) + +## SubProperties + + +## Other Logical Axioms + + * [is immediately upstream of sequence of](../../RO/31/RO_0002531.md) SubPropertyOf [is upstream of sequence of](../../RO/28/RO_0002528.md) + * [is immediately upstream of sequence of](../../RO/31/RO_0002531.md) SubPropertyOf [sequentially adjacent to](../../RO/15/RO_0002515.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of immediately downstream of + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://biorxiv.org/content/early/2014/06/27/006650.abstract + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is immediately upstream of sequence of + +## Usage + + * - + * [is immediately upstream of sequence of](../../RO/31/RO_0002531.md) SubPropertyOf [is upstream of sequence of](../../RO/28/RO_0002528.md) + * [is immediately upstream of sequence of](../../RO/31/RO_0002531.md) SubPropertyOf [sequentially adjacent to](../../RO/15/RO_0002515.md) + +## External Comments + diff --git a/src/ontology/md/RO/31/RO_HOM0000031.md b/src/ontology/md/RO/31/RO_HOM0000031.md new file mode 100644 index 00000000..b5c1ee7c --- /dev/null +++ b/src/ontology/md/RO/31/RO_HOM0000031.md @@ -0,0 +1,44 @@ + +## Class : in progenesis relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000031 + * *Label* = in progenesis relationship with + * *Definition* = Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:978-0674639416, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://en.wikipedia.org/wiki/Progenesis, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000031 ] + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in progenesis relationship with](../../RO/31/RO_HOM0000031.md) + * [in progenesis relationship with](../../RO/31/RO_HOM0000031.md) SubPropertyOf [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in progenesis relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000031 + +## Usage + + * - + * SymmetricObjectProperty [in progenesis relationship with](../../RO/31/RO_HOM0000031.md) + * [in progenesis relationship with](../../RO/31/RO_HOM0000031.md) SubPropertyOf [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## External Comments + diff --git a/src/ontology/md/RO/32/RO_0002132.md b/src/ontology/md/RO/32/RO_0002132.md new file mode 100644 index 00000000..2b209590 --- /dev/null +++ b/src/ontology/md/RO/32/RO_0002132.md @@ -0,0 +1,73 @@ + +## Class : has fasciculating neuron projection + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002132 + * *Label* = has fasciculating neuron projection + * *Definition* = The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) Domain [neuron projection bundle](../../CARO/01/CARO_0001001.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) InverseOf [fasciculates with](../../RO/01/RO_0002101.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) Range [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has fasciculating component + * *[first order logic expression](../../IAO/26/IAO_0000426.md)* = (forall (?x ?y) + (iff + (has_fasciculating_neuron_projection ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron projection bundle ; CARO_0001001" ?x) + ("neuron projection ; GO0043005" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500" ?npbs) + (part_of ?nps ?y) + (part_of ?npbs ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has fasciculating neuron projection + +## Usage + + * - + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) Domain [neuron projection bundle](../../CARO/01/CARO_0001001.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) InverseOf [fasciculates with](../../RO/01/RO_0002101.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) Range [neuron](../../CL/40/CL_0000540.md)or[part of](../../BFO/50/BFO_0000050.md) some [neuron](../../CL/40/CL_0000540.md) + * [has fasciculating neuron projection](../../RO/32/RO_0002132.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## External Comments + diff --git a/src/ontology/md/RO/32/RO_0002232.md b/src/ontology/md/RO/32/RO_0002232.md new file mode 100644 index 00000000..cb9dad77 --- /dev/null +++ b/src/ontology/md/RO/32/RO_0002232.md @@ -0,0 +1,49 @@ + +## Class : has end location + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002232 + * *Label* = has end location + * *Definition* = x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has part that occurs in](../../RO/79/RO_0002479.md) + +## SubProperties + + +## Other Logical Axioms + + * [has end location](../../RO/32/RO_0002232.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [has end location](../../RO/32/RO_0002232.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has end location](../../RO/32/RO_0002232.md) SubPropertyOf [has part that occurs in](../../RO/79/RO_0002479.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = ends with process that occurs in + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has end location + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has end location](../../RO/32/RO_0002232.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [has end location](../../RO/32/RO_0002232.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has end location](../../RO/32/RO_0002232.md) SubPropertyOf [has part that occurs in](../../RO/79/RO_0002479.md) + +## External Comments + diff --git a/src/ontology/md/RO/32/RO_0002332.md b/src/ontology/md/RO/32/RO_0002332.md new file mode 100644 index 00000000..05f10535 --- /dev/null +++ b/src/ontology/md/RO/32/RO_0002332.md @@ -0,0 +1,42 @@ + +## Class : regulates levels of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002332 + * *Label* = regulates levels of + * *Definition* = p regulates levels of c if p regulates some amount (PATO:0000070) of c + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [functionally related to](../../RO/28/RO_0002328.md) + +## SubProperties + + +## Other Logical Axioms + + * [regulates levels of](../../RO/32/RO_0002332.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid + * *[definition](../../IAO/15/IAO_0000115.md)* = p regulates levels of c if p regulates some amount (PATO:0000070) of c + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = regulates levels of (process to entity) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = regulates levels of + +## Usage + + * - + * [regulates levels of](../../RO/32/RO_0002332.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## External Comments + diff --git a/src/ontology/md/RO/32/RO_0002432.md b/src/ontology/md/RO/32/RO_0002432.md new file mode 100644 index 00000000..ae770f8d --- /dev/null +++ b/src/ontology/md/RO/32/RO_0002432.md @@ -0,0 +1,42 @@ + +## Class : enables activity in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002432 + * *Label* = enables activity in + * *Definition* = c executes activity in d if and only if c enables p and p occurs_in d + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [functionally related to](../../RO/28/RO_0002328.md) + +## SubProperties + + +## Other Logical Axioms + + * [enables activity in](../../RO/32/RO_0002432.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = c executes activity in d if and only if c enables p and p occurs_in d + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = executes activity in + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = enables activity in + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * [enables activity in](../../RO/32/RO_0002432.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## External Comments + diff --git a/src/ontology/md/RO/32/RO_0002532.md b/src/ontology/md/RO/32/RO_0002532.md new file mode 100644 index 00000000..be533205 --- /dev/null +++ b/src/ontology/md/RO/32/RO_0002532.md @@ -0,0 +1,43 @@ + +## Class : sequentially ordered entity + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002532 + * *Label* = sequentially ordered entity + * *Definition* = Any entity that is ordered in discrete units along a linear axis. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [has subsequence](../../RO/24/RO_0002524.md) some [sequence atomic unit](../../RO/33/RO_0002533.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Any entity that is ordered in discrete units along a linear axis. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = sequentially ordered entity + +## Usage + + * - + * [sequence atomic unit](../../RO/33/RO_0002533.md) SubClassOf [sequentially ordered entity](../../RO/32/RO_0002532.md) + * [sequence bearer](../../RO/34/RO_0002534.md) SubClassOf [sequentially ordered entity](../../RO/32/RO_0002532.md) + * [sequentially ordered entity](../../RO/32/RO_0002532.md) SubClassOf [has subsequence](../../RO/24/RO_0002524.md) some [sequence atomic unit](../../RO/33/RO_0002533.md) + * [sequentially related to](../../RO/14/RO_0002514.md) Domain [sequentially ordered entity](../../RO/32/RO_0002532.md) + * [sequentially related to](../../RO/14/RO_0002514.md) Range [sequentially ordered entity](../../RO/32/RO_0002532.md) + +## External Comments + diff --git a/src/ontology/md/RO/32/RO_HOM0000032.md b/src/ontology/md/RO/32/RO_HOM0000032.md new file mode 100644 index 00000000..37e6585c --- /dev/null +++ b/src/ontology/md/RO/32/RO_HOM0000032.md @@ -0,0 +1,48 @@ + +## Class : in neoteny relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000032 + * *Label* = in neoteny relationship with + * *Definition* = Paedomorphosis that is produced by a retardation of somatic development. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:978-0674639416, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://en.wikipedia.org/wiki/Neoteny, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000032 ] + +## Synonyms + + * juvenilization + * neotenous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in neoteny relationship with](../../RO/32/RO_HOM0000032.md) + * [in neoteny relationship with](../../RO/32/RO_HOM0000032.md) SubPropertyOf [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paedomorphosis that is produced by a retardation of somatic development. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = juvenilization + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = neotenous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in neoteny relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000032 + +## Usage + + * - + * SymmetricObjectProperty [in neoteny relationship with](../../RO/32/RO_HOM0000032.md) + * [in neoteny relationship with](../../RO/32/RO_HOM0000032.md) SubPropertyOf [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## External Comments + diff --git a/src/ontology/md/RO/33/RO_0002233.md b/src/ontology/md/RO/33/RO_0002233.md new file mode 100644 index 00000000..abab9f52 --- /dev/null +++ b/src/ontology/md/RO/33/RO_0002233.md @@ -0,0 +1,51 @@ + +## Class : has input + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002233 + * *Label* = has input + * *Definition* = p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [has input](../../RO/33/RO_0002233.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [input of](../../RO/52/RO_0002352.md) InverseOf [has input](../../RO/33/RO_0002233.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = consumes + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has input + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has direct input](../../RO/00/RO_0002400.md) SubPropertyOf [has input](../../RO/33/RO_0002233.md) + * [has input](../../RO/33/RO_0002233.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [input of](../../RO/52/RO_0002352.md) InverseOf [has input](../../RO/33/RO_0002233.md) + * [results in breakdown of](../../RO/86/RO_0002586.md) SubPropertyOf [has input](../../RO/33/RO_0002233.md) + * [results in remodeling of](../../RO/91/RO_0002591.md) SubPropertyOf [has input](../../RO/33/RO_0002233.md) + +## External Comments + diff --git a/src/ontology/md/RO/33/RO_0002333.md b/src/ontology/md/RO/33/RO_0002333.md new file mode 100644 index 00000000..583772dd --- /dev/null +++ b/src/ontology/md/RO/33/RO_0002333.md @@ -0,0 +1,49 @@ + +## Class : enabled by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002333 + * *Label* = enabled by + * *Definition* = inverse of enables + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * InverseOf() + * [functionally related to](../../RO/28/RO_0002328.md) + +## SubProperties + + +## Other Logical Axioms + + * [enabled by](../../RO/33/RO_0002333.md) InverseOf [enables](../../RO/27/RO_0002327.md) + * [enabled by](../../RO/33/RO_0002333.md) SubPropertyOf InverseOf() + * [enabled by](../../RO/33/RO_0002333.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of enables + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = enabled by + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [enabled by](../../RO/33/RO_0002333.md) InverseOf [enables](../../RO/27/RO_0002327.md) + * [enabled by](../../RO/33/RO_0002333.md) SubPropertyOf InverseOf() + * [enabled by](../../RO/33/RO_0002333.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## External Comments + diff --git a/src/ontology/md/RO/33/RO_0002433.md b/src/ontology/md/RO/33/RO_0002433.md new file mode 100644 index 00000000..d69bf37f --- /dev/null +++ b/src/ontology/md/RO/33/RO_0002433.md @@ -0,0 +1,40 @@ + +## Class : contributes to morphology of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002433 + * *Label* = contributes to morphology of + * *Definition* = p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [contributes to morphology of](../../RO/33/RO_0002433.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = contributes to morphology of + +## Usage + + * - + * [contributes to morphology of](../../RO/33/RO_0002433.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## External Comments + diff --git a/src/ontology/md/RO/33/RO_0002533.md b/src/ontology/md/RO/33/RO_0002533.md new file mode 100644 index 00000000..f9a00e3f --- /dev/null +++ b/src/ontology/md/RO/33/RO_0002533.md @@ -0,0 +1,41 @@ + +## Class : sequence atomic unit + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002533 + * *Label* = sequence atomic unit + * *Definition* = Any individual unit of a collection of like units arranged in a linear order + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [sequentially ordered entity](../../RO/32/RO_0002532.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Any individual unit of a collection of like units arranged in a linear order + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = sequence atomic unit + +## Usage + + * - + * [sequence atomic unit](../../RO/33/RO_0002533.md) SubClassOf [sequentially ordered entity](../../RO/32/RO_0002532.md) + * [sequentially ordered entity](../../RO/32/RO_0002532.md) SubClassOf [has subsequence](../../RO/24/RO_0002524.md) some [sequence atomic unit](../../RO/33/RO_0002533.md) + +## External Comments + diff --git a/src/ontology/md/RO/33/RO_HOM0000033.md b/src/ontology/md/RO/33/RO_HOM0000033.md new file mode 100644 index 00000000..0743efea --- /dev/null +++ b/src/ontology/md/RO/33/RO_HOM0000033.md @@ -0,0 +1,46 @@ + +## Class : in mimicry relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000033 + * *Label* = in mimicry relationship with + * *Definition* = Convergence that results from co-evolution usually involving an evolutionary arms race. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000033, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http:://en.wikipedia.org/wiki/Mimicry ] + +## Synonyms + + * mimicrous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in convergence relationship with](../../RO/04/RO_HOM0000004.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in mimicry relationship with](../../RO/33/RO_HOM0000033.md) + * [in mimicry relationship with](../../RO/33/RO_HOM0000033.md) SubPropertyOf [in convergence relationship with](../../RO/04/RO_HOM0000004.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Convergence that results from co-evolution usually involving an evolutionary arms race. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = mimicrous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in mimicry relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000033 + +## Usage + + * - + * SymmetricObjectProperty [in mimicry relationship with](../../RO/33/RO_HOM0000033.md) + * [in mimicry relationship with](../../RO/33/RO_HOM0000033.md) SubPropertyOf [in convergence relationship with](../../RO/04/RO_HOM0000004.md) + +## External Comments + diff --git a/src/ontology/md/RO/34/RO_0002134.md b/src/ontology/md/RO/34/RO_0002134.md new file mode 100644 index 00000000..03b5e61a --- /dev/null +++ b/src/ontology/md/RO/34/RO_0002134.md @@ -0,0 +1,53 @@ + +## Class : innervates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002134 + * *Label* = innervates + * *Definition* = Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. +T innervates some R +Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## SubProperties + + +## Other Logical Axioms + + * [innervated_by](../../RO/05/RO_0002005.md) InverseOf [innervates](../../RO/34/RO_0002134.md) + * [innervates](../../RO/34/RO_0002134.md) Domain [neuron projection bundle](../../CARO/01/CARO_0001001.md) + * [innervates](../../RO/34/RO_0002134.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. +T innervates some R +Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = some ( that ( some ( that some Y?))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[citesAsAuthority](../../ty/citesAsAuthority.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = innervates + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [innervated_by](../../RO/05/RO_0002005.md) InverseOf [innervates](../../RO/34/RO_0002134.md) + * [innervates](../../RO/34/RO_0002134.md) Domain [neuron projection bundle](../../CARO/01/CARO_0001001.md) + * [innervates](../../RO/34/RO_0002134.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## External Comments + diff --git a/src/ontology/md/RO/34/RO_0002234.md b/src/ontology/md/RO/34/RO_0002234.md new file mode 100644 index 00000000..d03785b8 --- /dev/null +++ b/src/ontology/md/RO/34/RO_0002234.md @@ -0,0 +1,50 @@ + +## Class : has output + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002234 + * *Label* = has output + * *Definition* = p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [has output](../../RO/34/RO_0002234.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [output of](../../RO/53/RO_0002353.md) InverseOf [has output](../../RO/34/RO_0002234.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = produces + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has output + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [has output](../../RO/34/RO_0002234.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [obsolete has indirect output](../../RO/03/RO_0002403.md) SubPropertyOf [has output](../../RO/34/RO_0002234.md) + * [output of](../../RO/53/RO_0002353.md) InverseOf [has output](../../RO/34/RO_0002234.md) + * [results in formation of](../../RO/97/RO_0002297.md) SubPropertyOf [has output](../../RO/34/RO_0002234.md) + +## External Comments + diff --git a/src/ontology/md/RO/34/RO_0002334.md b/src/ontology/md/RO/34/RO_0002334.md new file mode 100644 index 00000000..f2af1309 --- /dev/null +++ b/src/ontology/md/RO/34/RO_0002334.md @@ -0,0 +1,49 @@ + +## Class : regulated by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002334 + * *Label* = regulated by + * *Definition* = inverse of regulates + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causally downstream of or within](../../RO/27/RO_0002427.md) + +## SubProperties + + +## Other Logical Axioms + + * [regulated by](../../RO/34/RO_0002334.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulated by](../../RO/34/RO_0002334.md) InverseOf [regulates](../../RO/11/RO_0002211.md) + * [regulated by](../../RO/34/RO_0002334.md) Range [process](../../BFO/15/BFO_0000015.md) + * [regulated by](../../RO/34/RO_0002334.md) SubPropertyOf [causally downstream of or within](../../RO/27/RO_0002427.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of regulates + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = regulated by (processual) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = regulated by + +## Usage + + * - + * [negatively regulated by](../../RO/35/RO_0002335.md) SubPropertyOf [regulated by](../../RO/34/RO_0002334.md) + * [positively regulated by](../../RO/36/RO_0002336.md) SubPropertyOf [regulated by](../../RO/34/RO_0002334.md) + * [regulated by](../../RO/34/RO_0002334.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [regulated by](../../RO/34/RO_0002334.md) InverseOf [regulates](../../RO/11/RO_0002211.md) + * [regulated by](../../RO/34/RO_0002334.md) Range [process](../../BFO/15/BFO_0000015.md) + * [regulated by](../../RO/34/RO_0002334.md) SubPropertyOf [causally downstream of or within](../../RO/27/RO_0002427.md) + +## External Comments + diff --git a/src/ontology/md/RO/34/RO_0002434.md b/src/ontology/md/RO/34/RO_0002434.md new file mode 100644 index 00000000..3cb70f76 --- /dev/null +++ b/src/ontology/md/RO/34/RO_0002434.md @@ -0,0 +1,55 @@ + +## Class : interacts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002434 + * *Label* = interacts with + * *Definition* = A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + +## Synonyms + + * in pairwise interaction with + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [interacts with](../../RO/34/RO_0002434.md) + * [interacts with](../../RO/34/RO_0002434.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [interacts with](../../RO/34/RO_0002434.md) Range [material entity](../../BFO/40/BFO_0000040.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Considering relabeling as 'pairwise interacts with' + * *[editor note](../../IAO/16/IAO_0000116.md)* = This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = 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. + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = in pairwise interaction with + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = interacts with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/MI_0914 + * *[page](../../ge/page.md)* = https://code.google.com/p/obo-relations/wiki/InteractionRelations + +## Usage + + * - + * SymmetricObjectProperty [interacts with](../../RO/34/RO_0002434.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) SubPropertyOf [interacts with](../../RO/34/RO_0002434.md) + * [genetically interacts with](../../RO/35/RO_0002435.md) SubPropertyOf [interacts with](../../RO/34/RO_0002434.md) + * [interacts with](../../RO/34/RO_0002434.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [interacts with](../../RO/34/RO_0002434.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [molecularly interacts with](../../RO/36/RO_0002436.md) SubPropertyOf [interacts with](../../RO/34/RO_0002434.md) + +## External Comments + diff --git a/src/ontology/md/RO/34/RO_0002534.md b/src/ontology/md/RO/34/RO_0002534.md new file mode 100644 index 00000000..09e3ac46 --- /dev/null +++ b/src/ontology/md/RO/34/RO_0002534.md @@ -0,0 +1,40 @@ + +## Class : sequence bearer + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002534 + * *Label* = sequence bearer + * *Definition* = Any entity that can be divided into parts such that each part is an atomical unit of a sequence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [sequentially ordered entity](../../RO/32/RO_0002532.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Any entity that can be divided into parts such that each part is an atomical unit of a sequence + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = sequence bearer + +## Usage + + * - + * [sequence bearer](../../RO/34/RO_0002534.md) SubClassOf [sequentially ordered entity](../../RO/32/RO_0002532.md) + +## External Comments + diff --git a/src/ontology/md/RO/34/RO_HOM0000034.md b/src/ontology/md/RO/34/RO_HOM0000034.md new file mode 100644 index 00000000..8b1550ce --- /dev/null +++ b/src/ontology/md/RO/34/RO_HOM0000034.md @@ -0,0 +1,59 @@ + +## Class : in 1 to many orthology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000034 + * *Label* = in 1 to many orthology relationship with + * *Definition* = Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1038/415741a, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000034, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ensembl.org/info/docs/compara/homology_method.html ] + +## Synonyms + + * 1 to many orthologous to + * 1:many orthology + * one-to-many orthology + * co-orthology + * many to 1 orthology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in 1 to many homology relationship with](../../RO/37/RO_HOM0000037.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + * [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) SubPropertyOf [in 1 to many homology relationship with](../../RO/37/RO_HOM0000037.md) + * [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = 1 to many orthologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = 1:many orthology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = one-to-many orthology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = co-orthology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = many to 1 orthology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in 1 to many orthology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000034 + +## Usage + + * - + * SymmetricObjectProperty [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + * [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) SubPropertyOf [in 1 to many homology relationship with](../../RO/37/RO_HOM0000037.md) + * [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in pro-orthology relationship with](../../RO/25/RO_HOM0000025.md) SubPropertyOf [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + * [in semi-orthology relationship with](../../RO/26/RO_HOM0000026.md) SubPropertyOf [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) + +## External Comments + diff --git a/src/ontology/md/RO/35/RO_0002335.md b/src/ontology/md/RO/35/RO_0002335.md new file mode 100644 index 00000000..5a4b7f24 --- /dev/null +++ b/src/ontology/md/RO/35/RO_0002335.md @@ -0,0 +1,40 @@ + +## Class : negatively regulated by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002335 + * *Label* = negatively regulated by + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [regulated by](../../RO/34/RO_0002334.md) + +## SubProperties + + +## Other Logical Axioms + + * [negatively regulated by](../../RO/35/RO_0002335.md) InverseOf [negatively regulates](../../RO/12/RO_0002212.md) + * [negatively regulated by](../../RO/35/RO_0002335.md) SubPropertyOf [regulated by](../../RO/34/RO_0002334.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = negatively regulated by + +## Usage + + * - + * [negatively regulated by](../../RO/35/RO_0002335.md) InverseOf [negatively regulates](../../RO/12/RO_0002212.md) + * [negatively regulated by](../../RO/35/RO_0002335.md) SubPropertyOf [regulated by](../../RO/34/RO_0002334.md) + +## External Comments + diff --git a/src/ontology/md/RO/35/RO_0002435.md b/src/ontology/md/RO/35/RO_0002435.md new file mode 100644 index 00000000..59779e7a --- /dev/null +++ b/src/ontology/md/RO/35/RO_0002435.md @@ -0,0 +1,43 @@ + +## Class : genetically interacts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002435 + * *Label* = genetically interacts with + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [interacts with](../../RO/34/RO_0002434.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [genetically interacts with](../../RO/35/RO_0002435.md) + * [genetically interacts with](../../RO/35/RO_0002435.md) SubPropertyOf [interacts with](../../RO/34/RO_0002434.md) + +## Other Annotations + + * *[editor note](../../IAO/16/IAO_0000116.md)* = An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = genetically interacts with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/ECO_0000316 + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/MI_0208 + +## Usage + + * - + * SymmetricObjectProperty [genetically interacts with](../../RO/35/RO_0002435.md) + * [genetically interacts with](../../RO/35/RO_0002435.md) SubPropertyOf [interacts with](../../RO/34/RO_0002434.md) + +## External Comments + diff --git a/src/ontology/md/RO/35/RO_0002535.md b/src/ontology/md/RO/35/RO_0002535.md new file mode 100644 index 00000000..85f7ecdd --- /dev/null +++ b/src/ontology/md/RO/35/RO_0002535.md @@ -0,0 +1,45 @@ + +## Class : temporal logical macro assertion on a class + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002535 + * *Label* = temporal logical macro assertion on a class + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on a class](../../RO/20/RO_0002420.md) + +## SubProperties + + * [has end time value](../../RO/38/RO_0002538.md) + * [has start time value](../../RO/37/RO_0002537.md) + * [has developmental stage marker](../../RO/46/RO_0002546.md) + * [month of gestation](../../RO/45/RO_0002545.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[curator note](../../IAO/32/IAO_0000232.md)* = This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = temporal logical macro assertion on a class + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/36/RO_0002336.md b/src/ontology/md/RO/36/RO_0002336.md new file mode 100644 index 00000000..8c7ae19c --- /dev/null +++ b/src/ontology/md/RO/36/RO_0002336.md @@ -0,0 +1,40 @@ + +## Class : positively regulated by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002336 + * *Label* = positively regulated by + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [regulated by](../../RO/34/RO_0002334.md) + +## SubProperties + + +## Other Logical Axioms + + * [positively regulated by](../../RO/36/RO_0002336.md) InverseOf [positively regulates](../../RO/13/RO_0002213.md) + * [positively regulated by](../../RO/36/RO_0002336.md) SubPropertyOf [regulated by](../../RO/34/RO_0002334.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = positively regulated by + +## Usage + + * - + * [positively regulated by](../../RO/36/RO_0002336.md) InverseOf [positively regulates](../../RO/13/RO_0002213.md) + * [positively regulated by](../../RO/36/RO_0002336.md) SubPropertyOf [regulated by](../../RO/34/RO_0002334.md) + +## External Comments + diff --git a/src/ontology/md/RO/36/RO_0002436.md b/src/ontology/md/RO/36/RO_0002436.md new file mode 100644 index 00000000..9767caab --- /dev/null +++ b/src/ontology/md/RO/36/RO_0002436.md @@ -0,0 +1,49 @@ + +## Class : molecularly interacts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002436 + * *Label* = molecularly interacts with + * *Definition* = An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [interacts with](../../RO/34/RO_0002434.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [molecularly interacts with](../../RO/36/RO_0002436.md) + * [molecularly interacts with](../../RO/36/RO_0002436.md) SubPropertyOf [interacts with](../../RO/34/RO_0002434.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = binds + * *[alternative term](../../IAO/18/IAO_0000118.md)* = molecularly binds with + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = molecularly interacts with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/ECO_0000353 + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/MI_0915 + +## Usage + + * - + * SymmetricObjectProperty [molecularly interacts with](../../RO/36/RO_0002436.md) + * [molecularly controls](../../RO/48/RO_0002448.md) SubPropertyOf [molecularly interacts with](../../RO/36/RO_0002436.md) + * [molecularly interacts with](../../RO/36/RO_0002436.md) SubPropertyOf [interacts with](../../RO/34/RO_0002434.md) + * [phosphorylates](../../RO/47/RO_0002447.md) SubPropertyOf [molecularly interacts with](../../RO/36/RO_0002436.md) + * [ubiquitinates](../../RO/80/RO_0002480.md) SubPropertyOf [molecularly interacts with](../../RO/36/RO_0002436.md) + +## External Comments + diff --git a/src/ontology/md/RO/36/RO_0002536.md b/src/ontology/md/RO/36/RO_0002536.md new file mode 100644 index 00000000..a0b70d0b --- /dev/null +++ b/src/ontology/md/RO/36/RO_0002536.md @@ -0,0 +1,36 @@ + +## Class : measurement property has unit + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002536 + * *Label* = measurement property has unit + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on an annotation property](../../RO/23/RO_0002423.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = measurement property has unit + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/36/RO_HOM0000036.md b/src/ontology/md/RO/36/RO_HOM0000036.md new file mode 100644 index 00000000..43d82697 --- /dev/null +++ b/src/ontology/md/RO/36/RO_HOM0000036.md @@ -0,0 +1,51 @@ + +## Class : in many to many homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000036 + * *Label* = in many to many homology relationship with + * *Definition* = Historical homology that involves two members of a larger set of homologs. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1093/molbev/msp002, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000036 ] + +## Synonyms + + * many to many homologous to + * many-to-many homology + * many:many homology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in many to many homology relationship with](../../RO/36/RO_HOM0000036.md) + * [in many to many homology relationship with](../../RO/36/RO_HOM0000036.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves two members of a larger set of homologs. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = many to many homologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = many-to-many homology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = many:many homology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in many to many homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000036 + +## Usage + + * - + * SymmetricObjectProperty [in many to many homology relationship with](../../RO/36/RO_HOM0000036.md) + * [in many to many homology relationship with](../../RO/36/RO_HOM0000036.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in many to many orthology relationship with](../../RO/48/RO_HOM0000048.md) SubPropertyOf [in many to many homology relationship with](../../RO/36/RO_HOM0000036.md) + +## External Comments + diff --git a/src/ontology/md/RO/37/RO_0002337.md b/src/ontology/md/RO/37/RO_0002337.md new file mode 100644 index 00000000..eb621480 --- /dev/null +++ b/src/ontology/md/RO/37/RO_0002337.md @@ -0,0 +1,44 @@ + +## Class : related via localization to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002337 + * *Label* = related via localization to + * *Definition* = A relationship that holds via some process of localization + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [related via localization to](../../RO/37/RO_0002337.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [related via localization to](../../RO/37/RO_0002337.md) Range [continuant](../../BFO/02/BFO_0000002.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that holds via some process of localization + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = related via localization to + +## Usage + + * - + * [related via localization to](../../RO/37/RO_0002337.md) Domain [process](../../BFO/15/BFO_0000015.md) + * [related via localization to](../../RO/37/RO_0002337.md) Range [continuant](../../BFO/02/BFO_0000002.md) + * [results in transport along](../../RO/41/RO_0002341.md) SubPropertyOf [related via localization to](../../RO/37/RO_0002337.md) + * [results in transport to from or in](../../RO/44/RO_0002344.md) SubPropertyOf [related via localization to](../../RO/37/RO_0002337.md) + * [transports or maintains localization of](../../RO/13/RO_0002313.md) SubPropertyOf [related via localization to](../../RO/37/RO_0002337.md) + +## External Comments + diff --git a/src/ontology/md/RO/37/RO_0002437.md b/src/ontology/md/RO/37/RO_0002437.md new file mode 100644 index 00000000..2d0d1dc2 --- /dev/null +++ b/src/ontology/md/RO/37/RO_0002437.md @@ -0,0 +1,56 @@ + +## Class : biotically interacts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002437 + * *Label* = biotically interacts with + * *Definition* = An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [ecologically related to](../../RO/21/RO_0002321.md) + * [interacts with](../../RO/34/RO_0002434.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [biotically interacts with](../../RO/37/RO_0002437.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) SubPropertyOf [interacts with](../../RO/34/RO_0002434.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = interacts with on organism level + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = biotically interacts with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://eol.org/schema/terms/interactsWith + +## Usage + + * - + * SymmetricObjectProperty [biotically interacts with](../../RO/37/RO_0002437.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + * [biotically interacts with](../../RO/37/RO_0002437.md) SubPropertyOf [interacts with](../../RO/34/RO_0002434.md) + * [participates in a abiotic-biotic interaction with](../../RO/46/RO_0002446.md) SubPropertyOf [biotically interacts with](../../RO/37/RO_0002437.md) + * [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) SubPropertyOf [biotically interacts with](../../RO/37/RO_0002437.md) + +## External Comments + diff --git a/src/ontology/md/RO/37/RO_0002537.md b/src/ontology/md/RO/37/RO_0002537.md new file mode 100644 index 00000000..efae2849 --- /dev/null +++ b/src/ontology/md/RO/37/RO_0002537.md @@ -0,0 +1,46 @@ + +## Class : has start time value + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002537 + * *Label* = has start time value + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [temporal logical macro assertion on a class](../../RO/35/RO_0002535.md) + +## SubProperties + + * [start, days post fertilization](../../RO/39/RO_0002539.md) + * [start, weeks post birth](../../RO/49/RO_0002549.md) + * [start, months post birth](../../RO/43/RO_0002543.md) + * [start, days post coitum](../../RO/47/RO_0002547.md) + * [start, years post birth](../../RO/41/RO_0002541.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has start time value + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/37/RO_HOM0000037.md b/src/ontology/md/RO/37/RO_HOM0000037.md new file mode 100644 index 00000000..91bc6913 --- /dev/null +++ b/src/ontology/md/RO/37/RO_HOM0000037.md @@ -0,0 +1,51 @@ + +## Class : in 1 to many homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000037 + * *Label* = in 1 to many homology relationship with + * *Definition* = Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = BGEE:curator, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000037 ] + +## Synonyms + + * 1 to many homologous to + * one-to-many homology + * 1:many homology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in 1 to many homology relationship with](../../RO/37/RO_HOM0000037.md) + * [in 1 to many homology relationship with](../../RO/37/RO_HOM0000037.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = 1 to many homologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = one-to-many homology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = 1:many homology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in 1 to many homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000037 + +## Usage + + * - + * SymmetricObjectProperty [in 1 to many homology relationship with](../../RO/37/RO_HOM0000037.md) + * [in 1 to many homology relationship with](../../RO/37/RO_HOM0000037.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in 1 to many orthology relationship with](../../RO/34/RO_HOM0000034.md) SubPropertyOf [in 1 to many homology relationship with](../../RO/37/RO_HOM0000037.md) + +## External Comments + diff --git a/src/ontology/md/RO/38/RO_0002338.md b/src/ontology/md/RO/38/RO_0002338.md new file mode 100644 index 00000000..c4e80a34 --- /dev/null +++ b/src/ontology/md/RO/38/RO_0002338.md @@ -0,0 +1,41 @@ + +## Class : has target start location + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002338 + * *Label* = has target start location + * *Definition* = This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in transport to from or in](../../RO/44/RO_0002344.md) + +## SubProperties + + +## Other Logical Axioms + + * [has target start location](../../RO/38/RO_0002338.md) SubPropertyOf [results in transport to from or in](../../RO/44/RO_0002344.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has target start location + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has target start location](../../RO/38/RO_0002338.md) SubPropertyOf [results in transport to from or in](../../RO/44/RO_0002344.md) + +## External Comments + diff --git a/src/ontology/md/RO/38/RO_0002438.md b/src/ontology/md/RO/38/RO_0002438.md new file mode 100644 index 00000000..ccd1ee51 --- /dev/null +++ b/src/ontology/md/RO/38/RO_0002438.md @@ -0,0 +1,49 @@ + +## Class : trophically interacts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002438 + * *Label* = trophically interacts with + * *Definition* = An interaction relationship in which the partners are related via a feeding relationship. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## SubProperties + + +## Other Logical Axioms + + * [trophically interacts with](../../RO/38/RO_0002438.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An interaction relationship in which the partners are related via a feeding relationship. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = trophically interacts with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 + +## Usage + + * - + * [acquires nutrients from](../../RO/57/RO_0002457.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + * [eats](../../RO/70/RO_0002470.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + * [is eaten by](../../RO/71/RO_0002471.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + * [preyed upon by](../../RO/58/RO_0002458.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + * [preys on](../../RO/39/RO_0002439.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + * [provides nutrients for](../../RO/69/RO_0002469.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + * [trophically interacts with](../../RO/38/RO_0002438.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## External Comments + diff --git a/src/ontology/md/RO/38/RO_0002538.md b/src/ontology/md/RO/38/RO_0002538.md new file mode 100644 index 00000000..d1cf909d --- /dev/null +++ b/src/ontology/md/RO/38/RO_0002538.md @@ -0,0 +1,46 @@ + +## Class : has end time value + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002538 + * *Label* = has end time value + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [temporal logical macro assertion on a class](../../RO/35/RO_0002535.md) + +## SubProperties + + * [end, weeks post birth](../../RO/50/RO_0002550.md) + * [end, days post coitum](../../RO/48/RO_0002548.md) + * [end, years post birth](../../RO/42/RO_0002542.md) + * [end, months post birth](../../RO/44/RO_0002544.md) + * [end, days post fertilization](../../RO/40/RO_0002540.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has end time value + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/39/RO_0002339.md b/src/ontology/md/RO/39/RO_0002339.md new file mode 100644 index 00000000..3f045f11 --- /dev/null +++ b/src/ontology/md/RO/39/RO_0002339.md @@ -0,0 +1,41 @@ + +## Class : has target end location + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002339 + * *Label* = has target end location + * *Definition* = This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in transport to from or in](../../RO/44/RO_0002344.md) + +## SubProperties + + +## Other Logical Axioms + + * [has target end location](../../RO/39/RO_0002339.md) SubPropertyOf [results in transport to from or in](../../RO/44/RO_0002344.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has target end location + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has target end location](../../RO/39/RO_0002339.md) SubPropertyOf [results in transport to from or in](../../RO/44/RO_0002344.md) + +## External Comments + diff --git a/src/ontology/md/RO/39/RO_0002439.md b/src/ontology/md/RO/39/RO_0002439.md new file mode 100644 index 00000000..92b02d0f --- /dev/null +++ b/src/ontology/md/RO/39/RO_0002439.md @@ -0,0 +1,48 @@ + +## Class : preys on + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002439 + * *Label* = preys on + * *Definition* = An interaction relationship involving a predation process, where the subject consumes all or part of the target + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [trophically interacts with](../../RO/38/RO_0002438.md) + +## SubProperties + + +## Other Logical Axioms + + * [preyed upon by](../../RO/58/RO_0002458.md) InverseOf [preys on](../../RO/39/RO_0002439.md) + * [preys on](../../RO/39/RO_0002439.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Baleen whale preys on krill + * *[definition](../../IAO/15/IAO_0000115.md)* = An interaction relationship involving a predation process, where the subject consumes all or part of the target + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is subject of predation interaction with + * *[alternative term](../../IAO/18/IAO_0000118.md)* = preys upon + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = preys on + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://eol.org/schema/terms/preysUpon + +## Usage + + * - + * [preyed upon by](../../RO/58/RO_0002458.md) InverseOf [preys on](../../RO/39/RO_0002439.md) + * [preys on](../../RO/39/RO_0002439.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## External Comments + diff --git a/src/ontology/md/RO/39/RO_0002539.md b/src/ontology/md/RO/39/RO_0002539.md new file mode 100644 index 00000000..9980ae86 --- /dev/null +++ b/src/ontology/md/RO/39/RO_0002539.md @@ -0,0 +1,38 @@ + +## Class : start, days post fertilization + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002539 + * *Label* = start, days post fertilization + * *Definition* = Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has start time value](../../RO/37/RO_0002537.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = start, days post fertilization + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/40/RO_0002340.md b/src/ontology/md/RO/40/RO_0002340.md new file mode 100644 index 00000000..8a506e53 --- /dev/null +++ b/src/ontology/md/RO/40/RO_0002340.md @@ -0,0 +1,41 @@ + +## Class : imports + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002340 + * *Label* = imports + * *Definition* = Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [transports or maintains localization of](../../RO/13/RO_0002313.md) + +## SubProperties + + +## Other Logical Axioms + + * [imports](../../RO/40/RO_0002340.md) SubPropertyOf [transports or maintains localization of](../../RO/13/RO_0002313.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = imports + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [imports](../../RO/40/RO_0002340.md) SubPropertyOf [transports or maintains localization of](../../RO/13/RO_0002313.md) + +## External Comments + diff --git a/src/ontology/md/RO/40/RO_0002440.md b/src/ontology/md/RO/40/RO_0002440.md new file mode 100644 index 00000000..3669def7 --- /dev/null +++ b/src/ontology/md/RO/40/RO_0002440.md @@ -0,0 +1,53 @@ + +## Class : symbiotically interacts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002440 + * *Label* = symbiotically interacts with + * *Definition* = A biotic interaction in which the two organisms live together in more or less intimate association. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [symbiotically interacts with](../../RO/40/RO_0002440.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A biotic interaction in which the two organisms live together in more or less intimate association. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/19278549 + * *[curator note](../../IAO/32/IAO_0000232.md)* = We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism + * *[is symmetric relational form of process class](../../RO/61/RO_0002561.md)* = http://purl.obolibrary.org/obo/GO_0044403 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = symbiotically interacts with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * SymmetricObjectProperty [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [commensually interacts with](../../RO/41/RO_0002441.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [has host](../../RO/54/RO_0002454.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [host of](../../RO/53/RO_0002453.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [mutualistically interacts with](../../RO/42/RO_0002442.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [symbiotically interacts with](../../RO/40/RO_0002440.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## External Comments + diff --git a/src/ontology/md/RO/40/RO_0002540.md b/src/ontology/md/RO/40/RO_0002540.md new file mode 100644 index 00000000..39421117 --- /dev/null +++ b/src/ontology/md/RO/40/RO_0002540.md @@ -0,0 +1,38 @@ + +## Class : end, days post fertilization + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002540 + * *Label* = end, days post fertilization + * *Definition* = Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has end time value](../../RO/38/RO_0002538.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = end, days post fertilization + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/41/RO_0002341.md b/src/ontology/md/RO/41/RO_0002341.md new file mode 100644 index 00000000..719b549e --- /dev/null +++ b/src/ontology/md/RO/41/RO_0002341.md @@ -0,0 +1,40 @@ + +## Class : results in transport along + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002341 + * *Label* = results in transport along + * *Definition* = Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [related via localization to](../../RO/37/RO_0002337.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in transport along](../../RO/41/RO_0002341.md) SubPropertyOf [related via localization to](../../RO/37/RO_0002337.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in transport along + +## Usage + + * - + * [results in transport along](../../RO/41/RO_0002341.md) SubPropertyOf [related via localization to](../../RO/37/RO_0002337.md) + +## External Comments + diff --git a/src/ontology/md/RO/41/RO_0002441.md b/src/ontology/md/RO/41/RO_0002441.md new file mode 100644 index 00000000..47ab9bc4 --- /dev/null +++ b/src/ontology/md/RO/41/RO_0002441.md @@ -0,0 +1,45 @@ + +## Class : commensually interacts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002441 + * *Label* = commensually interacts with + * *Definition* = An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## SubProperties + + +## Other Logical Axioms + + * [commensually interacts with](../../RO/41/RO_0002441.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/19278549 + * *[is symmetric relational form of process class](../../RO/61/RO_0002561.md)* = http://purl.obolibrary.org/obo/GO_0085031 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = commensually interacts with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [commensually interacts with](../../RO/41/RO_0002441.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## External Comments + diff --git a/src/ontology/md/RO/41/RO_0002541.md b/src/ontology/md/RO/41/RO_0002541.md new file mode 100644 index 00000000..26521a80 --- /dev/null +++ b/src/ontology/md/RO/41/RO_0002541.md @@ -0,0 +1,38 @@ + +## Class : start, years post birth + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002541 + * *Label* = start, years post birth + * *Definition* = Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has start time value](../../RO/37/RO_0002537.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = start, years post birth + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/42/RO_0002342.md b/src/ontology/md/RO/42/RO_0002342.md new file mode 100644 index 00000000..01d04d8d --- /dev/null +++ b/src/ontology/md/RO/42/RO_0002342.md @@ -0,0 +1,40 @@ + +## Class : results in transport across + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002342 + * *Label* = results in transport across + * *Definition* = Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in transport to from or in](../../RO/44/RO_0002344.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in transport across](../../RO/42/RO_0002342.md) SubPropertyOf [results in transport to from or in](../../RO/44/RO_0002344.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in transport across + +## Usage + + * - + * [results in transport across](../../RO/42/RO_0002342.md) SubPropertyOf [results in transport to from or in](../../RO/44/RO_0002344.md) + +## External Comments + diff --git a/src/ontology/md/RO/42/RO_0002442.md b/src/ontology/md/RO/42/RO_0002442.md new file mode 100644 index 00000000..41f16b1e --- /dev/null +++ b/src/ontology/md/RO/42/RO_0002442.md @@ -0,0 +1,47 @@ + +## Class : mutualistically interacts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002442 + * *Label* = mutualistically interacts with + * *Definition* = An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## SubProperties + + +## Other Logical Axioms + + * [mutualistically interacts with](../../RO/42/RO_0002442.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/19278549 + * *[is symmetric relational form of process class](../../RO/61/RO_0002561.md)* = http://purl.obolibrary.org/obo/GO_0085030 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = mutualistically interacts with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [mutualistically interacts with](../../RO/42/RO_0002442.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [pollinated by](../../RO/56/RO_0002456.md) SubPropertyOf [mutualistically interacts with](../../RO/42/RO_0002442.md) + * [pollinates](../../RO/55/RO_0002455.md) SubPropertyOf [mutualistically interacts with](../../RO/42/RO_0002442.md) + +## External Comments + diff --git a/src/ontology/md/RO/42/RO_0002542.md b/src/ontology/md/RO/42/RO_0002542.md new file mode 100644 index 00000000..c41499c9 --- /dev/null +++ b/src/ontology/md/RO/42/RO_0002542.md @@ -0,0 +1,38 @@ + +## Class : end, years post birth + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002542 + * *Label* = end, years post birth + * *Definition* = Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has end time value](../../RO/38/RO_0002538.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = end, years post birth + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/42/RO_HOM0000042.md b/src/ontology/md/RO/42/RO_HOM0000042.md new file mode 100644 index 00000000..3c422f22 --- /dev/null +++ b/src/ontology/md/RO/42/RO_HOM0000042.md @@ -0,0 +1,50 @@ + +## Class : in apomorphy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000042 + * *Label* = in apomorphy relationship with + * *Definition* = Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:978-0252068140, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000042 ] + +## Synonyms + + * apomorphous to + * synapomorphy + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in apomorphy relationship with](../../RO/42/RO_HOM0000042.md) + * [in apomorphy relationship with](../../RO/42/RO_HOM0000042.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = apomorphous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = synapomorphy + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in apomorphy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000042 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in apomorphy relationship with](../../RO/42/RO_HOM0000042.md) + * [in apomorphy relationship with](../../RO/42/RO_HOM0000042.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## External Comments + diff --git a/src/ontology/md/RO/43/RO_0002343.md b/src/ontology/md/RO/43/RO_0002343.md new file mode 100644 index 00000000..8cf48949 --- /dev/null +++ b/src/ontology/md/RO/43/RO_0002343.md @@ -0,0 +1,42 @@ + +## Class : results in growth of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002343 + * *Label* = results in growth of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in growth of](../../RO/43/RO_0002343.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in growth of](../../RO/43/RO_0002343.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'pollen tube growth' results_in growth_of some 'pollen tube' + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in growth of + +## Usage + + * - + * [results in growth of](../../RO/43/RO_0002343.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in growth of](../../RO/43/RO_0002343.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/43/RO_0002443.md b/src/ontology/md/RO/43/RO_0002443.md new file mode 100644 index 00000000..38fbd2a2 --- /dev/null +++ b/src/ontology/md/RO/43/RO_0002443.md @@ -0,0 +1,48 @@ + +## Class : interacts with via parasite-host interaction + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002443 + * *Label* = interacts with via parasite-host interaction + * *Definition* = An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## SubProperties + + +## Other Logical Axioms + + * [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/19278549 + * *[curator note](../../IAO/32/IAO_0000232.md)* = This relation groups a pair of inverse relations, parasite of and parasitized by + * *[is symmetric relational form of process class](../../RO/61/RO_0002561.md)* = http://purl.obolibrary.org/obo/GO_0072519 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = interacts with via parasite-host interaction + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [parasite of](../../RO/44/RO_0002444.md) SubPropertyOf [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) + * [parasitized by](../../RO/45/RO_0002445.md) SubPropertyOf [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) + +## External Comments + diff --git a/src/ontology/md/RO/43/RO_0002543.md b/src/ontology/md/RO/43/RO_0002543.md new file mode 100644 index 00000000..7224c5da --- /dev/null +++ b/src/ontology/md/RO/43/RO_0002543.md @@ -0,0 +1,38 @@ + +## Class : start, months post birth + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002543 + * *Label* = start, months post birth + * *Definition* = Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has start time value](../../RO/37/RO_0002537.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = start, months post birth + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/43/RO_HOM0000043.md b/src/ontology/md/RO/43/RO_HOM0000043.md new file mode 100644 index 00000000..1c8110fd --- /dev/null +++ b/src/ontology/md/RO/43/RO_HOM0000043.md @@ -0,0 +1,52 @@ + +## Class : in plesiomorphy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000043 + * *Label* = in plesiomorphy relationship with + * *Definition* = Historical homology that is based on distant shared ancestry. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:978-0252068140, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000043 ] + * *Comment* = This term is usually contrasted to apomorphy. + +## Synonyms + + * plesiomorphous to + * symplesiomorphy + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in plesiomorphy relationship with](../../RO/43/RO_HOM0000043.md) + * [in plesiomorphy relationship with](../../RO/43/RO_HOM0000043.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that is based on distant shared ancestry. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = plesiomorphous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = symplesiomorphy + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = This term is usually contrasted to apomorphy. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in plesiomorphy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000043 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in plesiomorphy relationship with](../../RO/43/RO_HOM0000043.md) + * [in plesiomorphy relationship with](../../RO/43/RO_HOM0000043.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## External Comments + diff --git a/src/ontology/md/RO/44/RO_0002344.md b/src/ontology/md/RO/44/RO_0002344.md new file mode 100644 index 00000000..6c887ca9 --- /dev/null +++ b/src/ontology/md/RO/44/RO_0002344.md @@ -0,0 +1,42 @@ + +## Class : results in transport to from or in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002344 + * *Label* = results in transport to from or in + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [related via localization to](../../RO/37/RO_0002337.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in transport to from or in](../../RO/44/RO_0002344.md) SubPropertyOf [related via localization to](../../RO/37/RO_0002337.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in transport to from or in + +## Usage + + * - + * [has target end location](../../RO/39/RO_0002339.md) SubPropertyOf [results in transport to from or in](../../RO/44/RO_0002344.md) + * [has target start location](../../RO/38/RO_0002338.md) SubPropertyOf [results in transport to from or in](../../RO/44/RO_0002344.md) + * [results in transport across](../../RO/42/RO_0002342.md) SubPropertyOf [results in transport to from or in](../../RO/44/RO_0002344.md) + * [results in transport to from or in](../../RO/44/RO_0002344.md) SubPropertyOf [related via localization to](../../RO/37/RO_0002337.md) + +## External Comments + diff --git a/src/ontology/md/RO/44/RO_0002444.md b/src/ontology/md/RO/44/RO_0002444.md new file mode 100644 index 00000000..642530ca --- /dev/null +++ b/src/ontology/md/RO/44/RO_0002444.md @@ -0,0 +1,51 @@ + +## Class : parasite of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002444 + * *Label* = parasite of + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has host](../../RO/54/RO_0002454.md) + * [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) + +## SubProperties + + +## Other Logical Axioms + + * [parasite of](../../RO/44/RO_0002444.md) SubPropertyOf [has host](../../RO/54/RO_0002454.md) + * [parasite of](../../RO/44/RO_0002444.md) SubPropertyOf [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) + * [parasitized by](../../RO/45/RO_0002445.md) InverseOf [parasite of](../../RO/44/RO_0002444.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Pediculus humanus capitis parasite of human + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = parasitizes + * *[is asymmetric relational form of process class](../../RO/60/RO_0002560.md)* = http://purl.obolibrary.org/obo/GO_0072519 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = parasite of + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://eol.org/schema/terms/parasitizes + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [parasite of](../../RO/44/RO_0002444.md) SubPropertyOf [has host](../../RO/54/RO_0002454.md) + * [parasite of](../../RO/44/RO_0002444.md) SubPropertyOf [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) + * [parasitized by](../../RO/45/RO_0002445.md) InverseOf [parasite of](../../RO/44/RO_0002444.md) + +## External Comments + diff --git a/src/ontology/md/RO/44/RO_0002544.md b/src/ontology/md/RO/44/RO_0002544.md new file mode 100644 index 00000000..6702b2d0 --- /dev/null +++ b/src/ontology/md/RO/44/RO_0002544.md @@ -0,0 +1,38 @@ + +## Class : end, months post birth + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002544 + * *Label* = end, months post birth + * *Definition* = Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has end time value](../../RO/38/RO_0002538.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = end, months post birth + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/44/RO_HOM0000044.md b/src/ontology/md/RO/44/RO_HOM0000044.md new file mode 100644 index 00000000..d4828ead --- /dev/null +++ b/src/ontology/md/RO/44/RO_HOM0000044.md @@ -0,0 +1,57 @@ + +## Class : in deep homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000044 + * *Label* = in deep homology relationship with + * *Definition* = Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814485, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1038/nature07891, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000044 ] + * *Comment* = Used for structures in distantly related taxa. + +## Synonyms + + * deep genetic homology + * deep homologous to + * generative homology + * homoiology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + * [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in deep homology relationship with](../../RO/44/RO_HOM0000044.md) + * [in deep homology relationship with](../../RO/44/RO_HOM0000044.md) SubPropertyOf [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + * [in deep homology relationship with](../../RO/44/RO_HOM0000044.md) SubPropertyOf [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = deep genetic homology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = deep homologous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = generative homology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = homoiology + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Used for structures in distantly related taxa. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in deep homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000044 + +## Usage + + * - + * SymmetricObjectProperty [in deep homology relationship with](../../RO/44/RO_HOM0000044.md) + * [in deep homology relationship with](../../RO/44/RO_HOM0000044.md) SubPropertyOf [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + * [in deep homology relationship with](../../RO/44/RO_HOM0000044.md) SubPropertyOf [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + +## External Comments + diff --git a/src/ontology/md/RO/45/RO_0002345.md b/src/ontology/md/RO/45/RO_0002345.md new file mode 100644 index 00000000..58a70f10 --- /dev/null +++ b/src/ontology/md/RO/45/RO_0002345.md @@ -0,0 +1,39 @@ + +## Class : exports + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002345 + * *Label* = exports + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [transports or maintains localization of](../../RO/13/RO_0002313.md) + +## SubProperties + + +## Other Logical Axioms + + * [exports](../../RO/45/RO_0002345.md) SubPropertyOf [transports or maintains localization of](../../RO/13/RO_0002313.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = exports + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [exports](../../RO/45/RO_0002345.md) SubPropertyOf [transports or maintains localization of](../../RO/13/RO_0002313.md) + +## External Comments + diff --git a/src/ontology/md/RO/45/RO_0002445.md b/src/ontology/md/RO/45/RO_0002445.md new file mode 100644 index 00000000..c51d73f2 --- /dev/null +++ b/src/ontology/md/RO/45/RO_0002445.md @@ -0,0 +1,49 @@ + +## Class : parasitized by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002445 + * *Label* = parasitized by + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) + * [host of](../../RO/53/RO_0002453.md) + +## SubProperties + + +## Other Logical Axioms + + * [parasitized by](../../RO/45/RO_0002445.md) InverseOf [parasite of](../../RO/44/RO_0002444.md) + * [parasitized by](../../RO/45/RO_0002445.md) SubPropertyOf [host of](../../RO/53/RO_0002453.md) + * [parasitized by](../../RO/45/RO_0002445.md) SubPropertyOf [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has parasite + * *[alternative term](../../IAO/18/IAO_0000118.md)* = parasitised by + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = parasitized by + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://eol.org/schema/terms/hasParasite + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [parasitized by](../../RO/45/RO_0002445.md) InverseOf [parasite of](../../RO/44/RO_0002444.md) + * [parasitized by](../../RO/45/RO_0002445.md) SubPropertyOf [host of](../../RO/53/RO_0002453.md) + * [parasitized by](../../RO/45/RO_0002445.md) SubPropertyOf [interacts with via parasite-host interaction](../../RO/43/RO_0002443.md) + +## External Comments + diff --git a/src/ontology/md/RO/45/RO_0002545.md b/src/ontology/md/RO/45/RO_0002545.md new file mode 100644 index 00000000..36bac810 --- /dev/null +++ b/src/ontology/md/RO/45/RO_0002545.md @@ -0,0 +1,38 @@ + +## Class : month of gestation + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002545 + * *Label* = month of gestation + * *Definition* = Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [temporal logical macro assertion on a class](../../RO/35/RO_0002535.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = month of gestation + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/45/RO_HOM0000045.md b/src/ontology/md/RO/45/RO_HOM0000045.md new file mode 100644 index 00000000..67cc0780 --- /dev/null +++ b/src/ontology/md/RO/45/RO_HOM0000045.md @@ -0,0 +1,46 @@ + +## Class : in hemiplasy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000045 + * *Label* = in hemiplasy relationship with + * *Definition* = Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1073/pnas.0807433105, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000045 ] + +## Synonyms + + * hemiplasous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in hemiplasy relationship with](../../RO/45/RO_HOM0000045.md) + * [in hemiplasy relationship with](../../RO/45/RO_HOM0000045.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = hemiplasous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in hemiplasy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000045 + +## Usage + + * - + * SymmetricObjectProperty [in hemiplasy relationship with](../../RO/45/RO_HOM0000045.md) + * [in hemiplasy relationship with](../../RO/45/RO_HOM0000045.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## External Comments + diff --git a/src/ontology/md/RO/46/RO_0002446.md b/src/ontology/md/RO/46/RO_0002446.md new file mode 100644 index 00000000..a7c8828f --- /dev/null +++ b/src/ontology/md/RO/46/RO_0002446.md @@ -0,0 +1,46 @@ + +## Class : participates in a abiotic-biotic interaction with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002446 + * *Label* = participates in a abiotic-biotic interaction with + * *Definition* = A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. + +## Synonyms + + * semibiotically interacts with + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [biotically interacts with](../../RO/37/RO_0002437.md) + +## SubProperties + + +## Other Logical Axioms + + * [participates in a abiotic-biotic interaction with](../../RO/46/RO_0002446.md) SubPropertyOf [biotically interacts with](../../RO/37/RO_0002437.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Porifiera attaches to substrate + * *[definition](../../IAO/15/IAO_0000115.md)* = A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = semibiotically interacts with + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = participates in a abiotic-biotic interaction with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 + +## Usage + + * - + * [participates in a abiotic-biotic interaction with](../../RO/46/RO_0002446.md) SubPropertyOf [biotically interacts with](../../RO/37/RO_0002437.md) + +## External Comments + diff --git a/src/ontology/md/RO/46/RO_0002546.md b/src/ontology/md/RO/46/RO_0002546.md new file mode 100644 index 00000000..82757b5e --- /dev/null +++ b/src/ontology/md/RO/46/RO_0002546.md @@ -0,0 +1,38 @@ + +## Class : has developmental stage marker + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002546 + * *Label* = has developmental stage marker + * *Definition* = A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [temporal logical macro assertion on a class](../../RO/35/RO_0002535.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has developmental stage marker + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/46/RO_HOM0000046.md b/src/ontology/md/RO/46/RO_HOM0000046.md new file mode 100644 index 00000000..df955952 --- /dev/null +++ b/src/ontology/md/RO/46/RO_HOM0000046.md @@ -0,0 +1,46 @@ + +## Class : in gametology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000046 + * *Label* = in gametology relationship with + * *Definition* = Historical homology that involves not recombining and subsequently differentiated sex chromosomes. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000046, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ncbi.nlm.nih.gov/pubmed/11110898 ] + +## Synonyms + + * gametologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in chromosomal homology relationship with](../../RO/47/RO_HOM0000047.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in gametology relationship with](../../RO/46/RO_HOM0000046.md) + * [in gametology relationship with](../../RO/46/RO_HOM0000046.md) SubPropertyOf [in chromosomal homology relationship with](../../RO/47/RO_HOM0000047.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = gametologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in gametology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000046 + +## Usage + + * - + * SymmetricObjectProperty [in gametology relationship with](../../RO/46/RO_HOM0000046.md) + * [in gametology relationship with](../../RO/46/RO_HOM0000046.md) SubPropertyOf [in chromosomal homology relationship with](../../RO/47/RO_HOM0000047.md) + +## External Comments + diff --git a/src/ontology/md/RO/47/RO_0002447.md b/src/ontology/md/RO/47/RO_0002447.md new file mode 100644 index 00000000..43b00f2c --- /dev/null +++ b/src/ontology/md/RO/47/RO_0002447.md @@ -0,0 +1,41 @@ + +## Class : phosphorylates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002447 + * *Label* = phosphorylates + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [molecularly interacts with](../../RO/36/RO_0002436.md) + +## SubProperties + + +## Other Logical Axioms + + * [phosphorylates](../../RO/47/RO_0002447.md) SubPropertyOf [molecularly interacts with](../../RO/36/RO_0002436.md) + +## Other Annotations + + * *[editor note](../../IAO/16/IAO_0000116.md)* = Axiomatization to GO to be added later + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = phosphorylates + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [phosphorylates](../../RO/47/RO_0002447.md) SubPropertyOf [molecularly interacts with](../../RO/36/RO_0002436.md) + +## External Comments + diff --git a/src/ontology/md/RO/47/RO_0002547.md b/src/ontology/md/RO/47/RO_0002547.md new file mode 100644 index 00000000..e24c6aff --- /dev/null +++ b/src/ontology/md/RO/47/RO_0002547.md @@ -0,0 +1,39 @@ + +## Class : start, days post coitum + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002547 + * *Label* = start, days post coitum + * *Definition* = Count of number of days intervening between the start of the stage and the time of coitum. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has start time value](../../RO/37/RO_0002537.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Count of number of days intervening between the start of the stage and the time of coitum. + * *[curator note](../../IAO/32/IAO_0000232.md)* = For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = start, days post coitum + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/47/RO_HOM0000047.md b/src/ontology/md/RO/47/RO_HOM0000047.md new file mode 100644 index 00000000..3ad1c267 --- /dev/null +++ b/src/ontology/md/RO/47/RO_HOM0000047.md @@ -0,0 +1,49 @@ + +## Class : in chromosomal homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000047 + * *Label* = in chromosomal homology relationship with + * *Definition* = Historical homology that involves the chromosomes able to pair (synapse) during meiosis. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:0195307615, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000047 ] + +## Synonyms + + * chromosomal homologous to + +## Cross-references + + * MeSH:Chromosome_Pairing + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in chromosomal homology relationship with](../../RO/47/RO_HOM0000047.md) + * [in chromosomal homology relationship with](../../RO/47/RO_HOM0000047.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = MeSH:Chromosome_Pairing + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = chromosomal homologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in chromosomal homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000047 + +## Usage + + * - + * SymmetricObjectProperty [in chromosomal homology relationship with](../../RO/47/RO_HOM0000047.md) + * [in chromosomal homology relationship with](../../RO/47/RO_HOM0000047.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in gametology relationship with](../../RO/46/RO_HOM0000046.md) SubPropertyOf [in chromosomal homology relationship with](../../RO/47/RO_HOM0000047.md) + +## External Comments + diff --git a/src/ontology/md/RO/48/RO_0002348.md b/src/ontology/md/RO/48/RO_0002348.md new file mode 100644 index 00000000..d0c09316 --- /dev/null +++ b/src/ontology/md/RO/48/RO_0002348.md @@ -0,0 +1,44 @@ + +## Class : results in commitment to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002348 + * *Label* = results in commitment to + * *Definition* = p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in commitment to](../../RO/48/RO_0002348.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in commitment to](../../RO/48/RO_0002348.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. + * *[definition](../../IAO/15/IAO_0000115.md)* = p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.geneontology.org/GO.doc.development.shtml#fate + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in commitment to + +## Usage + + * - + * [results in commitment to](../../RO/48/RO_0002348.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in commitment to](../../RO/48/RO_0002348.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/48/RO_0002448.md b/src/ontology/md/RO/48/RO_0002448.md new file mode 100644 index 00000000..d42b5fa2 --- /dev/null +++ b/src/ontology/md/RO/48/RO_0002448.md @@ -0,0 +1,46 @@ + +## Class : molecularly controls + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002448 + * *Label* = molecularly controls + * *Definition* = Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [molecularly interacts with](../../RO/36/RO_0002436.md) + * [causally influences](../../RO/66/RO_0002566.md) + +## SubProperties + + +## Other Logical Axioms + + * [molecularly controls](../../RO/48/RO_0002448.md) SubPropertyOf [causally influences](../../RO/66/RO_0002566.md) + * [molecularly controls](../../RO/48/RO_0002448.md) SubPropertyOf [molecularly interacts with](../../RO/36/RO_0002436.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = molecularly controls + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [molecularly controls](../../RO/48/RO_0002448.md) SubPropertyOf [causally influences](../../RO/66/RO_0002566.md) + * [molecularly controls](../../RO/48/RO_0002448.md) SubPropertyOf [molecularly interacts with](../../RO/36/RO_0002436.md) + * [molecularly decreases activity of](../../RO/49/RO_0002449.md) SubPropertyOf [molecularly controls](../../RO/48/RO_0002448.md) + * [molecularly increases activity of](../../RO/50/RO_0002450.md) SubPropertyOf [molecularly controls](../../RO/48/RO_0002448.md) + +## External Comments + diff --git a/src/ontology/md/RO/48/RO_0002548.md b/src/ontology/md/RO/48/RO_0002548.md new file mode 100644 index 00000000..ed9aee10 --- /dev/null +++ b/src/ontology/md/RO/48/RO_0002548.md @@ -0,0 +1,38 @@ + +## Class : end, days post coitum + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002548 + * *Label* = end, days post coitum + * *Definition* = Count of number of days intervening between the end of the stage and the time of coitum. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has end time value](../../RO/38/RO_0002538.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Count of number of days intervening between the end of the stage and the time of coitum. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = end, days post coitum + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/48/RO_HOM0000048.md b/src/ontology/md/RO/48/RO_HOM0000048.md new file mode 100644 index 00000000..e1c07c4e --- /dev/null +++ b/src/ontology/md/RO/48/RO_HOM0000048.md @@ -0,0 +1,59 @@ + +## Class : in many to many orthology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000048 + * *Label* = in many to many orthology relationship with + * *Definition* = Orthology that involves two genes that experienced duplications more recent than the species split that created them. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1038/415741a, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000048, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ensembl.org/info/docs/compara/homology_method.html ] + +## Synonyms + + * many to many orthologous to + * many-to-many orthology + * many:many orthology + * trans-orthology + * co-orthology + * trans-homology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in many to many homology relationship with](../../RO/36/RO_HOM0000036.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in many to many orthology relationship with](../../RO/48/RO_HOM0000048.md) + * [in many to many orthology relationship with](../../RO/48/RO_HOM0000048.md) SubPropertyOf [in many to many homology relationship with](../../RO/36/RO_HOM0000036.md) + * [in many to many orthology relationship with](../../RO/48/RO_HOM0000048.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Orthology that involves two genes that experienced duplications more recent than the species split that created them. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = many to many orthologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = many-to-many orthology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = many:many orthology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = trans-orthology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = co-orthology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = trans-homology + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in many to many orthology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000048 + +## Usage + + * - + * SymmetricObjectProperty [in many to many orthology relationship with](../../RO/48/RO_HOM0000048.md) + * [in many to many orthology relationship with](../../RO/48/RO_HOM0000048.md) SubPropertyOf [in many to many homology relationship with](../../RO/36/RO_HOM0000036.md) + * [in many to many orthology relationship with](../../RO/48/RO_HOM0000048.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + +## External Comments + diff --git a/src/ontology/md/RO/49/RO_0002349.md b/src/ontology/md/RO/49/RO_0002349.md new file mode 100644 index 00000000..1539e647 --- /dev/null +++ b/src/ontology/md/RO/49/RO_0002349.md @@ -0,0 +1,43 @@ + +## Class : results in determination of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002349 + * *Label* = results in determination of + * *Definition* = p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in determination of](../../RO/49/RO_0002349.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in determination of](../../RO/49/RO_0002349.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.geneontology.org/GO.doc.development.shtml#fate + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in determination of + +## Usage + + * - + * [results in determination of](../../RO/49/RO_0002349.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in determination of](../../RO/49/RO_0002349.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/49/RO_0002449.md b/src/ontology/md/RO/49/RO_0002449.md new file mode 100644 index 00000000..e335d905 --- /dev/null +++ b/src/ontology/md/RO/49/RO_0002449.md @@ -0,0 +1,43 @@ + +## Class : molecularly decreases activity of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002449 + * *Label* = molecularly decreases activity of + * *Definition* = Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [molecularly controls](../../RO/48/RO_0002448.md) + +## SubProperties + + +## Other Logical Axioms + + * [molecularly decreases activity of](../../RO/49/RO_0002449.md) SubPropertyOf [molecularly controls](../../RO/48/RO_0002448.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between molecules a and b if and only if a executes a process that directly diminishes a process executed by b. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = inhibits + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = molecularly decreases activity of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [molecularly decreases activity of](../../RO/49/RO_0002449.md) SubPropertyOf [molecularly controls](../../RO/48/RO_0002448.md) + * [represses expression of](../../RO/02/RO_0003002.md) SubPropertyOf [molecularly decreases activity of](../../RO/49/RO_0002449.md) + +## External Comments + diff --git a/src/ontology/md/RO/49/RO_0002549.md b/src/ontology/md/RO/49/RO_0002549.md new file mode 100644 index 00000000..18e77a85 --- /dev/null +++ b/src/ontology/md/RO/49/RO_0002549.md @@ -0,0 +1,36 @@ + +## Class : start, weeks post birth + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002549 + * *Label* = start, weeks post birth + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has start time value](../../RO/37/RO_0002537.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = start, weeks post birth + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/49/RO_HOM0000049.md b/src/ontology/md/RO/49/RO_HOM0000049.md new file mode 100644 index 00000000..4cf94fc6 --- /dev/null +++ b/src/ontology/md/RO/49/RO_HOM0000049.md @@ -0,0 +1,48 @@ + +## Class : in within-species paralogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000049 + * *Label* = in within-species paralogy relationship with + * *Definition* = Paralogy that involves genes from the same species. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000049, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ensembl.org/info/docs/compara/homology_method.html ] + +## Synonyms + + * within-species paralogous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in within-species paralogy relationship with](../../RO/49/RO_HOM0000049.md) + * [in within-species paralogy relationship with](../../RO/49/RO_HOM0000049.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paralogy that involves genes from the same species. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = within-species paralogous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in within-species paralogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000049 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in within-species paralogy relationship with](../../RO/49/RO_HOM0000049.md) + * [in within-species paralogy relationship with](../../RO/49/RO_HOM0000049.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## External Comments + diff --git a/src/ontology/md/RO/50/RO_0002150.md b/src/ontology/md/RO/50/RO_0002150.md new file mode 100644 index 00000000..ec20ad3f --- /dev/null +++ b/src/ontology/md/RO/50/RO_0002150.md @@ -0,0 +1,49 @@ + +## Class : continuous with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002150 + * *Label* = continuous with + * *Definition* = X continuous_with Y if and only if X and Y share a fiat boundary. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [continuous with](../../RO/50/RO_0002150.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [continuous with](../../RO/50/RO_0002150.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [continuous with](../../RO/50/RO_0002150.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = X continuous_with Y if and only if X and Y share a fiat boundary. + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = connected to + * *[curator note](../../IAO/32/IAO_0000232.md)* = The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = continuous with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = FMA:85972 + +## Usage + + * - + * [continuous with](../../RO/50/RO_0002150.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [continuous with](../../RO/50/RO_0002150.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [continuous with](../../RO/50/RO_0002150.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## External Comments + diff --git a/src/ontology/md/RO/50/RO_0002350.md b/src/ontology/md/RO/50/RO_0002350.md new file mode 100644 index 00000000..2187ee13 --- /dev/null +++ b/src/ontology/md/RO/50/RO_0002350.md @@ -0,0 +1,46 @@ + +## Class : member of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002350 + * *Label* = member of + * *Definition* = is member of is a mereological relation between a item and a collection. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [part of](../../BFO/50/BFO_0000050.md) + +## SubProperties + + +## Other Logical Axioms + + * [member of](../../RO/50/RO_0002350.md) InverseOf [has member](../../RO/51/RO_0002351.md) + * [member of](../../RO/50/RO_0002350.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = An organism that is a member of a population of organisms + * *[definition](../../IAO/15/IAO_0000115.md)* = is member of is a mereological relation between a item and a collection. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is member of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = member part of + * *[definition source](../../IAO/19/IAO_0000119.md)* = SIO + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = member of + +## Usage + + * - + * [member of](../../RO/50/RO_0002350.md) InverseOf [has member](../../RO/51/RO_0002351.md) + * [member of](../../RO/50/RO_0002350.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## External Comments + diff --git a/src/ontology/md/RO/50/RO_0002450.md b/src/ontology/md/RO/50/RO_0002450.md new file mode 100644 index 00000000..39d19f25 --- /dev/null +++ b/src/ontology/md/RO/50/RO_0002450.md @@ -0,0 +1,43 @@ + +## Class : molecularly increases activity of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002450 + * *Label* = molecularly increases activity of + * *Definition* = Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [molecularly controls](../../RO/48/RO_0002448.md) + +## SubProperties + + +## Other Logical Axioms + + * [molecularly increases activity of](../../RO/50/RO_0002450.md) SubPropertyOf [molecularly controls](../../RO/48/RO_0002448.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between molecules a and b if and only if a executes a process that directly activates a process executed by b. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = activates + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = molecularly increases activity of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [increases expression of](../../RO/03/RO_0003003.md) SubPropertyOf [molecularly increases activity of](../../RO/50/RO_0002450.md) + * [molecularly increases activity of](../../RO/50/RO_0002450.md) SubPropertyOf [molecularly controls](../../RO/48/RO_0002448.md) + +## External Comments + diff --git a/src/ontology/md/RO/50/RO_0002550.md b/src/ontology/md/RO/50/RO_0002550.md new file mode 100644 index 00000000..41f189d5 --- /dev/null +++ b/src/ontology/md/RO/50/RO_0002550.md @@ -0,0 +1,36 @@ + +## Class : end, weeks post birth + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002550 + * *Label* = end, weeks post birth + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has end time value](../../RO/38/RO_0002538.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = end, weeks post birth + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/50/RO_HOM0000050.md b/src/ontology/md/RO/50/RO_HOM0000050.md new file mode 100644 index 00000000..10d58004 --- /dev/null +++ b/src/ontology/md/RO/50/RO_HOM0000050.md @@ -0,0 +1,51 @@ + +## Class : in between-species paralogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000050 + * *Label* = in between-species paralogy relationship with + * *Definition* = Paralogy that involves genes from different species. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000050, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ensembl.org/info/docs/compara/homology_method.html ] + * *Comment* = The genes have diverged before a speciation event. + +## Synonyms + + * between-species paralogous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in between-species paralogy relationship with](../../RO/50/RO_HOM0000050.md) + * [in between-species paralogy relationship with](../../RO/50/RO_HOM0000050.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paralogy that involves genes from different species. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = between-species paralogous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The genes have diverged before a speciation event. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in between-species paralogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000050 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in between-species paralogy relationship with](../../RO/50/RO_HOM0000050.md) + * [in apparent orthology relationship with](../../RO/60/RO_HOM0000060.md) SubPropertyOf [in between-species paralogy relationship with](../../RO/50/RO_HOM0000050.md) + * [in between-species paralogy relationship with](../../RO/50/RO_HOM0000050.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## External Comments + diff --git a/src/ontology/md/RO/51/RO_0002151.md b/src/ontology/md/RO/51/RO_0002151.md new file mode 100644 index 00000000..284e9257 --- /dev/null +++ b/src/ontology/md/RO/51/RO_0002151.md @@ -0,0 +1,52 @@ + +## Class : partially overlaps + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002151 + * *Label* = partially overlaps + * *Definition* = x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [partially overlaps](../../RO/51/RO_0002151.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x + * *[editor note](../../IAO/16/IAO_0000116.md)* = We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom + * *[alternative term](../../IAO/18/IAO_0000118.md)* = proper overlaps + * *[first order logic expression](../../IAO/26/IAO_0000426.md)* = (forall (?x ?y) + (iff + (proper_overlaps ?x ?y) + (and + (overlaps ?x ?y) + (not (part_of ?x ?y)) + (not (part_of ?y ?x))))) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = partially overlaps + +## Usage + + * - + * [partially overlaps](../../RO/51/RO_0002151.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## External Comments + diff --git a/src/ontology/md/RO/51/RO_0002351.md b/src/ontology/md/RO/51/RO_0002351.md new file mode 100644 index 00000000..02694c4a --- /dev/null +++ b/src/ontology/md/RO/51/RO_0002351.md @@ -0,0 +1,45 @@ + +## Class : has member + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002351 + * *Label* = has member + * *Definition* = has member is a mereological relation between a collection and an item. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has part](../../BFO/51/BFO_0000051.md) + +## SubProperties + + +## Other Logical Axioms + + * IrrefexiveObjectProperty [has member](../../RO/51/RO_0002351.md) + * [has member](../../RO/51/RO_0002351.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [member of](../../RO/50/RO_0002350.md) InverseOf [has member](../../RO/51/RO_0002351.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = has member is a mereological relation between a collection and an item. + * *[definition source](../../IAO/19/IAO_0000119.md)* = SIO + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has member + +## Usage + + * - + * IrrefexiveObjectProperty [has member](../../RO/51/RO_0002351.md) + * [has member](../../RO/51/RO_0002351.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [member of](../../RO/50/RO_0002350.md) InverseOf [has member](../../RO/51/RO_0002351.md) + +## External Comments + diff --git a/src/ontology/md/RO/51/RO_0002451.md b/src/ontology/md/RO/51/RO_0002451.md new file mode 100644 index 00000000..ba6d09e9 --- /dev/null +++ b/src/ontology/md/RO/51/RO_0002451.md @@ -0,0 +1,42 @@ + +## Class : transmitted by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002451 + * *Label* = transmitted by + * *Definition* = A relationship that holds between a disease and organism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [ecologically related to](../../RO/21/RO_0002321.md) + +## SubProperties + + +## Other Logical Axioms + + * [transmitted by](../../RO/51/RO_0002451.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = all dengue disease transmitted by some mosquito + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship that holds between a disease and organism + * *[editor note](../../IAO/16/IAO_0000116.md)* = Add domain and range constraints + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = transmitted by + +## Usage + + * - + * [transmitted by](../../RO/51/RO_0002451.md) SubPropertyOf [ecologically related to](../../RO/21/RO_0002321.md) + +## External Comments + diff --git a/src/ontology/md/RO/51/RO_0002551.md b/src/ontology/md/RO/51/RO_0002551.md new file mode 100644 index 00000000..58ca6b05 --- /dev/null +++ b/src/ontology/md/RO/51/RO_0002551.md @@ -0,0 +1,45 @@ + +## Class : has skeleton + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002551 + * *Label* = has skeleton + * *Definition* = A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has part](../../BFO/51/BFO_0000051.md) + +## SubProperties + + +## Other Logical Axioms + + * [has skeleton](../../RO/51/RO_0002551.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [skeleton of](../../RO/76/RO_0002576.md) InverseOf [has skeleton](../../RO/51/RO_0002551.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has supporting framework + * *[curator note](../../IAO/32/IAO_0000232.md)* = The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has skeleton + +## Usage + + * - + * [has skeleton](../../RO/51/RO_0002551.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + * [skeleton of](../../RO/76/RO_0002576.md) InverseOf [has skeleton](../../RO/51/RO_0002551.md) + +## External Comments + diff --git a/src/ontology/md/RO/51/RO_HOM0000051.md b/src/ontology/md/RO/51/RO_HOM0000051.md new file mode 100644 index 00000000..245d54d8 --- /dev/null +++ b/src/ontology/md/RO/51/RO_HOM0000051.md @@ -0,0 +1,46 @@ + +## Class : in postdisplacement relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000051 + * *Label* = in postdisplacement relationship with + * *Definition* = Paedomorphosis that is produced by delayed growth of immature structures into the adult form. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://en.wikipedia.org/wiki/Pedomorphosis, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000051 ] + +## Synonyms + + * post-displacement + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in postdisplacement relationship with](../../RO/51/RO_HOM0000051.md) + * [in postdisplacement relationship with](../../RO/51/RO_HOM0000051.md) SubPropertyOf [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = post-displacement + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in postdisplacement relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000051 + +## Usage + + * - + * SymmetricObjectProperty [in postdisplacement relationship with](../../RO/51/RO_HOM0000051.md) + * [in postdisplacement relationship with](../../RO/51/RO_HOM0000051.md) SubPropertyOf [in paedomorphorsis relationship with](../../RO/29/RO_HOM0000029.md) + +## External Comments + diff --git a/src/ontology/md/RO/52/RO_0000052.md b/src/ontology/md/RO/52/RO_0000052.md new file mode 100644 index 00000000..68062f0e --- /dev/null +++ b/src/ontology/md/RO/52/RO_0000052.md @@ -0,0 +1,52 @@ + +## Class : inheres in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000052 + * *Label* = inheres in + * *Definition* = a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [inheres in part of](../../RO/14/RO_0002314.md) + +## SubProperties + + +## Other Logical Axioms + + * [bearer of](../../RO/53/RO_0000053.md) InverseOf [inheres in](../../RO/52/RO_0000052.md) + * [inheres in](../../RO/52/RO_0000052.md) SubPropertyOf [inheres in part of](../../RO/14/RO_0002314.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = inheres in + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this fragility inheres in this vase + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this red color inheres in this apple + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + * *[editor note](../../IAO/16/IAO_0000116.md)* = A dependent inheres in its bearer at all times for which the dependent exists. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = inheres_in + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = inheres in + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [bearer of](../../RO/53/RO_0000053.md) InverseOf [inheres in](../../RO/52/RO_0000052.md) + * [function of](../../RO/79/RO_0000079.md) SubPropertyOf [inheres in](../../RO/52/RO_0000052.md) + * [inheres in](../../RO/52/RO_0000052.md) SubPropertyOf [inheres in part of](../../RO/14/RO_0002314.md) + * [quality of](../../RO/80/RO_0000080.md) SubPropertyOf [inheres in](../../RO/52/RO_0000052.md) + * [role of](../../RO/81/RO_0000081.md) SubPropertyOf [inheres in](../../RO/52/RO_0000052.md) + +## External Comments + diff --git a/src/ontology/md/RO/52/RO_0002352.md b/src/ontology/md/RO/52/RO_0002352.md new file mode 100644 index 00000000..19db4338 --- /dev/null +++ b/src/ontology/md/RO/52/RO_0002352.md @@ -0,0 +1,45 @@ + +## Class : input of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002352 + * *Label* = input of + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [functionally related to](../../RO/28/RO_0002328.md) + * [participates in](../../RO/56/RO_0000056.md) + +## SubProperties + + +## Other Logical Axioms + + * [input of](../../RO/52/RO_0002352.md) InverseOf [has input](../../RO/33/RO_0002233.md) + * [input of](../../RO/52/RO_0002352.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [input of](../../RO/52/RO_0002352.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = input of + +## Usage + + * - + * [input of](../../RO/52/RO_0002352.md) InverseOf [has input](../../RO/33/RO_0002233.md) + * [input of](../../RO/52/RO_0002352.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [input of](../../RO/52/RO_0002352.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + +## External Comments + diff --git a/src/ontology/md/RO/52/RO_0002452.md b/src/ontology/md/RO/52/RO_0002452.md new file mode 100644 index 00000000..d645708b --- /dev/null +++ b/src/ontology/md/RO/52/RO_0002452.md @@ -0,0 +1,40 @@ + +## Class : has symptom + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002452 + * *Label* = has symptom + * *Definition* = A relation that holds between a disease or an organism and a phenotype + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has phenotype](../../RO/00/RO_0002200.md) + +## SubProperties + + +## Other Logical Axioms + + * [has symptom](../../RO/52/RO_0002452.md) SubPropertyOf [has phenotype](../../RO/00/RO_0002200.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that holds between a disease or an organism and a phenotype + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has symptom + +## Usage + + * - + * [has symptom](../../RO/52/RO_0002452.md) SubPropertyOf [has phenotype](../../RO/00/RO_0002200.md) + +## External Comments + diff --git a/src/ontology/md/RO/52/RO_0002552.md b/src/ontology/md/RO/52/RO_0002552.md new file mode 100644 index 00000000..c0dc3afe --- /dev/null +++ b/src/ontology/md/RO/52/RO_0002552.md @@ -0,0 +1,45 @@ + +## Class : results in ending of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002552 + * *Label* = results in ending of + * *Definition* = p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in ending of](../../RO/52/RO_0002552.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in ending of](../../RO/52/RO_0002552.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in ending of + +## Usage + + * - + * [results in developmental regression of](../../RO/01/RO_0002301.md) SubPropertyOf [results in ending of](../../RO/52/RO_0002552.md) + * [results in disappearance of](../../RO/00/RO_0002300.md) SubPropertyOf [results in ending of](../../RO/52/RO_0002552.md) + * [results in ending of](../../RO/52/RO_0002552.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in ending of](../../RO/52/RO_0002552.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/52/RO_HOM0000052.md b/src/ontology/md/RO/52/RO_HOM0000052.md new file mode 100644 index 00000000..9acca951 --- /dev/null +++ b/src/ontology/md/RO/52/RO_HOM0000052.md @@ -0,0 +1,44 @@ + +## Class : in hypermorphosis relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000052 + * *Label* = in hypermorphosis relationship with + * *Definition* = Peramorphosis that is produced by a delay in the offset of development. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:978-0674639416, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://en.wikipedia.org/wiki/Peramorphosis, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000052 ] + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in peramorphosis relationship with](../../RO/30/RO_HOM0000030.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in hypermorphosis relationship with](../../RO/52/RO_HOM0000052.md) + * [in hypermorphosis relationship with](../../RO/52/RO_HOM0000052.md) SubPropertyOf [in peramorphosis relationship with](../../RO/30/RO_HOM0000030.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Peramorphosis that is produced by a delay in the offset of development. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in hypermorphosis relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000052 + +## Usage + + * - + * SymmetricObjectProperty [in hypermorphosis relationship with](../../RO/52/RO_HOM0000052.md) + * [in hypermorphosis relationship with](../../RO/52/RO_HOM0000052.md) SubPropertyOf [in peramorphosis relationship with](../../RO/30/RO_HOM0000030.md) + +## External Comments + diff --git a/src/ontology/md/RO/53/RO_0000053.md b/src/ontology/md/RO/53/RO_0000053.md new file mode 100644 index 00000000..802a670e --- /dev/null +++ b/src/ontology/md/RO/53/RO_0000053.md @@ -0,0 +1,54 @@ + +## Class : bearer of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000053 + * *Label* = bearer of + * *Definition* = a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [bearer of](../../RO/53/RO_0000053.md) InverseOf [inheres in](../../RO/52/RO_0000052.md) + * [bearer of](../../RO/53/RO_0000053.md) Range [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = bearer of + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this apple is bearer of this red color + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this vase is bearer of this fragility + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + * *[editor note](../../IAO/16/IAO_0000116.md)* = A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = bearer_of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is bearer of + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = bearer of + +## Usage + + * - + * [bearer of](../../RO/53/RO_0000053.md) InverseOf [inheres in](../../RO/52/RO_0000052.md) + * [bearer of](../../RO/53/RO_0000053.md) Range [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [bounding layer of](../../RO/07/RO_0002007.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [laminar](../../PATO/24/PATO_0002124.md) and [material entity](../../BFO/40/BFO_0000040.md) + * [branching part of](../../RO/80/RO_0002380.md) Range [bearer of](../../RO/53/RO_0000053.md) some [branched](../../PATO/02/PATO_0000402.md) + * [coincident with](../../RO/08/RO_0002008.md) Domain [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [coincident with](../../RO/08/RO_0002008.md) Range [bearer of](../../RO/53/RO_0000053.md) some [linear](../../PATO/99/PATO_0001199.md) and [continuant](../../BFO/02/BFO_0000002.md) + * [has function](../../RO/85/RO_0000085.md) SubPropertyOf [bearer of](../../RO/53/RO_0000053.md) + * [has quality](../../RO/86/RO_0000086.md) SubPropertyOf [bearer of](../../RO/53/RO_0000053.md) + * [has role](../../RO/87/RO_0000087.md) SubPropertyOf [bearer of](../../RO/53/RO_0000053.md) + +## External Comments + diff --git a/src/ontology/md/RO/53/RO_0002353.md b/src/ontology/md/RO/53/RO_0002353.md new file mode 100644 index 00000000..c5d1641d --- /dev/null +++ b/src/ontology/md/RO/53/RO_0002353.md @@ -0,0 +1,46 @@ + +## Class : output of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002353 + * *Label* = output of + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [functionally related to](../../RO/28/RO_0002328.md) + * [participates in](../../RO/56/RO_0000056.md) + +## SubProperties + + +## Other Logical Axioms + + * [output of](../../RO/53/RO_0002353.md) InverseOf [has output](../../RO/34/RO_0002234.md) + * [output of](../../RO/53/RO_0002353.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [output of](../../RO/53/RO_0002353.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = output of + +## Usage + + * - + * [formed as result of](../../RO/54/RO_0002354.md) SubPropertyOf [output of](../../RO/53/RO_0002353.md) + * [output of](../../RO/53/RO_0002353.md) InverseOf [has output](../../RO/34/RO_0002234.md) + * [output of](../../RO/53/RO_0002353.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [output of](../../RO/53/RO_0002353.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + +## External Comments + diff --git a/src/ontology/md/RO/53/RO_0002453.md b/src/ontology/md/RO/53/RO_0002453.md new file mode 100644 index 00000000..d84847ec --- /dev/null +++ b/src/ontology/md/RO/53/RO_0002453.md @@ -0,0 +1,44 @@ + +## Class : host of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002453 + * *Label* = host of + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## SubProperties + + +## Other Logical Axioms + + * [host of](../../RO/53/RO_0002453.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = host of + +## Usage + + * - + * [has pathogen](../../RO/57/RO_0002557.md) SubPropertyOf [host of](../../RO/53/RO_0002453.md) + * [host of](../../RO/53/RO_0002453.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [hyperparasitized by](../../RO/54/RO_0002554.md) SubPropertyOf [host of](../../RO/53/RO_0002453.md) + * [parasitized by](../../RO/45/RO_0002445.md) SubPropertyOf [host of](../../RO/53/RO_0002453.md) + +## External Comments + diff --git a/src/ontology/md/RO/53/RO_0002553.md b/src/ontology/md/RO/53/RO_0002553.md new file mode 100644 index 00000000..65df567a --- /dev/null +++ b/src/ontology/md/RO/53/RO_0002553.md @@ -0,0 +1,49 @@ + +## Class : hyperparasite of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002553 + * *Label* = hyperparasite of + * *Definition* = x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y + +## Synonyms + + * hyperparasitoid of + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has host](../../RO/54/RO_0002454.md) + +## SubProperties + + +## Other Logical Axioms + + * [hyperparasite of](../../RO/53/RO_0002553.md) SubPropertyOf [has host](../../RO/54/RO_0002454.md) + * [hyperparasitized by](../../RO/54/RO_0002554.md) InverseOf [hyperparasite of](../../RO/53/RO_0002553.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://eol.org/schema/terms/hyperparasitoidOf + * *[definition source](../../IAO/19/IAO_0000119.md)* = https://en.wikipedia.org/wiki/Hyperparasite + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = hyperparasitoid of + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = hyperparasite of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [hyperparasite of](../../RO/53/RO_0002553.md) SubPropertyOf [has host](../../RO/54/RO_0002454.md) + * [hyperparasitized by](../../RO/54/RO_0002554.md) InverseOf [hyperparasite of](../../RO/53/RO_0002553.md) + +## External Comments + diff --git a/src/ontology/md/RO/53/RO_HOM0000053.md b/src/ontology/md/RO/53/RO_HOM0000053.md new file mode 100644 index 00000000..723f969b --- /dev/null +++ b/src/ontology/md/RO/53/RO_HOM0000053.md @@ -0,0 +1,47 @@ + +## Class : in synology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000053 + * *Label* = in synology relationship with + * *Definition* = Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF00173425, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/S0168-9525(00)02005-9, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000053 ] + +## Synonyms + + * synologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in synology relationship with](../../RO/53/RO_HOM0000053.md) + * [in synology relationship with](../../RO/53/RO_HOM0000053.md) SubPropertyOf [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = synologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in synology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000053 + +## Usage + + * - + * SymmetricObjectProperty [in synology relationship with](../../RO/53/RO_HOM0000053.md) + * [in homoeology relationship with](../../RO/73/RO_HOM0000073.md) SubPropertyOf [in synology relationship with](../../RO/53/RO_HOM0000053.md) + * [in synology relationship with](../../RO/53/RO_HOM0000053.md) SubPropertyOf [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + +## External Comments + diff --git a/src/ontology/md/RO/54/RO_0002254.md b/src/ontology/md/RO/54/RO_0002254.md new file mode 100644 index 00000000..97a9e31c --- /dev/null +++ b/src/ontology/md/RO/54/RO_0002254.md @@ -0,0 +1,50 @@ + +## Class : has developmental contribution from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002254 + * *Label* = has developmental contribution from + * *Definition* = x has developmental contribution from y iff x has some part z such that z develops from y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally preceded by](../../RO/58/RO_0002258.md) + +## SubProperties + + +## Other Logical Axioms + + * [developmentally contributes to](../../RO/55/RO_0002255.md) InverseOf [has developmental contribution from](../../RO/54/RO_0002254.md) + * [has developmental contribution from](../../RO/54/RO_0002254.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [has developmental contribution from](../../RO/54/RO_0002254.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [has developmental contribution from](../../RO/54/RO_0002254.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has developmental contribution from y iff x has some part z such that z develops from y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has developmental contribution from + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [developmentally contributes to](../../RO/55/RO_0002255.md) InverseOf [has developmental contribution from](../../RO/54/RO_0002254.md) + * [has developmental contribution from](../../RO/54/RO_0002254.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [has developmental contribution from](../../RO/54/RO_0002254.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [has developmental contribution from](../../RO/54/RO_0002254.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## External Comments + diff --git a/src/ontology/md/RO/54/RO_0002354.md b/src/ontology/md/RO/54/RO_0002354.md new file mode 100644 index 00000000..bf0f68ee --- /dev/null +++ b/src/ontology/md/RO/54/RO_0002354.md @@ -0,0 +1,40 @@ + +## Class : formed as result of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002354 + * *Label* = formed as result of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [output of](../../RO/53/RO_0002353.md) + +## SubProperties + + +## Other Logical Axioms + + * [formed as result of](../../RO/54/RO_0002354.md) InverseOf [results in formation of](../../RO/97/RO_0002297.md) + * [formed as result of](../../RO/54/RO_0002354.md) SubPropertyOf [output of](../../RO/53/RO_0002353.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = formed as result of + +## Usage + + * - + * [formed as result of](../../RO/54/RO_0002354.md) InverseOf [results in formation of](../../RO/97/RO_0002297.md) + * [formed as result of](../../RO/54/RO_0002354.md) SubPropertyOf [output of](../../RO/53/RO_0002353.md) + +## External Comments + diff --git a/src/ontology/md/RO/54/RO_0002454.md b/src/ontology/md/RO/54/RO_0002454.md new file mode 100644 index 00000000..f6f38d5c --- /dev/null +++ b/src/ontology/md/RO/54/RO_0002454.md @@ -0,0 +1,44 @@ + +## Class : has host + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002454 + * *Label* = has host + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## SubProperties + + +## Other Logical Axioms + + * [has host](../../RO/54/RO_0002454.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has host + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://eol.org/schema/terms/hasHost + +## Usage + + * - + * [has host](../../RO/54/RO_0002454.md) SubPropertyOf [symbiotically interacts with](../../RO/40/RO_0002440.md) + * [hyperparasite of](../../RO/53/RO_0002553.md) SubPropertyOf [has host](../../RO/54/RO_0002454.md) + * [parasite of](../../RO/44/RO_0002444.md) SubPropertyOf [has host](../../RO/54/RO_0002454.md) + * [pathogen of](../../RO/56/RO_0002556.md) SubPropertyOf [has host](../../RO/54/RO_0002454.md) + +## External Comments + diff --git a/src/ontology/md/RO/54/RO_0002554.md b/src/ontology/md/RO/54/RO_0002554.md new file mode 100644 index 00000000..b97ee639 --- /dev/null +++ b/src/ontology/md/RO/54/RO_0002554.md @@ -0,0 +1,45 @@ + +## Class : hyperparasitized by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002554 + * *Label* = hyperparasitized by + +## Synonyms + + * hyperparasitoidized by + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [host of](../../RO/53/RO_0002453.md) + +## SubProperties + + +## Other Logical Axioms + + * [hyperparasitized by](../../RO/54/RO_0002554.md) InverseOf [hyperparasite of](../../RO/53/RO_0002553.md) + * [hyperparasitized by](../../RO/54/RO_0002554.md) SubPropertyOf [host of](../../RO/53/RO_0002453.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = hyperparasitoidized by + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = hyperparasitized by + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [hyperparasitized by](../../RO/54/RO_0002554.md) InverseOf [hyperparasite of](../../RO/53/RO_0002553.md) + * [hyperparasitized by](../../RO/54/RO_0002554.md) SubPropertyOf [host of](../../RO/53/RO_0002453.md) + +## External Comments + diff --git a/src/ontology/md/RO/54/RO_HOM0000054.md b/src/ontology/md/RO/54/RO_HOM0000054.md new file mode 100644 index 00000000..2a5f0622 --- /dev/null +++ b/src/ontology/md/RO/54/RO_HOM0000054.md @@ -0,0 +1,51 @@ + +## Class : in isoorthology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000054 + * *Label* = in isoorthology relationship with + * *Definition* = Orthology that involves functional equivalent genes with retention of the ancestral function. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/S0168-9525(00)02005-9, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000054 ] + +## Synonyms + + * isoorthologous to + +## Cross-references + + * ECO:0000080 + +## Subsets + + +## SuperProperties + + * [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + * [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in isoorthology relationship with](../../RO/54/RO_HOM0000054.md) + * [in isoorthology relationship with](../../RO/54/RO_HOM0000054.md) SubPropertyOf [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) + * [in isoorthology relationship with](../../RO/54/RO_HOM0000054.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Orthology that involves functional equivalent genes with retention of the ancestral function. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[database_cross_reference](../../ef/oboInOwl#hasDbXref.md)* = ECO:0000080 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = isoorthologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in isoorthology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000054 + +## Usage + + * - + * SymmetricObjectProperty [in isoorthology relationship with](../../RO/54/RO_HOM0000054.md) + * [in isoorthology relationship with](../../RO/54/RO_HOM0000054.md) SubPropertyOf [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) + * [in isoorthology relationship with](../../RO/54/RO_HOM0000054.md) SubPropertyOf [in orthology relationship with](../../RO/17/RO_HOM0000017.md) + +## External Comments + diff --git a/src/ontology/md/RO/55/RO_0002255.md b/src/ontology/md/RO/55/RO_0002255.md new file mode 100644 index 00000000..11a47757 --- /dev/null +++ b/src/ontology/md/RO/55/RO_0002255.md @@ -0,0 +1,45 @@ + +## Class : developmentally contributes to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002255 + * *Label* = developmentally contributes to + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [has potential to developmentally contribute to](../../RO/85/RO_0002385.md) + +## SubProperties + + +## Other Logical Axioms + + * [developmentally contributes to](../../RO/55/RO_0002255.md) InverseOf [has developmental contribution from](../../RO/54/RO_0002254.md) + * [developmentally contributes to](../../RO/55/RO_0002255.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [developmentally contributes to](../../RO/55/RO_0002255.md) SubPropertyOf [has potential to developmentally contribute to](../../RO/85/RO_0002385.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = developmentally contributes to + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [developmentally contributes to](../../RO/55/RO_0002255.md) InverseOf [has developmental contribution from](../../RO/54/RO_0002254.md) + * [developmentally contributes to](../../RO/55/RO_0002255.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [developmentally contributes to](../../RO/55/RO_0002255.md) SubPropertyOf [has potential to developmentally contribute to](../../RO/85/RO_0002385.md) + +## External Comments + diff --git a/src/ontology/md/RO/55/RO_0002355.md b/src/ontology/md/RO/55/RO_0002355.md new file mode 100644 index 00000000..a1138556 --- /dev/null +++ b/src/ontology/md/RO/55/RO_0002355.md @@ -0,0 +1,43 @@ + +## Class : results in structural organization of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002355 + * *Label* = results in structural organization of + * *Definition* = A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in structural organization of](../../RO/55/RO_0002355.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in structural organization of](../../RO/55/RO_0002355.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in structural organization of + +## Usage + + * - + * [results in structural organization of](../../RO/55/RO_0002355.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in structural organization of](../../RO/55/RO_0002355.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/55/RO_0002455.md b/src/ontology/md/RO/55/RO_0002455.md new file mode 100644 index 00000000..4f7d78a4 --- /dev/null +++ b/src/ontology/md/RO/55/RO_0002455.md @@ -0,0 +1,46 @@ + +## Class : pollinates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002455 + * *Label* = pollinates + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [mutualistically interacts with](../../RO/42/RO_0002442.md) + +## SubProperties + + +## Other Logical Axioms + + * [pollinated by](../../RO/56/RO_0002456.md) InverseOf [pollinates](../../RO/55/RO_0002455.md) + * [pollinates](../../RO/55/RO_0002455.md) SubPropertyOf [mutualistically interacts with](../../RO/42/RO_0002442.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Bees pollinate Flowers + * *[editor note](../../IAO/16/IAO_0000116.md)* = This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is subject of pollination interaction with + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = pollinates + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://eol.org/schema/terms/pollinates + +## Usage + + * - + * [pollinated by](../../RO/56/RO_0002456.md) InverseOf [pollinates](../../RO/55/RO_0002455.md) + * [pollinates](../../RO/55/RO_0002455.md) SubPropertyOf [mutualistically interacts with](../../RO/42/RO_0002442.md) + +## External Comments + diff --git a/src/ontology/md/RO/55/RO_0002555.md b/src/ontology/md/RO/55/RO_0002555.md new file mode 100644 index 00000000..6b407c5c --- /dev/null +++ b/src/ontology/md/RO/55/RO_0002555.md @@ -0,0 +1,43 @@ + +## Class : allelopath of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002555 + * *Label* = allelopath of + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## SubProperties + + +## Other Logical Axioms + + * [allelopath of](../../RO/55/RO_0002555.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://en.wikipedia.org/wiki/Allelopathy + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = allelopath of + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://eol.org/schema/terms/allelopathyYes + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y + +## Usage + + * - + * [allelopath of](../../RO/55/RO_0002555.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## External Comments + diff --git a/src/ontology/md/RO/55/RO_HOM0000055.md b/src/ontology/md/RO/55/RO_HOM0000055.md new file mode 100644 index 00000000..f3a283d0 --- /dev/null +++ b/src/ontology/md/RO/55/RO_HOM0000055.md @@ -0,0 +1,50 @@ + +## Class : in tandem paralogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000055 + * *Label* = in tandem paralogy relationship with + * *Definition* = Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:978-0878932665, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/S0168-9525(00)02005-9, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000055 ] + +## Synonyms + + * tandem paralogous to + * iterative paralogy + * serial paralogy + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in tandem paralogy relationship with](../../RO/55/RO_HOM0000055.md) + * [in tandem paralogy relationship with](../../RO/55/RO_HOM0000055.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = tandem paralogous to + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = iterative paralogy + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = serial paralogy + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in tandem paralogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000055 + +## Usage + + * - + * SymmetricObjectProperty [in tandem paralogy relationship with](../../RO/55/RO_HOM0000055.md) + * [in tandem paralogy relationship with](../../RO/55/RO_HOM0000055.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## External Comments + diff --git a/src/ontology/md/RO/56/RO_0000056.md b/src/ontology/md/RO/56/RO_0000056.md new file mode 100644 index 00000000..6fb5e409 --- /dev/null +++ b/src/ontology/md/RO/56/RO_0000056.md @@ -0,0 +1,52 @@ + +## Class : participates in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000056 + * *Label* = participates in + * *Definition* = a relation between a continuant and a process, in which the continuant is somehow involved in the process + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [has participant](../../RO/57/RO_0000057.md) InverseOf [participates in](../../RO/56/RO_0000056.md) + * [participates in](../../RO/56/RO_0000056.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [participates in](../../RO/56/RO_0000056.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = participates in + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this blood clot participates in this blood coagulation + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this input material (or this output material) participates in this process + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this investigator participates in this investigation + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between a continuant and a process, in which the continuant is somehow involved in the process + * *[alternative term](../../IAO/18/IAO_0000118.md)* = participates_in + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = participates in + +## Usage + + * - + * [actively participates in](../../RO/17/RO_0002217.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + * [causally influences](../../RO/66/RO_0002566.md) some [material entity](../../BFO/40/BFO_0000040.md) SubClassOf [capable of](../../RO/15/RO_0002215.md) some [participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md)or[participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md) + * [has participant](../../RO/57/RO_0000057.md) InverseOf [participates in](../../RO/56/RO_0000056.md) + * [input of](../../RO/52/RO_0002352.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + * [output of](../../RO/53/RO_0002353.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + * [participates in](../../RO/56/RO_0000056.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [participates in](../../RO/56/RO_0000056.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [partner in](../../RO/61/RO_0002461.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + +## External Comments + diff --git a/src/ontology/md/RO/56/RO_0002156.md b/src/ontology/md/RO/56/RO_0002156.md new file mode 100644 index 00000000..37c39374 --- /dev/null +++ b/src/ontology/md/RO/56/RO_0002156.md @@ -0,0 +1,47 @@ + +## Class : derived by descent from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002156 + * *Label* = derived by descent from + * *Definition* = d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [evolutionarily related to](../../RO/20/RO_0002320.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [derived by descent from](../../RO/56/RO_0002156.md) + * [derived by descent from](../../RO/56/RO_0002156.md) InverseOf [has derived by descendant](../../RO/57/RO_0002157.md) + * [derived by descent from](../../RO/56/RO_0002156.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = ancestral_stucture_of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = evolutionarily_descended_from + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = derived by descent from + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [derived by descent from](../../RO/56/RO_0002156.md) + * [derived by descent from](../../RO/56/RO_0002156.md) InverseOf [has derived by descendant](../../RO/57/RO_0002157.md) + * [derived by descent from](../../RO/56/RO_0002156.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## External Comments + diff --git a/src/ontology/md/RO/56/RO_0002256.md b/src/ontology/md/RO/56/RO_0002256.md new file mode 100644 index 00000000..30b6b4a4 --- /dev/null +++ b/src/ontology/md/RO/56/RO_0002256.md @@ -0,0 +1,54 @@ + +## Class : developmentally induced by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002256 + * *Label* = developmentally induced by + * *Definition* = t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally preceded by](../../RO/58/RO_0002258.md) + +## SubProperties + + +## Other Logical Axioms + + * [developmentally induced by](../../RO/56/RO_0002256.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [developmentally induced by](../../RO/56/RO_0002256.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [developmentally induced by](../../RO/56/RO_0002256.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [developmentally induces](../../RO/57/RO_0002257.md) InverseOf [developmentally induced by](../../RO/56/RO_0002256.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[term editor](../../IAO/17/IAO_0000117.md)* = Melissa Haendel + * *[alternative term](../../IAO/18/IAO_0000118.md)* = induced by + * *[definition source](../../IAO/19/IAO_0000119.md)* = Developmental Biology, Gilbert, 8th edition, figure 6.5(F) + * *[definition source](../../IAO/19/IAO_0000119.md)* = GO:0001759 + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * *[curator note](../../IAO/32/IAO_0000232.md)* = We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = developmentally induced by + +## Usage + + * - + * [developmentally induced by](../../RO/56/RO_0002256.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [developmentally induced by](../../RO/56/RO_0002256.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [developmentally induced by](../../RO/56/RO_0002256.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [developmentally induces](../../RO/57/RO_0002257.md) InverseOf [developmentally induced by](../../RO/56/RO_0002256.md) + +## External Comments + diff --git a/src/ontology/md/RO/56/RO_0002356.md b/src/ontology/md/RO/56/RO_0002356.md new file mode 100644 index 00000000..228f3acd --- /dev/null +++ b/src/ontology/md/RO/56/RO_0002356.md @@ -0,0 +1,43 @@ + +## Class : results in specification of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002356 + * *Label* = results in specification of + * *Definition* = The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in specification of](../../RO/56/RO_0002356.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in specification of](../../RO/56/RO_0002356.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.geneontology.org/GO.doc.development.shtml#fate + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in specification of + +## Usage + + * - + * [results in specification of](../../RO/56/RO_0002356.md) Range [cell](../../CL/00/CL_0000000.md) + * [results in specification of](../../RO/56/RO_0002356.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/56/RO_0002456.md b/src/ontology/md/RO/56/RO_0002456.md new file mode 100644 index 00000000..63cc64d9 --- /dev/null +++ b/src/ontology/md/RO/56/RO_0002456.md @@ -0,0 +1,45 @@ + +## Class : pollinated by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002456 + * *Label* = pollinated by + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [mutualistically interacts with](../../RO/42/RO_0002442.md) + +## SubProperties + + +## Other Logical Axioms + + * [pollinated by](../../RO/56/RO_0002456.md) InverseOf [pollinates](../../RO/55/RO_0002455.md) + * [pollinated by](../../RO/56/RO_0002456.md) SubPropertyOf [mutualistically interacts with](../../RO/42/RO_0002442.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has polinator + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is target of pollination interaction with + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = pollinated by + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://eol.org/schema/terms/hasPollinator + +## Usage + + * - + * [pollinated by](../../RO/56/RO_0002456.md) InverseOf [pollinates](../../RO/55/RO_0002455.md) + * [pollinated by](../../RO/56/RO_0002456.md) SubPropertyOf [mutualistically interacts with](../../RO/42/RO_0002442.md) + +## External Comments + diff --git a/src/ontology/md/RO/56/RO_0002556.md b/src/ontology/md/RO/56/RO_0002556.md new file mode 100644 index 00000000..f70bc118 --- /dev/null +++ b/src/ontology/md/RO/56/RO_0002556.md @@ -0,0 +1,42 @@ + +## Class : pathogen of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002556 + * *Label* = pathogen of + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has host](../../RO/54/RO_0002454.md) + +## SubProperties + + +## Other Logical Axioms + + * [pathogen of](../../RO/56/RO_0002556.md) InverseOf [has pathogen](../../RO/57/RO_0002557.md) + * [pathogen of](../../RO/56/RO_0002556.md) SubPropertyOf [has host](../../RO/54/RO_0002454.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = pathogen of + +## Usage + + * - + * [pathogen of](../../RO/56/RO_0002556.md) InverseOf [has pathogen](../../RO/57/RO_0002557.md) + * [pathogen of](../../RO/56/RO_0002556.md) SubPropertyOf [has host](../../RO/54/RO_0002454.md) + +## External Comments + diff --git a/src/ontology/md/RO/57/RO_0000057.md b/src/ontology/md/RO/57/RO_0000057.md new file mode 100644 index 00000000..9e092f90 --- /dev/null +++ b/src/ontology/md/RO/57/RO_0000057.md @@ -0,0 +1,66 @@ + +## Class : has participant + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000057 + * *Label* = has participant + * *Definition* = a relation between a process and a continuant, in which the continuant is somehow involved in the process + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [has participant](../../RO/57/RO_0000057.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [has participant](../../RO/57/RO_0000057.md) InverseOf [participates in](../../RO/56/RO_0000056.md) + * [has participant](../../RO/57/RO_0000057.md) Range [continuant](../../BFO/02/BFO_0000002.md) + +## Other Annotations + + * *[editor preferred term](../../IAO/11/IAO_0000111.md)* = has participant + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this blood coagulation has participant this blood clot + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this investigation has participant this investigator + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this process has participant this input material (or this output material) + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between a process and a continuant, in which the continuant is somehow involved in the process + * *[editor note](../../IAO/16/IAO_0000116.md)* = Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has_participant + * *[source](../../ce/source.md)* = http://www.obofoundry.org/ro/#OBO_REL:has_participant + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has participant + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has active participant](../../RO/18/RO_0002218.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [has input](../../RO/33/RO_0002233.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [has intermediate](../../RO/05/RO_0002505.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [has output](../../RO/34/RO_0002234.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [has participant](../../RO/57/RO_0000057.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [has participant](../../RO/57/RO_0000057.md) InverseOf [participates in](../../RO/56/RO_0000056.md) + * [has participant](../../RO/57/RO_0000057.md) Range [continuant](../../BFO/02/BFO_0000002.md) + * [results in acquisition of features of](../../RO/15/RO_0002315.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in closure of](../../RO/85/RO_0002585.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in development of](../../RO/96/RO_0002296.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in ending of](../../RO/52/RO_0002552.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in growth of](../../RO/43/RO_0002343.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in maturation of](../../RO/99/RO_0002299.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in morphogenesis of](../../RO/98/RO_0002298.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in movement of](../../RO/65/RO_0002565.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in organization of](../../RO/92/RO_0002592.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in structural organization of](../../RO/55/RO_0002355.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [transports or maintains localization of](../../RO/13/RO_0002313.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + +## External Comments + diff --git a/src/ontology/md/RO/57/RO_0002157.md b/src/ontology/md/RO/57/RO_0002157.md new file mode 100644 index 00000000..1cf3bc2b --- /dev/null +++ b/src/ontology/md/RO/57/RO_0002157.md @@ -0,0 +1,43 @@ + +## Class : has derived by descendant + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002157 + * *Label* = has derived by descendant + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [evolutionarily related to](../../RO/20/RO_0002320.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [has derived by descendant](../../RO/57/RO_0002157.md) + * [derived by descent from](../../RO/56/RO_0002156.md) InverseOf [has derived by descendant](../../RO/57/RO_0002157.md) + * [has derived by descendant](../../RO/57/RO_0002157.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has derived by descendant + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [has derived by descendant](../../RO/57/RO_0002157.md) + * [derived by descent from](../../RO/56/RO_0002156.md) InverseOf [has derived by descendant](../../RO/57/RO_0002157.md) + * [has derived by descendant](../../RO/57/RO_0002157.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## External Comments + diff --git a/src/ontology/md/RO/57/RO_0002257.md b/src/ontology/md/RO/57/RO_0002257.md new file mode 100644 index 00000000..c41c571c --- /dev/null +++ b/src/ontology/md/RO/57/RO_0002257.md @@ -0,0 +1,46 @@ + +## Class : developmentally induces + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002257 + * *Label* = developmentally induces + * *Definition* = Inverse of developmentally induced by + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [has potential to developmentally induce](../../RO/86/RO_0002386.md) + +## SubProperties + + +## Other Logical Axioms + + * [developmentally induces](../../RO/57/RO_0002257.md) InverseOf [developmentally induced by](../../RO/56/RO_0002256.md) + * [developmentally induces](../../RO/57/RO_0002257.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [developmentally induces](../../RO/57/RO_0002257.md) SubPropertyOf [has potential to developmentally induce](../../RO/86/RO_0002386.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Inverse of developmentally induced by + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = developmentally induces + +## Usage + + * - + * [developmentally induces](../../RO/57/RO_0002257.md) InverseOf [developmentally induced by](../../RO/56/RO_0002256.md) + * [developmentally induces](../../RO/57/RO_0002257.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [developmentally induces](../../RO/57/RO_0002257.md) SubPropertyOf [has potential to developmentally induce](../../RO/86/RO_0002386.md) + +## External Comments + diff --git a/src/ontology/md/RO/57/RO_0002357.md b/src/ontology/md/RO/57/RO_0002357.md new file mode 100644 index 00000000..c42fffa3 --- /dev/null +++ b/src/ontology/md/RO/57/RO_0002357.md @@ -0,0 +1,40 @@ + +## Class : results in developmental induction of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002357 + * *Label* = results in developmental induction of + * *Definition* = p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in developmental induction of](../../RO/57/RO_0002357.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in developmental induction of + +## Usage + + * - + * [results in developmental induction of](../../RO/57/RO_0002357.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/57/RO_0002457.md b/src/ontology/md/RO/57/RO_0002457.md new file mode 100644 index 00000000..de4097c1 --- /dev/null +++ b/src/ontology/md/RO/57/RO_0002457.md @@ -0,0 +1,43 @@ + +## Class : acquires nutrients from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002457 + * *Label* = acquires nutrients from + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [trophically interacts with](../../RO/38/RO_0002438.md) + +## SubProperties + + +## Other Logical Axioms + + * [acquires nutrients from](../../RO/57/RO_0002457.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + * [provides nutrients for](../../RO/69/RO_0002469.md) InverseOf [acquires nutrients from](../../RO/57/RO_0002457.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = acquires nutrients from + +## Usage + + * - + * [acquires nutrients from](../../RO/57/RO_0002457.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + * [provides nutrients for](../../RO/69/RO_0002469.md) InverseOf [acquires nutrients from](../../RO/57/RO_0002457.md) + +## External Comments + diff --git a/src/ontology/md/RO/57/RO_0002557.md b/src/ontology/md/RO/57/RO_0002557.md new file mode 100644 index 00000000..f3b0d039 --- /dev/null +++ b/src/ontology/md/RO/57/RO_0002557.md @@ -0,0 +1,42 @@ + +## Class : has pathogen + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002557 + * *Label* = has pathogen + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [host of](../../RO/53/RO_0002453.md) + +## SubProperties + + +## Other Logical Axioms + + * [has pathogen](../../RO/57/RO_0002557.md) SubPropertyOf [host of](../../RO/53/RO_0002453.md) + * [pathogen of](../../RO/56/RO_0002556.md) InverseOf [has pathogen](../../RO/57/RO_0002557.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has pathogen + +## Usage + + * - + * [has pathogen](../../RO/57/RO_0002557.md) SubPropertyOf [host of](../../RO/53/RO_0002453.md) + * [pathogen of](../../RO/56/RO_0002556.md) InverseOf [has pathogen](../../RO/57/RO_0002557.md) + +## External Comments + diff --git a/src/ontology/md/RO/57/RO_HOM0000057.md b/src/ontology/md/RO/57/RO_HOM0000057.md new file mode 100644 index 00000000..4311cb54 --- /dev/null +++ b/src/ontology/md/RO/57/RO_HOM0000057.md @@ -0,0 +1,63 @@ + +## Class : in latent homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000057 + * *Label* = in latent homology relationship with + * *Definition* = Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:0199141118, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814485, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/j.jhevol.2006.11.010, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1186/1742-9994-2-15, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000057 ] + * *Comment* = Used for structures in closely related taxa. + +## Synonyms + + * apomorphic tendency + * cryptic homology + * latent homologous to + * underlying synapomorphy + * homoiology + * homoplastic tendency + * re-awakening + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + * [in syngeny relationship with](../../RO/58/RO_HOM0000058.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in latent homology relationship with](../../RO/57/RO_HOM0000057.md) + * [in latent homology relationship with](../../RO/57/RO_HOM0000057.md) SubPropertyOf [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + * [in latent homology relationship with](../../RO/57/RO_HOM0000057.md) SubPropertyOf [in syngeny relationship with](../../RO/58/RO_HOM0000058.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = apomorphic tendency + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = cryptic homology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = latent homologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = underlying synapomorphy + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = homoiology + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = homoplastic tendency + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = re-awakening + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Used for structures in closely related taxa. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in latent homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000057 + +## Usage + + * - + * SymmetricObjectProperty [in latent homology relationship with](../../RO/57/RO_HOM0000057.md) + * [in latent homology relationship with](../../RO/57/RO_HOM0000057.md) SubPropertyOf [in parallelism relationship with](../../RO/05/RO_HOM0000005.md) + * [in latent homology relationship with](../../RO/57/RO_HOM0000057.md) SubPropertyOf [in syngeny relationship with](../../RO/58/RO_HOM0000058.md) + +## External Comments + diff --git a/src/ontology/md/RO/58/RO_0000058.md b/src/ontology/md/RO/58/RO_0000058.md new file mode 100644 index 00000000..170d1fe7 --- /dev/null +++ b/src/ontology/md/RO/58/RO_0000058.md @@ -0,0 +1,44 @@ + +## Class : is concretized as + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000058 + * *Label* = is concretized as + * *Definition* = A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [is concretized as](../../RO/58/RO_0000058.md) Domain [generically dependent continuant](../../BFO/31/BFO_0000031.md) + * [is concretized as](../../RO/58/RO_0000058.md) InverseOf [concretizes](../../RO/59/RO_0000059.md) + * [is concretized as](../../RO/58/RO_0000058.md) Range [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 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). + * *[definition](../../IAO/15/IAO_0000115.md)* = 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. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is concretized as + +## Usage + + * - + * [is concretized as](../../RO/58/RO_0000058.md) Domain [generically dependent continuant](../../BFO/31/BFO_0000031.md) + * [is concretized as](../../RO/58/RO_0000058.md) InverseOf [concretizes](../../RO/59/RO_0000059.md) + * [is concretized as](../../RO/58/RO_0000058.md) Range [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + +## External Comments + diff --git a/src/ontology/md/RO/58/RO_0002158.md b/src/ontology/md/RO/58/RO_0002158.md new file mode 100644 index 00000000..e70b43ba --- /dev/null +++ b/src/ontology/md/RO/58/RO_0002158.md @@ -0,0 +1,49 @@ + +## Class : shares ancestor with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002158 + * *Label* = shares ancestor with + * *Definition* = two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + * *Comment* = VBO calls this homologous_to + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [evolutionarily related to](../../RO/20/RO_0002320.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [shares ancestor with](../../RO/58/RO_0002158.md) + * TransitiveObjectProperty [shares ancestor with](../../RO/58/RO_0002158.md) + * [shares ancestor with](../../RO/58/RO_0002158.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + * *[curator note](../../IAO/32/IAO_0000232.md)* = Consider obsoleting and merging with child relation, 'in homology relationship with' + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = VBO calls this homologous_to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = shares ancestor with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SymmetricObjectProperty [shares ancestor with](../../RO/58/RO_0002158.md) + * TransitiveObjectProperty [shares ancestor with](../../RO/58/RO_0002158.md) + * [in homology relationship with](../../RO/01/RO_HOM0000001.md) SubPropertyOf [shares ancestor with](../../RO/58/RO_0002158.md) + * [shares ancestor with](../../RO/58/RO_0002158.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## External Comments + diff --git a/src/ontology/md/RO/58/RO_0002258.md b/src/ontology/md/RO/58/RO_0002258.md new file mode 100644 index 00000000..4a497084 --- /dev/null +++ b/src/ontology/md/RO/58/RO_0002258.md @@ -0,0 +1,54 @@ + +## Class : developmentally preceded by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002258 + * *Label* = developmentally preceded by + * *Definition* = Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + * *Comment* = This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally related to](../../RO/24/RO_0002324.md) + +## SubProperties + + +## Other Logical Axioms + + * [developmentally preceded by](../../RO/58/RO_0002258.md) SubPropertyOf [developmentally related to](../../RO/24/RO_0002324.md) + * [developmentally succeeded by](../../RO/86/RO_0002286.md) InverseOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + * *[editor note](../../IAO/16/IAO_0000116.md)* = false + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = In general you should not use this relation to make assertions - use one of the more specific relations below this one + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = developmentally preceded by + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [child nucleus of](../../RO/76/RO_0002476.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [developmentally induced by](../../RO/56/RO_0002256.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [developmentally preceded by](../../RO/58/RO_0002258.md) SubPropertyOf [developmentally related to](../../RO/24/RO_0002324.md) + * [developmentally replaces](../../RO/85/RO_0002285.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [developmentally succeeded by](../../RO/86/RO_0002286.md) InverseOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [develops from](../../RO/02/RO_0002202.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [develops in](../../RO/26/RO_0002226.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [has developmental contribution from](../../RO/54/RO_0002254.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## External Comments + diff --git a/src/ontology/md/RO/58/RO_0002458.md b/src/ontology/md/RO/58/RO_0002458.md new file mode 100644 index 00000000..cc7a83b4 --- /dev/null +++ b/src/ontology/md/RO/58/RO_0002458.md @@ -0,0 +1,46 @@ + +## Class : preyed upon by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002458 + * *Label* = preyed upon by + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [trophically interacts with](../../RO/38/RO_0002438.md) + +## SubProperties + + +## Other Logical Axioms + + * [preyed upon by](../../RO/58/RO_0002458.md) InverseOf [preys on](../../RO/39/RO_0002439.md) + * [preyed upon by](../../RO/58/RO_0002458.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has predator + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is target of predation interaction with + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = preyed upon by + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://eol.org/schema/terms/HasPredator + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://polytraits.lifewatchgreece.eu/terms/PRED + +## Usage + + * - + * [preyed upon by](../../RO/58/RO_0002458.md) InverseOf [preys on](../../RO/39/RO_0002439.md) + * [preyed upon by](../../RO/58/RO_0002458.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## External Comments + diff --git a/src/ontology/md/RO/58/RO_0002558.md b/src/ontology/md/RO/58/RO_0002558.md new file mode 100644 index 00000000..22659e25 --- /dev/null +++ b/src/ontology/md/RO/58/RO_0002558.md @@ -0,0 +1,42 @@ + +## Class : has evidence + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002558 + * *Label* = has evidence + * *Comment* = x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [has evidence](../../RO/58/RO_0002558.md) InverseOf [is evidence for](../../RO/72/RO_0002472.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/25052702 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has evidence + +## Usage + + * - + * [has evidence](../../RO/58/RO_0002558.md) InverseOf [is evidence for](../../RO/72/RO_0002472.md) + +## External Comments + diff --git a/src/ontology/md/RO/58/RO_HOM0000058.md b/src/ontology/md/RO/58/RO_HOM0000058.md new file mode 100644 index 00000000..cdd9a45c --- /dev/null +++ b/src/ontology/md/RO/58/RO_HOM0000058.md @@ -0,0 +1,51 @@ + +## Class : in syngeny relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000058 + * *Label* = in syngeny relationship with + * *Definition* = Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1186/1742-9994-2-15, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000058 ] + * *Comment* = Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + +## Synonyms + + * generative homology + * syngenous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in syngeny relationship with](../../RO/58/RO_HOM0000058.md) + * [in syngeny relationship with](../../RO/58/RO_HOM0000058.md) SubPropertyOf [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = generative homology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = syngenous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in syngeny relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000058 + +## Usage + + * - + * SymmetricObjectProperty [in syngeny relationship with](../../RO/58/RO_HOM0000058.md) + * [in latent homology relationship with](../../RO/57/RO_HOM0000057.md) SubPropertyOf [in syngeny relationship with](../../RO/58/RO_HOM0000058.md) + * [in syngeny relationship with](../../RO/58/RO_HOM0000058.md) SubPropertyOf [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + +## External Comments + diff --git a/src/ontology/md/RO/59/RO_0000059.md b/src/ontology/md/RO/59/RO_0000059.md new file mode 100644 index 00000000..ea7990b8 --- /dev/null +++ b/src/ontology/md/RO/59/RO_0000059.md @@ -0,0 +1,44 @@ + +## Class : concretizes + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000059 + * *Label* = concretizes + * *Definition* = A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [concretizes](../../RO/59/RO_0000059.md) Domain [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [concretizes](../../RO/59/RO_0000059.md) Range [generically dependent continuant](../../BFO/31/BFO_0000031.md) + * [is concretized as](../../RO/58/RO_0000058.md) InverseOf [concretizes](../../RO/59/RO_0000059.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 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). + * *[definition](../../IAO/15/IAO_0000115.md)* = 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. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = concretizes + +## Usage + + * - + * [concretizes](../../RO/59/RO_0000059.md) Domain [specifically dependent continuant](../../BFO/20/BFO_0000020.md) + * [concretizes](../../RO/59/RO_0000059.md) Range [generically dependent continuant](../../BFO/31/BFO_0000031.md) + * [is concretized as](../../RO/58/RO_0000058.md) InverseOf [concretizes](../../RO/59/RO_0000059.md) + +## External Comments + diff --git a/src/ontology/md/RO/59/RO_0002159.md b/src/ontology/md/RO/59/RO_0002159.md new file mode 100644 index 00000000..bfc7979e --- /dev/null +++ b/src/ontology/md/RO/59/RO_0002159.md @@ -0,0 +1,42 @@ + +## Class : serially homologous to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002159 + * *Label* = serially homologous to + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [evolutionarily related to](../../RO/20/RO_0002320.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [serially homologous to](../../RO/59/RO_0002159.md) + * TransitiveObjectProperty [serially homologous to](../../RO/59/RO_0002159.md) + * [serially homologous to](../../RO/59/RO_0002159.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = serially homologous to + +## Usage + + * - + * SymmetricObjectProperty [serially homologous to](../../RO/59/RO_0002159.md) + * TransitiveObjectProperty [serially homologous to](../../RO/59/RO_0002159.md) + * [serially homologous to](../../RO/59/RO_0002159.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## External Comments + diff --git a/src/ontology/md/RO/59/RO_0002459.md b/src/ontology/md/RO/59/RO_0002459.md new file mode 100644 index 00000000..d4c7f126 --- /dev/null +++ b/src/ontology/md/RO/59/RO_0002459.md @@ -0,0 +1,45 @@ + +## Class : is vector for + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002459 + * *Label* = is vector for + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## SubProperties + + +## Other Logical Axioms + + * [is vector for](../../RO/59/RO_0002459.md) InverseOf [has vector](../../RO/60/RO_0002460.md) + * [is vector for](../../RO/59/RO_0002459.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Anopheles is a vector for Plasmodium + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = a is a vector for b if a carries and transmits an infectious pathogen b into another living organism + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is vector for + +## Usage + + * - + * [has vector](../../RO/60/RO_0002460.md) SubPropertyOf [is vector for](../../RO/59/RO_0002459.md) + * [is vector for](../../RO/59/RO_0002459.md) InverseOf [has vector](../../RO/60/RO_0002460.md) + * [is vector for](../../RO/59/RO_0002459.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## External Comments + diff --git a/src/ontology/md/RO/59/RO_0002559.md b/src/ontology/md/RO/59/RO_0002559.md new file mode 100644 index 00000000..f173b45c --- /dev/null +++ b/src/ontology/md/RO/59/RO_0002559.md @@ -0,0 +1,42 @@ + +## Class : causally influenced by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002559 + * *Label* = causally influenced by + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causal relation between material entities](../../RO/06/RO_0002506.md) + +## SubProperties + + +## Other Logical Axioms + + * [causally influenced by](../../RO/59/RO_0002559.md) SubPropertyOf [causal relation between material entities](../../RO/06/RO_0002506.md) + * [causally influences](../../RO/66/RO_0002566.md) InverseOf [causally influenced by](../../RO/59/RO_0002559.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = causally influenced by (material entity to material entity) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causally influenced by + +## Usage + + * - + * [causally influenced by](../../RO/59/RO_0002559.md) SubPropertyOf [causal relation between material entities](../../RO/06/RO_0002506.md) + * [causally influences](../../RO/66/RO_0002566.md) InverseOf [causally influenced by](../../RO/59/RO_0002559.md) + * [determined by](../../RO/07/RO_0002507.md) SubPropertyOf [causally influenced by](../../RO/59/RO_0002559.md) + +## External Comments + diff --git a/src/ontology/md/RO/60/RO_0002160.md b/src/ontology/md/RO/60/RO_0002160.md new file mode 100644 index 00000000..dce25306 --- /dev/null +++ b/src/ontology/md/RO/60/RO_0002160.md @@ -0,0 +1,48 @@ + +## Class : only in taxon + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002160 + * *Label* = only in taxon + * *Definition* = x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in taxon](../../RO/62/RO_0002162.md) + +## SubProperties + + +## Other Logical Axioms + + * [only in taxon](../../RO/60/RO_0002160.md) SubPropertyOf [in taxon](../../RO/62/RO_0002162.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = lactation SubClassOf 'only in taxon' some 'Mammalia' + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + * *[editor note](../../IAO/16/IAO_0000116.md)* = The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. + + 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/17921072 + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20973947 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = only in taxon + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +## Usage + + * - + * [only in taxon](../../RO/60/RO_0002160.md) SubPropertyOf [in taxon](../../RO/62/RO_0002162.md) + +## External Comments + diff --git a/src/ontology/md/RO/60/RO_0002360.md b/src/ontology/md/RO/60/RO_0002360.md new file mode 100644 index 00000000..e044530b --- /dev/null +++ b/src/ontology/md/RO/60/RO_0002360.md @@ -0,0 +1,39 @@ + +## Class : has dendrite location + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002360 + * *Label* = has dendrite location + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [has dendrite location](../../RO/60/RO_0002360.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[source](../../ce/source.md)* = http://neurolex.org/wiki/Property:DendriteLocation + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has dendrite location + +## Usage + + * - + * [has dendrite location](../../RO/60/RO_0002360.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## External Comments + diff --git a/src/ontology/md/RO/60/RO_0002460.md b/src/ontology/md/RO/60/RO_0002460.md new file mode 100644 index 00000000..eb064dc4 --- /dev/null +++ b/src/ontology/md/RO/60/RO_0002460.md @@ -0,0 +1,42 @@ + +## Class : has vector + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002460 + * *Label* = has vector + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [is vector for](../../RO/59/RO_0002459.md) + +## SubProperties + + +## Other Logical Axioms + + * [has vector](../../RO/60/RO_0002460.md) SubPropertyOf [is vector for](../../RO/59/RO_0002459.md) + * [is vector for](../../RO/59/RO_0002459.md) InverseOf [has vector](../../RO/60/RO_0002460.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has vector + +## Usage + + * - + * [has vector](../../RO/60/RO_0002460.md) SubPropertyOf [is vector for](../../RO/59/RO_0002459.md) + * [is vector for](../../RO/59/RO_0002459.md) InverseOf [has vector](../../RO/60/RO_0002460.md) + +## External Comments + diff --git a/src/ontology/md/RO/60/RO_0002560.md b/src/ontology/md/RO/60/RO_0002560.md new file mode 100644 index 00000000..317c5292 --- /dev/null +++ b/src/ontology/md/RO/60/RO_0002560.md @@ -0,0 +1,40 @@ + +## Class : is asymmetric relational form of process class + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002560 + * *Label* = is asymmetric relational form of process class + * *Definition* = If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is relational form of process class](../../RO/62/RO_0002562.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is asymmetric relational form of process class + * *[page](../../ge/page.md)* = https://code.google.com/p/obo-relations/wiki/InteractionRelations + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * http://purl.obolibrary.org/obo/RO_0002444 [is asymmetric relational form of process class](../../RO/60/RO_0002560.md) http://purl.obolibrary.org/obo/GO_0072519 + +## External Comments + diff --git a/src/ontology/md/RO/60/RO_HOM0000060.md b/src/ontology/md/RO/60/RO_HOM0000060.md new file mode 100644 index 00000000..bbdef141 --- /dev/null +++ b/src/ontology/md/RO/60/RO_HOM0000060.md @@ -0,0 +1,57 @@ + +## Class : in apparent orthology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000060 + * *Label* = in apparent orthology relationship with + * *Definition* = Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000060, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ensembl.org/info/docs/compara/homology_method.html ] + * *Comment* = The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + +## Synonyms + + * 1:1 paralogy + * apparent 1:1 orthology + * apparent orthologous to + * pseudoorthology + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + * [in between-species paralogy relationship with](../../RO/50/RO_HOM0000050.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in apparent orthology relationship with](../../RO/60/RO_HOM0000060.md) + * [in apparent orthology relationship with](../../RO/60/RO_HOM0000060.md) SubPropertyOf [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + * [in apparent orthology relationship with](../../RO/60/RO_HOM0000060.md) SubPropertyOf [in between-species paralogy relationship with](../../RO/50/RO_HOM0000050.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = 1:1 paralogy + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = apparent 1:1 orthology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = apparent orthologous to + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = pseudoorthology + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in apparent orthology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000060 + +## Usage + + * - + * SymmetricObjectProperty [in apparent orthology relationship with](../../RO/60/RO_HOM0000060.md) + * [in apparent orthology relationship with](../../RO/60/RO_HOM0000060.md) SubPropertyOf [in 1 to 1 homology relationship with](../../RO/19/RO_HOM0000019.md) + * [in apparent orthology relationship with](../../RO/60/RO_HOM0000060.md) SubPropertyOf [in between-species paralogy relationship with](../../RO/50/RO_HOM0000050.md) + +## External Comments + diff --git a/src/ontology/md/RO/61/RO_0002161.md b/src/ontology/md/RO/61/RO_0002161.md new file mode 100644 index 00000000..923de898 --- /dev/null +++ b/src/ontology/md/RO/61/RO_0002161.md @@ -0,0 +1,44 @@ + +## Class : never in taxon + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002161 + * *Label* = never in taxon + * *Definition* = x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [taxonomic class assertion](../../RO/72/RO_0002172.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = tooth SubClassOf 'never in taxon' value 'Aves' + * *[definition](../../IAO/15/IAO_0000115.md)* = x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/17921072 + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20973947 + * *[expand assertion to](../../IAO/25/IAO_0000425.md)* = ?X DisjointWith RO_0002162 some ?Y + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = never in taxon + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/61/RO_0002461.md b/src/ontology/md/RO/61/RO_0002461.md new file mode 100644 index 00000000..22b25480 --- /dev/null +++ b/src/ontology/md/RO/61/RO_0002461.md @@ -0,0 +1,45 @@ + +## Class : partner in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002461 + * *Label* = partner in + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [participates in](../../RO/56/RO_0000056.md) + +## SubProperties + + +## Other Logical Axioms + + * [partner in](../../RO/61/RO_0002461.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = partner in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [partner in](../../RO/61/RO_0002461.md) SubPropertyOf [participates in](../../RO/56/RO_0000056.md) + * [subject participant in](../../RO/62/RO_0002462.md) SubPropertyOf [partner in](../../RO/61/RO_0002461.md) + * [target participant in](../../RO/63/RO_0002463.md) SubPropertyOf [partner in](../../RO/61/RO_0002461.md) + +## External Comments + diff --git a/src/ontology/md/RO/61/RO_0002561.md b/src/ontology/md/RO/61/RO_0002561.md new file mode 100644 index 00000000..bcfef1b6 --- /dev/null +++ b/src/ontology/md/RO/61/RO_0002561.md @@ -0,0 +1,43 @@ + +## Class : is symmetric relational form of process class + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002561 + * *Label* = is symmetric relational form of process class + * *Definition* = If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is relational form of process class](../../RO/62/RO_0002562.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is symmetric relational form of process class + * *[page](../../ge/page.md)* = https://code.google.com/p/obo-relations/wiki/InteractionRelations + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * http://purl.obolibrary.org/obo/RO_0002440 [is symmetric relational form of process class](../../RO/61/RO_0002561.md) http://purl.obolibrary.org/obo/GO_0044403 + * http://purl.obolibrary.org/obo/RO_0002441 [is symmetric relational form of process class](../../RO/61/RO_0002561.md) http://purl.obolibrary.org/obo/GO_0085031 + * http://purl.obolibrary.org/obo/RO_0002442 [is symmetric relational form of process class](../../RO/61/RO_0002561.md) http://purl.obolibrary.org/obo/GO_0085030 + * http://purl.obolibrary.org/obo/RO_0002443 [is symmetric relational form of process class](../../RO/61/RO_0002561.md) http://purl.obolibrary.org/obo/GO_0072519 + +## External Comments + diff --git a/src/ontology/md/RO/61/RO_HOM0000061.md b/src/ontology/md/RO/61/RO_HOM0000061.md new file mode 100644 index 00000000..43c398ab --- /dev/null +++ b/src/ontology/md/RO/61/RO_HOM0000061.md @@ -0,0 +1,48 @@ + +## Class : in pseudoparalogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000061 + * *Label* = in pseudoparalogy relationship with + * *Definition* = Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000061 ] + * *Comment* = These genes may come out as paralogs in a single-genome analysis. + +## Synonyms + + * pseudoparalogous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in pseudoparalogy relationship with](../../RO/61/RO_HOM0000061.md) + * [in pseudoparalogy relationship with](../../RO/61/RO_HOM0000061.md) SubPropertyOf [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = pseudoparalogous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = These genes may come out as paralogs in a single-genome analysis. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in pseudoparalogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000061 + +## Usage + + * - + * SymmetricObjectProperty [in pseudoparalogy relationship with](../../RO/61/RO_HOM0000061.md) + * [in pseudoparalogy relationship with](../../RO/61/RO_HOM0000061.md) SubPropertyOf [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + +## External Comments + diff --git a/src/ontology/md/RO/62/RO_0002162.md b/src/ontology/md/RO/62/RO_0002162.md new file mode 100644 index 00000000..da2adec5 --- /dev/null +++ b/src/ontology/md/RO/62/RO_0002162.md @@ -0,0 +1,61 @@ + +## Class : in taxon + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002162 + * *Label* = in taxon + * *Definition* = x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + * *Comment* = Connects a biological entity to its taxon of origin. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [evolutionarily related to](../../RO/20/RO_0002320.md) + +## SubProperties + + +## Other Logical Axioms + + * [in taxon](../../RO/62/RO_0002162.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [in taxon](../../RO/62/RO_0002162.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = Jennifer Deegan + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/17921072 + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20973947 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Connects a biological entity to its taxon of origin. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in taxon + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [in taxon](../../RO/62/RO_0002162.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [in taxon](../../RO/62/RO_0002162.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + * [only in taxon](../../RO/60/RO_0002160.md) SubPropertyOf [in taxon](../../RO/62/RO_0002162.md) + +## External Comments + diff --git a/src/ontology/md/RO/62/RO_0002462.md b/src/ontology/md/RO/62/RO_0002462.md new file mode 100644 index 00000000..264a62b8 --- /dev/null +++ b/src/ontology/md/RO/62/RO_0002462.md @@ -0,0 +1,40 @@ + +## Class : subject participant in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002462 + * *Label* = subject participant in + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [partner in](../../RO/61/RO_0002461.md) + +## SubProperties + + +## Other Logical Axioms + + * [subject participant in](../../RO/62/RO_0002462.md) SubPropertyOf [partner in](../../RO/61/RO_0002461.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = subject participant in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [subject participant in](../../RO/62/RO_0002462.md) SubPropertyOf [partner in](../../RO/61/RO_0002461.md) + +## External Comments + diff --git a/src/ontology/md/RO/62/RO_0002562.md b/src/ontology/md/RO/62/RO_0002562.md new file mode 100644 index 00000000..5a3872a3 --- /dev/null +++ b/src/ontology/md/RO/62/RO_0002562.md @@ -0,0 +1,43 @@ + +## Class : is relational form of process class + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002562 + * *Label* = is relational form of process class + * *Definition* = R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is relational form of a class](../../RO/94/RO_0002594.md) + +## SubProperties + + * [is symmetric relational form of process class](../../RO/61/RO_0002561.md) + * [is asymmetric relational form of process class](../../RO/60/RO_0002560.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is relational form of process class + * *[page](../../ge/page.md)* = https://code.google.com/p/obo-relations/wiki/InteractionRelations + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/62/RO_HOM0000062.md b/src/ontology/md/RO/62/RO_HOM0000062.md new file mode 100644 index 00000000..94b77a92 --- /dev/null +++ b/src/ontology/md/RO/62/RO_HOM0000062.md @@ -0,0 +1,54 @@ + +## Class : in equivalogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000062 + * *Label* = in equivalogy relationship with + * *Definition* = Historical homology that involves functional equivalent genes with retention of the ancestral function. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1093/nar/gkl1043, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000062 ] + * *Comment* = This may include examples of orthology, paralogy and xenology. + +## Synonyms + + * equivalogous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in functional equivalence relationship with](../../RO/65/RO_HOM0000065.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) + * [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) SubPropertyOf [in functional equivalence relationship with](../../RO/65/RO_HOM0000065.md) + * [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves functional equivalent genes with retention of the ancestral function. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = equivalogous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = This may include examples of orthology, paralogy and xenology. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in equivalogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000062 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) + * [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) SubPropertyOf [in functional equivalence relationship with](../../RO/65/RO_HOM0000065.md) + * [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + * [in isoorthology relationship with](../../RO/54/RO_HOM0000054.md) SubPropertyOf [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) + +## External Comments + diff --git a/src/ontology/md/RO/63/RO_0002163.md b/src/ontology/md/RO/63/RO_0002163.md new file mode 100644 index 00000000..9c8bb9df --- /dev/null +++ b/src/ontology/md/RO/63/RO_0002163.md @@ -0,0 +1,50 @@ + +## Class : spatially disjoint from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002163 + * *Label* = spatially disjoint from + * *Definition* = A is spatially_disjoint_from B if and only if they have no parts in common + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [spatially disjoint from](../../RO/63/RO_0002163.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = A is spatially_disjoint_from B if and only if they have no parts in common + * *[editor note](../../IAO/16/IAO_0000116.md)* = There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * *[curator note](../../IAO/32/IAO_0000232.md)* = Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy + * *[expand expression to](../../IAO/24/IAO_0000424.md)* = BFO_0000051 exactly 0 (BFO_0000050 some ?Y) + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = spatially disjoint from + * *[page](../../ge/page.md)* = https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + +## Usage + + * - + * [adjacent to](../../RO/20/RO_0002220.md) SubPropertyOf [spatially disjoint from](../../RO/63/RO_0002163.md) + * [spatially disjoint from](../../RO/63/RO_0002163.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## External Comments + diff --git a/src/ontology/md/RO/63/RO_0002463.md b/src/ontology/md/RO/63/RO_0002463.md new file mode 100644 index 00000000..8a79e9a4 --- /dev/null +++ b/src/ontology/md/RO/63/RO_0002463.md @@ -0,0 +1,40 @@ + +## Class : target participant in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002463 + * *Label* = target participant in + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [partner in](../../RO/61/RO_0002461.md) + +## SubProperties + + +## Other Logical Axioms + + * [target participant in](../../RO/63/RO_0002463.md) SubPropertyOf [partner in](../../RO/61/RO_0002461.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = target participant in + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [target participant in](../../RO/63/RO_0002463.md) SubPropertyOf [partner in](../../RO/61/RO_0002461.md) + +## External Comments + diff --git a/src/ontology/md/RO/63/RO_0002563.md b/src/ontology/md/RO/63/RO_0002563.md new file mode 100644 index 00000000..e3d110c2 --- /dev/null +++ b/src/ontology/md/RO/63/RO_0002563.md @@ -0,0 +1,42 @@ + +## Class : interaction relation helper property + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002563 + * *Label* = interaction relation helper property + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [helper property](../../RO/64/RO_0002464.md) + +## SubProperties + + +## Other Logical Axioms + + * [interaction relation helper property](../../RO/63/RO_0002563.md) SubPropertyOf [helper property](../../RO/64/RO_0002464.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = interaction relation helper property + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 + * *[page](../../ge/page.md)* = https://code.google.com/p/obo-relations/wiki/InteractionRelations + +## Usage + + * - + * [interaction relation helper property](../../RO/63/RO_0002563.md) SubPropertyOf [helper property](../../RO/64/RO_0002464.md) + * [is symbiosis](../../RO/65/RO_0002465.md) SubPropertyOf [interaction relation helper property](../../RO/63/RO_0002563.md) + * [molecular interaction relation helper property](../../RO/64/RO_0002564.md) SubPropertyOf [interaction relation helper property](../../RO/63/RO_0002563.md) + +## External Comments + diff --git a/src/ontology/md/RO/63/RO_HOM0000063.md b/src/ontology/md/RO/63/RO_HOM0000063.md new file mode 100644 index 00000000..fb8f23c1 --- /dev/null +++ b/src/ontology/md/RO/63/RO_HOM0000063.md @@ -0,0 +1,46 @@ + +## Class : in interology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000063 + * *Label* = in interology relationship with + * *Definition* = Historical homology that involves orthologous pairs of interacting molecules in different organisms. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1101/gr.1774904, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1126/science.287.5450.116, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000063 ] + +## Synonyms + + * interologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in interology relationship with](../../RO/63/RO_HOM0000063.md) + * [in interology relationship with](../../RO/63/RO_HOM0000063.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves orthologous pairs of interacting molecules in different organisms. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = interologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in interology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000063 + +## Usage + + * - + * SymmetricObjectProperty [in interology relationship with](../../RO/63/RO_HOM0000063.md) + * [in interology relationship with](../../RO/63/RO_HOM0000063.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## External Comments + diff --git a/src/ontology/md/RO/64/RO_0002464.md b/src/ontology/md/RO/64/RO_0002464.md new file mode 100644 index 00000000..40cd34fa --- /dev/null +++ b/src/ontology/md/RO/64/RO_0002464.md @@ -0,0 +1,38 @@ + +## Class : helper property + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002464 + * *Label* = helper property + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = helper property + +## Usage + + * - + * [interaction relation helper property](../../RO/63/RO_0002563.md) SubPropertyOf [helper property](../../RO/64/RO_0002464.md) + +## External Comments + diff --git a/src/ontology/md/RO/64/RO_0002564.md b/src/ontology/md/RO/64/RO_0002564.md new file mode 100644 index 00000000..abff6365 --- /dev/null +++ b/src/ontology/md/RO/64/RO_0002564.md @@ -0,0 +1,40 @@ + +## Class : molecular interaction relation helper property + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002564 + * *Label* = molecular interaction relation helper property + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [interaction relation helper property](../../RO/63/RO_0002563.md) + +## SubProperties + + +## Other Logical Axioms + + * [molecular interaction relation helper property](../../RO/64/RO_0002564.md) SubPropertyOf [interaction relation helper property](../../RO/63/RO_0002563.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = molecular interaction relation helper property + +## Usage + + * - + * [is kinase activity](../../RO/81/RO_0002481.md) SubPropertyOf [molecular interaction relation helper property](../../RO/64/RO_0002564.md) + * [is ubiquitination](../../RO/82/RO_0002482.md) SubPropertyOf [molecular interaction relation helper property](../../RO/64/RO_0002564.md) + * [molecular interaction relation helper property](../../RO/64/RO_0002564.md) SubPropertyOf [interaction relation helper property](../../RO/63/RO_0002563.md) + +## External Comments + diff --git a/src/ontology/md/RO/65/RO_0002465.md b/src/ontology/md/RO/65/RO_0002465.md new file mode 100644 index 00000000..50d38484 --- /dev/null +++ b/src/ontology/md/RO/65/RO_0002465.md @@ -0,0 +1,43 @@ + +## Class : is symbiosis + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002465 + * *Label* = is symbiosis + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [interaction relation helper property](../../RO/63/RO_0002563.md) + +## SubProperties + + +## Other Logical Axioms + + * [is symbiosis](../../RO/65/RO_0002465.md) SubPropertyOf [interaction relation helper property](../../RO/63/RO_0002563.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is symbiosis + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [is commensalism](../../RO/66/RO_0002466.md) SubPropertyOf [is symbiosis](../../RO/65/RO_0002465.md) + * [is mutualism](../../RO/67/RO_0002467.md) SubPropertyOf [is symbiosis](../../RO/65/RO_0002465.md) + * [is parasitism](../../RO/68/RO_0002468.md) SubPropertyOf [is symbiosis](../../RO/65/RO_0002465.md) + * [is symbiosis](../../RO/65/RO_0002465.md) SubPropertyOf [interaction relation helper property](../../RO/63/RO_0002563.md) + * [symbiosis, encompassing mutualism through parasitism](../../GO/03/GO_0044403.md) SubClassOf ObjectHasSelf() + +## External Comments + diff --git a/src/ontology/md/RO/65/RO_0002565.md b/src/ontology/md/RO/65/RO_0002565.md new file mode 100644 index 00000000..7eefdd3f --- /dev/null +++ b/src/ontology/md/RO/65/RO_0002565.md @@ -0,0 +1,43 @@ + +## Class : results in movement of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002565 + * *Label* = results in movement of + * *Definition* = Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = GOC:mtg_berkeley_2013 ] + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in movement of](../../RO/65/RO_0002565.md) Domain [GO_0040011](../../GO/11/GO_0040011.md) + * [results in movement of](../../RO/65/RO_0002565.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in movement of + +## Usage + + * - + * [results in movement of](../../RO/65/RO_0002565.md) Domain [GO_0040011](../../GO/11/GO_0040011.md) + * [results in movement of](../../RO/65/RO_0002565.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + +## External Comments + diff --git a/src/ontology/md/RO/65/RO_HOM0000065.md b/src/ontology/md/RO/65/RO_HOM0000065.md new file mode 100644 index 00000000..c89fa1b1 --- /dev/null +++ b/src/ontology/md/RO/65/RO_HOM0000065.md @@ -0,0 +1,47 @@ + +## Class : in functional equivalence relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000065 + * *Label* = in functional equivalence relationship with + * *Definition* = Similarity that is characterized by interchangeability in function. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814484, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1038/415741a, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000065 ] + +## Synonyms + + * functional similarity + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in functional equivalence relationship with](../../RO/65/RO_HOM0000065.md) + * [in functional equivalence relationship with](../../RO/65/RO_HOM0000065.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Similarity that is characterized by interchangeability in function. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = functional similarity + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in functional equivalence relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000065 + +## Usage + + * - + * SymmetricObjectProperty [in functional equivalence relationship with](../../RO/65/RO_HOM0000065.md) + * [in equivalogy relationship with](../../RO/62/RO_HOM0000062.md) SubPropertyOf [in functional equivalence relationship with](../../RO/65/RO_HOM0000065.md) + * [in functional equivalence relationship with](../../RO/65/RO_HOM0000065.md) SubPropertyOf [in similarity relationship with](../../RO/00/RO_HOM0000000.md) + +## External Comments + diff --git a/src/ontology/md/RO/66/RO_0002466.md b/src/ontology/md/RO/66/RO_0002466.md new file mode 100644 index 00000000..87868a58 --- /dev/null +++ b/src/ontology/md/RO/66/RO_0002466.md @@ -0,0 +1,40 @@ + +## Class : is commensalism + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002466 + * *Label* = is commensalism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is symbiosis](../../RO/65/RO_0002465.md) + +## SubProperties + + +## Other Logical Axioms + + * [is commensalism](../../RO/66/RO_0002466.md) SubPropertyOf [is symbiosis](../../RO/65/RO_0002465.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is commensalism + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [commensalism](../../GO/31/GO_0085031.md) SubClassOf ObjectHasSelf() + * [is commensalism](../../RO/66/RO_0002466.md) SubPropertyOf [is symbiosis](../../RO/65/RO_0002465.md) + +## External Comments + diff --git a/src/ontology/md/RO/66/RO_0002566.md b/src/ontology/md/RO/66/RO_0002566.md new file mode 100644 index 00000000..c84a685b --- /dev/null +++ b/src/ontology/md/RO/66/RO_0002566.md @@ -0,0 +1,48 @@ + +## Class : causally influences + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002566 + * *Label* = causally influences + * *Definition* = Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causal relation between material entities](../../RO/06/RO_0002506.md) + +## SubProperties + + +## Other Logical Axioms + + * [causally influences](../../RO/66/RO_0002566.md) InverseOf [causally influenced by](../../RO/59/RO_0002559.md) + * [causally influences](../../RO/66/RO_0002566.md) SubPropertyOf [causal relation between material entities](../../RO/06/RO_0002506.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = causally influences (material entity to material entity) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causally influences + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [causally influences](../../RO/66/RO_0002566.md) InverseOf [causally influenced by](../../RO/59/RO_0002559.md) + * [causally influences](../../RO/66/RO_0002566.md) SubPropertyOf [causal relation between material entities](../../RO/06/RO_0002506.md) + * [causally influences](../../RO/66/RO_0002566.md) some [material entity](../../BFO/40/BFO_0000040.md) SubClassOf [capable of](../../RO/15/RO_0002215.md) some [participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md)or[participates in](../../RO/56/RO_0000056.md) some [causally upstream of or within](../../RO/18/RO_0002418.md) some [process](../../BFO/15/BFO_0000015.md) + * [determines](../../RO/08/RO_0002508.md) SubPropertyOf [causally influences](../../RO/66/RO_0002566.md) + * [molecularly controls](../../RO/48/RO_0002448.md) SubPropertyOf [causally influences](../../RO/66/RO_0002566.md) + +## External Comments + diff --git a/src/ontology/md/RO/66/RO_HOM0000066.md b/src/ontology/md/RO/66/RO_HOM0000066.md new file mode 100644 index 00000000..1c179e34 --- /dev/null +++ b/src/ontology/md/RO/66/RO_HOM0000066.md @@ -0,0 +1,48 @@ + +## Class : in iterative homology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000066 + * *Label* = in iterative homology relationship with + * *Definition* = Biological homology that involves parts of the same organism. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1146/annurev.es.20.110189.000411, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000066 ] + +## Synonyms + + * iterative homologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + * [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) SubPropertyOf [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Biological homology that involves parts of the same organism. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = iterative homologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in iterative homology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000066 + +## Usage + + * - + * SymmetricObjectProperty [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + * [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) SubPropertyOf [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + * [in paramorphism relationship with](../../RO/74/RO_HOM0000074.md) SubPropertyOf [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + * [in serial homology relationship with](../../RO/27/RO_HOM0000027.md) SubPropertyOf [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + +## External Comments + diff --git a/src/ontology/md/RO/67/RO_0002467.md b/src/ontology/md/RO/67/RO_0002467.md new file mode 100644 index 00000000..70389901 --- /dev/null +++ b/src/ontology/md/RO/67/RO_0002467.md @@ -0,0 +1,40 @@ + +## Class : is mutualism + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002467 + * *Label* = is mutualism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is symbiosis](../../RO/65/RO_0002465.md) + +## SubProperties + + +## Other Logical Axioms + + * [is mutualism](../../RO/67/RO_0002467.md) SubPropertyOf [is symbiosis](../../RO/65/RO_0002465.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is mutualism + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [is mutualism](../../RO/67/RO_0002467.md) SubPropertyOf [is symbiosis](../../RO/65/RO_0002465.md) + * [mutualism](../../GO/30/GO_0085030.md) SubClassOf ObjectHasSelf() + +## External Comments + diff --git a/src/ontology/md/RO/67/RO_0002567.md b/src/ontology/md/RO/67/RO_0002567.md new file mode 100644 index 00000000..94d26c7e --- /dev/null +++ b/src/ontology/md/RO/67/RO_0002567.md @@ -0,0 +1,43 @@ + +## Class : biomechanically related to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002567 + * *Label* = biomechanically related to + * *Definition* = A relation that holds between elements of a musculoskeletal system or its analogs. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [functionally related to](../../RO/28/RO_0002328.md) + +## SubProperties + + +## Other Logical Axioms + + * [biomechanically related to](../../RO/67/RO_0002567.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that holds between elements of a musculoskeletal system or its analogs. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = biomechanically related to + +## Usage + + * - + * [biomechanically related to](../../RO/67/RO_0002567.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + * [has muscle antagonist](../../RO/68/RO_0002568.md) SubPropertyOf [biomechanically related to](../../RO/67/RO_0002567.md) + * [has muscle insertion](../../RO/73/RO_0002373.md) SubPropertyOf [biomechanically related to](../../RO/67/RO_0002567.md) + * [has muscle origin](../../RO/72/RO_0002372.md) SubPropertyOf [biomechanically related to](../../RO/67/RO_0002567.md) + +## External Comments + diff --git a/src/ontology/md/RO/68/RO_0002468.md b/src/ontology/md/RO/68/RO_0002468.md new file mode 100644 index 00000000..1d7b3334 --- /dev/null +++ b/src/ontology/md/RO/68/RO_0002468.md @@ -0,0 +1,41 @@ + +## Class : is parasitism + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002468 + * *Label* = is parasitism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is symbiosis](../../RO/65/RO_0002465.md) + +## SubProperties + + +## Other Logical Axioms + + * [is parasitism](../../RO/68/RO_0002468.md) SubPropertyOf [is symbiosis](../../RO/65/RO_0002465.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is parasitism + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [is parasitism](../../RO/68/RO_0002468.md) SubPropertyOf [is symbiosis](../../RO/65/RO_0002465.md) + * [parasitism](../../GO/19/GO_0072519.md) SubClassOf ObjectHasSelf() + +## External Comments + diff --git a/src/ontology/md/RO/68/RO_0002568.md b/src/ontology/md/RO/68/RO_0002568.md new file mode 100644 index 00000000..d8ecbbea --- /dev/null +++ b/src/ontology/md/RO/68/RO_0002568.md @@ -0,0 +1,41 @@ + +## Class : has muscle antagonist + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002568 + * *Label* = has muscle antagonist + * *Definition* = m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [biomechanically related to](../../RO/67/RO_0002567.md) + +## SubProperties + + +## Other Logical Axioms + + * [has muscle antagonist](../../RO/68/RO_0002568.md) SubPropertyOf [biomechanically related to](../../RO/67/RO_0002567.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = Wikipedia:Antagonist_(muscle) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has muscle antagonist + +## Usage + + * - + * [has muscle antagonist](../../RO/68/RO_0002568.md) SubPropertyOf [biomechanically related to](../../RO/67/RO_0002567.md) + +## External Comments + diff --git a/src/ontology/md/RO/68/RO_HOM0000068.md b/src/ontology/md/RO/68/RO_HOM0000068.md new file mode 100644 index 00000000..facd671c --- /dev/null +++ b/src/ontology/md/RO/68/RO_HOM0000068.md @@ -0,0 +1,50 @@ + +## Class : in paraxenology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000068 + * *Label* = in paraxenology relationship with + * *Definition* = Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000068, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ncbi.nlm.nih.gov/pubmed/3065587 ] + +## Synonyms + + * duplicate xenology + * multiple xenology + * paraxenologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in paraxenology relationship with](../../RO/68/RO_HOM0000068.md) + * [in paraxenology relationship with](../../RO/68/RO_HOM0000068.md) SubPropertyOf [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = duplicate xenology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = multiple xenology + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = paraxenologous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in paraxenology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000068 + +## Usage + + * - + * SymmetricObjectProperty [in paraxenology relationship with](../../RO/68/RO_HOM0000068.md) + * [in paraxenology relationship with](../../RO/68/RO_HOM0000068.md) SubPropertyOf [in xenology relationship with](../../RO/18/RO_HOM0000018.md) + +## External Comments + diff --git a/src/ontology/md/RO/69/RO_0002469.md b/src/ontology/md/RO/69/RO_0002469.md new file mode 100644 index 00000000..ee1434b1 --- /dev/null +++ b/src/ontology/md/RO/69/RO_0002469.md @@ -0,0 +1,42 @@ + +## Class : provides nutrients for + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002469 + * *Label* = provides nutrients for + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [trophically interacts with](../../RO/38/RO_0002438.md) + +## SubProperties + + +## Other Logical Axioms + + * [provides nutrients for](../../RO/69/RO_0002469.md) InverseOf [acquires nutrients from](../../RO/57/RO_0002457.md) + * [provides nutrients for](../../RO/69/RO_0002469.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = provides nutrients for + +## Usage + + * - + * [provides nutrients for](../../RO/69/RO_0002469.md) InverseOf [acquires nutrients from](../../RO/57/RO_0002457.md) + * [provides nutrients for](../../RO/69/RO_0002469.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## External Comments + diff --git a/src/ontology/md/RO/69/RO_0002569.md b/src/ontology/md/RO/69/RO_0002569.md new file mode 100644 index 00000000..d020cb79 --- /dev/null +++ b/src/ontology/md/RO/69/RO_0002569.md @@ -0,0 +1,42 @@ + +## Class : has branching part + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002569 + * *Label* = has branching part + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [in branching relationship with](../../RO/75/RO_0002375.md) + +## SubProperties + + +## Other Logical Axioms + + * [has branching part](../../RO/69/RO_0002569.md) InverseOf [branching part of](../../RO/80/RO_0002380.md) + * [has branching part](../../RO/69/RO_0002569.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has branching part + +## Usage + + * - + * [has branching part](../../RO/69/RO_0002569.md) InverseOf [branching part of](../../RO/80/RO_0002380.md) + * [has branching part](../../RO/69/RO_0002569.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + +## External Comments + diff --git a/src/ontology/md/RO/69/RO_HOM0000069.md b/src/ontology/md/RO/69/RO_HOM0000069.md new file mode 100644 index 00000000..78e5024b --- /dev/null +++ b/src/ontology/md/RO/69/RO_HOM0000069.md @@ -0,0 +1,48 @@ + +## Class : in plerology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000069 + * *Label* = in plerology relationship with + * *Definition* = Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000069, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://www.ncbi.nlm.nih.gov/pubmed/3065587 ] + * *Comment* = This phenomenon is usually due to gene conversion process. + +## Synonyms + + * plerologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in plerology relationship with](../../RO/69/RO_HOM0000069.md) + * [in plerology relationship with](../../RO/69/RO_HOM0000069.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = plerologous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = This phenomenon is usually due to gene conversion process. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in plerology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000069 + +## Usage + + * - + * SymmetricObjectProperty [in plerology relationship with](../../RO/69/RO_HOM0000069.md) + * [in plerology relationship with](../../RO/69/RO_HOM0000069.md) SubPropertyOf [in paralogy relationship with](../../RO/11/RO_HOM0000011.md) + +## External Comments + diff --git a/src/ontology/md/RO/70/RO_0002170.md b/src/ontology/md/RO/70/RO_0002170.md new file mode 100644 index 00000000..ab1b6008 --- /dev/null +++ b/src/ontology/md/RO/70/RO_0002170.md @@ -0,0 +1,53 @@ + +## Class : connected to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002170 + * *Label* = connected to + * *Definition* = a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [connected to](../../RO/70/RO_0002170.md) Domain [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connected to](../../RO/70/RO_0002170.md) Range [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connected to](../../RO/70/RO_0002170.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + * *[definition](../../IAO/15/IAO_0000115.md)* = a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = connected to + * *[page](../../ge/page.md)* = https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + * *[page](../../ge/page.md)* = https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [attached to](../../RO/71/RO_0002371.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + * [connected to](../../RO/70/RO_0002170.md) Domain [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connected to](../../RO/70/RO_0002170.md) Range [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connected to](../../RO/70/RO_0002170.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [drains](../../RO/79/RO_0002179.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + * [receives input from](../../RO/85/RO_0002485.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + * [sends output to](../../RO/86/RO_0002486.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + * [supplies](../../RO/78/RO_0002178.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## External Comments + diff --git a/src/ontology/md/RO/70/RO_0002470.md b/src/ontology/md/RO/70/RO_0002470.md new file mode 100644 index 00000000..8c77f7d8 --- /dev/null +++ b/src/ontology/md/RO/70/RO_0002470.md @@ -0,0 +1,41 @@ + +## Class : eats + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002470 + * *Label* = eats + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [trophically interacts with](../../RO/38/RO_0002438.md) + +## SubProperties + + +## Other Logical Axioms + + * [eats](../../RO/70/RO_0002470.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is subject of eating interaction with + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = eats + +## Usage + + * - + * [eats](../../RO/70/RO_0002470.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## External Comments + diff --git a/src/ontology/md/RO/70/RO_0002570.md b/src/ontology/md/RO/70/RO_0002570.md new file mode 100644 index 00000000..d3b0ad0e --- /dev/null +++ b/src/ontology/md/RO/70/RO_0002570.md @@ -0,0 +1,48 @@ + +## Class : conduit for + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002570 + * *Label* = conduit for + * *Definition* = x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [conduit for](../../RO/70/RO_0002570.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [conduit for](../../RO/70/RO_0002570.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [conduit for](../../RO/70/RO_0002570.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = UBERON:cjm + * *[curator note](../../IAO/32/IAO_0000232.md)* = This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = conduit for + +## Usage + + * - + * [conduit for](../../RO/70/RO_0002570.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [conduit for](../../RO/70/RO_0002570.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [conduit for](../../RO/70/RO_0002570.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## External Comments + diff --git a/src/ontology/md/RO/71/RO_0002171.md b/src/ontology/md/RO/71/RO_0002171.md new file mode 100644 index 00000000..5a1757a7 --- /dev/null +++ b/src/ontology/md/RO/71/RO_0002171.md @@ -0,0 +1,44 @@ + +## Class : mutually spatially disjoint with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002171 + * *Label* = mutually spatially disjoint with + * *Definition* = A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on a class](../../RO/20/RO_0002420.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = non-overlapping with + * *[alternative term](../../IAO/18/IAO_0000118.md)* = shares no parts with + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * *[expand assertion to](../../IAO/25/IAO_0000425.md)* = Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = mutually spatially disjoint with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/RO_0002163 + * *[page](../../ge/page.md)* = https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/71/RO_0002371.md b/src/ontology/md/RO/71/RO_0002371.md new file mode 100644 index 00000000..06700978 --- /dev/null +++ b/src/ontology/md/RO/71/RO_0002371.md @@ -0,0 +1,50 @@ + +## Class : attached to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002371 + * *Label* = attached to + * *Definition* = a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [connected to](../../RO/70/RO_0002170.md) + * [attached to part of](../../RO/77/RO_0002177.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [attached to](../../RO/71/RO_0002371.md) + * [attached to](../../RO/71/RO_0002371.md) SubPropertyOf [attached to part of](../../RO/77/RO_0002177.md) + * [attached to](../../RO/71/RO_0002371.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = attached to + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SymmetricObjectProperty [attached to](../../RO/71/RO_0002371.md) + * [attached to](../../RO/71/RO_0002371.md) SubPropertyOf [attached to part of](../../RO/77/RO_0002177.md) + * [attached to](../../RO/71/RO_0002371.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + * [has muscle insertion](../../RO/73/RO_0002373.md) SubPropertyOf [attached to](../../RO/71/RO_0002371.md) + * [has muscle origin](../../RO/72/RO_0002372.md) SubPropertyOf [attached to](../../RO/71/RO_0002371.md) + +## External Comments + diff --git a/src/ontology/md/RO/71/RO_0002471.md b/src/ontology/md/RO/71/RO_0002471.md new file mode 100644 index 00000000..66910344 --- /dev/null +++ b/src/ontology/md/RO/71/RO_0002471.md @@ -0,0 +1,41 @@ + +## Class : is eaten by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002471 + * *Label* = is eaten by + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [trophically interacts with](../../RO/38/RO_0002438.md) + +## SubProperties + + +## Other Logical Axioms + + * [is eaten by](../../RO/71/RO_0002471.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is target of eating interaction with + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is eaten by + +## Usage + + * - + * [is eaten by](../../RO/71/RO_0002471.md) SubPropertyOf [trophically interacts with](../../RO/38/RO_0002438.md) + +## External Comments + diff --git a/src/ontology/md/RO/71/RO_0002571.md b/src/ontology/md/RO/71/RO_0002571.md new file mode 100644 index 00000000..c4b72e09 --- /dev/null +++ b/src/ontology/md/RO/71/RO_0002571.md @@ -0,0 +1,46 @@ + +## Class : lumen of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002571 + * *Label* = lumen of + * *Definition* = x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [part of](../../BFO/50/BFO_0000050.md) + +## SubProperties + + +## Other Logical Axioms + + * [lumen of](../../RO/71/RO_0002571.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [lumen of](../../RO/71/RO_0002571.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = GOC:cjm + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = lumen of + +## Usage + + * - + * [lumen of](../../RO/71/RO_0002571.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [lumen of](../../RO/71/RO_0002571.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [luminal space of](../../RO/72/RO_0002572.md) SubPropertyOf [lumen of](../../RO/71/RO_0002571.md) + +## External Comments + diff --git a/src/ontology/md/RO/71/RO_HOM0000071.md b/src/ontology/md/RO/71/RO_HOM0000071.md new file mode 100644 index 00000000..617a44ed --- /dev/null +++ b/src/ontology/md/RO/71/RO_HOM0000071.md @@ -0,0 +1,50 @@ + +## Class : in homotopy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000071 + * *Label* = in homotopy relationship with + * *Definition* = Structural homology that involves structures with the same or similar relative positions. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = ISBN:0123195837, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814484, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814485, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000071 ] + * *Comment* = Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + +## Synonyms + + * homotopous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in homotopy relationship with](../../RO/71/RO_HOM0000071.md) + * [in homotopy relationship with](../../RO/71/RO_HOM0000071.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Structural homology that involves structures with the same or similar relative positions. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = homotopous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in homotopy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000071 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in homotopy relationship with](../../RO/71/RO_HOM0000071.md) + * [in homotopy relationship with](../../RO/71/RO_HOM0000071.md) SubPropertyOf [in structural homology relationship with](../../RO/06/RO_HOM0000006.md) + +## External Comments + diff --git a/src/ontology/md/RO/72/RO_0002172.md b/src/ontology/md/RO/72/RO_0002172.md new file mode 100644 index 00000000..7c7eb3b0 --- /dev/null +++ b/src/ontology/md/RO/72/RO_0002172.md @@ -0,0 +1,47 @@ + +## Class : taxonomic class assertion + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002172 + * *Label* = taxonomic class assertion + * *Definition* = An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on a class](../../RO/20/RO_0002420.md) + +## SubProperties + + * [never in taxon](../../RO/61/RO_0002161.md) + * [ambiguous for taxon](../../RO/73/RO_0002173.md) + * [dubious for taxon](../../RO/74/RO_0002174.md) + * [present in taxon](../../RO/75/RO_0002175.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = taxonomic class assertion + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/72/RO_0002372.md b/src/ontology/md/RO/72/RO_0002372.md new file mode 100644 index 00000000..8d3b36b5 --- /dev/null +++ b/src/ontology/md/RO/72/RO_0002372.md @@ -0,0 +1,45 @@ + +## Class : has muscle origin + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002372 + * *Label* = has muscle origin + * *Definition* = m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [attached to](../../RO/71/RO_0002371.md) + * [biomechanically related to](../../RO/67/RO_0002567.md) + +## SubProperties + + +## Other Logical Axioms + + * [has muscle origin](../../RO/72/RO_0002372.md) SubPropertyOf [attached to](../../RO/71/RO_0002371.md) + * [has muscle origin](../../RO/72/RO_0002372.md) SubPropertyOf [biomechanically related to](../../RO/67/RO_0002567.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = Wikipedia:Insertion_(anatomy) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has muscle origin + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://dbpedia.org/property/origin + +## Usage + + * - + * [has muscle origin](../../RO/72/RO_0002372.md) SubPropertyOf [attached to](../../RO/71/RO_0002371.md) + * [has muscle origin](../../RO/72/RO_0002372.md) SubPropertyOf [biomechanically related to](../../RO/67/RO_0002567.md) + +## External Comments + diff --git a/src/ontology/md/RO/72/RO_0002472.md b/src/ontology/md/RO/72/RO_0002472.md new file mode 100644 index 00000000..ee090d99 --- /dev/null +++ b/src/ontology/md/RO/72/RO_0002472.md @@ -0,0 +1,43 @@ + +## Class : is evidence for + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002472 + * *Label* = is evidence for + * *Definition* = A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and +the a supports either the existence of b, or the truth value of b. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [has evidence](../../RO/58/RO_0002558.md) InverseOf [is evidence for](../../RO/72/RO_0002472.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and +the a supports either the existence of b, or the truth value of b. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is evidence for + +## Usage + + * - + * [has evidence](../../RO/58/RO_0002558.md) InverseOf [is evidence for](../../RO/72/RO_0002472.md) + +## External Comments + diff --git a/src/ontology/md/RO/72/RO_0002572.md b/src/ontology/md/RO/72/RO_0002572.md new file mode 100644 index 00000000..3f24dae1 --- /dev/null +++ b/src/ontology/md/RO/72/RO_0002572.md @@ -0,0 +1,44 @@ + +## Class : luminal space of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002572 + * *Label* = luminal space of + * *Definition* = s is luminal space of x iff s is lumen_of x and s is an immaterial entity + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [lumen of](../../RO/71/RO_0002571.md) + +## SubProperties + + +## Other Logical Axioms + + * [luminal space of](../../RO/72/RO_0002572.md) Domain [immaterial entity](../../BFO/41/BFO_0000141.md) + * [luminal space of](../../RO/72/RO_0002572.md) SubPropertyOf [lumen of](../../RO/71/RO_0002571.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = s is luminal space of x iff s is lumen_of x and s is an immaterial entity + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = luminal space of + +## Usage + + * - + * [luminal space of](../../RO/72/RO_0002572.md) Domain [immaterial entity](../../BFO/41/BFO_0000141.md) + * [luminal space of](../../RO/72/RO_0002572.md) SubPropertyOf [lumen of](../../RO/71/RO_0002571.md) + +## External Comments + diff --git a/src/ontology/md/RO/72/RO_HOM0000072.md b/src/ontology/md/RO/72/RO_HOM0000072.md new file mode 100644 index 00000000..9359cd65 --- /dev/null +++ b/src/ontology/md/RO/72/RO_HOM0000072.md @@ -0,0 +1,48 @@ + +## Class : in homeosis relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000072 + * *Label* = in homeosis relationship with + * *Definition* = Biological homology that involves an ectopic structure and the normally positioned structure. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/BF02814485, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1016/j.cell.2008.06.030, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000072 ] + +## Synonyms + + * heterotopy + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in homeosis relationship with](../../RO/72/RO_HOM0000072.md) + * [in homeosis relationship with](../../RO/72/RO_HOM0000072.md) SubPropertyOf [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Biological homology that involves an ectopic structure and the normally positioned structure. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = heterotopy + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in homeosis relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000072 + +## Usage + + * - + * DisjointObjectProperties( ) + * SymmetricObjectProperty [in homeosis relationship with](../../RO/72/RO_HOM0000072.md) + * [in homeosis relationship with](../../RO/72/RO_HOM0000072.md) SubPropertyOf [in biological homology relationship with](../../RO/08/RO_HOM0000008.md) + +## External Comments + diff --git a/src/ontology/md/RO/73/RO_0002173.md b/src/ontology/md/RO/73/RO_0002173.md new file mode 100644 index 00000000..df3b8cc2 --- /dev/null +++ b/src/ontology/md/RO/73/RO_0002173.md @@ -0,0 +1,39 @@ + +## Class : ambiguous for taxon + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002173 + * *Label* = ambiguous for taxon + * *Definition* = S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [taxonomic class assertion](../../RO/72/RO_0002172.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ambiguous for taxon + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/73/RO_0002373.md b/src/ontology/md/RO/73/RO_0002373.md new file mode 100644 index 00000000..69121bf2 --- /dev/null +++ b/src/ontology/md/RO/73/RO_0002373.md @@ -0,0 +1,45 @@ + +## Class : has muscle insertion + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002373 + * *Label* = has muscle insertion + * *Definition* = m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [attached to](../../RO/71/RO_0002371.md) + * [biomechanically related to](../../RO/67/RO_0002567.md) + +## SubProperties + + +## Other Logical Axioms + + * [has muscle insertion](../../RO/73/RO_0002373.md) SubPropertyOf [attached to](../../RO/71/RO_0002371.md) + * [has muscle insertion](../../RO/73/RO_0002373.md) SubPropertyOf [biomechanically related to](../../RO/67/RO_0002567.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = Wikipedia:Insertion_(anatomy) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has muscle insertion + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://dbpedia.org/property/insertion + +## Usage + + * - + * [has muscle insertion](../../RO/73/RO_0002373.md) SubPropertyOf [attached to](../../RO/71/RO_0002371.md) + * [has muscle insertion](../../RO/73/RO_0002373.md) SubPropertyOf [biomechanically related to](../../RO/67/RO_0002567.md) + +## External Comments + diff --git a/src/ontology/md/RO/73/RO_0002473.md b/src/ontology/md/RO/73/RO_0002473.md new file mode 100644 index 00000000..7de1a88f --- /dev/null +++ b/src/ontology/md/RO/73/RO_0002473.md @@ -0,0 +1,45 @@ + +## Class : composed primarily of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002473 + * *Label* = composed primarily of + * *Definition* = x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has part](../../BFO/51/BFO_0000051.md) + +## SubProperties + + +## Other Logical Axioms + + * [composed primarily of](../../RO/73/RO_0002473.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' + * *[definition](../../IAO/15/IAO_0000115.md)* = x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = composed primarily of + +## Usage + + * - + * [composed primarily of](../../RO/73/RO_0002473.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + +## External Comments + diff --git a/src/ontology/md/RO/73/RO_0002573.md b/src/ontology/md/RO/73/RO_0002573.md new file mode 100644 index 00000000..fe52fabc --- /dev/null +++ b/src/ontology/md/RO/73/RO_0002573.md @@ -0,0 +1,43 @@ + +## Class : has modifier + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002573 + * *Label* = has modifier + * *Definition* = A relation that holds between an attribute or a qualifier and another attribute. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [has modifier](../../RO/73/RO_0002573.md) Domain [quality](../../PATO/01/PATO_0000001.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A relation that holds between an attribute or a qualifier and another attribute. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * *[curator note](../../IAO/32/IAO_0000232.md)* = This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has modifier + +## Usage + + * - + * [has modifier](../../RO/73/RO_0002573.md) Domain [quality](../../PATO/01/PATO_0000001.md) + +## External Comments + diff --git a/src/ontology/md/RO/73/RO_HOM0000073.md b/src/ontology/md/RO/73/RO_HOM0000073.md new file mode 100644 index 00000000..b4e8c6e8 --- /dev/null +++ b/src/ontology/md/RO/73/RO_HOM0000073.md @@ -0,0 +1,51 @@ + +## Class : in homoeology relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000073 + * *Label* = in homoeology relationship with + * *Definition* = Synology that results from allopolyploidy. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1073/pnas.0505156102, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000073 ] + * *Comment* = On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + +## Synonyms + + * homoeologous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in synology relationship with](../../RO/53/RO_HOM0000053.md) + * [in ohnology relationship with](../../RO/22/RO_HOM0000022.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in homoeology relationship with](../../RO/73/RO_HOM0000073.md) + * [in homoeology relationship with](../../RO/73/RO_HOM0000073.md) SubPropertyOf [in ohnology relationship with](../../RO/22/RO_HOM0000022.md) + * [in homoeology relationship with](../../RO/73/RO_HOM0000073.md) SubPropertyOf [in synology relationship with](../../RO/53/RO_HOM0000053.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Synology that results from allopolyploidy. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = homoeologous to + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in homoeology relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000073 + +## Usage + + * - + * SymmetricObjectProperty [in homoeology relationship with](../../RO/73/RO_HOM0000073.md) + * [in homoeology relationship with](../../RO/73/RO_HOM0000073.md) SubPropertyOf [in ohnology relationship with](../../RO/22/RO_HOM0000022.md) + * [in homoeology relationship with](../../RO/73/RO_HOM0000073.md) SubPropertyOf [in synology relationship with](../../RO/53/RO_HOM0000053.md) + +## External Comments + diff --git a/src/ontology/md/RO/74/RO_0002174.md b/src/ontology/md/RO/74/RO_0002174.md new file mode 100644 index 00000000..c5fe0e36 --- /dev/null +++ b/src/ontology/md/RO/74/RO_0002174.md @@ -0,0 +1,43 @@ + +## Class : dubious for taxon + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002174 + * *Label* = dubious for taxon + * *Definition* = S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. + * *Comment* = This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [taxonomic class assertion](../../RO/72/RO_0002172.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. + * *[term editor](../../IAO/17/IAO_0000117.md)* = https://orcid.org/0000-0002-6601-2165 + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = dubious for taxon + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/74/RO_0002374.md b/src/ontology/md/RO/74/RO_0002374.md new file mode 100644 index 00000000..39e7b7a7 --- /dev/null +++ b/src/ontology/md/RO/74/RO_0002374.md @@ -0,0 +1,46 @@ + +## Class : has fused element + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002374 + * *Label* = has fused element + * *Definition* = x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + * *Comment* = A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [evolutionarily related to](../../RO/20/RO_0002320.md) + +## SubProperties + + +## Other Logical Axioms + + * [has fused element](../../RO/74/RO_0002374.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = false + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has fused element + +## Usage + + * - + * [has fused element](../../RO/74/RO_0002374.md) SubPropertyOf [evolutionarily related to](../../RO/20/RO_0002320.md) + +## External Comments + diff --git a/src/ontology/md/RO/74/RO_0002474.md b/src/ontology/md/RO/74/RO_0002474.md new file mode 100644 index 00000000..1b83f7c9 --- /dev/null +++ b/src/ontology/md/RO/74/RO_0002474.md @@ -0,0 +1,38 @@ + +## Class : dispositional interpretation + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002474 + * *Label* = dispositional interpretation + * *Definition* = An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on an object property](../../RO/22/RO_0002422.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = dispositional interpretation + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/74/RO_0002574.md b/src/ontology/md/RO/74/RO_0002574.md new file mode 100644 index 00000000..c1805f42 --- /dev/null +++ b/src/ontology/md/RO/74/RO_0002574.md @@ -0,0 +1,45 @@ + +## Class : participates in a biotic-biotic interaction with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002574 + * *Label* = participates in a biotic-biotic interaction with + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [biotically interacts with](../../RO/37/RO_0002437.md) + +## SubProperties + + +## Other Logical Axioms + + * [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) SubPropertyOf [biotically interacts with](../../RO/37/RO_0002437.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = participates in a biotic-biotic interaction with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 + +## Usage + + * - + * [allelopath of](../../RO/55/RO_0002555.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + * [is vector for](../../RO/59/RO_0002459.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + * [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) SubPropertyOf [biotically interacts with](../../RO/37/RO_0002437.md) + * [symbiotically interacts with](../../RO/40/RO_0002440.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + * [trophically interacts with](../../RO/38/RO_0002438.md) SubPropertyOf [participates in a biotic-biotic interaction with](../../RO/74/RO_0002574.md) + +## External Comments + diff --git a/src/ontology/md/RO/74/RO_HOM0000074.md b/src/ontology/md/RO/74/RO_HOM0000074.md new file mode 100644 index 00000000..ef314db1 --- /dev/null +++ b/src/ontology/md/RO/74/RO_HOM0000074.md @@ -0,0 +1,49 @@ + +## Class : in paramorphism relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000074 + * *Label* = in paramorphism relationship with + * *Definition* = Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1007/s10441-007-9023-8, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000074 ] + +## Synonyms + + * axis paramorphism + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + * [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in paramorphism relationship with](../../RO/74/RO_HOM0000074.md) + * [in paramorphism relationship with](../../RO/74/RO_HOM0000074.md) SubPropertyOf [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + * [in paramorphism relationship with](../../RO/74/RO_HOM0000074.md) SubPropertyOf [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md)* = axis paramorphism + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in paramorphism relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000074 + +## Usage + + * - + * SymmetricObjectProperty [in paramorphism relationship with](../../RO/74/RO_HOM0000074.md) + * [in paramorphism relationship with](../../RO/74/RO_HOM0000074.md) SubPropertyOf [in homocracy relationship with](../../RO/03/RO_HOM0000003.md) + * [in paramorphism relationship with](../../RO/74/RO_HOM0000074.md) SubPropertyOf [in iterative homology relationship with](../../RO/66/RO_HOM0000066.md) + +## External Comments + diff --git a/src/ontology/md/RO/75/RO_0002175.md b/src/ontology/md/RO/75/RO_0002175.md new file mode 100644 index 00000000..e6a2ef96 --- /dev/null +++ b/src/ontology/md/RO/75/RO_0002175.md @@ -0,0 +1,43 @@ + +## Class : present in taxon + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002175 + * *Label* = present in taxon + * *Definition* = S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [taxonomic class assertion](../../RO/72/RO_0002172.md) + +## SubProperties + + * [always present in taxon](../../RO/04/RO_0002504.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S + * *[term editor](../../IAO/17/IAO_0000117.md)* = https://orcid.org/0000-0002-6601-2165 + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = present in taxon + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/75/RO_0002375.md b/src/ontology/md/RO/75/RO_0002375.md new file mode 100644 index 00000000..bad8bb72 --- /dev/null +++ b/src/ontology/md/RO/75/RO_0002375.md @@ -0,0 +1,53 @@ + +## Class : in branching relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002375 + * *Label* = in branching relationship with + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [part of](../../BFO/50/BFO_0000050.md) + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [in branching relationship with](../../RO/75/RO_0002375.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in branching relationship with + * *[page](../../ge/page.md)* = https://github.com/obophenotype/uberon/issues/170 + +## Usage + + * - + * [branching part of](../../RO/80/RO_0002380.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + * [distributary of](../../RO/77/RO_0002377.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + * [has branching part](../../RO/69/RO_0002569.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) Range [material entity](../../BFO/40/BFO_0000040.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [main stem of](../../RO/81/RO_0002381.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + * [tributary of](../../RO/76/RO_0002376.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + +## External Comments + diff --git a/src/ontology/md/RO/75/RO_0002475.md b/src/ontology/md/RO/75/RO_0002475.md new file mode 100644 index 00000000..dae42bef --- /dev/null +++ b/src/ontology/md/RO/75/RO_0002475.md @@ -0,0 +1,41 @@ + +## Class : has no connections with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002475 + * *Label* = has no connections with + * *Definition* = A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on a class](../../RO/20/RO_0002420.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' + * *[definition](../../IAO/15/IAO_0000115.md)* = A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = shares no connection with + * *[expand assertion to](../../IAO/25/IAO_0000425.md)* = Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has no connections with + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/75/RO_0002575.md b/src/ontology/md/RO/75/RO_0002575.md new file mode 100644 index 00000000..64e3c886 --- /dev/null +++ b/src/ontology/md/RO/75/RO_0002575.md @@ -0,0 +1,54 @@ + +## Class : is direct form of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002575 + * *Label* = is direct form of + * *Definition* = relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on an object property](../../RO/22/RO_0002422.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y + * *[editor note](../../IAO/16/IAO_0000116.md)* = The general property hierarchy is: + + "directly P" SubPropertyOf "P" + Transitive(P) + +Where we have an annotation assertion + + "directly P" "is direct form of" "P" + * *[logical macro assertion on an annotation property](../../RO/23/RO_0002423.md)* = If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' + * *[creator](../../or/creator.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is direct form of + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * http://purl.obolibrary.org/obo/RO_0002090 [is direct form of](../../RO/75/RO_0002575.md) http://purl.obolibrary.org/obo/BFO_0000063 + * http://purl.obolibrary.org/obo/RO_0002207 [is direct form of](../../RO/75/RO_0002575.md) http://purl.obolibrary.org/obo/RO_0002202 + * http://purl.obolibrary.org/obo/RO_0002412 [is direct form of](../../RO/75/RO_0002575.md) http://purl.obolibrary.org/obo/RO_0002411 + * http://purl.obolibrary.org/obo/RO_0002495 [is direct form of](../../RO/75/RO_0002575.md) http://purl.obolibrary.org/obo/RO_0002494 + * http://purl.obolibrary.org/obo/RO_0002530 [is direct form of](../../RO/75/RO_0002575.md) http://purl.obolibrary.org/obo/RO_0002529 + * http://purl.obolibrary.org/obo/RO_0002578 [is direct form of](../../RO/75/RO_0002575.md) http://purl.obolibrary.org/obo/RO_0002211 + +## External Comments + diff --git a/src/ontology/md/RO/75/RO_HOM0000075.md b/src/ontology/md/RO/75/RO_HOM0000075.md new file mode 100644 index 00000000..f3a45e11 --- /dev/null +++ b/src/ontology/md/RO/75/RO_HOM0000075.md @@ -0,0 +1,46 @@ + +## Class : in regulogy relationship with + + * *IRI* = http://purl.obolibrary.org/obo/RO_HOM0000075 + * *Label* = in regulogy relationship with + * *Definition* = Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. [ [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://dx.doi.org/10.1101/gr.1774904, [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) = http://purl.obolibrary.org/obo/HOM_0000075 ] + +## Synonyms + + * regulogous to + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## SubProperties + + +## Other Logical Axioms + + * SymmetricObjectProperty [in regulogy relationship with](../../RO/75/RO_HOM0000075.md) + * [in regulogy relationship with](../../RO/75/RO_HOM0000075.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + * *[creator](../../or/creator.md)* = http://bgee.unil.ch + * *[source](../../ce/source.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * *[has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md)* = regulogous to + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in regulogy relationship with + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://purl.obolibrary.org/obo/HOM_0000075 + +## Usage + + * - + * SymmetricObjectProperty [in regulogy relationship with](../../RO/75/RO_HOM0000075.md) + * [in regulogy relationship with](../../RO/75/RO_HOM0000075.md) SubPropertyOf [in historical homology relationship with](../../RO/07/RO_HOM0000007.md) + +## External Comments + diff --git a/src/ontology/md/RO/76/RO_0002176.md b/src/ontology/md/RO/76/RO_0002176.md new file mode 100644 index 00000000..a4d9bd37 --- /dev/null +++ b/src/ontology/md/RO/76/RO_0002176.md @@ -0,0 +1,49 @@ + +## Class : connects + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002176 + * *Label* = connects + * *Definition* = c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [connects](../../RO/76/RO_0002176.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [connects](../../RO/76/RO_0002176.md) Range [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connects](../../RO/76/RO_0002176.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = The M8 connects Glasgow and Edinburgh + * *[example of usage](../../IAO/12/IAO_0000112.md)* = a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + * *[definition](../../IAO/15/IAO_0000115.md)* = c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/22293552 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = connects + * *[page](../../ge/page.md)* = https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + * *[page](../../ge/page.md)* = https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [connects](../../RO/76/RO_0002176.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [connects](../../RO/76/RO_0002176.md) Range [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connects](../../RO/76/RO_0002176.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## External Comments + diff --git a/src/ontology/md/RO/76/RO_0002376.md b/src/ontology/md/RO/76/RO_0002376.md new file mode 100644 index 00000000..3e988799 --- /dev/null +++ b/src/ontology/md/RO/76/RO_0002376.md @@ -0,0 +1,55 @@ + +## Class : tributary of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002376 + * *Label* = tributary of + * *Definition* = x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [in branching relationship with](../../RO/75/RO_0002375.md) + +## SubProperties + + +## Other Logical Axioms + + * [tributary of](../../RO/76/RO_0002376.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Deschutes River tributary_of Columbia River + * *[example of usage](../../IAO/12/IAO_0000112.md)* = inferior epigastric vein tributary_of external iliac vein + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = drains into + * *[alternative term](../../IAO/18/IAO_0000118.md)* = drains to + * *[alternative term](../../IAO/18/IAO_0000118.md)* = tributary channel of + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://en.wikipedia.org/wiki/Tributary + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.medindia.net/glossary/venous_tributary.htm + * *[curator note](../../IAO/32/IAO_0000232.md)* = This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = tributary of + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://dbpedia.org/ontology/drainsTo + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://en.wikipedia.org/wiki/Tributary + +## Usage + + * - + * [anabranch of](../../RO/78/RO_0002378.md) SubPropertyOf InverseOf() + * [proper tributary of](../../RO/83/RO_0002383.md) SubPropertyOf [tributary of](../../RO/76/RO_0002376.md) + * [tributary of](../../RO/76/RO_0002376.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + +## External Comments + diff --git a/src/ontology/md/RO/76/RO_0002476.md b/src/ontology/md/RO/76/RO_0002476.md new file mode 100644 index 00000000..ca3a8c4c --- /dev/null +++ b/src/ontology/md/RO/76/RO_0002476.md @@ -0,0 +1,48 @@ + +## Class : child nucleus of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002476 + * *Label* = child nucleus of + * *Definition* = c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally preceded by](../../RO/58/RO_0002258.md) + +## SubProperties + + +## Other Logical Axioms + + * [child nucleus of](../../RO/76/RO_0002476.md) Domain [nucleus](../../GO/34/GO_0005634.md) + * [child nucleus of](../../RO/76/RO_0002476.md) Range [nucleus](../../GO/34/GO_0005634.md) + * [child nucleus of](../../RO/76/RO_0002476.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = ABal nucleus child nucleus of ABa nucleus (in C elegans) + * *[definition](../../IAO/15/IAO_0000115.md)* = c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = child nucleus of + +## Usage + + * - + * [child nucleus of in hermaphrodite](../../RO/77/RO_0002477.md) SubPropertyOf [child nucleus of](../../RO/76/RO_0002476.md) + * [child nucleus of in male](../../RO/78/RO_0002478.md) SubPropertyOf [child nucleus of](../../RO/76/RO_0002476.md) + * [child nucleus of](../../RO/76/RO_0002476.md) Domain [nucleus](../../GO/34/GO_0005634.md) + * [child nucleus of](../../RO/76/RO_0002476.md) Range [nucleus](../../GO/34/GO_0005634.md) + * [child nucleus of](../../RO/76/RO_0002476.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## External Comments + diff --git a/src/ontology/md/RO/76/RO_0002576.md b/src/ontology/md/RO/76/RO_0002576.md new file mode 100644 index 00000000..4f749060 --- /dev/null +++ b/src/ontology/md/RO/76/RO_0002576.md @@ -0,0 +1,44 @@ + +## Class : skeleton of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002576 + * *Label* = skeleton of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [part of](../../BFO/50/BFO_0000050.md) + +## SubProperties + + +## Other Logical Axioms + + * [skeleton of](../../RO/76/RO_0002576.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [skeleton of](../../RO/76/RO_0002576.md) InverseOf [has skeleton](../../RO/51/RO_0002551.md) + * [skeleton of](../../RO/76/RO_0002576.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [skeleton of](../../RO/76/RO_0002576.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = skeleton of + +## Usage + + * - + * [skeleton of](../../RO/76/RO_0002576.md) Domain [anatomical structure](../../CARO/03/CARO_0000003.md) + * [skeleton of](../../RO/76/RO_0002576.md) InverseOf [has skeleton](../../RO/51/RO_0002551.md) + * [skeleton of](../../RO/76/RO_0002576.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [skeleton of](../../RO/76/RO_0002576.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + +## External Comments + diff --git a/src/ontology/md/RO/77/RO_0002177.md b/src/ontology/md/RO/77/RO_0002177.md new file mode 100644 index 00000000..e37f6ce3 --- /dev/null +++ b/src/ontology/md/RO/77/RO_0002177.md @@ -0,0 +1,41 @@ + +## Class : attached to part of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002177 + * *Label* = attached to part of + * *Definition* = a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [mereotopologically related to](../../RO/23/RO_0002323.md) + +## SubProperties + + +## Other Logical Axioms + + * [attached to part of](../../RO/77/RO_0002177.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = attached to part of + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * [attached to part of](../../RO/77/RO_0002177.md) SubPropertyOf [mereotopologically related to](../../RO/23/RO_0002323.md) + * [attached to](../../RO/71/RO_0002371.md) SubPropertyOf [attached to part of](../../RO/77/RO_0002177.md) + +## External Comments + diff --git a/src/ontology/md/RO/77/RO_0002377.md b/src/ontology/md/RO/77/RO_0002377.md new file mode 100644 index 00000000..4ab30727 --- /dev/null +++ b/src/ontology/md/RO/77/RO_0002377.md @@ -0,0 +1,50 @@ + +## Class : distributary of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002377 + * *Label* = distributary of + * *Definition* = x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [in branching relationship with](../../RO/75/RO_0002375.md) + +## SubProperties + + +## Other Logical Axioms + + * [distributary of](../../RO/77/RO_0002377.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = Deschutes River distributary_of Little Lava Lake + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = branch of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = distributary channel of + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://en.wikipedia.org/wiki/Distributary + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = distributary of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [anabranch of](../../RO/78/RO_0002378.md) SubPropertyOf [distributary of](../../RO/77/RO_0002377.md) + * [distributary of](../../RO/77/RO_0002377.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + * [proper distributary of](../../RO/82/RO_0002382.md) SubPropertyOf [distributary of](../../RO/77/RO_0002377.md) + +## External Comments + diff --git a/src/ontology/md/RO/77/RO_0002477.md b/src/ontology/md/RO/77/RO_0002477.md new file mode 100644 index 00000000..cd21a095 --- /dev/null +++ b/src/ontology/md/RO/77/RO_0002477.md @@ -0,0 +1,40 @@ + +## Class : child nucleus of in hermaphrodite + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002477 + * *Label* = child nucleus of in hermaphrodite + * *Definition* = A child nucleus relationship in which the cells are part of a hermaphroditic organism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [child nucleus of](../../RO/76/RO_0002476.md) + +## SubProperties + + +## Other Logical Axioms + + * [child nucleus of in hermaphrodite](../../RO/77/RO_0002477.md) SubPropertyOf [child nucleus of](../../RO/76/RO_0002476.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A child nucleus relationship in which the cells are part of a hermaphroditic organism + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = child nucleus of in hermaphrodite + +## Usage + + * - + * [child nucleus of in hermaphrodite](../../RO/77/RO_0002477.md) SubPropertyOf [child nucleus of](../../RO/76/RO_0002476.md) + +## External Comments + diff --git a/src/ontology/md/RO/77/RO_0002577.md b/src/ontology/md/RO/77/RO_0002577.md new file mode 100644 index 00000000..55328712 --- /dev/null +++ b/src/ontology/md/RO/77/RO_0002577.md @@ -0,0 +1,48 @@ + +## Class : system + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002577 + * *Label* = system + * *Definition* = A material entity consisting of multiple components that are causally integrated. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + * [material entity](../../BFO/40/BFO_0000040.md) + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A material entity consisting of multiple components that are causally integrated. + * *[editor note](../../IAO/16/IAO_0000116.md)* = May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.jbiomedsem.com/content/4/1/43 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = system + +## Usage + + * - + * [connected anatomical system](../../CARO/11/CARO_0000011.md) SubClassOf [system](../../RO/77/RO_0002577.md) + * [connected to](../../RO/70/RO_0002170.md) Domain [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connected to](../../RO/70/RO_0002170.md) Range [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [connects](../../RO/76/RO_0002176.md) Range [part of](../../BFO/50/BFO_0000050.md) some [system](../../RO/77/RO_0002577.md) + * [determined by part of](../../RO/09/RO_0002509.md) Domain [system](../../RO/77/RO_0002577.md) + * [determined by](../../RO/07/RO_0002507.md) Domain [system](../../RO/77/RO_0002577.md) + * [environmental system](../../ENVO/54/ENVO_01000254.md) SubClassOf [system](../../RO/77/RO_0002577.md) + * [system](../../RO/77/RO_0002577.md) SubClassOf [material entity](../../BFO/40/BFO_0000040.md) + +## External Comments + diff --git a/src/ontology/md/RO/78/RO_0002178.md b/src/ontology/md/RO/78/RO_0002178.md new file mode 100644 index 00000000..50a4d874 --- /dev/null +++ b/src/ontology/md/RO/78/RO_0002178.md @@ -0,0 +1,41 @@ + +## Class : supplies + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002178 + * *Label* = supplies + * *Definition* = Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [connected to](../../RO/70/RO_0002170.md) + +## SubProperties + + +## Other Logical Axioms + + * [supplies](../../RO/78/RO_0002178.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = supplies + +## Usage + + * - + * [supplies](../../RO/78/RO_0002178.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## External Comments + diff --git a/src/ontology/md/RO/78/RO_0002378.md b/src/ontology/md/RO/78/RO_0002378.md new file mode 100644 index 00000000..867d1ed3 --- /dev/null +++ b/src/ontology/md/RO/78/RO_0002378.md @@ -0,0 +1,51 @@ + +## Class : anabranch of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002378 + * *Label* = anabranch of + * *Definition* = x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [distributary of](../../RO/77/RO_0002377.md) + * InverseOf() + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * DisjointObjectProperties( ) + * [anabranch of](../../RO/78/RO_0002378.md) SubPropertyOf InverseOf() + * [anabranch of](../../RO/78/RO_0002378.md) SubPropertyOf [distributary of](../../RO/77/RO_0002377.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = anastomoses with + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = anabranch of + +## Usage + + * - + * DisjointObjectProperties( ) + * DisjointObjectProperties( ) + * [anabranch of](../../RO/78/RO_0002378.md) SubPropertyOf InverseOf() + * [anabranch of](../../RO/78/RO_0002378.md) SubPropertyOf [distributary of](../../RO/77/RO_0002377.md) + +## External Comments + diff --git a/src/ontology/md/RO/78/RO_0002478.md b/src/ontology/md/RO/78/RO_0002478.md new file mode 100644 index 00000000..8b49e96c --- /dev/null +++ b/src/ontology/md/RO/78/RO_0002478.md @@ -0,0 +1,40 @@ + +## Class : child nucleus of in male + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002478 + * *Label* = child nucleus of in male + * *Definition* = A child nucleus relationship in which the cells are part of a male organism + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [child nucleus of](../../RO/76/RO_0002476.md) + +## SubProperties + + +## Other Logical Axioms + + * [child nucleus of in male](../../RO/78/RO_0002478.md) SubPropertyOf [child nucleus of](../../RO/76/RO_0002476.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = A child nucleus relationship in which the cells are part of a male organism + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = child nucleus of in male + +## Usage + + * - + * [child nucleus of in male](../../RO/78/RO_0002478.md) SubPropertyOf [child nucleus of](../../RO/76/RO_0002476.md) + +## External Comments + diff --git a/src/ontology/md/RO/78/RO_0002578.md b/src/ontology/md/RO/78/RO_0002578.md new file mode 100644 index 00000000..5c14b9c4 --- /dev/null +++ b/src/ontology/md/RO/78/RO_0002578.md @@ -0,0 +1,48 @@ + +## Class : directly regulates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002578 + * *Label* = directly regulates + * *Definition* = p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [regulates](../../RO/11/RO_0002211.md) + +## SubProperties + + +## Other Logical Axioms + + * [directly regulates](../../RO/78/RO_0002578.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly regulates](../../RO/78/RO_0002578.md) SubPropertyOf [regulates](../../RO/11/RO_0002211.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[OBO foundry unique label](../../IAO/89/IAO_0000589.md)* = directly regulates (processual) + * *[is direct form of](../../RO/75/RO_0002575.md)* = http://purl.obolibrary.org/obo/RO_0002211 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = directly regulates + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [directly activates](../../RO/06/RO_0002406.md) SubPropertyOf [directly regulates](../../RO/78/RO_0002578.md) + * [directly inhibits](../../RO/08/RO_0002408.md) SubPropertyOf [directly regulates](../../RO/78/RO_0002578.md) + * [directly regulates](../../RO/78/RO_0002578.md) SubPropertyOf [immediately causally upstream of](../../RO/12/RO_0002412.md) + * [directly regulates](../../RO/78/RO_0002578.md) SubPropertyOf [regulates](../../RO/11/RO_0002211.md) + +## External Comments + diff --git a/src/ontology/md/RO/79/RO_0000079.md b/src/ontology/md/RO/79/RO_0000079.md new file mode 100644 index 00000000..371f2a4d --- /dev/null +++ b/src/ontology/md/RO/79/RO_0000079.md @@ -0,0 +1,47 @@ + +## Class : function of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000079 + * *Label* = function of + * *Definition* = a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [inheres in](../../RO/52/RO_0000052.md) + +## SubProperties + + +## Other Logical Axioms + + * [function of](../../RO/79/RO_0000079.md) Domain [function](../../BFO/34/BFO_0000034.md) + * [function of](../../RO/79/RO_0000079.md) SubPropertyOf [inheres in](../../RO/52/RO_0000052.md) + * [has function](../../RO/85/RO_0000085.md) InverseOf [function of](../../RO/79/RO_0000079.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this catalysis function is a function of this enzyme + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + * *[editor note](../../IAO/16/IAO_0000116.md)* = A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = function_of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is function of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = function of + +## Usage + + * - + * [function of](../../RO/79/RO_0000079.md) Domain [function](../../BFO/34/BFO_0000034.md) + * [function of](../../RO/79/RO_0000079.md) SubPropertyOf [inheres in](../../RO/52/RO_0000052.md) + * [has function](../../RO/85/RO_0000085.md) InverseOf [function of](../../RO/79/RO_0000079.md) + +## External Comments + diff --git a/src/ontology/md/RO/79/RO_0002179.md b/src/ontology/md/RO/79/RO_0002179.md new file mode 100644 index 00000000..60e1a598 --- /dev/null +++ b/src/ontology/md/RO/79/RO_0002179.md @@ -0,0 +1,41 @@ + +## Class : drains + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002179 + * *Label* = drains + * *Definition* = Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [connected to](../../RO/70/RO_0002170.md) + +## SubProperties + + +## Other Logical Axioms + + * [drains](../../RO/79/RO_0002179.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. + * *[editor note](../../IAO/16/IAO_0000116.md)* = Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.ncbi.nlm.nih.gov/pubmed/20064205 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = drains + +## Usage + + * - + * [drains](../../RO/79/RO_0002179.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## External Comments + diff --git a/src/ontology/md/RO/79/RO_0002379.md b/src/ontology/md/RO/79/RO_0002379.md new file mode 100644 index 00000000..9774fd7c --- /dev/null +++ b/src/ontology/md/RO/79/RO_0002379.md @@ -0,0 +1,43 @@ + +## Class : spatially coextensive with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002379 + * *Label* = spatially coextensive with + * *Definition* = x spatially_coextensive_with y if and inly if x and y have the same location + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [overlaps](../../RO/31/RO_0002131.md) + +## SubProperties + + +## Other Logical Axioms + + * [spatially coextensive with](../../RO/79/RO_0002379.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = A lump of clay and a statue + * *[definition](../../IAO/15/IAO_0000115.md)* = x spatially_coextensive_with y if and inly if x and y have the same location + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = This relation is added for formal completeness. It is unlikely to be used in many practical scenarios + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = spatially coextensive with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [spatially coextensive with](../../RO/79/RO_0002379.md) SubPropertyOf [overlaps](../../RO/31/RO_0002131.md) + +## External Comments + diff --git a/src/ontology/md/RO/79/RO_0002479.md b/src/ontology/md/RO/79/RO_0002479.md new file mode 100644 index 00000000..88f051d8 --- /dev/null +++ b/src/ontology/md/RO/79/RO_0002479.md @@ -0,0 +1,46 @@ + +## Class : has part that occurs in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002479 + * *Label* = has part that occurs in + * *Definition* = p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [has part that occurs in](../../RO/79/RO_0002479.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [has part that occurs in](../../RO/79/RO_0002479.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has part that occurs in + +## Usage + + * - + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * [has end location](../../RO/32/RO_0002232.md) SubPropertyOf [has part that occurs in](../../RO/79/RO_0002479.md) + * [has part that occurs in](../../RO/79/RO_0002479.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [has part that occurs in](../../RO/79/RO_0002479.md) Range [independent continuant](../../BFO/04/BFO_0000004.md) + * [has start location](../../RO/31/RO_0002231.md) SubPropertyOf [has part that occurs in](../../RO/79/RO_0002479.md) + +## External Comments + diff --git a/src/ontology/md/RO/79/RO_0002579.md b/src/ontology/md/RO/79/RO_0002579.md new file mode 100644 index 00000000..ab059db0 --- /dev/null +++ b/src/ontology/md/RO/79/RO_0002579.md @@ -0,0 +1,41 @@ + +## Class : is indirect form of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002579 + * *Label* = is indirect form of + * *Definition* = relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on an object property](../../RO/22/RO_0002422.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y + * *[creator](../../or/creator.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is indirect form of + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * http://purl.obolibrary.org/obo/RO_0002407 [is indirect form of](../../RO/79/RO_0002579.md) http://purl.obolibrary.org/obo/RO_0002213 + * http://purl.obolibrary.org/obo/RO_0002409 [is indirect form of](../../RO/79/RO_0002579.md) http://purl.obolibrary.org/obo/RO_0002212 + +## External Comments + diff --git a/src/ontology/md/RO/80/RO_0000080.md b/src/ontology/md/RO/80/RO_0000080.md new file mode 100644 index 00000000..4e1f2d01 --- /dev/null +++ b/src/ontology/md/RO/80/RO_0000080.md @@ -0,0 +1,45 @@ + +## Class : quality of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000080 + * *Label* = quality of + * *Definition* = a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [inheres in](../../RO/52/RO_0000052.md) + +## SubProperties + + +## Other Logical Axioms + + * [quality of](../../RO/80/RO_0000080.md) InverseOf [has quality](../../RO/86/RO_0000086.md) + * [quality of](../../RO/80/RO_0000080.md) SubPropertyOf [inheres in](../../RO/52/RO_0000052.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this red color is a quality of this apple + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + * *[editor note](../../IAO/16/IAO_0000116.md)* = A quality inheres in its bearer at all times for which the quality exists. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is quality of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = quality_of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = quality of + +## Usage + + * - + * [quality of](../../RO/80/RO_0000080.md) InverseOf [has quality](../../RO/86/RO_0000086.md) + * [quality of](../../RO/80/RO_0000080.md) SubPropertyOf [inheres in](../../RO/52/RO_0000052.md) + +## External Comments + diff --git a/src/ontology/md/RO/80/RO_0002180.md b/src/ontology/md/RO/80/RO_0002180.md new file mode 100644 index 00000000..52331865 --- /dev/null +++ b/src/ontology/md/RO/80/RO_0002180.md @@ -0,0 +1,46 @@ + +## Class : has component + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002180 + * *Label* = has component + * *Definition* = w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [has part](../../BFO/51/BFO_0000051.md) + +## SubProperties + + +## Other Logical Axioms + + * [has component](../../RO/80/RO_0002180.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + * *[editor note](../../IAO/16/IAO_0000116.md)* = The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + * *[curator note](../../IAO/32/IAO_0000232.md)* = 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. + * *[temporal interpretation](../../RO/00/RO_0001900.md)* = http://purl.obolibrary.org/obo/RO_0001901 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has component + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://ontologydesignpatterns.org/wiki/Submissions:Componency + +## Usage + + * - + * [has component](../../RO/80/RO_0002180.md) SubPropertyOf [has part](../../BFO/51/BFO_0000051.md) + +## External Comments + diff --git a/src/ontology/md/RO/80/RO_0002380.md b/src/ontology/md/RO/80/RO_0002380.md new file mode 100644 index 00000000..229d87ac --- /dev/null +++ b/src/ontology/md/RO/80/RO_0002380.md @@ -0,0 +1,52 @@ + +## Class : branching part of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002380 + * *Label* = branching part of + * *Definition* = x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [part of](../../BFO/50/BFO_0000050.md) + * [in branching relationship with](../../RO/75/RO_0002375.md) + +## SubProperties + + +## Other Logical Axioms + + * [branching part of](../../RO/80/RO_0002380.md) Range [bearer of](../../RO/53/RO_0000053.md) some [branched](../../PATO/02/PATO_0000402.md) + * [branching part of](../../RO/80/RO_0002380.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + * [branching part of](../../RO/80/RO_0002380.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [has branching part](../../RO/69/RO_0002569.md) InverseOf [branching part of](../../RO/80/RO_0002380.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = branching part of + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = FMA:85994 + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [branching part of](../../RO/80/RO_0002380.md) Range [bearer of](../../RO/53/RO_0000053.md) some [branched](../../PATO/02/PATO_0000402.md) + * [branching part of](../../RO/80/RO_0002380.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + * [branching part of](../../RO/80/RO_0002380.md) SubPropertyOf [part of](../../BFO/50/BFO_0000050.md) + * [has branching part](../../RO/69/RO_0002569.md) InverseOf [branching part of](../../RO/80/RO_0002380.md) + +## External Comments + diff --git a/src/ontology/md/RO/80/RO_0002480.md b/src/ontology/md/RO/80/RO_0002480.md new file mode 100644 index 00000000..ef76ed40 --- /dev/null +++ b/src/ontology/md/RO/80/RO_0002480.md @@ -0,0 +1,42 @@ + +## Class : ubiquitinates + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002480 + * *Label* = ubiquitinates + * *Definition* = An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [molecularly interacts with](../../RO/36/RO_0002436.md) + +## SubProperties + + +## Other Logical Axioms + + * [ubiquitinates](../../RO/80/RO_0002480.md) SubPropertyOf [molecularly interacts with](../../RO/36/RO_0002436.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y + * *[editor note](../../IAO/16/IAO_0000116.md)* = Axiomatization to GO to be added later + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ubiquitinates + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [ubiquitinates](../../RO/80/RO_0002480.md) SubPropertyOf [molecularly interacts with](../../RO/36/RO_0002436.md) + +## External Comments + diff --git a/src/ontology/md/RO/80/RO_0002580.md b/src/ontology/md/RO/80/RO_0002580.md new file mode 100644 index 00000000..0978a689 --- /dev/null +++ b/src/ontology/md/RO/80/RO_0002580.md @@ -0,0 +1,38 @@ + +## Class : logical macro assertion on an axiom + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002580 + * *Label* = logical macro assertion on an axiom + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion](../../RO/16/RO_0002416.md) + +## SubProperties + + * [is a defining property chain axiom](../../RO/81/RO_0002581.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = logical macro assertion on an axiom + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/81/RO_0000081.md b/src/ontology/md/RO/81/RO_0000081.md new file mode 100644 index 00000000..b5cf8f68 --- /dev/null +++ b/src/ontology/md/RO/81/RO_0000081.md @@ -0,0 +1,45 @@ + +## Class : role of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000081 + * *Label* = role of + * *Definition* = a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [inheres in](../../RO/52/RO_0000052.md) + +## SubProperties + + +## Other Logical Axioms + + * [has role](../../RO/87/RO_0000087.md) InverseOf [role of](../../RO/81/RO_0000081.md) + * [role of](../../RO/81/RO_0000081.md) SubPropertyOf [inheres in](../../RO/52/RO_0000052.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this investigator role is a role of this person + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + * *[editor note](../../IAO/16/IAO_0000116.md)* = A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = is role of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = role_of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = role of + +## Usage + + * - + * [has role](../../RO/87/RO_0000087.md) InverseOf [role of](../../RO/81/RO_0000081.md) + * [role of](../../RO/81/RO_0000081.md) SubPropertyOf [inheres in](../../RO/52/RO_0000052.md) + +## External Comments + diff --git a/src/ontology/md/RO/81/RO_0002081.md b/src/ontology/md/RO/81/RO_0002081.md new file mode 100644 index 00000000..8968bae0 --- /dev/null +++ b/src/ontology/md/RO/81/RO_0002081.md @@ -0,0 +1,45 @@ + +## Class : before or simultaneous with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002081 + * *Label* = before or simultaneous with + * *Comment* = Primitive instance level timing relation between events + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * [before or simultaneous with](../../RO/81/RO_0002081.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = <= + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Primitive instance level timing relation between events + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = before or simultaneous with + +## Usage + + * - + * [before or simultaneous with](../../RO/81/RO_0002081.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [before](../../RO/83/RO_0002083.md) SubPropertyOf [before or simultaneous with](../../RO/81/RO_0002081.md) + * [simultaneous with](../../RO/82/RO_0002082.md) SubPropertyOf [before or simultaneous with](../../RO/81/RO_0002081.md) + +## External Comments + diff --git a/src/ontology/md/RO/81/RO_0002381.md b/src/ontology/md/RO/81/RO_0002381.md new file mode 100644 index 00000000..0728e7ad --- /dev/null +++ b/src/ontology/md/RO/81/RO_0002381.md @@ -0,0 +1,44 @@ + +## Class : main stem of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002381 + * *Label* = main stem of + * *Definition* = x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [in branching relationship with](../../RO/75/RO_0002375.md) + +## SubProperties + + +## Other Logical Axioms + + * [main stem of](../../RO/81/RO_0002381.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = main stem of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [main stem of](../../RO/81/RO_0002381.md) SubPropertyOf [in branching relationship with](../../RO/75/RO_0002375.md) + +## External Comments + diff --git a/src/ontology/md/RO/81/RO_0002481.md b/src/ontology/md/RO/81/RO_0002481.md new file mode 100644 index 00000000..e05b7ee4 --- /dev/null +++ b/src/ontology/md/RO/81/RO_0002481.md @@ -0,0 +1,40 @@ + +## Class : is kinase activity + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002481 + * *Label* = is kinase activity + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [molecular interaction relation helper property](../../RO/64/RO_0002564.md) + +## SubProperties + + +## Other Logical Axioms + + * [is kinase activity](../../RO/81/RO_0002481.md) SubPropertyOf [molecular interaction relation helper property](../../RO/64/RO_0002564.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is kinase activity + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [is kinase activity](../../RO/81/RO_0002481.md) SubPropertyOf [molecular interaction relation helper property](../../RO/64/RO_0002564.md) + * [kinase activity](../../GO/01/GO_0016301.md) SubClassOf ObjectHasSelf() + +## External Comments + diff --git a/src/ontology/md/RO/81/RO_0002581.md b/src/ontology/md/RO/81/RO_0002581.md new file mode 100644 index 00000000..942c1886 --- /dev/null +++ b/src/ontology/md/RO/81/RO_0002581.md @@ -0,0 +1,43 @@ + +## Class : is a defining property chain axiom + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002581 + * *Label* = is a defining property chain axiom + * *Definition* = If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on an axiom](../../RO/80/RO_0002580.md) + +## SubProperties + + * [is a defining property chain axiom where second argument is reflexive](../../RO/82/RO_0002582.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is a defining property chain axiom + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + +## External Comments + diff --git a/src/ontology/md/RO/82/RO_0002082.md b/src/ontology/md/RO/82/RO_0002082.md new file mode 100644 index 00000000..98db4e56 --- /dev/null +++ b/src/ontology/md/RO/82/RO_0002082.md @@ -0,0 +1,46 @@ + +## Class : simultaneous with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002082 + * *Label* = simultaneous with + * *Comment* = t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [before or simultaneous with](../../RO/81/RO_0002081.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [simultaneous with](../../RO/82/RO_0002082.md) + * [simultaneous with](../../RO/82/RO_0002082.md) SubPropertyOf [before or simultaneous with](../../RO/81/RO_0002081.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = simultaneous with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [simultaneous with](../../RO/82/RO_0002082.md) + * [simultaneous with](../../RO/82/RO_0002082.md) SubPropertyOf [before or simultaneous with](../../RO/81/RO_0002081.md) + +## External Comments + diff --git a/src/ontology/md/RO/82/RO_0002382.md b/src/ontology/md/RO/82/RO_0002382.md new file mode 100644 index 00000000..a5bed2ff --- /dev/null +++ b/src/ontology/md/RO/82/RO_0002382.md @@ -0,0 +1,45 @@ + +## Class : proper distributary of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002382 + * *Label* = proper distributary of + * *Definition* = x proper_distributary_of y iff x distributary_of y and x does not flow back into y + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [distributary of](../../RO/77/RO_0002377.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * [proper distributary of](../../RO/82/RO_0002382.md) SubPropertyOf [distributary of](../../RO/77/RO_0002377.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x proper_distributary_of y iff x distributary_of y and x does not flow back into y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = proper distributary of + +## Usage + + * - + * DisjointObjectProperties( ) + * [proper distributary of](../../RO/82/RO_0002382.md) SubPropertyOf [distributary of](../../RO/77/RO_0002377.md) + +## External Comments + diff --git a/src/ontology/md/RO/82/RO_0002482.md b/src/ontology/md/RO/82/RO_0002482.md new file mode 100644 index 00000000..89894092 --- /dev/null +++ b/src/ontology/md/RO/82/RO_0002482.md @@ -0,0 +1,40 @@ + +## Class : is ubiquitination + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002482 + * *Label* = is ubiquitination + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [molecular interaction relation helper property](../../RO/64/RO_0002564.md) + +## SubProperties + + +## Other Logical Axioms + + * [is ubiquitination](../../RO/82/RO_0002482.md) SubPropertyOf [molecular interaction relation helper property](../../RO/64/RO_0002564.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is ubiquitination + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [is ubiquitination](../../RO/82/RO_0002482.md) SubPropertyOf [molecular interaction relation helper property](../../RO/64/RO_0002564.md) + * [ubiquitin-protein ligase activity](../../GO/42/GO_0004842.md) SubClassOf ObjectHasSelf() + +## External Comments + diff --git a/src/ontology/md/RO/82/RO_0002582.md b/src/ontology/md/RO/82/RO_0002582.md new file mode 100644 index 00000000..83457ff1 --- /dev/null +++ b/src/ontology/md/RO/82/RO_0002582.md @@ -0,0 +1,43 @@ + +## Class : is a defining property chain axiom where second argument is reflexive + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002582 + * *Label* = is a defining property chain axiom where second argument is reflexive + * *Definition* = If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [is a defining property chain axiom](../../RO/81/RO_0002581.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = 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. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is a defining property chain axiom where second argument is reflexive + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + * SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) + +## External Comments + diff --git a/src/ontology/md/RO/83/RO_0002083.md b/src/ontology/md/RO/83/RO_0002083.md new file mode 100644 index 00000000..cf241cb4 --- /dev/null +++ b/src/ontology/md/RO/83/RO_0002083.md @@ -0,0 +1,44 @@ + +## Class : before + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002083 + * *Label* = before + * *Comment* = t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [before or simultaneous with](../../RO/81/RO_0002081.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [before](../../RO/83/RO_0002083.md) + * [before](../../RO/83/RO_0002083.md) SubPropertyOf [before or simultaneous with](../../RO/81/RO_0002081.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = before + +## Usage + + * - + * TransitiveObjectProperty [before](../../RO/83/RO_0002083.md) + * [before](../../RO/83/RO_0002083.md) SubPropertyOf [before or simultaneous with](../../RO/81/RO_0002081.md) + +## External Comments + diff --git a/src/ontology/md/RO/83/RO_0002383.md b/src/ontology/md/RO/83/RO_0002383.md new file mode 100644 index 00000000..9fcb0f89 --- /dev/null +++ b/src/ontology/md/RO/83/RO_0002383.md @@ -0,0 +1,45 @@ + +## Class : proper tributary of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002383 + * *Label* = proper tributary of + * *Definition* = x proper_tributary_of y iff x tributary_of y and x does not originate from y + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [tributary of](../../RO/76/RO_0002376.md) + +## SubProperties + + +## Other Logical Axioms + + * DisjointObjectProperties( ) + * [proper tributary of](../../RO/83/RO_0002383.md) SubPropertyOf [tributary of](../../RO/76/RO_0002376.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x proper_tributary_of y iff x tributary_of y and x does not originate from y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = proper tributary of + +## Usage + + * - + * DisjointObjectProperties( ) + * [proper tributary of](../../RO/83/RO_0002383.md) SubPropertyOf [tributary of](../../RO/76/RO_0002376.md) + +## External Comments + diff --git a/src/ontology/md/RO/83/RO_0002483.md b/src/ontology/md/RO/83/RO_0002483.md new file mode 100644 index 00000000..ffa76cae --- /dev/null +++ b/src/ontology/md/RO/83/RO_0002483.md @@ -0,0 +1,36 @@ + +## Class : inherited annotation property + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002483 + * *Label* = inherited annotation property + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + * [curator guidance link](../../RO/84/RO_0002484.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = inherited annotation property + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/83/RO_0002583.md b/src/ontology/md/RO/83/RO_0002583.md new file mode 100644 index 00000000..93b989c5 --- /dev/null +++ b/src/ontology/md/RO/83/RO_0002583.md @@ -0,0 +1,42 @@ + +## Class : existence starts at point + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002583 + * *Label* = existence starts at point + * *Definition* = x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [relation between structure and stage](../../RO/87/RO_0002487.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence starts at point](../../RO/83/RO_0002583.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence starts at point + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [existence starts at point](../../RO/83/RO_0002583.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + +## External Comments + diff --git a/src/ontology/md/RO/84/RO_0002084.md b/src/ontology/md/RO/84/RO_0002084.md new file mode 100644 index 00000000..8ee38df7 --- /dev/null +++ b/src/ontology/md/RO/84/RO_0002084.md @@ -0,0 +1,44 @@ + +## Class : during which ends + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002084 + * *Label* = during which ends + * *Comment* = Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * [during which ends](../../RO/84/RO_0002084.md) InverseOf [ends during](../../RO/93/RO_0002093.md) + * [during which ends](../../RO/84/RO_0002084.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = during which ends + +## Usage + + * - + * [during which ends](../../RO/84/RO_0002084.md) InverseOf [ends during](../../RO/93/RO_0002093.md) + * [during which ends](../../RO/84/RO_0002084.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## External Comments + diff --git a/src/ontology/md/RO/84/RO_0002384.md b/src/ontology/md/RO/84/RO_0002384.md new file mode 100644 index 00000000..97c1eb37 --- /dev/null +++ b/src/ontology/md/RO/84/RO_0002384.md @@ -0,0 +1,45 @@ + +## Class : has developmental potential involving + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002384 + * *Label* = has developmental potential involving + * *Definition* = x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally related to](../../RO/24/RO_0002324.md) + +## SubProperties + + +## Other Logical Axioms + + * [has developmental potential involving](../../RO/84/RO_0002384.md) SubPropertyOf [developmentally related to](../../RO/24/RO_0002324.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has developmental potential involving + +## Usage + + * - + * [developmentally succeeded by](../../RO/86/RO_0002286.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + * [has developmental potential involving](../../RO/84/RO_0002384.md) SubPropertyOf [developmentally related to](../../RO/24/RO_0002324.md) + * [has potential to develop into](../../RO/87/RO_0002387.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + * [has potential to developmentally contribute to](../../RO/85/RO_0002385.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + * [has potential to developmentally induce](../../RO/86/RO_0002386.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + +## External Comments + diff --git a/src/ontology/md/RO/84/RO_0002484.md b/src/ontology/md/RO/84/RO_0002484.md new file mode 100644 index 00000000..4c482eff --- /dev/null +++ b/src/ontology/md/RO/84/RO_0002484.md @@ -0,0 +1,38 @@ + +## Class : curator guidance link + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002484 + * *Label* = curator guidance link + * *Definition* = Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [inherited annotation property](../../RO/83/RO_0002483.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = curator guidance link + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/84/RO_0002584.md b/src/ontology/md/RO/84/RO_0002584.md new file mode 100644 index 00000000..448ca5fd --- /dev/null +++ b/src/ontology/md/RO/84/RO_0002584.md @@ -0,0 +1,45 @@ + +## Class : has part structure that is capable of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002584 + * *Label* = has part structure that is capable of + * *Definition* = s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [functionally related to](../../RO/28/RO_0002328.md) + +## SubProperties + + +## Other Logical Axioms + + * [has part structure that is capable of](../../RO/84/RO_0002584.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [has part structure that is capable of](../../RO/84/RO_0002584.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + * *[definition](../../IAO/15/IAO_0000115.md)* = s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has part structure that is capable of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [has part structure that is capable of](../../RO/84/RO_0002584.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [has part structure that is capable of](../../RO/84/RO_0002584.md) SubPropertyOf [functionally related to](../../RO/28/RO_0002328.md) + +## External Comments + diff --git a/src/ontology/md/RO/85/RO_0000085.md b/src/ontology/md/RO/85/RO_0000085.md new file mode 100644 index 00000000..50cbdf7a --- /dev/null +++ b/src/ontology/md/RO/85/RO_0000085.md @@ -0,0 +1,46 @@ + +## Class : has function + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000085 + * *Label* = has function + * *Definition* = a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [bearer of](../../RO/53/RO_0000053.md) + +## SubProperties + + +## Other Logical Axioms + + * [has function](../../RO/85/RO_0000085.md) InverseOf [function of](../../RO/79/RO_0000079.md) + * [has function](../../RO/85/RO_0000085.md) Range [function](../../BFO/34/BFO_0000034.md) + * [has function](../../RO/85/RO_0000085.md) SubPropertyOf [bearer of](../../RO/53/RO_0000053.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + * *[editor note](../../IAO/16/IAO_0000116.md)* = A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has_function + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has function + +## Usage + + * - + * [has function](../../RO/85/RO_0000085.md) InverseOf [function of](../../RO/79/RO_0000079.md) + * [has function](../../RO/85/RO_0000085.md) Range [function](../../BFO/34/BFO_0000034.md) + * [has function](../../RO/85/RO_0000085.md) SubPropertyOf [bearer of](../../RO/53/RO_0000053.md) + +## External Comments + diff --git a/src/ontology/md/RO/85/RO_0002085.md b/src/ontology/md/RO/85/RO_0002085.md new file mode 100644 index 00000000..ca529349 --- /dev/null +++ b/src/ontology/md/RO/85/RO_0002085.md @@ -0,0 +1,45 @@ + +## Class : encompasses + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002085 + * *Label* = encompasses + * *Comment* = Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [during which starts](../../RO/88/RO_0002088.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [encompasses](../../RO/85/RO_0002085.md) + * [encompasses](../../RO/85/RO_0002085.md) InverseOf [happens during](../../RO/92/RO_0002092.md) + * [encompasses](../../RO/85/RO_0002085.md) SubPropertyOf [during which starts](../../RO/88/RO_0002088.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = di + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = encompasses + +## Usage + + * - + * TransitiveObjectProperty [encompasses](../../RO/85/RO_0002085.md) + * [encompasses](../../RO/85/RO_0002085.md) InverseOf [happens during](../../RO/92/RO_0002092.md) + * [encompasses](../../RO/85/RO_0002085.md) SubPropertyOf [during which starts](../../RO/88/RO_0002088.md) + +## External Comments + diff --git a/src/ontology/md/RO/85/RO_0002285.md b/src/ontology/md/RO/85/RO_0002285.md new file mode 100644 index 00000000..305a7fdb --- /dev/null +++ b/src/ontology/md/RO/85/RO_0002285.md @@ -0,0 +1,43 @@ + +## Class : developmentally replaces + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002285 + * *Label* = developmentally replaces + * *Definition* = x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally preceded by](../../RO/58/RO_0002258.md) + +## SubProperties + + +## Other Logical Axioms + + * [developmentally replaces](../../RO/85/RO_0002285.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else + * *[editor note](../../IAO/16/IAO_0000116.md)* = This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[alternative term](../../IAO/18/IAO_0000118.md)* = replaces + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = developmentally replaces + +## Usage + + * - + * [developmentally replaces](../../RO/85/RO_0002285.md) SubPropertyOf [developmentally preceded by](../../RO/58/RO_0002258.md) + +## External Comments + diff --git a/src/ontology/md/RO/85/RO_0002385.md b/src/ontology/md/RO/85/RO_0002385.md new file mode 100644 index 00000000..6daa071f --- /dev/null +++ b/src/ontology/md/RO/85/RO_0002385.md @@ -0,0 +1,42 @@ + +## Class : has potential to developmentally contribute to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002385 + * *Label* = has potential to developmentally contribute to + * *Definition* = x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has developmental potential involving](../../RO/84/RO_0002384.md) + +## SubProperties + + +## Other Logical Axioms + + * [has potential to developmentally contribute to](../../RO/85/RO_0002385.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has potential to developmentally contribute to + +## Usage + + * - + * [developmentally contributes to](../../RO/55/RO_0002255.md) SubPropertyOf [has potential to developmentally contribute to](../../RO/85/RO_0002385.md) + * [has potential to developmentally contribute to](../../RO/85/RO_0002385.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + +## External Comments + diff --git a/src/ontology/md/RO/85/RO_0002485.md b/src/ontology/md/RO/85/RO_0002485.md new file mode 100644 index 00000000..6eb32a93 --- /dev/null +++ b/src/ontology/md/RO/85/RO_0002485.md @@ -0,0 +1,41 @@ + +## Class : receives input from + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002485 + * *Label* = receives input from + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [connected to](../../RO/70/RO_0002170.md) + +## SubProperties + + +## Other Logical Axioms + + * [receives input from](../../RO/85/RO_0002485.md) InverseOf [sends output to](../../RO/86/RO_0002486.md) + * [receives input from](../../RO/85/RO_0002485.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## Other Annotations + + * *[editor note](../../IAO/16/IAO_0000116.md)* = See notes for inverse relation + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = receives input from + +## Usage + + * - + * [receives input from](../../RO/85/RO_0002485.md) InverseOf [sends output to](../../RO/86/RO_0002486.md) + * [receives input from](../../RO/85/RO_0002485.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## External Comments + diff --git a/src/ontology/md/RO/85/RO_0002585.md b/src/ontology/md/RO/85/RO_0002585.md new file mode 100644 index 00000000..3045c8d5 --- /dev/null +++ b/src/ontology/md/RO/85/RO_0002585.md @@ -0,0 +1,41 @@ + +## Class : results in closure of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002585 + * *Label* = results in closure of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in closure of](../../RO/85/RO_0002585.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in closure of](../../RO/85/RO_0002585.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[editor note](../../IAO/16/IAO_0000116.md)* = p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in closure of + +## Usage + + * - + * [results in closure of](../../RO/85/RO_0002585.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in closure of](../../RO/85/RO_0002585.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/86/RO_0000086.md b/src/ontology/md/RO/86/RO_0000086.md new file mode 100644 index 00000000..61b5fdfd --- /dev/null +++ b/src/ontology/md/RO/86/RO_0000086.md @@ -0,0 +1,46 @@ + +## Class : has quality + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000086 + * *Label* = has quality + * *Definition* = a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [bearer of](../../RO/53/RO_0000053.md) + +## SubProperties + + +## Other Logical Axioms + + * [has quality](../../RO/86/RO_0000086.md) Range [quality](../../BFO/19/BFO_0000019.md) + * [has quality](../../RO/86/RO_0000086.md) SubPropertyOf [bearer of](../../RO/53/RO_0000053.md) + * [quality of](../../RO/80/RO_0000080.md) InverseOf [has quality](../../RO/86/RO_0000086.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this apple has quality this red color + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + * *[editor note](../../IAO/16/IAO_0000116.md)* = A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has_quality + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has quality + +## Usage + + * - + * [has quality](../../RO/86/RO_0000086.md) Range [quality](../../BFO/19/BFO_0000019.md) + * [has quality](../../RO/86/RO_0000086.md) SubPropertyOf [bearer of](../../RO/53/RO_0000053.md) + * [quality of](../../RO/80/RO_0000080.md) InverseOf [has quality](../../RO/86/RO_0000086.md) + +## External Comments + diff --git a/src/ontology/md/RO/86/RO_0002086.md b/src/ontology/md/RO/86/RO_0002086.md new file mode 100644 index 00000000..7b770167 --- /dev/null +++ b/src/ontology/md/RO/86/RO_0002086.md @@ -0,0 +1,46 @@ + +## Class : ends after + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002086 + * *Label* = ends after + * *Comment* = X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [ends after](../../RO/86/RO_0002086.md) + * [ends after](../../RO/86/RO_0002086.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ends after + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [ends after](../../RO/86/RO_0002086.md) + * [ends after](../../RO/86/RO_0002086.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [preceded by](../../BFO/62/BFO_0000062.md) SubPropertyOf [ends after](../../RO/86/RO_0002086.md) + +## External Comments + diff --git a/src/ontology/md/RO/86/RO_0002286.md b/src/ontology/md/RO/86/RO_0002286.md new file mode 100644 index 00000000..1dd1ad5f --- /dev/null +++ b/src/ontology/md/RO/86/RO_0002286.md @@ -0,0 +1,48 @@ + +## Class : developmentally succeeded by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002286 + * *Label* = developmentally succeeded by + * *Definition* = Inverse of developmentally preceded by + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has developmental potential involving](../../RO/84/RO_0002384.md) + +## SubProperties + + +## Other Logical Axioms + + * [developmentally succeeded by](../../RO/86/RO_0002286.md) InverseOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [developmentally succeeded by](../../RO/86/RO_0002286.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Inverse of developmentally preceded by + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = developmentally succeeded by + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [developmentally contributes to](../../RO/55/RO_0002255.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [developmentally induces](../../RO/57/RO_0002257.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [developmentally succeeded by](../../RO/86/RO_0002286.md) InverseOf [developmentally preceded by](../../RO/58/RO_0002258.md) + * [developmentally succeeded by](../../RO/86/RO_0002286.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + * [develops into](../../RO/03/RO_0002203.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + * [part of developmental precursor of](../../RO/87/RO_0002287.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + +## External Comments + diff --git a/src/ontology/md/RO/86/RO_0002386.md b/src/ontology/md/RO/86/RO_0002386.md new file mode 100644 index 00000000..24a34f77 --- /dev/null +++ b/src/ontology/md/RO/86/RO_0002386.md @@ -0,0 +1,42 @@ + +## Class : has potential to developmentally induce + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002386 + * *Label* = has potential to developmentally induce + * *Definition* = x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has developmental potential involving](../../RO/84/RO_0002384.md) + +## SubProperties + + +## Other Logical Axioms + + * [has potential to developmentally induce](../../RO/86/RO_0002386.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has potential to developmentally induce + +## Usage + + * - + * [developmentally induces](../../RO/57/RO_0002257.md) SubPropertyOf [has potential to developmentally induce](../../RO/86/RO_0002386.md) + * [has potential to developmentally induce](../../RO/86/RO_0002386.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + +## External Comments + diff --git a/src/ontology/md/RO/86/RO_0002486.md b/src/ontology/md/RO/86/RO_0002486.md new file mode 100644 index 00000000..b59d1de8 --- /dev/null +++ b/src/ontology/md/RO/86/RO_0002486.md @@ -0,0 +1,41 @@ + +## Class : sends output to + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002486 + * *Label* = sends output to + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [connected to](../../RO/70/RO_0002170.md) + +## SubProperties + + +## Other Logical Axioms + + * [receives input from](../../RO/85/RO_0002485.md) InverseOf [sends output to](../../RO/86/RO_0002486.md) + * [sends output to](../../RO/86/RO_0002486.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## Other Annotations + + * *[editor note](../../IAO/16/IAO_0000116.md)* = This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = sends output to + +## Usage + + * - + * [receives input from](../../RO/85/RO_0002485.md) InverseOf [sends output to](../../RO/86/RO_0002486.md) + * [sends output to](../../RO/86/RO_0002486.md) SubPropertyOf [connected to](../../RO/70/RO_0002170.md) + +## External Comments + diff --git a/src/ontology/md/RO/86/RO_0002586.md b/src/ontology/md/RO/86/RO_0002586.md new file mode 100644 index 00000000..6b63b45c --- /dev/null +++ b/src/ontology/md/RO/86/RO_0002586.md @@ -0,0 +1,41 @@ + +## Class : results in breakdown of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002586 + * *Label* = results in breakdown of + * *Definition* = p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has input](../../RO/33/RO_0002233.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in breakdown of](../../RO/86/RO_0002586.md) SubPropertyOf [has input](../../RO/33/RO_0002233.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in breakdown of + +## Usage + + * - + * [results in breakdown of](../../RO/86/RO_0002586.md) SubPropertyOf [has input](../../RO/33/RO_0002233.md) + * [results in catabolism of](../../RO/89/RO_0002589.md) SubPropertyOf [results in breakdown of](../../RO/86/RO_0002586.md) + * [results in disassembly of](../../RO/90/RO_0002590.md) SubPropertyOf [results in breakdown of](../../RO/86/RO_0002586.md) + +## External Comments + diff --git a/src/ontology/md/RO/87/RO_0000087.md b/src/ontology/md/RO/87/RO_0000087.md new file mode 100644 index 00000000..e5ee7442 --- /dev/null +++ b/src/ontology/md/RO/87/RO_0000087.md @@ -0,0 +1,48 @@ + +## Class : has role + + * *IRI* = http://purl.obolibrary.org/obo/RO_0000087 + * *Label* = has role + * *Definition* = a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [bearer of](../../RO/53/RO_0000053.md) + +## SubProperties + + +## Other Logical Axioms + + * [has role](../../RO/87/RO_0000087.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [has role](../../RO/87/RO_0000087.md) InverseOf [role of](../../RO/81/RO_0000081.md) + * [has role](../../RO/87/RO_0000087.md) Range [role](../../BFO/23/BFO_0000023.md) + * [has role](../../RO/87/RO_0000087.md) SubPropertyOf [bearer of](../../RO/53/RO_0000053.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = this person has role this investigator role (more colloquially: this person has this role of investigator) + * *[definition](../../IAO/15/IAO_0000115.md)* = a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + * *[editor note](../../IAO/16/IAO_0000116.md)* = A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = has_role + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has role + +## Usage + + * - + * [has role](../../RO/87/RO_0000087.md) Domain [independent continuant](../../BFO/04/BFO_0000004.md) + * [has role](../../RO/87/RO_0000087.md) InverseOf [role of](../../RO/81/RO_0000081.md) + * [has role](../../RO/87/RO_0000087.md) Range [role](../../BFO/23/BFO_0000023.md) + * [has role](../../RO/87/RO_0000087.md) SubPropertyOf [bearer of](../../RO/53/RO_0000053.md) + +## External Comments + diff --git a/src/ontology/md/RO/87/RO_0002087.md b/src/ontology/md/RO/87/RO_0002087.md new file mode 100644 index 00000000..465cc9b7 --- /dev/null +++ b/src/ontology/md/RO/87/RO_0002087.md @@ -0,0 +1,45 @@ + +## Class : immediately preceded by + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002087 + * *Label* = immediately preceded by + * *Comment* = X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [preceded by](../../BFO/62/BFO_0000062.md) + +## SubProperties + + +## Other Logical Axioms + + * [immediately preceded by](../../RO/87/RO_0002087.md) InverseOf [immediately precedes](../../RO/90/RO_0002090.md) + * [immediately preceded by](../../RO/87/RO_0002087.md) SubPropertyOf [preceded by](../../BFO/62/BFO_0000062.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = starts_at_end_of + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = immediately preceded by + +## Usage + + * - + * [immediate transformation of](../../RO/95/RO_0002495.md) SubPropertyOf [immediately preceded by](../../RO/87/RO_0002087.md) + * [immediately causally downstream of](../../RO/05/RO_0002405.md) SubPropertyOf [immediately preceded by](../../RO/87/RO_0002087.md) + * [immediately preceded by](../../RO/87/RO_0002087.md) InverseOf [immediately precedes](../../RO/90/RO_0002090.md) + * [immediately preceded by](../../RO/87/RO_0002087.md) SubPropertyOf [preceded by](../../BFO/62/BFO_0000062.md) + +## External Comments + diff --git a/src/ontology/md/RO/87/RO_0002287.md b/src/ontology/md/RO/87/RO_0002287.md new file mode 100644 index 00000000..77bc4ee2 --- /dev/null +++ b/src/ontology/md/RO/87/RO_0002287.md @@ -0,0 +1,41 @@ + +## Class : part of developmental precursor of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002287 + * *Label* = part of developmental precursor of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally succeeded by](../../RO/86/RO_0002286.md) + +## SubProperties + + +## Other Logical Axioms + + * [part of developmental precursor of](../../RO/87/RO_0002287.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = part of developmental precursor of + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [part of developmental precursor of](../../RO/87/RO_0002287.md) SubPropertyOf [developmentally succeeded by](../../RO/86/RO_0002286.md) + +## External Comments + diff --git a/src/ontology/md/RO/87/RO_0002387.md b/src/ontology/md/RO/87/RO_0002387.md new file mode 100644 index 00000000..8fa778e7 --- /dev/null +++ b/src/ontology/md/RO/87/RO_0002387.md @@ -0,0 +1,43 @@ + +## Class : has potential to develop into + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002387 + * *Label* = has potential to develop into + * *Definition* = x has the potential to develop into y iff x develops into y or if x is capable of developing into y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has developmental potential involving](../../RO/84/RO_0002384.md) + +## SubProperties + + +## Other Logical Axioms + + * [has potential to develop into](../../RO/87/RO_0002387.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has the potential to develop into y iff x develops into y or if x is capable of developing into y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has potential to develop into + +## Usage + + * - + * [develops into](../../RO/03/RO_0002203.md) SubPropertyOf [has potential to develop into](../../RO/87/RO_0002387.md) + * [has potential to develop into](../../RO/87/RO_0002387.md) SubPropertyOf [has developmental potential involving](../../RO/84/RO_0002384.md) + * [has potential to directly develop into](../../RO/88/RO_0002388.md) SubPropertyOf [has potential to develop into](../../RO/87/RO_0002387.md) + +## External Comments + diff --git a/src/ontology/md/RO/87/RO_0002487.md b/src/ontology/md/RO/87/RO_0002487.md new file mode 100644 index 00000000..ae83d48d --- /dev/null +++ b/src/ontology/md/RO/87/RO_0002487.md @@ -0,0 +1,45 @@ + +## Class : relation between structure and stage + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002487 + * *Label* = relation between structure and stage + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + * [relation between structure and stage](../../RO/87/RO_0002487.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [relation between structure and stage](../../RO/87/RO_0002487.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[curator note](../../IAO/32/IAO_0000232.md)* = Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = relation between structure and stage + +## Usage + + * - + * [existence ends at point](../../RO/93/RO_0002593.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + * [existence ends during or before](../../RO/97/RO_0002497.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + * [existence overlaps](../../RO/90/RO_0002490.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + * [existence starts at point](../../RO/83/RO_0002583.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + * [existence starts during or after](../../RO/96/RO_0002496.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + * [relation between structure and stage](../../RO/87/RO_0002487.md) Domain [continuant](../../BFO/02/BFO_0000002.md) + * [relation between structure and stage](../../RO/87/RO_0002487.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + +## External Comments + diff --git a/src/ontology/md/RO/87/RO_0002587.md b/src/ontology/md/RO/87/RO_0002587.md new file mode 100644 index 00000000..09144f84 --- /dev/null +++ b/src/ontology/md/RO/87/RO_0002587.md @@ -0,0 +1,37 @@ + +## Class : results in synthesis of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002587 + * *Label* = results in synthesis of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in formation of](../../RO/97/RO_0002297.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in synthesis of](../../RO/87/RO_0002587.md) SubPropertyOf [results in formation of](../../RO/97/RO_0002297.md) + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in synthesis of + +## Usage + + * - + * [results in synthesis of](../../RO/87/RO_0002587.md) SubPropertyOf [results in formation of](../../RO/97/RO_0002297.md) + +## External Comments + diff --git a/src/ontology/md/RO/88/RO_0002088.md b/src/ontology/md/RO/88/RO_0002088.md new file mode 100644 index 00000000..810c7859 --- /dev/null +++ b/src/ontology/md/RO/88/RO_0002088.md @@ -0,0 +1,45 @@ + +## Class : during which starts + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002088 + * *Label* = during which starts + * *Comment* = Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * [during which starts](../../RO/88/RO_0002088.md) InverseOf [starts during](../../RO/91/RO_0002091.md) + * [during which starts](../../RO/88/RO_0002088.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = during which starts + +## Usage + + * - + * [during which starts](../../RO/88/RO_0002088.md) InverseOf [starts during](../../RO/91/RO_0002091.md) + * [during which starts](../../RO/88/RO_0002088.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [encompasses](../../RO/85/RO_0002085.md) SubPropertyOf [during which starts](../../RO/88/RO_0002088.md) + +## External Comments + diff --git a/src/ontology/md/RO/88/RO_0002388.md b/src/ontology/md/RO/88/RO_0002388.md new file mode 100644 index 00000000..fe488441 --- /dev/null +++ b/src/ontology/md/RO/88/RO_0002388.md @@ -0,0 +1,42 @@ + +## Class : has potential to directly develop into + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002388 + * *Label* = has potential to directly develop into + * *Definition* = x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has potential to develop into](../../RO/87/RO_0002387.md) + +## SubProperties + + +## Other Logical Axioms + + * [has potential to directly develop into](../../RO/88/RO_0002388.md) SubPropertyOf [has potential to develop into](../../RO/87/RO_0002387.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000428 + * *[definition](../../IAO/15/IAO_0000115.md)* = x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has potential to directly develop into + +## Usage + + * - + * [develops into](../../RO/03/RO_0002203.md) SubPropertyOf [has potential to directly develop into](../../RO/88/RO_0002388.md) + * [has potential to directly develop into](../../RO/88/RO_0002388.md) SubPropertyOf [has potential to develop into](../../RO/87/RO_0002387.md) + +## External Comments + diff --git a/src/ontology/md/RO/88/RO_0002488.md b/src/ontology/md/RO/88/RO_0002488.md new file mode 100644 index 00000000..42a78e2d --- /dev/null +++ b/src/ontology/md/RO/88/RO_0002488.md @@ -0,0 +1,47 @@ + +## Class : existence starts during + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002488 + * *Label* = existence starts during + * *Definition* = x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [existence overlaps](../../RO/90/RO_0002490.md) + * [existence starts during or after](../../RO/96/RO_0002496.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence starts during](../../RO/88/RO_0002488.md) SubPropertyOf [existence overlaps](../../RO/90/RO_0002490.md) + * [existence starts during](../../RO/88/RO_0002488.md) SubPropertyOf [existence starts during or after](../../RO/96/RO_0002496.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence starts during + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [existence starts and ends during](../../RO/91/RO_0002491.md) SubPropertyOf [existence starts during](../../RO/88/RO_0002488.md) + * [existence starts during](../../RO/88/RO_0002488.md) SubPropertyOf [existence overlaps](../../RO/90/RO_0002490.md) + * [existence starts during](../../RO/88/RO_0002488.md) SubPropertyOf [existence starts during or after](../../RO/96/RO_0002496.md) + * [existence starts with](../../RO/89/RO_0002489.md) SubPropertyOf [existence starts during](../../RO/88/RO_0002488.md) + +## External Comments + diff --git a/src/ontology/md/RO/88/RO_0002588.md b/src/ontology/md/RO/88/RO_0002588.md new file mode 100644 index 00000000..8eb62ddb --- /dev/null +++ b/src/ontology/md/RO/88/RO_0002588.md @@ -0,0 +1,40 @@ + +## Class : results in assembly of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002588 + * *Label* = results in assembly of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in formation of](../../RO/97/RO_0002297.md) + * [results in organization of](../../RO/92/RO_0002592.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in assembly of](../../RO/88/RO_0002588.md) SubPropertyOf [results in formation of](../../RO/97/RO_0002297.md) + * [results in assembly of](../../RO/88/RO_0002588.md) SubPropertyOf [results in organization of](../../RO/92/RO_0002592.md) + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in assembly of + +## Usage + + * - + * [results in assembly of](../../RO/88/RO_0002588.md) SubPropertyOf [results in formation of](../../RO/97/RO_0002297.md) + * [results in assembly of](../../RO/88/RO_0002588.md) SubPropertyOf [results in organization of](../../RO/92/RO_0002592.md) + +## External Comments + diff --git a/src/ontology/md/RO/89/RO_0002089.md b/src/ontology/md/RO/89/RO_0002089.md new file mode 100644 index 00000000..2fbef5f6 --- /dev/null +++ b/src/ontology/md/RO/89/RO_0002089.md @@ -0,0 +1,43 @@ + +## Class : starts before + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002089 + * *Label* = starts before + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [starts before](../../RO/89/RO_0002089.md) + * [starts before](../../RO/89/RO_0002089.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = starts before + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [starts before](../../RO/89/RO_0002089.md) + * [starts before](../../RO/89/RO_0002089.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## External Comments + diff --git a/src/ontology/md/RO/89/RO_0002489.md b/src/ontology/md/RO/89/RO_0002489.md new file mode 100644 index 00000000..59ddefcc --- /dev/null +++ b/src/ontology/md/RO/89/RO_0002489.md @@ -0,0 +1,41 @@ + +## Class : existence starts with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002489 + * *Label* = existence starts with + * *Definition* = x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [existence starts during](../../RO/88/RO_0002488.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence starts with](../../RO/89/RO_0002489.md) SubPropertyOf [existence starts during](../../RO/88/RO_0002488.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence starts with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [existence starts with](../../RO/89/RO_0002489.md) SubPropertyOf [existence starts during](../../RO/88/RO_0002488.md) + +## External Comments + diff --git a/src/ontology/md/RO/89/RO_0002589.md b/src/ontology/md/RO/89/RO_0002589.md new file mode 100644 index 00000000..74ae306f --- /dev/null +++ b/src/ontology/md/RO/89/RO_0002589.md @@ -0,0 +1,39 @@ + +## Class : results in catabolism of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002589 + * *Label* = results in catabolism of + * *Definition* = p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in breakdown of](../../RO/86/RO_0002586.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in catabolism of](../../RO/89/RO_0002589.md) SubPropertyOf [results in breakdown of](../../RO/86/RO_0002586.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in catabolism of + +## Usage + + * - + * [results in catabolism of](../../RO/89/RO_0002589.md) SubPropertyOf [results in breakdown of](../../RO/86/RO_0002586.md) + +## External Comments + diff --git a/src/ontology/md/RO/90/RO_0002090.md b/src/ontology/md/RO/90/RO_0002090.md new file mode 100644 index 00000000..fece743b6 --- /dev/null +++ b/src/ontology/md/RO/90/RO_0002090.md @@ -0,0 +1,49 @@ + +## Class : immediately precedes + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002090 + * *Label* = immediately precedes + * *Comment* = X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [precedes](../../BFO/63/BFO_0000063.md) + +## SubProperties + + +## Other Logical Axioms + + * [immediately preceded by](../../RO/87/RO_0002087.md) InverseOf [immediately precedes](../../RO/90/RO_0002090.md) + * [immediately precedes](../../RO/90/RO_0002090.md) SubPropertyOf [precedes](../../BFO/63/BFO_0000063.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = ends_at_start_of + * *[alternative term](../../IAO/18/IAO_0000118.md)* = meets + * *[is direct form of](../../RO/75/RO_0002575.md)* = http://purl.obolibrary.org/obo/BFO_0000063 + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = immediately precedes + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [immediately causally upstream of](../../RO/12/RO_0002412.md) SubPropertyOf [immediately precedes](../../RO/90/RO_0002090.md) + * [immediately preceded by](../../RO/87/RO_0002087.md) InverseOf [immediately precedes](../../RO/90/RO_0002090.md) + * [immediately precedes](../../RO/90/RO_0002090.md) SubPropertyOf [precedes](../../BFO/63/BFO_0000063.md) + +## External Comments + diff --git a/src/ontology/md/RO/90/RO_0002490.md b/src/ontology/md/RO/90/RO_0002490.md new file mode 100644 index 00000000..d876fcb8 --- /dev/null +++ b/src/ontology/md/RO/90/RO_0002490.md @@ -0,0 +1,44 @@ + +## Class : existence overlaps + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002490 + * *Label* = existence overlaps + * *Definition* = x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + * *Comment* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [relation between structure and stage](../../RO/87/RO_0002487.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence overlaps](../../RO/90/RO_0002490.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence overlaps + +## Usage + + * - + * [existence ends during](../../RO/92/RO_0002492.md) SubPropertyOf [existence overlaps](../../RO/90/RO_0002490.md) + * [existence overlaps](../../RO/90/RO_0002490.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + * [existence starts during](../../RO/88/RO_0002488.md) SubPropertyOf [existence overlaps](../../RO/90/RO_0002490.md) + +## External Comments + diff --git a/src/ontology/md/RO/90/RO_0002590.md b/src/ontology/md/RO/90/RO_0002590.md new file mode 100644 index 00000000..ecdb36ae --- /dev/null +++ b/src/ontology/md/RO/90/RO_0002590.md @@ -0,0 +1,40 @@ + +## Class : results in disassembly of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002590 + * *Label* = results in disassembly of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in breakdown of](../../RO/86/RO_0002586.md) + * [results in organization of](../../RO/92/RO_0002592.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in disassembly of](../../RO/90/RO_0002590.md) SubPropertyOf [results in breakdown of](../../RO/86/RO_0002586.md) + * [results in disassembly of](../../RO/90/RO_0002590.md) SubPropertyOf [results in organization of](../../RO/92/RO_0002592.md) + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in disassembly of + +## Usage + + * - + * [results in disassembly of](../../RO/90/RO_0002590.md) SubPropertyOf [results in breakdown of](../../RO/86/RO_0002586.md) + * [results in disassembly of](../../RO/90/RO_0002590.md) SubPropertyOf [results in organization of](../../RO/92/RO_0002592.md) + +## External Comments + diff --git a/src/ontology/md/RO/91/RO_0002091.md b/src/ontology/md/RO/91/RO_0002091.md new file mode 100644 index 00000000..61a6525f --- /dev/null +++ b/src/ontology/md/RO/91/RO_0002091.md @@ -0,0 +1,51 @@ + +## Class : starts during + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002091 + * *Label* = starts during + * *Comment* = X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * [during which starts](../../RO/88/RO_0002088.md) InverseOf [starts during](../../RO/91/RO_0002091.md) + * [starts during](../../RO/91/RO_0002091.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [starts during](../../RO/91/RO_0002091.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [starts during](../../RO/91/RO_0002091.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = io + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = starts during + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [during which starts](../../RO/88/RO_0002088.md) InverseOf [starts during](../../RO/91/RO_0002091.md) + * [starts during](../../RO/91/RO_0002091.md) Domain [occurrent](../../BFO/03/BFO_0000003.md) + * [starts during](../../RO/91/RO_0002091.md) Range [occurrent](../../BFO/03/BFO_0000003.md) + * [starts during](../../RO/91/RO_0002091.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## External Comments + diff --git a/src/ontology/md/RO/91/RO_0002291.md b/src/ontology/md/RO/91/RO_0002291.md new file mode 100644 index 00000000..ee92dd38 --- /dev/null +++ b/src/ontology/md/RO/91/RO_0002291.md @@ -0,0 +1,44 @@ + +## Class : ubiquitously expressed in + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002291 + * *Label* = ubiquitously expressed in + * *Definition* = x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [expressed in](../../RO/06/RO_0002206.md) + +## SubProperties + + +## Other Logical Axioms + + * [ubiquitously expressed in](../../RO/91/RO_0002291.md) SubPropertyOf [expressed in](../../RO/06/RO_0002206.md) + * [ubiquitously expresses](../../RO/93/RO_0002293.md) InverseOf [ubiquitously expressed in](../../RO/91/RO_0002291.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x + * *[editor note](../../IAO/16/IAO_0000116.md)* = Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ubiquitously expressed in + +## Usage + + * - + * [ubiquitously expressed in](../../RO/91/RO_0002291.md) SubPropertyOf [expressed in](../../RO/06/RO_0002206.md) + * [ubiquitously expresses](../../RO/93/RO_0002293.md) InverseOf [ubiquitously expressed in](../../RO/91/RO_0002291.md) + +## External Comments + diff --git a/src/ontology/md/RO/91/RO_0002491.md b/src/ontology/md/RO/91/RO_0002491.md new file mode 100644 index 00000000..0de81cf2 --- /dev/null +++ b/src/ontology/md/RO/91/RO_0002491.md @@ -0,0 +1,45 @@ + +## Class : existence starts and ends during + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002491 + * *Label* = existence starts and ends during + * *Definition* = x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + * *Comment* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [existence ends during](../../RO/92/RO_0002492.md) + * [existence starts during](../../RO/88/RO_0002488.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence starts and ends during](../../RO/91/RO_0002491.md) SubPropertyOf [existence ends during](../../RO/92/RO_0002492.md) + * [existence starts and ends during](../../RO/91/RO_0002491.md) SubPropertyOf [existence starts during](../../RO/88/RO_0002488.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence starts and ends during + +## Usage + + * - + * [existence starts and ends during](../../RO/91/RO_0002491.md) SubPropertyOf [existence ends during](../../RO/92/RO_0002492.md) + * [existence starts and ends during](../../RO/91/RO_0002491.md) SubPropertyOf [existence starts during](../../RO/88/RO_0002488.md) + +## External Comments + diff --git a/src/ontology/md/RO/91/RO_0002591.md b/src/ontology/md/RO/91/RO_0002591.md new file mode 100644 index 00000000..555dff39 --- /dev/null +++ b/src/ontology/md/RO/91/RO_0002591.md @@ -0,0 +1,40 @@ + +## Class : results in remodeling of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002591 + * *Label* = results in remodeling of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has input](../../RO/33/RO_0002233.md) + * [results in organization of](../../RO/92/RO_0002592.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in remodeling of](../../RO/91/RO_0002591.md) SubPropertyOf [has input](../../RO/33/RO_0002233.md) + * [results in remodeling of](../../RO/91/RO_0002591.md) SubPropertyOf [results in organization of](../../RO/92/RO_0002592.md) + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in remodeling of + +## Usage + + * - + * [results in remodeling of](../../RO/91/RO_0002591.md) SubPropertyOf [has input](../../RO/33/RO_0002233.md) + * [results in remodeling of](../../RO/91/RO_0002591.md) SubPropertyOf [results in organization of](../../RO/92/RO_0002592.md) + +## External Comments + diff --git a/src/ontology/md/RO/92/RO_0002092.md b/src/ontology/md/RO/92/RO_0002092.md new file mode 100644 index 00000000..10503d94 --- /dev/null +++ b/src/ontology/md/RO/92/RO_0002092.md @@ -0,0 +1,49 @@ + +## Class : happens during + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002092 + * *Label* = happens during + * *Comment* = X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [ends during](../../RO/93/RO_0002093.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [happens during](../../RO/92/RO_0002092.md) + * [encompasses](../../RO/85/RO_0002085.md) InverseOf [happens during](../../RO/92/RO_0002092.md) + * [happens during](../../RO/92/RO_0002092.md) SubPropertyOf [ends during](../../RO/93/RO_0002093.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = d + * *[alternative term](../../IAO/18/IAO_0000118.md)* = during + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = happens during + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * TransitiveObjectProperty [happens during](../../RO/92/RO_0002092.md) + * [encompasses](../../RO/85/RO_0002085.md) InverseOf [happens during](../../RO/92/RO_0002092.md) + * [happens during](../../RO/92/RO_0002092.md) SubPropertyOf [ends during](../../RO/93/RO_0002093.md) + +## External Comments + diff --git a/src/ontology/md/RO/92/RO_0002292.md b/src/ontology/md/RO/92/RO_0002292.md new file mode 100644 index 00000000..7cde500e --- /dev/null +++ b/src/ontology/md/RO/92/RO_0002292.md @@ -0,0 +1,45 @@ + +## Class : expresses + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002292 + * *Label* = expresses + * *Definition* = Inverse of 'expressed in' + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [genomically related to](../../RO/30/RO_0002330.md) + +## SubProperties + + +## Other Logical Axioms + + * [expresses](../../RO/92/RO_0002292.md) InverseOf [expressed in](../../RO/06/RO_0002206.md) + * [expresses](../../RO/92/RO_0002292.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = Inverse of 'expressed in' + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = expresses + +## Usage + + * - + * [cell expresses](../../RO/09/RO_0002009.md) SubPropertyOf [expresses](../../RO/92/RO_0002292.md) + * [expresses](../../RO/92/RO_0002292.md) InverseOf [expressed in](../../RO/06/RO_0002206.md) + * [expresses](../../RO/92/RO_0002292.md) SubPropertyOf [genomically related to](../../RO/30/RO_0002330.md) + * [ubiquitously expresses](../../RO/93/RO_0002293.md) SubPropertyOf [expresses](../../RO/92/RO_0002292.md) + +## External Comments + diff --git a/src/ontology/md/RO/92/RO_0002492.md b/src/ontology/md/RO/92/RO_0002492.md new file mode 100644 index 00000000..81d0560a --- /dev/null +++ b/src/ontology/md/RO/92/RO_0002492.md @@ -0,0 +1,49 @@ + +## Class : existence ends during + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002492 + * *Label* = existence ends during + * *Definition* = x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + * *Comment* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [existence overlaps](../../RO/90/RO_0002490.md) + * [existence ends during or before](../../RO/97/RO_0002497.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence ends during](../../RO/92/RO_0002492.md) SubPropertyOf [existence ends during or before](../../RO/97/RO_0002497.md) + * [existence ends during](../../RO/92/RO_0002492.md) SubPropertyOf [existence overlaps](../../RO/90/RO_0002490.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence ends during + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [existence ends during](../../RO/92/RO_0002492.md) SubPropertyOf [existence ends during or before](../../RO/97/RO_0002497.md) + * [existence ends during](../../RO/92/RO_0002492.md) SubPropertyOf [existence overlaps](../../RO/90/RO_0002490.md) + * [existence ends with](../../RO/93/RO_0002493.md) SubPropertyOf [existence ends during](../../RO/92/RO_0002492.md) + * [existence starts and ends during](../../RO/91/RO_0002491.md) SubPropertyOf [existence ends during](../../RO/92/RO_0002492.md) + +## External Comments + diff --git a/src/ontology/md/RO/92/RO_0002592.md b/src/ontology/md/RO/92/RO_0002592.md new file mode 100644 index 00000000..bd561cc7 --- /dev/null +++ b/src/ontology/md/RO/92/RO_0002592.md @@ -0,0 +1,42 @@ + +## Class : results in organization of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002592 + * *Label* = results in organization of + * *Definition* = p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in organization of](../../RO/92/RO_0002592.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in organization of + +## Usage + + * - + * [results in assembly of](../../RO/88/RO_0002588.md) SubPropertyOf [results in organization of](../../RO/92/RO_0002592.md) + * [results in disassembly of](../../RO/90/RO_0002590.md) SubPropertyOf [results in organization of](../../RO/92/RO_0002592.md) + * [results in organization of](../../RO/92/RO_0002592.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in remodeling of](../../RO/91/RO_0002591.md) SubPropertyOf [results in organization of](../../RO/92/RO_0002592.md) + +## External Comments + diff --git a/src/ontology/md/RO/93/RO_0002093.md b/src/ontology/md/RO/93/RO_0002093.md new file mode 100644 index 00000000..0ff05d6d --- /dev/null +++ b/src/ontology/md/RO/93/RO_0002093.md @@ -0,0 +1,48 @@ + +## Class : ends during + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002093 + * *Label* = ends during + * *Comment* = X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + +## Synonyms + + +## Cross-references + + +## Subsets + + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## SuperProperties + + * [temporally related to](../../RO/22/RO_0002222.md) + +## SubProperties + + +## Other Logical Axioms + + * [during which ends](../../RO/84/RO_0002084.md) InverseOf [ends during](../../RO/93/RO_0002093.md) + * [ends during](../../RO/93/RO_0002093.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + +## Other Annotations + + * *[term editor](../../IAO/17/IAO_0000117.md)* = David Osumi-Sutherland + * *[alternative term](../../IAO/18/IAO_0000118.md)* = o + * *[alternative term](../../IAO/18/IAO_0000118.md)* = overlaps + * *[in_subset](../../et/oboInOwl#inSubset.md)* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ends during + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [during which ends](../../RO/84/RO_0002084.md) InverseOf [ends during](../../RO/93/RO_0002093.md) + * [ends during](../../RO/93/RO_0002093.md) SubPropertyOf [temporally related to](../../RO/22/RO_0002222.md) + * [happens during](../../RO/92/RO_0002092.md) SubPropertyOf [ends during](../../RO/93/RO_0002093.md) + +## External Comments + diff --git a/src/ontology/md/RO/93/RO_0002293.md b/src/ontology/md/RO/93/RO_0002293.md new file mode 100644 index 00000000..c58d6290 --- /dev/null +++ b/src/ontology/md/RO/93/RO_0002293.md @@ -0,0 +1,43 @@ + +## Class : ubiquitously expresses + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002293 + * *Label* = ubiquitously expresses + * *Definition* = inverse of ubiquiotously expressed in + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [expresses](../../RO/92/RO_0002292.md) + +## SubProperties + + +## Other Logical Axioms + + * [ubiquitously expresses](../../RO/93/RO_0002293.md) InverseOf [ubiquitously expressed in](../../RO/91/RO_0002291.md) + * [ubiquitously expresses](../../RO/93/RO_0002293.md) SubPropertyOf [expresses](../../RO/92/RO_0002292.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = inverse of ubiquiotously expressed in + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = ubiquitously expresses + +## Usage + + * - + * [ubiquitously expresses](../../RO/93/RO_0002293.md) InverseOf [ubiquitously expressed in](../../RO/91/RO_0002291.md) + * [ubiquitously expresses](../../RO/93/RO_0002293.md) SubPropertyOf [expresses](../../RO/92/RO_0002292.md) + +## External Comments + diff --git a/src/ontology/md/RO/93/RO_0002493.md b/src/ontology/md/RO/93/RO_0002493.md new file mode 100644 index 00000000..631b6578 --- /dev/null +++ b/src/ontology/md/RO/93/RO_0002493.md @@ -0,0 +1,43 @@ + +## Class : existence ends with + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002493 + * *Label* = existence ends with + * *Definition* = x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). + * *Comment* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [existence ends during](../../RO/92/RO_0002492.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence ends with](../../RO/93/RO_0002493.md) SubPropertyOf [existence ends during](../../RO/92/RO_0002492.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence ends with + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [existence ends with](../../RO/93/RO_0002493.md) SubPropertyOf [existence ends during](../../RO/92/RO_0002492.md) + +## External Comments + diff --git a/src/ontology/md/RO/93/RO_0002593.md b/src/ontology/md/RO/93/RO_0002593.md new file mode 100644 index 00000000..f6f6dce0 --- /dev/null +++ b/src/ontology/md/RO/93/RO_0002593.md @@ -0,0 +1,42 @@ + +## Class : existence ends at point + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002593 + * *Label* = existence ends at point + * *Definition* = x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [relation between structure and stage](../../RO/87/RO_0002487.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence ends at point](../../RO/93/RO_0002593.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x existence starts at point y if and only if the time point at which x starts is equivalent to the time point at which y ends. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence ends at point + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [existence ends at point](../../RO/93/RO_0002593.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + +## External Comments + diff --git a/src/ontology/md/RO/94/RO_0002494.md b/src/ontology/md/RO/94/RO_0002494.md new file mode 100644 index 00000000..0290eb77 --- /dev/null +++ b/src/ontology/md/RO/94/RO_0002494.md @@ -0,0 +1,46 @@ + +## Class : transformation of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002494 + * *Label* = transformation of + * *Definition* = x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [preceded by](../../BFO/62/BFO_0000062.md) + * [develops from](../../RO/02/RO_0002202.md) + +## SubProperties + + +## Other Logical Axioms + + * TransitiveObjectProperty [transformation of](../../RO/94/RO_0002494.md) + * [transformation of](../../RO/94/RO_0002494.md) SubPropertyOf [develops from](../../RO/02/RO_0002202.md) + * [transformation of](../../RO/94/RO_0002494.md) SubPropertyOf [preceded by](../../BFO/62/BFO_0000062.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = transformation of + +## Usage + + * - + * TransitiveObjectProperty [transformation of](../../RO/94/RO_0002494.md) + * [immediate transformation of](../../RO/95/RO_0002495.md) SubPropertyOf [transformation of](../../RO/94/RO_0002494.md) + * [transformation of](../../RO/94/RO_0002494.md) SubPropertyOf [develops from](../../RO/02/RO_0002202.md) + * [transformation of](../../RO/94/RO_0002494.md) SubPropertyOf [preceded by](../../BFO/62/BFO_0000062.md) + +## External Comments + diff --git a/src/ontology/md/RO/94/RO_0002594.md b/src/ontology/md/RO/94/RO_0002594.md new file mode 100644 index 00000000..cf1bcd79 --- /dev/null +++ b/src/ontology/md/RO/94/RO_0002594.md @@ -0,0 +1,40 @@ + +## Class : is relational form of a class + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002594 + * *Label* = is relational form of a class + * *Definition* = An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [logical macro assertion on an object property](../../RO/22/RO_0002422.md) + +## SubProperties + + * [is relational form of process class](../../RO/62/RO_0002562.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = is relational form of a class + +## Usage + + * - + * SubAnnotationPropertyOf( ) + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/RO/95/RO_0002295.md b/src/ontology/md/RO/95/RO_0002295.md new file mode 100644 index 00000000..f4ddb692 --- /dev/null +++ b/src/ontology/md/RO/95/RO_0002295.md @@ -0,0 +1,61 @@ + +## Class : results in developmental progression of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002295 + * *Label* = results in developmental progression of + * *Definition* = p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [developmentally related to](../../RO/24/RO_0002324.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in developmental progression of](../../RO/95/RO_0002295.md) Domain [biological_process](../../GO/50/GO_0008150.md) + * [results in developmental progression of](../../RO/95/RO_0002295.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [results in developmental progression of](../../RO/95/RO_0002295.md) SubPropertyOf [developmentally related to](../../RO/24/RO_0002324.md) + +## Other Annotations + + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + * *[editor note](../../IAO/16/IAO_0000116.md)* = This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[shorthand](../../nd/oboInOwl#shorthand.md)* = results_in_developmental_progression_of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in developmental progression of + * *[rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md)* = http://wiki.geneontology.org/index.php/Ontology_extensions + +## Usage + + * - + * [results in acquisition of features of](../../RO/15/RO_0002315.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in closure of](../../RO/85/RO_0002585.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in commitment to](../../RO/48/RO_0002348.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in determination of](../../RO/49/RO_0002349.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in development of](../../RO/96/RO_0002296.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in developmental induction of](../../RO/57/RO_0002357.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in developmental progression of](../../RO/95/RO_0002295.md) Domain [biological_process](../../GO/50/GO_0008150.md) + * [results in developmental progression of](../../RO/95/RO_0002295.md) Range [anatomical structure](../../CARO/03/CARO_0000003.md) + * [results in developmental progression of](../../RO/95/RO_0002295.md) SubPropertyOf [developmentally related to](../../RO/24/RO_0002324.md) + * [results in ending of](../../RO/52/RO_0002552.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in formation of](../../RO/97/RO_0002297.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in growth of](../../RO/43/RO_0002343.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in maturation of](../../RO/99/RO_0002299.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in morphogenesis of](../../RO/98/RO_0002298.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in specification of](../../RO/56/RO_0002356.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in structural organization of](../../RO/55/RO_0002355.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/95/RO_0002495.md b/src/ontology/md/RO/95/RO_0002495.md new file mode 100644 index 00000000..9c387ac6 --- /dev/null +++ b/src/ontology/md/RO/95/RO_0002495.md @@ -0,0 +1,47 @@ + +## Class : immediate transformation of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002495 + * *Label* = immediate transformation of + * *Definition* = x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [directly develops from](../../RO/07/RO_0002207.md) + * [transformation of](../../RO/94/RO_0002494.md) + * [immediately preceded by](../../RO/87/RO_0002087.md) + +## SubProperties + + +## Other Logical Axioms + + * [immediate transformation of](../../RO/95/RO_0002495.md) SubPropertyOf [directly develops from](../../RO/07/RO_0002207.md) + * [immediate transformation of](../../RO/95/RO_0002495.md) SubPropertyOf [immediately preceded by](../../RO/87/RO_0002087.md) + * [immediate transformation of](../../RO/95/RO_0002495.md) SubPropertyOf [transformation of](../../RO/94/RO_0002494.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[is direct form of](../../RO/75/RO_0002575.md)* = http://purl.obolibrary.org/obo/RO_0002494 + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = immediate transformation of + +## Usage + + * - + * [immediate transformation of](../../RO/95/RO_0002495.md) SubPropertyOf [directly develops from](../../RO/07/RO_0002207.md) + * [immediate transformation of](../../RO/95/RO_0002495.md) SubPropertyOf [immediately preceded by](../../RO/87/RO_0002087.md) + * [immediate transformation of](../../RO/95/RO_0002495.md) SubPropertyOf [transformation of](../../RO/94/RO_0002494.md) + +## External Comments + diff --git a/src/ontology/md/RO/95/RO_0002595.md b/src/ontology/md/RO/95/RO_0002595.md new file mode 100644 index 00000000..34a20284 --- /dev/null +++ b/src/ontology/md/RO/95/RO_0002595.md @@ -0,0 +1,47 @@ + +## Class : causal relation between material entity and a process + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002595 + * *Label* = causal relation between material entity and a process + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causally related to](../../RO/10/RO_0002410.md) + +## SubProperties + + +## Other Logical Axioms + + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) Range [process](../../BFO/15/BFO_0000015.md) + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) SubPropertyOf [causally related to](../../RO/10/RO_0002410.md) + +## Other Annotations + + * *[editor note](../../IAO/16/IAO_0000116.md)* = Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = causal relation between material entity and a process + +## Usage + + * - + * [capable of part of](../../RO/16/RO_0002216.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [capable of regulating](../../RO/96/RO_0002596.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [capable of](../../RO/15/RO_0002215.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) Domain [material entity](../../BFO/40/BFO_0000040.md) + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) Range [process](../../BFO/15/BFO_0000015.md) + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) SubPropertyOf [causally related to](../../RO/10/RO_0002410.md) + * [has part structure that is capable of](../../RO/84/RO_0002584.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + +## External Comments + diff --git a/src/ontology/md/RO/96/RO_0002296.md b/src/ontology/md/RO/96/RO_0002296.md new file mode 100644 index 00000000..8264969c --- /dev/null +++ b/src/ontology/md/RO/96/RO_0002296.md @@ -0,0 +1,47 @@ + +## Class : results in development of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002296 + * *Label* = results in development of + * *Definition* = p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in development of](../../RO/96/RO_0002296.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in development of](../../RO/96/RO_0002296.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = every flower development (GO:0009908) results in development of some flower (PO:0009046) + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = http://www.geneontology.org/GO.doc.development.shtml + * *[shorthand](../../nd/oboInOwl#shorthand.md)* = results_in_development_of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in development of + +## Usage + + * - + * [results in development of](../../RO/96/RO_0002296.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in development of](../../RO/96/RO_0002296.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/96/RO_0002496.md b/src/ontology/md/RO/96/RO_0002496.md new file mode 100644 index 00000000..a05d734f --- /dev/null +++ b/src/ontology/md/RO/96/RO_0002496.md @@ -0,0 +1,49 @@ + +## Class : existence starts during or after + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002496 + * *Label* = existence starts during or after + * *Definition* = x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + * *Comment* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [relation between structure and stage](../../RO/87/RO_0002487.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence starts during or after](../../RO/96/RO_0002496.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence starts during or after + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [existence starts during or after](../../RO/96/RO_0002496.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + * [existence starts during](../../RO/88/RO_0002488.md) SubPropertyOf [existence starts during or after](../../RO/96/RO_0002496.md) + +## External Comments + diff --git a/src/ontology/md/RO/96/RO_0002596.md b/src/ontology/md/RO/96/RO_0002596.md new file mode 100644 index 00000000..6eed2f13 --- /dev/null +++ b/src/ontology/md/RO/96/RO_0002596.md @@ -0,0 +1,43 @@ + +## Class : capable of regulating + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002596 + * *Label* = capable of regulating + * *Definition* = Holds between c and p if and only if c is capable of some activity a, and a regulates p. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + +## SubProperties + + +## Other Logical Axioms + + * [capable of regulating](../../RO/96/RO_0002596.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = pyrethroid -> growth + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between c and p if and only if c is capable of some activity a, and a regulates p. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = capable of regulating + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [capable of negatively regulating](../../RO/97/RO_0002597.md) SubPropertyOf [capable of regulating](../../RO/96/RO_0002596.md) + * [capable of positively regulating](../../RO/98/RO_0002598.md) SubPropertyOf [capable of regulating](../../RO/96/RO_0002596.md) + * [capable of regulating](../../RO/96/RO_0002596.md) SubPropertyOf [causal relation between material entity and a process](../../RO/95/RO_0002595.md) + +## External Comments + diff --git a/src/ontology/md/RO/97/RO_0002297.md b/src/ontology/md/RO/97/RO_0002297.md new file mode 100644 index 00000000..310e745c --- /dev/null +++ b/src/ontology/md/RO/97/RO_0002297.md @@ -0,0 +1,50 @@ + +## Class : results in formation of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002297 + * *Label* = results in formation of + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + * [has output](../../RO/34/RO_0002234.md) + +## SubProperties + + +## Other Logical Axioms + + * [formed as result of](../../RO/54/RO_0002354.md) InverseOf [results in formation of](../../RO/97/RO_0002297.md) + * [results in formation of](../../RO/97/RO_0002297.md) SubPropertyOf [has output](../../RO/34/RO_0002234.md) + * [results in formation of](../../RO/97/RO_0002297.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. + * *[example of usage](../../IAO/12/IAO_0000112.md)* = every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = GOC:mtg_berkeley_2013 + * *[shorthand](../../nd/oboInOwl#shorthand.md)* = results_in_formation_of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in formation of + +## Usage + + * - + * [formed as result of](../../RO/54/RO_0002354.md) InverseOf [results in formation of](../../RO/97/RO_0002297.md) + * [results in assembly of](../../RO/88/RO_0002588.md) SubPropertyOf [results in formation of](../../RO/97/RO_0002297.md) + * [results in formation of](../../RO/97/RO_0002297.md) SubPropertyOf [has output](../../RO/34/RO_0002234.md) + * [results in formation of](../../RO/97/RO_0002297.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + * [results in synthesis of](../../RO/87/RO_0002587.md) SubPropertyOf [results in formation of](../../RO/97/RO_0002297.md) + +## External Comments + diff --git a/src/ontology/md/RO/97/RO_0002497.md b/src/ontology/md/RO/97/RO_0002497.md new file mode 100644 index 00000000..d40b56a2 --- /dev/null +++ b/src/ontology/md/RO/97/RO_0002497.md @@ -0,0 +1,49 @@ + +## Class : existence ends during or before + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002497 + * *Label* = existence ends during or before + * *Definition* = x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. + * *Comment* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [relation between structure and stage](../../RO/87/RO_0002487.md) + +## SubProperties + + +## Other Logical Axioms + + * [existence ends during or before](../../RO/97/RO_0002497.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[rdf-schema#comment](../../nt/rdf-schema#comment.md)* = The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = existence ends during or before + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * SubObjectPropertyOf(ObjectPropertyChain( InverseOf() ) ) + * [existence ends during or before](../../RO/97/RO_0002497.md) SubPropertyOf [relation between structure and stage](../../RO/87/RO_0002487.md) + * [existence ends during](../../RO/92/RO_0002492.md) SubPropertyOf [existence ends during or before](../../RO/97/RO_0002497.md) + +## External Comments + diff --git a/src/ontology/md/RO/97/RO_0002597.md b/src/ontology/md/RO/97/RO_0002597.md new file mode 100644 index 00000000..ed6b6dab --- /dev/null +++ b/src/ontology/md/RO/97/RO_0002597.md @@ -0,0 +1,41 @@ + +## Class : capable of negatively regulating + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002597 + * *Label* = capable of negatively regulating + * *Definition* = Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [capable of regulating](../../RO/96/RO_0002596.md) + +## SubProperties + + +## Other Logical Axioms + + * [capable of negatively regulating](../../RO/97/RO_0002597.md) SubPropertyOf [capable of regulating](../../RO/96/RO_0002596.md) + +## Other Annotations + + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = capable of negatively regulating + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [capable of inhibiting or preventing pathological process](../../RO/99/RO_0002599.md) SubPropertyOf [capable of negatively regulating](../../RO/97/RO_0002597.md) + * [capable of negatively regulating](../../RO/97/RO_0002597.md) SubPropertyOf [capable of regulating](../../RO/96/RO_0002596.md) + +## External Comments + diff --git a/src/ontology/md/RO/98/RO_0002298.md b/src/ontology/md/RO/98/RO_0002298.md new file mode 100644 index 00000000..36a5fe62 --- /dev/null +++ b/src/ontology/md/RO/98/RO_0002298.md @@ -0,0 +1,48 @@ + +## Class : results in morphogenesis of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002298 + * *Label* = results in morphogenesis of + * *Definition* = The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in morphogenesis of](../../RO/98/RO_0002298.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in morphogenesis of](../../RO/98/RO_0002298.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. + * *[example of usage](../../IAO/12/IAO_0000112.md)* = tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = GOC:mtg_berkeley_2013 + * *[shorthand](../../nd/oboInOwl#shorthand.md)* = results_in_morphogenesis_of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in morphogenesis of + +## Usage + + * - + * [results in morphogenesis of](../../RO/98/RO_0002298.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in morphogenesis of](../../RO/98/RO_0002298.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/98/RO_0002598.md b/src/ontology/md/RO/98/RO_0002598.md new file mode 100644 index 00000000..5fe935c3 --- /dev/null +++ b/src/ontology/md/RO/98/RO_0002598.md @@ -0,0 +1,42 @@ + +## Class : capable of positively regulating + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002598 + * *Label* = capable of positively regulating + * *Definition* = Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [capable of regulating](../../RO/96/RO_0002596.md) + +## SubProperties + + +## Other Logical Axioms + + * [capable of positively regulating](../../RO/98/RO_0002598.md) SubPropertyOf [capable of regulating](../../RO/96/RO_0002596.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = renin -> arteriolar smooth muscle contraction + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = capable of positively regulating + +## Usage + + * - + * SubObjectPropertyOf(ObjectPropertyChain( ) ) + * [capable of positively regulating](../../RO/98/RO_0002598.md) SubPropertyOf [capable of regulating](../../RO/96/RO_0002596.md) + * [capable of upregulating or causing pathological process](../../RO/00/RO_0002600.md) SubPropertyOf [capable of positively regulating](../../RO/98/RO_0002598.md) + +## External Comments + diff --git a/src/ontology/md/RO/99/RO_0002299.md b/src/ontology/md/RO/99/RO_0002299.md new file mode 100644 index 00000000..76673560 --- /dev/null +++ b/src/ontology/md/RO/99/RO_0002299.md @@ -0,0 +1,48 @@ + +## Class : results in maturation of + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002299 + * *Label* = results in maturation of + * *Definition* = The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [results in developmental progression of](../../RO/95/RO_0002295.md) + * [has participant](../../RO/57/RO_0000057.md) + +## SubProperties + + +## Other Logical Axioms + + * [results in maturation of](../../RO/99/RO_0002299.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in maturation of](../../RO/99/RO_0002299.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process + * *[example of usage](../../IAO/12/IAO_0000112.md)* = bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) + * *[has curation status](../../IAO/14/IAO_0000114.md)* = http://purl.obolibrary.org/obo/IAO_0000125 + * *[definition](../../IAO/15/IAO_0000115.md)* = The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + * *[term editor](../../IAO/17/IAO_0000117.md)* = Chris Mungall + * *[definition source](../../IAO/19/IAO_0000119.md)* = GOC:mtg_berkeley_2013 + * *[shorthand](../../nd/oboInOwl#shorthand.md)* = results_in_maturation_of + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = results in maturation of + +## Usage + + * - + * [results in maturation of](../../RO/99/RO_0002299.md) SubPropertyOf [has participant](../../RO/57/RO_0000057.md) + * [results in maturation of](../../RO/99/RO_0002299.md) SubPropertyOf [results in developmental progression of](../../RO/95/RO_0002295.md) + +## External Comments + diff --git a/src/ontology/md/RO/99/RO_0002599.md b/src/ontology/md/RO/99/RO_0002599.md new file mode 100644 index 00000000..f8419b19 --- /dev/null +++ b/src/ontology/md/RO/99/RO_0002599.md @@ -0,0 +1,43 @@ + +## Class : capable of inhibiting or preventing pathological process + + * *IRI* = http://purl.obolibrary.org/obo/RO_0002599 + * *Label* = capable of inhibiting or preventing pathological process + * *Definition* = Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [capable of negatively regulating](../../RO/97/RO_0002597.md) + +## SubProperties + + +## Other Logical Axioms + + * [capable of inhibiting or preventing pathological process](../../RO/99/RO_0002599.md) SubPropertyOf [capable of negatively regulating](../../RO/97/RO_0002597.md) + +## Other Annotations + + * *[example of usage](../../IAO/12/IAO_0000112.md)* = pazopanib -> pathological angiogenesis + * *[definition](../../IAO/15/IAO_0000115.md)* = Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. + * *[alternative term](../../IAO/18/IAO_0000118.md)* = treats + * *[curator note](../../IAO/32/IAO_0000232.md)* = The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = capable of inhibiting or preventing pathological process + +## Usage + + * - + * [capable of inhibiting or preventing pathological process](../../RO/99/RO_0002599.md) SubPropertyOf [capable of negatively regulating](../../RO/97/RO_0002597.md) + * [is substance that treats](../../RO/06/RO_0002606.md) SubPropertyOf [capable of inhibiting or preventing pathological process](../../RO/99/RO_0002599.md) + +## External Comments + diff --git a/src/ontology/md/ce/source.md b/src/ontology/md/ce/source.md new file mode 100644 index 00000000..d915e07e --- /dev/null +++ b/src/ontology/md/ce/source.md @@ -0,0 +1,108 @@ + +## Class : null + + * *IRI* = http://purl.org/dc/elements/1.1/source + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000062 [source](../../ce/source.md) http://www.obofoundry.org/ro/#OBO_REL:preceded_by + * http://purl.obolibrary.org/obo/RO_0000057 [source](../../ce/source.md) http://www.obofoundry.org/ro/#OBO_REL:has_participant + * http://purl.obolibrary.org/obo/RO_0001025 [source](../../ce/source.md) http://www.obofoundry.org/ro/#OBO_REL:located_in + * http://purl.obolibrary.org/obo/RO_0002150 [curator note](../../IAO/32/IAO_0000232.md) The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) + * http://purl.obolibrary.org/obo/RO_0002222 [source](../../ce/source.md) https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + * http://purl.obolibrary.org/obo/RO_0002360 [source](../../ce/source.md) http://neurolex.org/wiki/Property:DendriteLocation + * http://purl.obolibrary.org/obo/RO_0002376 [alternative term](../../IAO/18/IAO_0000118.md) drains to + * http://purl.obolibrary.org/obo/RO_0002376 [example of usage](../../IAO/12/IAO_0000112.md) Deschutes River tributary_of Columbia River + * http://purl.obolibrary.org/obo/RO_0002376 [example of usage](../../IAO/12/IAO_0000112.md) inferior epigastric vein tributary_of external iliac vein + * http://purl.obolibrary.org/obo/RO_0002377 [example of usage](../../IAO/12/IAO_0000112.md) Deschutes River distributary_of Little Lava Lake + * http://purl.obolibrary.org/obo/RO_0002440 [curator note](../../IAO/32/IAO_0000232.md) We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism + * http://purl.obolibrary.org/obo/RO_HOM0000000 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000001 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000002 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000003 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000004 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000005 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000006 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000007 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000008 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000009 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000010 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000011 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000012 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000013 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000014 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000015 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000016 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000017 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000018 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000019 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000020 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000022 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000023 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000024 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000025 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000026 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000027 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000028 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000029 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000030 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000031 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000032 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000033 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000034 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000036 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000037 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000042 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000043 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000044 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000045 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000046 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000047 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000048 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000049 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000050 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000051 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000052 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000053 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000054 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000055 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000057 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000058 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000060 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000061 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000062 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000063 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000065 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000066 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000068 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000069 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000071 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000072 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000073 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000074 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + * http://purl.obolibrary.org/obo/RO_HOM0000075 [source](../../ce/source.md) http://www.ncbi.nlm.nih.gov/pubmed/20116127 + +## External Comments + diff --git a/src/ontology/md/co/subsets#ro-eco.md b/src/ontology/md/co/subsets#ro-eco.md new file mode 100644 index 00000000..b1eada98 --- /dev/null +++ b/src/ontology/md/co/subsets#ro-eco.md @@ -0,0 +1,36 @@ + +## Class : eco subset + + * *IRI* = http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * *Label* = eco subset + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + * [subset_property](../../ty/oboInOwl#SubsetProperty.md) + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = eco subset + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/ed/owl#deprecated.md b/src/ontology/md/ed/owl#deprecated.md new file mode 100644 index 00000000..6b1b6929 --- /dev/null +++ b/src/ontology/md/ed/owl#deprecated.md @@ -0,0 +1,35 @@ + +## Class : null + + * *IRI* = http://www.w3.org/2002/07/owl#deprecated + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * http://purl.obolibrary.org/obo/BFO_0000005 [owl#deprecated](../../ed/owl#deprecated.md) true + * http://purl.obolibrary.org/obo/RO_0002401 [owl#deprecated](../../ed/owl#deprecated.md) true + * http://purl.obolibrary.org/obo/RO_0002402 [owl#deprecated](../../ed/owl#deprecated.md) true + * http://purl.obolibrary.org/obo/RO_0002403 [owl#deprecated](../../ed/owl#deprecated.md) true + +## External Comments + diff --git a/src/ontology/md/ef/oboInOwl#hasDbXref.md b/src/ontology/md/ef/oboInOwl#hasDbXref.md new file mode 100644 index 00000000..cf3ced7e --- /dev/null +++ b/src/ontology/md/ef/oboInOwl#hasDbXref.md @@ -0,0 +1,129 @@ + +## Class : database_cross_reference + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#hasDbXref + * *Label* = database_cross_reference + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = database_cross_reference + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002011 [definition](../../IAO/15/IAO_0000115.md) A relationship that holds between a process that regulates a transport process and the entity transported by that process. + * http://purl.obolibrary.org/obo/RO_0002565 [definition](../../IAO/15/IAO_0000115.md) Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c + * http://purl.obolibrary.org/obo/RO_HOM0000000 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) ECO:0000041 + * http://purl.obolibrary.org/obo/RO_HOM0000000 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:similar_to + * http://purl.obolibrary.org/obo/RO_HOM0000000 [definition](../../IAO/15/IAO_0000115.md) Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + * http://purl.obolibrary.org/obo/RO_HOM0000000 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) correspondence + * http://purl.obolibrary.org/obo/RO_HOM0000001 [definition](../../IAO/15/IAO_0000115.md) Similarity that results from common evolutionary origin. + * http://purl.obolibrary.org/obo/RO_HOM0000002 [definition](../../IAO/15/IAO_0000115.md) Similarity that results from independent evolution. + * http://purl.obolibrary.org/obo/RO_HOM0000003 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) ECO:0000075 + * http://purl.obolibrary.org/obo/RO_HOM0000003 [definition](../../IAO/15/IAO_0000115.md) Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + * http://purl.obolibrary.org/obo/RO_HOM0000004 [definition](../../IAO/15/IAO_0000115.md) Homoplasy that involves different underlying mechanisms or structures. + * http://purl.obolibrary.org/obo/RO_HOM0000005 [definition](../../IAO/15/IAO_0000115.md) Homoplasy that involves homologous underlying mechanisms or structures. + * http://purl.obolibrary.org/obo/RO_HOM0000006 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) ECO:0000071 + * http://purl.obolibrary.org/obo/RO_HOM0000006 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) MI:2163 + * http://purl.obolibrary.org/obo/RO_HOM0000006 [definition](../../IAO/15/IAO_0000115.md) Homology that is defined by similarity with regard to selected structural parameters. + * http://purl.obolibrary.org/obo/RO_HOM0000007 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) ECO:0000080 + * http://purl.obolibrary.org/obo/RO_HOM0000007 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) RO_proposed_relation:homologous_to + * http://purl.obolibrary.org/obo/RO_HOM0000007 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:0000330 + * http://purl.obolibrary.org/obo/RO_HOM0000007 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:0000853 + * http://purl.obolibrary.org/obo/RO_HOM0000007 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:0000857 + * http://purl.obolibrary.org/obo/RO_HOM0000007 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:homologous_to + * http://purl.obolibrary.org/obo/RO_HOM0000007 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) TAO:homologous_to + * http://purl.obolibrary.org/obo/RO_HOM0000007 [definition](../../IAO/15/IAO_0000115.md) Homology that is defined by common descent. + * http://purl.obolibrary.org/obo/RO_HOM0000008 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) ECO:0000067 + * http://purl.obolibrary.org/obo/RO_HOM0000008 [definition](../../IAO/15/IAO_0000115.md) Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + * http://purl.obolibrary.org/obo/RO_HOM0000009 [definition](../../IAO/15/IAO_0000115.md) Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + * http://purl.obolibrary.org/obo/RO_HOM0000010 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) MeSH:Synteny + * http://purl.obolibrary.org/obo/RO_HOM0000010 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:0000860 + * http://purl.obolibrary.org/obo/RO_HOM0000010 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:0005858 + * http://purl.obolibrary.org/obo/RO_HOM0000010 [definition](../../IAO/15/IAO_0000115.md) Structural homology that is detected by similarity in content and organization between chromosomes. + * http://purl.obolibrary.org/obo/RO_HOM0000011 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:0000854 + * http://purl.obolibrary.org/obo/RO_HOM0000011 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:0000859 + * http://purl.obolibrary.org/obo/RO_HOM0000011 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:paralogous_to + * http://purl.obolibrary.org/obo/RO_HOM0000011 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves genes that diverged after a duplication event. + * http://purl.obolibrary.org/obo/RO_HOM0000012 [definition](../../IAO/15/IAO_0000115.md) Paralogy that involves sets of syntenic blocks. + * http://purl.obolibrary.org/obo/RO_HOM0000013 [definition](../../IAO/15/IAO_0000115.md) Syntenic homology that involves chromosomes of different species. + * http://purl.obolibrary.org/obo/RO_HOM0000014 [definition](../../IAO/15/IAO_0000115.md) Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + * http://purl.obolibrary.org/obo/RO_HOM0000015 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) MeSH:Structural_Homology,_Protein + * http://purl.obolibrary.org/obo/RO_HOM0000015 [definition](../../IAO/15/IAO_0000115.md) Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + * http://purl.obolibrary.org/obo/RO_HOM0000016 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:non_functional_homolog_of + * http://purl.obolibrary.org/obo/RO_HOM0000016 [definition](../../IAO/15/IAO_0000115.md) Structural homology that involves a pseudogenic feature and its functional ancestor. + * http://purl.obolibrary.org/obo/RO_HOM0000017 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) ECO:00000060 + * http://purl.obolibrary.org/obo/RO_HOM0000017 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:0000855 + * http://purl.obolibrary.org/obo/RO_HOM0000017 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:0000858 + * http://purl.obolibrary.org/obo/RO_HOM0000017 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) SO:orthologous_to + * http://purl.obolibrary.org/obo/RO_HOM0000017 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves genes that diverged after a speciation event. + * http://purl.obolibrary.org/obo/RO_HOM0000018 [definition](../../IAO/15/IAO_0000115.md) Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + * http://purl.obolibrary.org/obo/RO_HOM0000019 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves two members sharing no other homologs in the lineages considered. + * http://purl.obolibrary.org/obo/RO_HOM0000020 [definition](../../IAO/15/IAO_0000115.md) Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + * http://purl.obolibrary.org/obo/RO_HOM0000022 [definition](../../IAO/15/IAO_0000115.md) Paralogy that results from a whole genome duplication event. + * http://purl.obolibrary.org/obo/RO_HOM0000023 [definition](../../IAO/15/IAO_0000115.md) Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + * http://purl.obolibrary.org/obo/RO_HOM0000024 [definition](../../IAO/15/IAO_0000115.md) Paralogy that results from a duplication preceding a given speciation event. + * http://purl.obolibrary.org/obo/RO_HOM0000025 [definition](../../IAO/15/IAO_0000115.md) 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + * http://purl.obolibrary.org/obo/RO_HOM0000026 [definition](../../IAO/15/IAO_0000115.md) 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + * http://purl.obolibrary.org/obo/RO_HOM0000027 [definition](../../IAO/15/IAO_0000115.md) Iterative homology that involves structures arranged along the main body axis. + * http://purl.obolibrary.org/obo/RO_HOM0000028 [definition](../../IAO/15/IAO_0000115.md) Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + * http://purl.obolibrary.org/obo/RO_HOM0000029 [definition](../../IAO/15/IAO_0000115.md) Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + * http://purl.obolibrary.org/obo/RO_HOM0000030 [definition](../../IAO/15/IAO_0000115.md) Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + * http://purl.obolibrary.org/obo/RO_HOM0000031 [definition](../../IAO/15/IAO_0000115.md) Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + * http://purl.obolibrary.org/obo/RO_HOM0000032 [definition](../../IAO/15/IAO_0000115.md) Paedomorphosis that is produced by a retardation of somatic development. + * http://purl.obolibrary.org/obo/RO_HOM0000033 [definition](../../IAO/15/IAO_0000115.md) Convergence that results from co-evolution usually involving an evolutionary arms race. + * http://purl.obolibrary.org/obo/RO_HOM0000034 [definition](../../IAO/15/IAO_0000115.md) Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + * http://purl.obolibrary.org/obo/RO_HOM0000036 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves two members of a larger set of homologs. + * http://purl.obolibrary.org/obo/RO_HOM0000037 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + * http://purl.obolibrary.org/obo/RO_HOM0000042 [definition](../../IAO/15/IAO_0000115.md) Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + * http://purl.obolibrary.org/obo/RO_HOM0000043 [definition](../../IAO/15/IAO_0000115.md) Historical homology that is based on distant shared ancestry. + * http://purl.obolibrary.org/obo/RO_HOM0000044 [definition](../../IAO/15/IAO_0000115.md) Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + * http://purl.obolibrary.org/obo/RO_HOM0000045 [definition](../../IAO/15/IAO_0000115.md) Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + * http://purl.obolibrary.org/obo/RO_HOM0000046 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + * http://purl.obolibrary.org/obo/RO_HOM0000047 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) MeSH:Chromosome_Pairing + * http://purl.obolibrary.org/obo/RO_HOM0000047 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + * http://purl.obolibrary.org/obo/RO_HOM0000048 [definition](../../IAO/15/IAO_0000115.md) Orthology that involves two genes that experienced duplications more recent than the species split that created them. + * http://purl.obolibrary.org/obo/RO_HOM0000049 [definition](../../IAO/15/IAO_0000115.md) Paralogy that involves genes from the same species. + * http://purl.obolibrary.org/obo/RO_HOM0000050 [definition](../../IAO/15/IAO_0000115.md) Paralogy that involves genes from different species. + * http://purl.obolibrary.org/obo/RO_HOM0000051 [definition](../../IAO/15/IAO_0000115.md) Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + * http://purl.obolibrary.org/obo/RO_HOM0000052 [definition](../../IAO/15/IAO_0000115.md) Peramorphosis that is produced by a delay in the offset of development. + * http://purl.obolibrary.org/obo/RO_HOM0000053 [definition](../../IAO/15/IAO_0000115.md) Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + * http://purl.obolibrary.org/obo/RO_HOM0000054 [database_cross_reference](../../ef/oboInOwl#hasDbXref.md) ECO:0000080 + * http://purl.obolibrary.org/obo/RO_HOM0000054 [definition](../../IAO/15/IAO_0000115.md) Orthology that involves functional equivalent genes with retention of the ancestral function. + * http://purl.obolibrary.org/obo/RO_HOM0000055 [definition](../../IAO/15/IAO_0000115.md) Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + * http://purl.obolibrary.org/obo/RO_HOM0000057 [definition](../../IAO/15/IAO_0000115.md) Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + * http://purl.obolibrary.org/obo/RO_HOM0000058 [definition](../../IAO/15/IAO_0000115.md) Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + * http://purl.obolibrary.org/obo/RO_HOM0000060 [definition](../../IAO/15/IAO_0000115.md) Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + * http://purl.obolibrary.org/obo/RO_HOM0000061 [definition](../../IAO/15/IAO_0000115.md) Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + * http://purl.obolibrary.org/obo/RO_HOM0000062 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves functional equivalent genes with retention of the ancestral function. + * http://purl.obolibrary.org/obo/RO_HOM0000063 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves orthologous pairs of interacting molecules in different organisms. + * http://purl.obolibrary.org/obo/RO_HOM0000065 [definition](../../IAO/15/IAO_0000115.md) Similarity that is characterized by interchangeability in function. + * http://purl.obolibrary.org/obo/RO_HOM0000066 [definition](../../IAO/15/IAO_0000115.md) Biological homology that involves parts of the same organism. + * http://purl.obolibrary.org/obo/RO_HOM0000068 [definition](../../IAO/15/IAO_0000115.md) Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + * http://purl.obolibrary.org/obo/RO_HOM0000069 [definition](../../IAO/15/IAO_0000115.md) Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + * http://purl.obolibrary.org/obo/RO_HOM0000071 [definition](../../IAO/15/IAO_0000115.md) Structural homology that involves structures with the same or similar relative positions. + * http://purl.obolibrary.org/obo/RO_HOM0000072 [definition](../../IAO/15/IAO_0000115.md) Biological homology that involves an ectopic structure and the normally positioned structure. + * http://purl.obolibrary.org/obo/RO_HOM0000073 [definition](../../IAO/15/IAO_0000115.md) Synology that results from allopolyploidy. + * http://purl.obolibrary.org/obo/RO_HOM0000074 [definition](../../IAO/15/IAO_0000115.md) Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + * http://purl.obolibrary.org/obo/RO_HOM0000075 [definition](../../IAO/15/IAO_0000115.md) Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + +## External Comments + diff --git a/src/ontology/md/el/rdf-schema#label.md b/src/ontology/md/el/rdf-schema#label.md new file mode 100644 index 00000000..b85eae58 --- /dev/null +++ b/src/ontology/md/el/rdf-schema#label.md @@ -0,0 +1,619 @@ + +## Class : null + + * *IRI* = http://www.w3.org/2000/01/rdf-schema#label + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000002 [rdf-schema#label](../../el/rdf-schema#label.md) continuant + * http://purl.obolibrary.org/obo/BFO_0000003 [rdf-schema#label](../../el/rdf-schema#label.md) occurrent + * http://purl.obolibrary.org/obo/BFO_0000004 [rdf-schema#label](../../el/rdf-schema#label.md) independent continuant + * http://purl.obolibrary.org/obo/BFO_0000005 [rdf-schema#label](../../el/rdf-schema#label.md) obsolete dependent continuant + * http://purl.obolibrary.org/obo/BFO_0000015 [rdf-schema#label](../../el/rdf-schema#label.md) process + * http://purl.obolibrary.org/obo/BFO_0000017 [rdf-schema#label](../../el/rdf-schema#label.md) realizable entity + * http://purl.obolibrary.org/obo/BFO_0000019 [rdf-schema#label](../../el/rdf-schema#label.md) quality + * http://purl.obolibrary.org/obo/BFO_0000020 [rdf-schema#label](../../el/rdf-schema#label.md) specifically dependent continuant + * http://purl.obolibrary.org/obo/BFO_0000023 [rdf-schema#label](../../el/rdf-schema#label.md) role + * http://purl.obolibrary.org/obo/BFO_0000031 [rdf-schema#label](../../el/rdf-schema#label.md) generically dependent continuant + * http://purl.obolibrary.org/obo/BFO_0000034 [rdf-schema#label](../../el/rdf-schema#label.md) function + * http://purl.obolibrary.org/obo/BFO_0000040 [rdf-schema#label](../../el/rdf-schema#label.md) material entity + * http://purl.obolibrary.org/obo/BFO_0000050 [rdf-schema#label](../../el/rdf-schema#label.md) part of + * http://purl.obolibrary.org/obo/BFO_0000051 [rdf-schema#label](../../el/rdf-schema#label.md) has part + * http://purl.obolibrary.org/obo/BFO_0000054 [rdf-schema#label](../../el/rdf-schema#label.md) realized in + * http://purl.obolibrary.org/obo/BFO_0000055 [rdf-schema#label](../../el/rdf-schema#label.md) realizes + * http://purl.obolibrary.org/obo/BFO_0000060 [rdf-schema#label](../../el/rdf-schema#label.md) obsolete preceded by + * http://purl.obolibrary.org/obo/BFO_0000062 [rdf-schema#label](../../el/rdf-schema#label.md) preceded by + * http://purl.obolibrary.org/obo/BFO_0000063 [rdf-schema#label](../../el/rdf-schema#label.md) precedes + * http://purl.obolibrary.org/obo/BFO_0000066 [rdf-schema#label](../../el/rdf-schema#label.md) occurs in + * http://purl.obolibrary.org/obo/BFO_0000067 [rdf-schema#label](../../el/rdf-schema#label.md) contains process + * http://purl.obolibrary.org/obo/BFO_0000141 [rdf-schema#label](../../el/rdf-schema#label.md) immaterial entity + * http://purl.obolibrary.org/obo/CARO_0000003 [rdf-schema#label](../../el/rdf-schema#label.md) anatomical structure + * http://purl.obolibrary.org/obo/CARO_0000006 [rdf-schema#label](../../el/rdf-schema#label.md) material anatomical entity + * http://purl.obolibrary.org/obo/CARO_0000007 [rdf-schema#label](../../el/rdf-schema#label.md) immaterial anatomical entity + * http://purl.obolibrary.org/obo/CARO_0000011 [rdf-schema#label](../../el/rdf-schema#label.md) connected anatomical system + * http://purl.obolibrary.org/obo/CARO_0000014 [rdf-schema#label](../../el/rdf-schema#label.md) cell part + * http://purl.obolibrary.org/obo/CARO_0001000 [rdf-schema#label](../../el/rdf-schema#label.md) multi-cell-part structure + * http://purl.obolibrary.org/obo/CARO_0001001 [rdf-schema#label](../../el/rdf-schema#label.md) neuron projection bundle + * http://purl.obolibrary.org/obo/CARO_0010000 [rdf-schema#label](../../el/rdf-schema#label.md) multicellular anatomical structure + * http://purl.obolibrary.org/obo/CL_0000000 [rdf-schema#label](../../el/rdf-schema#label.md) cell + * http://purl.obolibrary.org/obo/CL_0000540 [rdf-schema#label](../../el/rdf-schema#label.md) neuron + * http://purl.obolibrary.org/obo/ENVO_00000428 [rdf-schema#label](../../el/rdf-schema#label.md) biome + * http://purl.obolibrary.org/obo/ENVO_00002036 [rdf-schema#label](../../el/rdf-schema#label.md) habitat + * http://purl.obolibrary.org/obo/ENVO_01000254 [rdf-schema#label](../../el/rdf-schema#label.md) environmental system + * http://purl.obolibrary.org/obo/GO_0003674 [rdf-schema#label](../../el/rdf-schema#label.md) molecular_function + * http://purl.obolibrary.org/obo/GO_0003824 [rdf-schema#label](../../el/rdf-schema#label.md) catalytic activity + * http://purl.obolibrary.org/obo/GO_0004842 [rdf-schema#label](../../el/rdf-schema#label.md) ubiquitin-protein ligase activity + * http://purl.obolibrary.org/obo/GO_0005634 [rdf-schema#label](../../el/rdf-schema#label.md) nucleus + * http://purl.obolibrary.org/obo/GO_0007610 [rdf-schema#label](../../el/rdf-schema#label.md) behavior + * http://purl.obolibrary.org/obo/GO_0007631 [rdf-schema#label](../../el/rdf-schema#label.md) feeding behavior + * http://purl.obolibrary.org/obo/GO_0008150 [rdf-schema#label](../../el/rdf-schema#label.md) biological_process + * http://purl.obolibrary.org/obo/GO_0016020 [rdf-schema#label](../../el/rdf-schema#label.md) membrane + * http://purl.obolibrary.org/obo/GO_0016301 [rdf-schema#label](../../el/rdf-schema#label.md) kinase activity + * http://purl.obolibrary.org/obo/GO_0016740 [rdf-schema#label](../../el/rdf-schema#label.md) transferase activity + * http://purl.obolibrary.org/obo/GO_0016772 [rdf-schema#label](../../el/rdf-schema#label.md) transferase activity, transferring phosphorus-containing groups + * http://purl.obolibrary.org/obo/GO_0016874 [rdf-schema#label](../../el/rdf-schema#label.md) ligase activity + * http://purl.obolibrary.org/obo/GO_0016879 [rdf-schema#label](../../el/rdf-schema#label.md) ligase activity, forming carbon-nitrogen bonds + * http://purl.obolibrary.org/obo/GO_0016881 [rdf-schema#label](../../el/rdf-schema#label.md) acid-amino acid ligase activity + * http://purl.obolibrary.org/obo/GO_0019787 [rdf-schema#label](../../el/rdf-schema#label.md) small conjugating protein ligase activity + * http://purl.obolibrary.org/obo/GO_0030424 [rdf-schema#label](../../el/rdf-schema#label.md) axon + * http://purl.obolibrary.org/obo/GO_0030425 [rdf-schema#label](../../el/rdf-schema#label.md) dendrite + * http://purl.obolibrary.org/obo/GO_0042734 [rdf-schema#label](../../el/rdf-schema#label.md) presynaptic membrane + * http://purl.obolibrary.org/obo/GO_0042995 [rdf-schema#label](../../el/rdf-schema#label.md) cell projection + * http://purl.obolibrary.org/obo/GO_0043005 [rdf-schema#label](../../el/rdf-schema#label.md) neuron projection + * http://purl.obolibrary.org/obo/GO_0044403 [rdf-schema#label](../../el/rdf-schema#label.md) symbiosis, encompassing mutualism through parasitism + * http://purl.obolibrary.org/obo/GO_0044419 [rdf-schema#label](../../el/rdf-schema#label.md) interspecies interaction between organisms + * http://purl.obolibrary.org/obo/GO_0044456 [rdf-schema#label](../../el/rdf-schema#label.md) synapse part + * http://purl.obolibrary.org/obo/GO_0044464 [rdf-schema#label](../../el/rdf-schema#label.md) cell part + * http://purl.obolibrary.org/obo/GO_0045202 [rdf-schema#label](../../el/rdf-schema#label.md) synapse + * http://purl.obolibrary.org/obo/GO_0045211 [rdf-schema#label](../../el/rdf-schema#label.md) postsynaptic membrane + * http://purl.obolibrary.org/obo/GO_0050896 [rdf-schema#label](../../el/rdf-schema#label.md) response to stimulus + * http://purl.obolibrary.org/obo/GO_0051702 [rdf-schema#label](../../el/rdf-schema#label.md) interaction with symbiont + * http://purl.obolibrary.org/obo/GO_0051704 [rdf-schema#label](../../el/rdf-schema#label.md) multi-organism process + * http://purl.obolibrary.org/obo/GO_0051705 [rdf-schema#label](../../el/rdf-schema#label.md) multi-organism behavior + * http://purl.obolibrary.org/obo/GO_0051816 [rdf-schema#label](../../el/rdf-schema#label.md) acquisition of nutrients from other organism during symbiotic interaction + * http://purl.obolibrary.org/obo/GO_0051850 [rdf-schema#label](../../el/rdf-schema#label.md) acquisition of nutrients from symbiont + * http://purl.obolibrary.org/obo/GO_0072519 [rdf-schema#label](../../el/rdf-schema#label.md) parasitism + * http://purl.obolibrary.org/obo/GO_0085030 [rdf-schema#label](../../el/rdf-schema#label.md) mutualism + * http://purl.obolibrary.org/obo/GO_0085031 [rdf-schema#label](../../el/rdf-schema#label.md) commensalism + * http://purl.obolibrary.org/obo/IAO_0000078 [rdf-schema#label](../../el/rdf-schema#label.md) curation status specification + * http://purl.obolibrary.org/obo/IAO_0000111 [rdf-schema#label](../../el/rdf-schema#label.md) editor preferred term + * http://purl.obolibrary.org/obo/IAO_0000112 [rdf-schema#label](../../el/rdf-schema#label.md) example of usage + * http://purl.obolibrary.org/obo/IAO_0000114 [rdf-schema#label](../../el/rdf-schema#label.md) has curation status + * http://purl.obolibrary.org/obo/IAO_0000115 [rdf-schema#label](../../el/rdf-schema#label.md) definition + * http://purl.obolibrary.org/obo/IAO_0000115 [rdf-schema#label](../../el/rdf-schema#label.md) definition + * http://purl.obolibrary.org/obo/IAO_0000116 [rdf-schema#label](../../el/rdf-schema#label.md) editor note + * http://purl.obolibrary.org/obo/IAO_0000117 [rdf-schema#label](../../el/rdf-schema#label.md) term editor + * http://purl.obolibrary.org/obo/IAO_0000118 [rdf-schema#label](../../el/rdf-schema#label.md) alternative term + * http://purl.obolibrary.org/obo/IAO_0000119 [rdf-schema#label](../../el/rdf-schema#label.md) definition source + * http://purl.obolibrary.org/obo/IAO_0000122 [rdf-schema#label](../../el/rdf-schema#label.md) ready for release + * http://purl.obolibrary.org/obo/IAO_0000125 [rdf-schema#label](../../el/rdf-schema#label.md) pending final vetting + * http://purl.obolibrary.org/obo/IAO_0000225 [rdf-schema#label](../../el/rdf-schema#label.md) obsolescence reason specification + * http://purl.obolibrary.org/obo/IAO_0000232 [rdf-schema#label](../../el/rdf-schema#label.md) curator note + * http://purl.obolibrary.org/obo/IAO_0000412 [rdf-schema#label](../../el/rdf-schema#label.md) imported from + * http://purl.obolibrary.org/obo/IAO_0000424 [rdf-schema#label](../../el/rdf-schema#label.md) expand expression to + * http://purl.obolibrary.org/obo/IAO_0000425 [rdf-schema#label](../../el/rdf-schema#label.md) expand assertion to + * http://purl.obolibrary.org/obo/IAO_0000426 [rdf-schema#label](../../el/rdf-schema#label.md) first order logic expression + * http://purl.obolibrary.org/obo/IAO_0000428 [rdf-schema#label](../../el/rdf-schema#label.md) requires discussion + * http://purl.obolibrary.org/obo/IAO_0000589 [rdf-schema#label](../../el/rdf-schema#label.md) OBO foundry unique label + * http://purl.obolibrary.org/obo/IAO_0000600 [rdf-schema#label](../../el/rdf-schema#label.md) elucidation + * http://purl.obolibrary.org/obo/IAO_0100001 [rdf-schema#label](../../el/rdf-schema#label.md) term replaced by + * http://purl.obolibrary.org/obo/PATO_0000001 [rdf-schema#label](../../el/rdf-schema#label.md) quality + * http://purl.obolibrary.org/obo/PATO_0000051 [rdf-schema#label](../../el/rdf-schema#label.md) morphology + * http://purl.obolibrary.org/obo/PATO_0000052 [rdf-schema#label](../../el/rdf-schema#label.md) shape + * http://purl.obolibrary.org/obo/PATO_0000141 [rdf-schema#label](../../el/rdf-schema#label.md) structure + * http://purl.obolibrary.org/obo/PATO_0000402 [rdf-schema#label](../../el/rdf-schema#label.md) branched + * http://purl.obolibrary.org/obo/PATO_0001199 [rdf-schema#label](../../el/rdf-schema#label.md) linear + * http://purl.obolibrary.org/obo/PATO_0001241 [rdf-schema#label](../../el/rdf-schema#label.md) physical object quality + * http://purl.obolibrary.org/obo/PATO_0002009 [rdf-schema#label](../../el/rdf-schema#label.md) branchiness + * http://purl.obolibrary.org/obo/PATO_0002124 [rdf-schema#label](../../el/rdf-schema#label.md) laminar + * http://purl.obolibrary.org/obo/RO_0000052 [rdf-schema#label](../../el/rdf-schema#label.md) inheres in + * http://purl.obolibrary.org/obo/RO_0000053 [rdf-schema#label](../../el/rdf-schema#label.md) bearer of + * http://purl.obolibrary.org/obo/RO_0000056 [rdf-schema#label](../../el/rdf-schema#label.md) participates in + * http://purl.obolibrary.org/obo/RO_0000057 [rdf-schema#label](../../el/rdf-schema#label.md) has participant + * http://purl.obolibrary.org/obo/RO_0000058 [rdf-schema#label](../../el/rdf-schema#label.md) is concretized as + * http://purl.obolibrary.org/obo/RO_0000059 [rdf-schema#label](../../el/rdf-schema#label.md) concretizes + * http://purl.obolibrary.org/obo/RO_0000079 [rdf-schema#label](../../el/rdf-schema#label.md) function of + * http://purl.obolibrary.org/obo/RO_0000080 [rdf-schema#label](../../el/rdf-schema#label.md) quality of + * http://purl.obolibrary.org/obo/RO_0000081 [rdf-schema#label](../../el/rdf-schema#label.md) role of + * http://purl.obolibrary.org/obo/RO_0000085 [rdf-schema#label](../../el/rdf-schema#label.md) has function + * http://purl.obolibrary.org/obo/RO_0000086 [rdf-schema#label](../../el/rdf-schema#label.md) has quality + * http://purl.obolibrary.org/obo/RO_0000087 [rdf-schema#label](../../el/rdf-schema#label.md) has role + * http://purl.obolibrary.org/obo/RO_0000300 [rdf-schema#label](../../el/rdf-schema#label.md) in neural circuit with + * http://purl.obolibrary.org/obo/RO_0000301 [rdf-schema#label](../../el/rdf-schema#label.md) upstream in neural circuit with + * http://purl.obolibrary.org/obo/RO_0000302 [rdf-schema#label](../../el/rdf-schema#label.md) downstream in neural circuit with + * http://purl.obolibrary.org/obo/RO_0001000 [rdf-schema#label](../../el/rdf-schema#label.md) derives from + * http://purl.obolibrary.org/obo/RO_0001001 [rdf-schema#label](../../el/rdf-schema#label.md) derives into + * http://purl.obolibrary.org/obo/RO_0001015 [rdf-schema#label](../../el/rdf-schema#label.md) location of + * http://purl.obolibrary.org/obo/RO_0001018 [rdf-schema#label](../../el/rdf-schema#label.md) contained in + * http://purl.obolibrary.org/obo/RO_0001019 [rdf-schema#label](../../el/rdf-schema#label.md) contains + * http://purl.obolibrary.org/obo/RO_0001025 [rdf-schema#label](../../el/rdf-schema#label.md) located in + * http://purl.obolibrary.org/obo/RO_0001900 [rdf-schema#label](../../el/rdf-schema#label.md) temporal interpretation + * http://purl.obolibrary.org/obo/RO_0001901 [rdf-schema#label](../../el/rdf-schema#label.md) axiom holds for all times + * http://purl.obolibrary.org/obo/RO_0001902 [rdf-schema#label](../../el/rdf-schema#label.md) relation has no temporal argument + * http://purl.obolibrary.org/obo/RO_0002000 [rdf-schema#label](../../el/rdf-schema#label.md) 2D boundary of + * http://purl.obolibrary.org/obo/RO_0002001 [rdf-schema#label](../../el/rdf-schema#label.md) aligned with + * http://purl.obolibrary.org/obo/RO_0002002 [rdf-schema#label](../../el/rdf-schema#label.md) has 2D boundary + * http://purl.obolibrary.org/obo/RO_0002003 [rdf-schema#label](../../el/rdf-schema#label.md) electrically_synapsed_to + * http://purl.obolibrary.org/obo/RO_0002004 [rdf-schema#label](../../el/rdf-schema#label.md) tracheates + * http://purl.obolibrary.org/obo/RO_0002005 [rdf-schema#label](../../el/rdf-schema#label.md) innervated_by + * http://purl.obolibrary.org/obo/RO_0002006 [rdf-schema#label](../../el/rdf-schema#label.md) has synaptic terminal of + * http://purl.obolibrary.org/obo/RO_0002007 [rdf-schema#label](../../el/rdf-schema#label.md) bounding layer of + * http://purl.obolibrary.org/obo/RO_0002008 [rdf-schema#label](../../el/rdf-schema#label.md) coincident with + * http://purl.obolibrary.org/obo/RO_0002009 [rdf-schema#label](../../el/rdf-schema#label.md) cell expresses + * http://purl.obolibrary.org/obo/RO_0002010 [rdf-schema#label](../../el/rdf-schema#label.md) regulates in other organism + * http://purl.obolibrary.org/obo/RO_0002011 [rdf-schema#label](../../el/rdf-schema#label.md) regulates transport of + * http://purl.obolibrary.org/obo/RO_0002081 [rdf-schema#label](../../el/rdf-schema#label.md) before or simultaneous with + * http://purl.obolibrary.org/obo/RO_0002082 [rdf-schema#label](../../el/rdf-schema#label.md) simultaneous with + * http://purl.obolibrary.org/obo/RO_0002083 [rdf-schema#label](../../el/rdf-schema#label.md) before + * http://purl.obolibrary.org/obo/RO_0002084 [rdf-schema#label](../../el/rdf-schema#label.md) during which ends + * http://purl.obolibrary.org/obo/RO_0002085 [rdf-schema#label](../../el/rdf-schema#label.md) encompasses + * http://purl.obolibrary.org/obo/RO_0002086 [rdf-schema#label](../../el/rdf-schema#label.md) ends after + * http://purl.obolibrary.org/obo/RO_0002087 [rdf-schema#label](../../el/rdf-schema#label.md) immediately preceded by + * http://purl.obolibrary.org/obo/RO_0002088 [rdf-schema#label](../../el/rdf-schema#label.md) during which starts + * http://purl.obolibrary.org/obo/RO_0002089 [rdf-schema#label](../../el/rdf-schema#label.md) starts before + * http://purl.obolibrary.org/obo/RO_0002090 [rdf-schema#label](../../el/rdf-schema#label.md) immediately precedes + * http://purl.obolibrary.org/obo/RO_0002091 [rdf-schema#label](../../el/rdf-schema#label.md) starts during + * http://purl.obolibrary.org/obo/RO_0002092 [rdf-schema#label](../../el/rdf-schema#label.md) happens during + * http://purl.obolibrary.org/obo/RO_0002093 [rdf-schema#label](../../el/rdf-schema#label.md) ends during + * http://purl.obolibrary.org/obo/RO_0002100 [rdf-schema#label](../../el/rdf-schema#label.md) has soma location + * http://purl.obolibrary.org/obo/RO_0002101 [rdf-schema#label](../../el/rdf-schema#label.md) fasciculates with + * http://purl.obolibrary.org/obo/RO_0002102 [rdf-schema#label](../../el/rdf-schema#label.md) axon synapses in + * http://purl.obolibrary.org/obo/RO_0002103 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed by + * http://purl.obolibrary.org/obo/RO_0002104 [rdf-schema#label](../../el/rdf-schema#label.md) has plasma membrane part + * http://purl.obolibrary.org/obo/RO_0002105 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed_via_type_Ib_bouton_to + * http://purl.obolibrary.org/obo/RO_0002106 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed_via_type_Is_bouton_to + * http://purl.obolibrary.org/obo/RO_0002107 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed_via_type_II_bouton_to + * http://purl.obolibrary.org/obo/RO_0002108 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed_by_via_type_II_bouton + * http://purl.obolibrary.org/obo/RO_0002109 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed_by_via_type_Ib_bouton + * http://purl.obolibrary.org/obo/RO_0002110 [rdf-schema#label](../../el/rdf-schema#label.md) has postsynaptic terminal in + * http://purl.obolibrary.org/obo/RO_0002111 [rdf-schema#label](../../el/rdf-schema#label.md) releases neurotransmitter + * http://purl.obolibrary.org/obo/RO_0002112 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed_by_via_type_Is_bouton + * http://purl.obolibrary.org/obo/RO_0002113 [rdf-schema#label](../../el/rdf-schema#label.md) has presynaptic terminal in + * http://purl.obolibrary.org/obo/RO_0002114 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed_via_type_III_bouton_to + * http://purl.obolibrary.org/obo/RO_0002115 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed_by_via_type_III_bouton + * http://purl.obolibrary.org/obo/RO_0002120 [rdf-schema#label](../../el/rdf-schema#label.md) synapsed to + * http://purl.obolibrary.org/obo/RO_0002121 [rdf-schema#label](../../el/rdf-schema#label.md) dendrite synapsed in + * http://purl.obolibrary.org/obo/RO_0002130 [rdf-schema#label](../../el/rdf-schema#label.md) has synaptic terminal in + * http://purl.obolibrary.org/obo/RO_0002131 [rdf-schema#label](../../el/rdf-schema#label.md) overlaps + * http://purl.obolibrary.org/obo/RO_0002132 [rdf-schema#label](../../el/rdf-schema#label.md) has fasciculating neuron projection + * http://purl.obolibrary.org/obo/RO_0002134 [rdf-schema#label](../../el/rdf-schema#label.md) innervates + * http://purl.obolibrary.org/obo/RO_0002150 [rdf-schema#label](../../el/rdf-schema#label.md) continuous with + * http://purl.obolibrary.org/obo/RO_0002151 [rdf-schema#label](../../el/rdf-schema#label.md) partially overlaps + * http://purl.obolibrary.org/obo/RO_0002156 [rdf-schema#label](../../el/rdf-schema#label.md) derived by descent from + * http://purl.obolibrary.org/obo/RO_0002157 [rdf-schema#label](../../el/rdf-schema#label.md) has derived by descendant + * http://purl.obolibrary.org/obo/RO_0002158 [rdf-schema#label](../../el/rdf-schema#label.md) shares ancestor with + * http://purl.obolibrary.org/obo/RO_0002159 [rdf-schema#label](../../el/rdf-schema#label.md) serially homologous to + * http://purl.obolibrary.org/obo/RO_0002160 [rdf-schema#label](../../el/rdf-schema#label.md) only in taxon + * http://purl.obolibrary.org/obo/RO_0002161 [rdf-schema#label](../../el/rdf-schema#label.md) never in taxon + * http://purl.obolibrary.org/obo/RO_0002162 [rdf-schema#label](../../el/rdf-schema#label.md) in taxon + * http://purl.obolibrary.org/obo/RO_0002163 [rdf-schema#label](../../el/rdf-schema#label.md) spatially disjoint from + * http://purl.obolibrary.org/obo/RO_0002170 [rdf-schema#label](../../el/rdf-schema#label.md) connected to + * http://purl.obolibrary.org/obo/RO_0002171 [rdf-schema#label](../../el/rdf-schema#label.md) mutually spatially disjoint with + * http://purl.obolibrary.org/obo/RO_0002172 [rdf-schema#label](../../el/rdf-schema#label.md) taxonomic class assertion + * http://purl.obolibrary.org/obo/RO_0002173 [rdf-schema#label](../../el/rdf-schema#label.md) ambiguous for taxon + * http://purl.obolibrary.org/obo/RO_0002174 [rdf-schema#label](../../el/rdf-schema#label.md) dubious for taxon + * http://purl.obolibrary.org/obo/RO_0002175 [rdf-schema#label](../../el/rdf-schema#label.md) present in taxon + * http://purl.obolibrary.org/obo/RO_0002176 [rdf-schema#label](../../el/rdf-schema#label.md) connects + * http://purl.obolibrary.org/obo/RO_0002177 [rdf-schema#label](../../el/rdf-schema#label.md) attached to part of + * http://purl.obolibrary.org/obo/RO_0002178 [rdf-schema#label](../../el/rdf-schema#label.md) supplies + * http://purl.obolibrary.org/obo/RO_0002179 [rdf-schema#label](../../el/rdf-schema#label.md) drains + * http://purl.obolibrary.org/obo/RO_0002180 [rdf-schema#label](../../el/rdf-schema#label.md) has component + * http://purl.obolibrary.org/obo/RO_0002200 [rdf-schema#label](../../el/rdf-schema#label.md) has phenotype + * http://purl.obolibrary.org/obo/RO_0002201 [rdf-schema#label](../../el/rdf-schema#label.md) phenotype of + * http://purl.obolibrary.org/obo/RO_0002202 [rdf-schema#label](../../el/rdf-schema#label.md) develops from + * http://purl.obolibrary.org/obo/RO_0002203 [rdf-schema#label](../../el/rdf-schema#label.md) develops into + * http://purl.obolibrary.org/obo/RO_0002204 [rdf-schema#label](../../el/rdf-schema#label.md) gene product of + * http://purl.obolibrary.org/obo/RO_0002205 [rdf-schema#label](../../el/rdf-schema#label.md) has gene product + * http://purl.obolibrary.org/obo/RO_0002206 [rdf-schema#label](../../el/rdf-schema#label.md) expressed in + * http://purl.obolibrary.org/obo/RO_0002207 [rdf-schema#label](../../el/rdf-schema#label.md) directly develops from + * http://purl.obolibrary.org/obo/RO_0002210 [rdf-schema#label](../../el/rdf-schema#label.md) directly develops into + * http://purl.obolibrary.org/obo/RO_0002211 [rdf-schema#label](../../el/rdf-schema#label.md) regulates + * http://purl.obolibrary.org/obo/RO_0002212 [rdf-schema#label](../../el/rdf-schema#label.md) negatively regulates + * http://purl.obolibrary.org/obo/RO_0002213 [rdf-schema#label](../../el/rdf-schema#label.md) positively regulates + * http://purl.obolibrary.org/obo/RO_0002214 [rdf-schema#label](../../el/rdf-schema#label.md) has prototype + * http://purl.obolibrary.org/obo/RO_0002215 [rdf-schema#label](../../el/rdf-schema#label.md) capable of + * http://purl.obolibrary.org/obo/RO_0002216 [rdf-schema#label](../../el/rdf-schema#label.md) capable of part of + * http://purl.obolibrary.org/obo/RO_0002217 [rdf-schema#label](../../el/rdf-schema#label.md) actively participates in + * http://purl.obolibrary.org/obo/RO_0002218 [rdf-schema#label](../../el/rdf-schema#label.md) has active participant + * http://purl.obolibrary.org/obo/RO_0002219 [rdf-schema#label](../../el/rdf-schema#label.md) surrounded by + * http://purl.obolibrary.org/obo/RO_0002220 [rdf-schema#label](../../el/rdf-schema#label.md) adjacent to + * http://purl.obolibrary.org/obo/RO_0002221 [rdf-schema#label](../../el/rdf-schema#label.md) surrounds + * http://purl.obolibrary.org/obo/RO_0002222 [rdf-schema#label](../../el/rdf-schema#label.md) temporally related to + * http://purl.obolibrary.org/obo/RO_0002223 [rdf-schema#label](../../el/rdf-schema#label.md) starts + * http://purl.obolibrary.org/obo/RO_0002224 [rdf-schema#label](../../el/rdf-schema#label.md) starts with + * http://purl.obolibrary.org/obo/RO_0002225 [rdf-schema#label](../../el/rdf-schema#label.md) develops from part of + * http://purl.obolibrary.org/obo/RO_0002226 [rdf-schema#label](../../el/rdf-schema#label.md) develops in + * http://purl.obolibrary.org/obo/RO_0002229 [rdf-schema#label](../../el/rdf-schema#label.md) ends + * http://purl.obolibrary.org/obo/RO_0002230 [rdf-schema#label](../../el/rdf-schema#label.md) ends with + * http://purl.obolibrary.org/obo/RO_0002231 [rdf-schema#label](../../el/rdf-schema#label.md) has start location + * http://purl.obolibrary.org/obo/RO_0002232 [rdf-schema#label](../../el/rdf-schema#label.md) has end location + * http://purl.obolibrary.org/obo/RO_0002233 [rdf-schema#label](../../el/rdf-schema#label.md) has input + * http://purl.obolibrary.org/obo/RO_0002234 [rdf-schema#label](../../el/rdf-schema#label.md) has output + * http://purl.obolibrary.org/obo/RO_0002254 [rdf-schema#label](../../el/rdf-schema#label.md) has developmental contribution from + * http://purl.obolibrary.org/obo/RO_0002255 [rdf-schema#label](../../el/rdf-schema#label.md) developmentally contributes to + * http://purl.obolibrary.org/obo/RO_0002256 [rdf-schema#label](../../el/rdf-schema#label.md) developmentally induced by + * http://purl.obolibrary.org/obo/RO_0002257 [rdf-schema#label](../../el/rdf-schema#label.md) developmentally induces + * http://purl.obolibrary.org/obo/RO_0002258 [rdf-schema#label](../../el/rdf-schema#label.md) developmentally preceded by + * http://purl.obolibrary.org/obo/RO_0002285 [rdf-schema#label](../../el/rdf-schema#label.md) developmentally replaces + * http://purl.obolibrary.org/obo/RO_0002286 [rdf-schema#label](../../el/rdf-schema#label.md) developmentally succeeded by + * http://purl.obolibrary.org/obo/RO_0002287 [rdf-schema#label](../../el/rdf-schema#label.md) part of developmental precursor of + * http://purl.obolibrary.org/obo/RO_0002291 [rdf-schema#label](../../el/rdf-schema#label.md) ubiquitously expressed in + * http://purl.obolibrary.org/obo/RO_0002292 [rdf-schema#label](../../el/rdf-schema#label.md) expresses + * http://purl.obolibrary.org/obo/RO_0002293 [rdf-schema#label](../../el/rdf-schema#label.md) ubiquitously expresses + * http://purl.obolibrary.org/obo/RO_0002295 [rdf-schema#label](../../el/rdf-schema#label.md) results in developmental progression of + * http://purl.obolibrary.org/obo/RO_0002296 [rdf-schema#label](../../el/rdf-schema#label.md) results in development of + * http://purl.obolibrary.org/obo/RO_0002297 [rdf-schema#label](../../el/rdf-schema#label.md) results in formation of + * http://purl.obolibrary.org/obo/RO_0002298 [rdf-schema#label](../../el/rdf-schema#label.md) results in morphogenesis of + * http://purl.obolibrary.org/obo/RO_0002299 [rdf-schema#label](../../el/rdf-schema#label.md) results in maturation of + * http://purl.obolibrary.org/obo/RO_0002300 [rdf-schema#label](../../el/rdf-schema#label.md) results in disappearance of + * http://purl.obolibrary.org/obo/RO_0002301 [rdf-schema#label](../../el/rdf-schema#label.md) results in developmental regression of + * http://purl.obolibrary.org/obo/RO_0002303 [rdf-schema#label](../../el/rdf-schema#label.md) has habitat + * http://purl.obolibrary.org/obo/RO_0002312 [rdf-schema#label](../../el/rdf-schema#label.md) evolutionary variant of + * http://purl.obolibrary.org/obo/RO_0002313 [rdf-schema#label](../../el/rdf-schema#label.md) transports or maintains localization of + * http://purl.obolibrary.org/obo/RO_0002314 [rdf-schema#label](../../el/rdf-schema#label.md) inheres in part of + * http://purl.obolibrary.org/obo/RO_0002315 [rdf-schema#label](../../el/rdf-schema#label.md) results in acquisition of features of + * http://purl.obolibrary.org/obo/RO_0002320 [rdf-schema#label](../../el/rdf-schema#label.md) evolutionarily related to + * http://purl.obolibrary.org/obo/RO_0002321 [rdf-schema#label](../../el/rdf-schema#label.md) ecologically related to + * http://purl.obolibrary.org/obo/RO_0002322 [rdf-schema#label](../../el/rdf-schema#label.md) confers advantage in + * http://purl.obolibrary.org/obo/RO_0002323 [rdf-schema#label](../../el/rdf-schema#label.md) mereotopologically related to + * http://purl.obolibrary.org/obo/RO_0002324 [rdf-schema#label](../../el/rdf-schema#label.md) developmentally related to + * http://purl.obolibrary.org/obo/RO_0002325 [rdf-schema#label](../../el/rdf-schema#label.md) colocalizes with + * http://purl.obolibrary.org/obo/RO_0002326 [rdf-schema#label](../../el/rdf-schema#label.md) contributes to + * http://purl.obolibrary.org/obo/RO_0002327 [rdf-schema#label](../../el/rdf-schema#label.md) enables + * http://purl.obolibrary.org/obo/RO_0002328 [rdf-schema#label](../../el/rdf-schema#label.md) functionally related to + * http://purl.obolibrary.org/obo/RO_0002329 [rdf-schema#label](../../el/rdf-schema#label.md) part of structure that is capable of + * http://purl.obolibrary.org/obo/RO_0002330 [rdf-schema#label](../../el/rdf-schema#label.md) genomically related to + * http://purl.obolibrary.org/obo/RO_0002331 [rdf-schema#label](../../el/rdf-schema#label.md) involved in + * http://purl.obolibrary.org/obo/RO_0002332 [rdf-schema#label](../../el/rdf-schema#label.md) regulates levels of + * http://purl.obolibrary.org/obo/RO_0002333 [rdf-schema#label](../../el/rdf-schema#label.md) enabled by + * http://purl.obolibrary.org/obo/RO_0002334 [rdf-schema#label](../../el/rdf-schema#label.md) regulated by + * http://purl.obolibrary.org/obo/RO_0002335 [rdf-schema#label](../../el/rdf-schema#label.md) negatively regulated by + * http://purl.obolibrary.org/obo/RO_0002336 [rdf-schema#label](../../el/rdf-schema#label.md) positively regulated by + * http://purl.obolibrary.org/obo/RO_0002337 [rdf-schema#label](../../el/rdf-schema#label.md) related via localization to + * http://purl.obolibrary.org/obo/RO_0002338 [rdf-schema#label](../../el/rdf-schema#label.md) has target start location + * http://purl.obolibrary.org/obo/RO_0002339 [rdf-schema#label](../../el/rdf-schema#label.md) has target end location + * http://purl.obolibrary.org/obo/RO_0002340 [rdf-schema#label](../../el/rdf-schema#label.md) imports + * http://purl.obolibrary.org/obo/RO_0002341 [rdf-schema#label](../../el/rdf-schema#label.md) results in transport along + * http://purl.obolibrary.org/obo/RO_0002342 [rdf-schema#label](../../el/rdf-schema#label.md) results in transport across + * http://purl.obolibrary.org/obo/RO_0002343 [rdf-schema#label](../../el/rdf-schema#label.md) results in growth of + * http://purl.obolibrary.org/obo/RO_0002344 [rdf-schema#label](../../el/rdf-schema#label.md) results in transport to from or in + * http://purl.obolibrary.org/obo/RO_0002345 [rdf-schema#label](../../el/rdf-schema#label.md) exports + * http://purl.obolibrary.org/obo/RO_0002348 [rdf-schema#label](../../el/rdf-schema#label.md) results in commitment to + * http://purl.obolibrary.org/obo/RO_0002349 [rdf-schema#label](../../el/rdf-schema#label.md) results in determination of + * http://purl.obolibrary.org/obo/RO_0002350 [rdf-schema#label](../../el/rdf-schema#label.md) member of + * http://purl.obolibrary.org/obo/RO_0002351 [rdf-schema#label](../../el/rdf-schema#label.md) has member + * http://purl.obolibrary.org/obo/RO_0002352 [rdf-schema#label](../../el/rdf-schema#label.md) input of + * http://purl.obolibrary.org/obo/RO_0002353 [rdf-schema#label](../../el/rdf-schema#label.md) output of + * http://purl.obolibrary.org/obo/RO_0002354 [rdf-schema#label](../../el/rdf-schema#label.md) formed as result of + * http://purl.obolibrary.org/obo/RO_0002355 [rdf-schema#label](../../el/rdf-schema#label.md) results in structural organization of + * http://purl.obolibrary.org/obo/RO_0002356 [rdf-schema#label](../../el/rdf-schema#label.md) results in specification of + * http://purl.obolibrary.org/obo/RO_0002357 [rdf-schema#label](../../el/rdf-schema#label.md) results in developmental induction of + * http://purl.obolibrary.org/obo/RO_0002360 [rdf-schema#label](../../el/rdf-schema#label.md) has dendrite location + * http://purl.obolibrary.org/obo/RO_0002371 [rdf-schema#label](../../el/rdf-schema#label.md) attached to + * http://purl.obolibrary.org/obo/RO_0002372 [rdf-schema#label](../../el/rdf-schema#label.md) has muscle origin + * http://purl.obolibrary.org/obo/RO_0002373 [rdf-schema#label](../../el/rdf-schema#label.md) has muscle insertion + * http://purl.obolibrary.org/obo/RO_0002374 [rdf-schema#label](../../el/rdf-schema#label.md) has fused element + * http://purl.obolibrary.org/obo/RO_0002375 [rdf-schema#label](../../el/rdf-schema#label.md) in branching relationship with + * http://purl.obolibrary.org/obo/RO_0002376 [rdf-schema#label](../../el/rdf-schema#label.md) tributary of + * http://purl.obolibrary.org/obo/RO_0002377 [rdf-schema#label](../../el/rdf-schema#label.md) distributary of + * http://purl.obolibrary.org/obo/RO_0002378 [rdf-schema#label](../../el/rdf-schema#label.md) anabranch of + * http://purl.obolibrary.org/obo/RO_0002379 [rdf-schema#label](../../el/rdf-schema#label.md) spatially coextensive with + * http://purl.obolibrary.org/obo/RO_0002380 [rdf-schema#label](../../el/rdf-schema#label.md) branching part of + * http://purl.obolibrary.org/obo/RO_0002381 [rdf-schema#label](../../el/rdf-schema#label.md) main stem of + * http://purl.obolibrary.org/obo/RO_0002382 [rdf-schema#label](../../el/rdf-schema#label.md) proper distributary of + * http://purl.obolibrary.org/obo/RO_0002383 [rdf-schema#label](../../el/rdf-schema#label.md) proper tributary of + * http://purl.obolibrary.org/obo/RO_0002384 [rdf-schema#label](../../el/rdf-schema#label.md) has developmental potential involving + * http://purl.obolibrary.org/obo/RO_0002385 [rdf-schema#label](../../el/rdf-schema#label.md) has potential to developmentally contribute to + * http://purl.obolibrary.org/obo/RO_0002386 [rdf-schema#label](../../el/rdf-schema#label.md) has potential to developmentally induce + * http://purl.obolibrary.org/obo/RO_0002387 [rdf-schema#label](../../el/rdf-schema#label.md) has potential to develop into + * http://purl.obolibrary.org/obo/RO_0002388 [rdf-schema#label](../../el/rdf-schema#label.md) has potential to directly develop into + * http://purl.obolibrary.org/obo/RO_0002400 [rdf-schema#label](../../el/rdf-schema#label.md) has direct input + * http://purl.obolibrary.org/obo/RO_0002401 [rdf-schema#label](../../el/rdf-schema#label.md) obsolete has indirect input + * http://purl.obolibrary.org/obo/RO_0002402 [rdf-schema#label](../../el/rdf-schema#label.md) obsolete has direct output + * http://purl.obolibrary.org/obo/RO_0002403 [rdf-schema#label](../../el/rdf-schema#label.md) obsolete has indirect output + * http://purl.obolibrary.org/obo/RO_0002404 [rdf-schema#label](../../el/rdf-schema#label.md) causally downstream of + * http://purl.obolibrary.org/obo/RO_0002405 [rdf-schema#label](../../el/rdf-schema#label.md) immediately causally downstream of + * http://purl.obolibrary.org/obo/RO_0002406 [rdf-schema#label](../../el/rdf-schema#label.md) directly activates + * http://purl.obolibrary.org/obo/RO_0002407 [rdf-schema#label](../../el/rdf-schema#label.md) indirectly activates + * http://purl.obolibrary.org/obo/RO_0002408 [rdf-schema#label](../../el/rdf-schema#label.md) directly inhibits + * http://purl.obolibrary.org/obo/RO_0002409 [rdf-schema#label](../../el/rdf-schema#label.md) indirectly inhibits + * http://purl.obolibrary.org/obo/RO_0002410 [rdf-schema#label](../../el/rdf-schema#label.md) causally related to + * http://purl.obolibrary.org/obo/RO_0002411 [rdf-schema#label](../../el/rdf-schema#label.md) causally upstream of + * http://purl.obolibrary.org/obo/RO_0002412 [rdf-schema#label](../../el/rdf-schema#label.md) immediately causally upstream of + * http://purl.obolibrary.org/obo/RO_0002413 [rdf-schema#label](../../el/rdf-schema#label.md) directly provides input for + * http://purl.obolibrary.org/obo/RO_0002414 [rdf-schema#label](../../el/rdf-schema#label.md) transitively provides input for + * http://purl.obolibrary.org/obo/RO_0002416 [rdf-schema#label](../../el/rdf-schema#label.md) logical macro assertion + * http://purl.obolibrary.org/obo/RO_0002418 [rdf-schema#label](../../el/rdf-schema#label.md) causally upstream of or within + * http://purl.obolibrary.org/obo/RO_0002419 [rdf-schema#label](../../el/rdf-schema#label.md) annotation property cardinality + * http://purl.obolibrary.org/obo/RO_0002420 [rdf-schema#label](../../el/rdf-schema#label.md) logical macro assertion on a class + * http://purl.obolibrary.org/obo/RO_0002421 [rdf-schema#label](../../el/rdf-schema#label.md) logical macro assertion on a property + * http://purl.obolibrary.org/obo/RO_0002422 [rdf-schema#label](../../el/rdf-schema#label.md) logical macro assertion on an object property + * http://purl.obolibrary.org/obo/RO_0002423 [rdf-schema#label](../../el/rdf-schema#label.md) logical macro assertion on an annotation property + * http://purl.obolibrary.org/obo/RO_0002424 [rdf-schema#label](../../el/rdf-schema#label.md) differs in + * http://purl.obolibrary.org/obo/RO_0002425 [rdf-schema#label](../../el/rdf-schema#label.md) differs in attribute of + * http://purl.obolibrary.org/obo/RO_0002426 [rdf-schema#label](../../el/rdf-schema#label.md) differs in attribute + * http://purl.obolibrary.org/obo/RO_0002427 [rdf-schema#label](../../el/rdf-schema#label.md) causally downstream of or within + * http://purl.obolibrary.org/obo/RO_0002428 [rdf-schema#label](../../el/rdf-schema#label.md) involved in regulation of + * http://purl.obolibrary.org/obo/RO_0002429 [rdf-schema#label](../../el/rdf-schema#label.md) involved in positive regulation of + * http://purl.obolibrary.org/obo/RO_0002430 [rdf-schema#label](../../el/rdf-schema#label.md) involved in negative regulation of + * http://purl.obolibrary.org/obo/RO_0002431 [rdf-schema#label](../../el/rdf-schema#label.md) involved in or regulates + * http://purl.obolibrary.org/obo/RO_0002432 [rdf-schema#label](../../el/rdf-schema#label.md) enables activity in + * http://purl.obolibrary.org/obo/RO_0002433 [rdf-schema#label](../../el/rdf-schema#label.md) contributes to morphology of + * http://purl.obolibrary.org/obo/RO_0002434 [rdf-schema#label](../../el/rdf-schema#label.md) interacts with + * http://purl.obolibrary.org/obo/RO_0002435 [rdf-schema#label](../../el/rdf-schema#label.md) genetically interacts with + * http://purl.obolibrary.org/obo/RO_0002436 [rdf-schema#label](../../el/rdf-schema#label.md) molecularly interacts with + * http://purl.obolibrary.org/obo/RO_0002437 [rdf-schema#label](../../el/rdf-schema#label.md) biotically interacts with + * http://purl.obolibrary.org/obo/RO_0002438 [rdf-schema#label](../../el/rdf-schema#label.md) trophically interacts with + * http://purl.obolibrary.org/obo/RO_0002439 [rdf-schema#label](../../el/rdf-schema#label.md) preys on + * http://purl.obolibrary.org/obo/RO_0002440 [rdf-schema#label](../../el/rdf-schema#label.md) symbiotically interacts with + * http://purl.obolibrary.org/obo/RO_0002441 [rdf-schema#label](../../el/rdf-schema#label.md) commensually interacts with + * http://purl.obolibrary.org/obo/RO_0002442 [rdf-schema#label](../../el/rdf-schema#label.md) mutualistically interacts with + * http://purl.obolibrary.org/obo/RO_0002443 [rdf-schema#label](../../el/rdf-schema#label.md) interacts with via parasite-host interaction + * http://purl.obolibrary.org/obo/RO_0002444 [rdf-schema#label](../../el/rdf-schema#label.md) parasite of + * http://purl.obolibrary.org/obo/RO_0002445 [rdf-schema#label](../../el/rdf-schema#label.md) parasitized by + * http://purl.obolibrary.org/obo/RO_0002446 [rdf-schema#label](../../el/rdf-schema#label.md) participates in a abiotic-biotic interaction with + * http://purl.obolibrary.org/obo/RO_0002447 [rdf-schema#label](../../el/rdf-schema#label.md) phosphorylates + * http://purl.obolibrary.org/obo/RO_0002448 [rdf-schema#label](../../el/rdf-schema#label.md) molecularly controls + * http://purl.obolibrary.org/obo/RO_0002449 [rdf-schema#label](../../el/rdf-schema#label.md) molecularly decreases activity of + * http://purl.obolibrary.org/obo/RO_0002450 [rdf-schema#label](../../el/rdf-schema#label.md) molecularly increases activity of + * http://purl.obolibrary.org/obo/RO_0002451 [rdf-schema#label](../../el/rdf-schema#label.md) transmitted by + * http://purl.obolibrary.org/obo/RO_0002452 [rdf-schema#label](../../el/rdf-schema#label.md) has symptom + * http://purl.obolibrary.org/obo/RO_0002453 [rdf-schema#label](../../el/rdf-schema#label.md) host of + * http://purl.obolibrary.org/obo/RO_0002454 [rdf-schema#label](../../el/rdf-schema#label.md) has host + * http://purl.obolibrary.org/obo/RO_0002455 [rdf-schema#label](../../el/rdf-schema#label.md) pollinates + * http://purl.obolibrary.org/obo/RO_0002456 [rdf-schema#label](../../el/rdf-schema#label.md) pollinated by + * http://purl.obolibrary.org/obo/RO_0002457 [rdf-schema#label](../../el/rdf-schema#label.md) acquires nutrients from + * http://purl.obolibrary.org/obo/RO_0002458 [rdf-schema#label](../../el/rdf-schema#label.md) preyed upon by + * http://purl.obolibrary.org/obo/RO_0002459 [rdf-schema#label](../../el/rdf-schema#label.md) is vector for + * http://purl.obolibrary.org/obo/RO_0002460 [rdf-schema#label](../../el/rdf-schema#label.md) has vector + * http://purl.obolibrary.org/obo/RO_0002461 [rdf-schema#label](../../el/rdf-schema#label.md) partner in + * http://purl.obolibrary.org/obo/RO_0002462 [rdf-schema#label](../../el/rdf-schema#label.md) subject participant in + * http://purl.obolibrary.org/obo/RO_0002463 [rdf-schema#label](../../el/rdf-schema#label.md) target participant in + * http://purl.obolibrary.org/obo/RO_0002464 [rdf-schema#label](../../el/rdf-schema#label.md) helper property + * http://purl.obolibrary.org/obo/RO_0002465 [rdf-schema#label](../../el/rdf-schema#label.md) is symbiosis + * http://purl.obolibrary.org/obo/RO_0002466 [rdf-schema#label](../../el/rdf-schema#label.md) is commensalism + * http://purl.obolibrary.org/obo/RO_0002467 [rdf-schema#label](../../el/rdf-schema#label.md) is mutualism + * http://purl.obolibrary.org/obo/RO_0002468 [rdf-schema#label](../../el/rdf-schema#label.md) is parasitism + * http://purl.obolibrary.org/obo/RO_0002469 [rdf-schema#label](../../el/rdf-schema#label.md) provides nutrients for + * http://purl.obolibrary.org/obo/RO_0002470 [rdf-schema#label](../../el/rdf-schema#label.md) eats + * http://purl.obolibrary.org/obo/RO_0002471 [rdf-schema#label](../../el/rdf-schema#label.md) is eaten by + * http://purl.obolibrary.org/obo/RO_0002472 [rdf-schema#label](../../el/rdf-schema#label.md) is evidence for + * http://purl.obolibrary.org/obo/RO_0002473 [rdf-schema#label](../../el/rdf-schema#label.md) composed primarily of + * http://purl.obolibrary.org/obo/RO_0002474 [rdf-schema#label](../../el/rdf-schema#label.md) dispositional interpretation + * http://purl.obolibrary.org/obo/RO_0002475 [rdf-schema#label](../../el/rdf-schema#label.md) has no connections with + * http://purl.obolibrary.org/obo/RO_0002476 [rdf-schema#label](../../el/rdf-schema#label.md) child nucleus of + * http://purl.obolibrary.org/obo/RO_0002477 [rdf-schema#label](../../el/rdf-schema#label.md) child nucleus of in hermaphrodite + * http://purl.obolibrary.org/obo/RO_0002478 [rdf-schema#label](../../el/rdf-schema#label.md) child nucleus of in male + * http://purl.obolibrary.org/obo/RO_0002479 [rdf-schema#label](../../el/rdf-schema#label.md) has part that occurs in + * http://purl.obolibrary.org/obo/RO_0002480 [rdf-schema#label](../../el/rdf-schema#label.md) ubiquitinates + * http://purl.obolibrary.org/obo/RO_0002481 [rdf-schema#label](../../el/rdf-schema#label.md) is kinase activity + * http://purl.obolibrary.org/obo/RO_0002482 [rdf-schema#label](../../el/rdf-schema#label.md) is ubiquitination + * http://purl.obolibrary.org/obo/RO_0002483 [rdf-schema#label](../../el/rdf-schema#label.md) inherited annotation property + * http://purl.obolibrary.org/obo/RO_0002484 [rdf-schema#label](../../el/rdf-schema#label.md) curator guidance link + * http://purl.obolibrary.org/obo/RO_0002485 [rdf-schema#label](../../el/rdf-schema#label.md) receives input from + * http://purl.obolibrary.org/obo/RO_0002486 [rdf-schema#label](../../el/rdf-schema#label.md) sends output to + * http://purl.obolibrary.org/obo/RO_0002487 [rdf-schema#label](../../el/rdf-schema#label.md) relation between structure and stage + * http://purl.obolibrary.org/obo/RO_0002488 [rdf-schema#label](../../el/rdf-schema#label.md) existence starts during + * http://purl.obolibrary.org/obo/RO_0002489 [rdf-schema#label](../../el/rdf-schema#label.md) existence starts with + * http://purl.obolibrary.org/obo/RO_0002490 [rdf-schema#label](../../el/rdf-schema#label.md) existence overlaps + * http://purl.obolibrary.org/obo/RO_0002491 [rdf-schema#label](../../el/rdf-schema#label.md) existence starts and ends during + * http://purl.obolibrary.org/obo/RO_0002492 [rdf-schema#label](../../el/rdf-schema#label.md) existence ends during + * http://purl.obolibrary.org/obo/RO_0002493 [rdf-schema#label](../../el/rdf-schema#label.md) existence ends with + * http://purl.obolibrary.org/obo/RO_0002494 [rdf-schema#label](../../el/rdf-schema#label.md) transformation of + * http://purl.obolibrary.org/obo/RO_0002495 [rdf-schema#label](../../el/rdf-schema#label.md) immediate transformation of + * http://purl.obolibrary.org/obo/RO_0002496 [rdf-schema#label](../../el/rdf-schema#label.md) existence starts during or after + * http://purl.obolibrary.org/obo/RO_0002497 [rdf-schema#label](../../el/rdf-schema#label.md) existence ends during or before + * http://purl.obolibrary.org/obo/RO_0002501 [rdf-schema#label](../../el/rdf-schema#label.md) causal relation between processes + * http://purl.obolibrary.org/obo/RO_0002502 [rdf-schema#label](../../el/rdf-schema#label.md) depends on + * http://purl.obolibrary.org/obo/RO_0002503 [rdf-schema#label](../../el/rdf-schema#label.md) towards + * http://purl.obolibrary.org/obo/RO_0002504 [rdf-schema#label](../../el/rdf-schema#label.md) always present in taxon + * http://purl.obolibrary.org/obo/RO_0002505 [rdf-schema#label](../../el/rdf-schema#label.md) has intermediate + * http://purl.obolibrary.org/obo/RO_0002506 [rdf-schema#label](../../el/rdf-schema#label.md) causal relation between material entities + * http://purl.obolibrary.org/obo/RO_0002507 [rdf-schema#label](../../el/rdf-schema#label.md) determined by + * http://purl.obolibrary.org/obo/RO_0002508 [rdf-schema#label](../../el/rdf-schema#label.md) determines + * http://purl.obolibrary.org/obo/RO_0002509 [rdf-schema#label](../../el/rdf-schema#label.md) determined by part of + * http://purl.obolibrary.org/obo/RO_0002510 [rdf-schema#label](../../el/rdf-schema#label.md) transcribed from + * http://purl.obolibrary.org/obo/RO_0002511 [rdf-schema#label](../../el/rdf-schema#label.md) transcribed to + * http://purl.obolibrary.org/obo/RO_0002512 [rdf-schema#label](../../el/rdf-schema#label.md) ribosomal translation of + * http://purl.obolibrary.org/obo/RO_0002513 [rdf-schema#label](../../el/rdf-schema#label.md) ribosomally translates to + * http://purl.obolibrary.org/obo/RO_0002514 [rdf-schema#label](../../el/rdf-schema#label.md) sequentially related to + * http://purl.obolibrary.org/obo/RO_0002515 [rdf-schema#label](../../el/rdf-schema#label.md) sequentially adjacent to + * http://purl.obolibrary.org/obo/RO_0002516 [rdf-schema#label](../../el/rdf-schema#label.md) has start sequence + * http://purl.obolibrary.org/obo/RO_0002517 [rdf-schema#label](../../el/rdf-schema#label.md) is start sequence of + * http://purl.obolibrary.org/obo/RO_0002518 [rdf-schema#label](../../el/rdf-schema#label.md) has end sequence + * http://purl.obolibrary.org/obo/RO_0002519 [rdf-schema#label](../../el/rdf-schema#label.md) is end sequence of + * http://purl.obolibrary.org/obo/RO_0002520 [rdf-schema#label](../../el/rdf-schema#label.md) is consecutive sequence of + * http://purl.obolibrary.org/obo/RO_0002521 [rdf-schema#label](../../el/rdf-schema#label.md) is sequentially aligned with + * http://purl.obolibrary.org/obo/RO_0002522 [rdf-schema#label](../../el/rdf-schema#label.md) bounds sequence of + * http://purl.obolibrary.org/obo/RO_0002523 [rdf-schema#label](../../el/rdf-schema#label.md) is bound by sequence of + * http://purl.obolibrary.org/obo/RO_0002524 [rdf-schema#label](../../el/rdf-schema#label.md) has subsequence + * http://purl.obolibrary.org/obo/RO_0002525 [rdf-schema#label](../../el/rdf-schema#label.md) is subsequence of + * http://purl.obolibrary.org/obo/RO_0002526 [rdf-schema#label](../../el/rdf-schema#label.md) overlaps sequence of + * http://purl.obolibrary.org/obo/RO_0002527 [rdf-schema#label](../../el/rdf-schema#label.md) does not overlap sequence of + * http://purl.obolibrary.org/obo/RO_0002528 [rdf-schema#label](../../el/rdf-schema#label.md) is upstream of sequence of + * http://purl.obolibrary.org/obo/RO_0002529 [rdf-schema#label](../../el/rdf-schema#label.md) is downstream of sequence of + * http://purl.obolibrary.org/obo/RO_0002530 [rdf-schema#label](../../el/rdf-schema#label.md) is immediately downstream of sequence of + * http://purl.obolibrary.org/obo/RO_0002531 [rdf-schema#label](../../el/rdf-schema#label.md) is immediately upstream of sequence of + * http://purl.obolibrary.org/obo/RO_0002532 [rdf-schema#label](../../el/rdf-schema#label.md) sequentially ordered entity + * http://purl.obolibrary.org/obo/RO_0002533 [rdf-schema#label](../../el/rdf-schema#label.md) sequence atomic unit + * http://purl.obolibrary.org/obo/RO_0002534 [rdf-schema#label](../../el/rdf-schema#label.md) sequence bearer + * http://purl.obolibrary.org/obo/RO_0002535 [rdf-schema#label](../../el/rdf-schema#label.md) temporal logical macro assertion on a class + * http://purl.obolibrary.org/obo/RO_0002536 [rdf-schema#label](../../el/rdf-schema#label.md) measurement property has unit + * http://purl.obolibrary.org/obo/RO_0002537 [rdf-schema#label](../../el/rdf-schema#label.md) has start time value + * http://purl.obolibrary.org/obo/RO_0002538 [rdf-schema#label](../../el/rdf-schema#label.md) has end time value + * http://purl.obolibrary.org/obo/RO_0002539 [rdf-schema#label](../../el/rdf-schema#label.md) start, days post fertilization + * http://purl.obolibrary.org/obo/RO_0002540 [rdf-schema#label](../../el/rdf-schema#label.md) end, days post fertilization + * http://purl.obolibrary.org/obo/RO_0002541 [rdf-schema#label](../../el/rdf-schema#label.md) start, years post birth + * http://purl.obolibrary.org/obo/RO_0002542 [rdf-schema#label](../../el/rdf-schema#label.md) end, years post birth + * http://purl.obolibrary.org/obo/RO_0002543 [rdf-schema#label](../../el/rdf-schema#label.md) start, months post birth + * http://purl.obolibrary.org/obo/RO_0002544 [rdf-schema#label](../../el/rdf-schema#label.md) end, months post birth + * http://purl.obolibrary.org/obo/RO_0002545 [rdf-schema#label](../../el/rdf-schema#label.md) month of gestation + * http://purl.obolibrary.org/obo/RO_0002546 [rdf-schema#label](../../el/rdf-schema#label.md) has developmental stage marker + * http://purl.obolibrary.org/obo/RO_0002547 [rdf-schema#label](../../el/rdf-schema#label.md) start, days post coitum + * http://purl.obolibrary.org/obo/RO_0002548 [rdf-schema#label](../../el/rdf-schema#label.md) end, days post coitum + * http://purl.obolibrary.org/obo/RO_0002549 [rdf-schema#label](../../el/rdf-schema#label.md) start, weeks post birth + * http://purl.obolibrary.org/obo/RO_0002550 [rdf-schema#label](../../el/rdf-schema#label.md) end, weeks post birth + * http://purl.obolibrary.org/obo/RO_0002551 [rdf-schema#label](../../el/rdf-schema#label.md) has skeleton + * http://purl.obolibrary.org/obo/RO_0002552 [rdf-schema#label](../../el/rdf-schema#label.md) results in ending of + * http://purl.obolibrary.org/obo/RO_0002553 [rdf-schema#label](../../el/rdf-schema#label.md) hyperparasite of + * http://purl.obolibrary.org/obo/RO_0002554 [rdf-schema#label](../../el/rdf-schema#label.md) hyperparasitized by + * http://purl.obolibrary.org/obo/RO_0002555 [rdf-schema#label](../../el/rdf-schema#label.md) allelopath of + * http://purl.obolibrary.org/obo/RO_0002556 [rdf-schema#label](../../el/rdf-schema#label.md) pathogen of + * http://purl.obolibrary.org/obo/RO_0002557 [rdf-schema#label](../../el/rdf-schema#label.md) has pathogen + * http://purl.obolibrary.org/obo/RO_0002558 [rdf-schema#label](../../el/rdf-schema#label.md) has evidence + * http://purl.obolibrary.org/obo/RO_0002559 [rdf-schema#label](../../el/rdf-schema#label.md) causally influenced by + * http://purl.obolibrary.org/obo/RO_0002560 [rdf-schema#label](../../el/rdf-schema#label.md) is asymmetric relational form of process class + * http://purl.obolibrary.org/obo/RO_0002561 [rdf-schema#label](../../el/rdf-schema#label.md) is symmetric relational form of process class + * http://purl.obolibrary.org/obo/RO_0002562 [rdf-schema#label](../../el/rdf-schema#label.md) is relational form of process class + * http://purl.obolibrary.org/obo/RO_0002563 [rdf-schema#label](../../el/rdf-schema#label.md) interaction relation helper property + * http://purl.obolibrary.org/obo/RO_0002564 [rdf-schema#label](../../el/rdf-schema#label.md) molecular interaction relation helper property + * http://purl.obolibrary.org/obo/RO_0002565 [rdf-schema#label](../../el/rdf-schema#label.md) results in movement of + * http://purl.obolibrary.org/obo/RO_0002566 [rdf-schema#label](../../el/rdf-schema#label.md) causally influences + * http://purl.obolibrary.org/obo/RO_0002567 [rdf-schema#label](../../el/rdf-schema#label.md) biomechanically related to + * http://purl.obolibrary.org/obo/RO_0002568 [rdf-schema#label](../../el/rdf-schema#label.md) has muscle antagonist + * http://purl.obolibrary.org/obo/RO_0002569 [rdf-schema#label](../../el/rdf-schema#label.md) has branching part + * http://purl.obolibrary.org/obo/RO_0002570 [rdf-schema#label](../../el/rdf-schema#label.md) conduit for + * http://purl.obolibrary.org/obo/RO_0002571 [rdf-schema#label](../../el/rdf-schema#label.md) lumen of + * http://purl.obolibrary.org/obo/RO_0002572 [rdf-schema#label](../../el/rdf-schema#label.md) luminal space of + * http://purl.obolibrary.org/obo/RO_0002573 [rdf-schema#label](../../el/rdf-schema#label.md) has modifier + * http://purl.obolibrary.org/obo/RO_0002574 [rdf-schema#label](../../el/rdf-schema#label.md) participates in a biotic-biotic interaction with + * http://purl.obolibrary.org/obo/RO_0002575 [rdf-schema#label](../../el/rdf-schema#label.md) is direct form of + * http://purl.obolibrary.org/obo/RO_0002576 [rdf-schema#label](../../el/rdf-schema#label.md) skeleton of + * http://purl.obolibrary.org/obo/RO_0002577 [rdf-schema#label](../../el/rdf-schema#label.md) system + * http://purl.obolibrary.org/obo/RO_0002578 [rdf-schema#label](../../el/rdf-schema#label.md) directly regulates + * http://purl.obolibrary.org/obo/RO_0002579 [rdf-schema#label](../../el/rdf-schema#label.md) is indirect form of + * http://purl.obolibrary.org/obo/RO_0002580 [rdf-schema#label](../../el/rdf-schema#label.md) logical macro assertion on an axiom + * http://purl.obolibrary.org/obo/RO_0002581 [rdf-schema#label](../../el/rdf-schema#label.md) is a defining property chain axiom + * http://purl.obolibrary.org/obo/RO_0002582 [rdf-schema#label](../../el/rdf-schema#label.md) is a defining property chain axiom where second argument is reflexive + * http://purl.obolibrary.org/obo/RO_0002583 [rdf-schema#label](../../el/rdf-schema#label.md) existence starts at point + * http://purl.obolibrary.org/obo/RO_0002584 [rdf-schema#label](../../el/rdf-schema#label.md) has part structure that is capable of + * http://purl.obolibrary.org/obo/RO_0002585 [rdf-schema#label](../../el/rdf-schema#label.md) results in closure of + * http://purl.obolibrary.org/obo/RO_0002586 [rdf-schema#label](../../el/rdf-schema#label.md) results in breakdown of + * http://purl.obolibrary.org/obo/RO_0002587 [rdf-schema#label](../../el/rdf-schema#label.md) results in synthesis of + * http://purl.obolibrary.org/obo/RO_0002588 [rdf-schema#label](../../el/rdf-schema#label.md) results in assembly of + * http://purl.obolibrary.org/obo/RO_0002589 [rdf-schema#label](../../el/rdf-schema#label.md) results in catabolism of + * http://purl.obolibrary.org/obo/RO_0002590 [rdf-schema#label](../../el/rdf-schema#label.md) results in disassembly of + * http://purl.obolibrary.org/obo/RO_0002591 [rdf-schema#label](../../el/rdf-schema#label.md) results in remodeling of + * http://purl.obolibrary.org/obo/RO_0002592 [rdf-schema#label](../../el/rdf-schema#label.md) results in organization of + * http://purl.obolibrary.org/obo/RO_0002593 [rdf-schema#label](../../el/rdf-schema#label.md) existence ends at point + * http://purl.obolibrary.org/obo/RO_0002594 [rdf-schema#label](../../el/rdf-schema#label.md) is relational form of a class + * http://purl.obolibrary.org/obo/RO_0002595 [rdf-schema#label](../../el/rdf-schema#label.md) causal relation between material entity and a process + * http://purl.obolibrary.org/obo/RO_0002596 [rdf-schema#label](../../el/rdf-schema#label.md) capable of regulating + * http://purl.obolibrary.org/obo/RO_0002597 [rdf-schema#label](../../el/rdf-schema#label.md) capable of negatively regulating + * http://purl.obolibrary.org/obo/RO_0002598 [rdf-schema#label](../../el/rdf-schema#label.md) capable of positively regulating + * http://purl.obolibrary.org/obo/RO_0002599 [rdf-schema#label](../../el/rdf-schema#label.md) capable of inhibiting or preventing pathological process + * http://purl.obolibrary.org/obo/RO_0002600 [rdf-schema#label](../../el/rdf-schema#label.md) capable of upregulating or causing pathological process + * http://purl.obolibrary.org/obo/RO_0002601 [rdf-schema#label](../../el/rdf-schema#label.md) logical macro assertion involving identity + * http://purl.obolibrary.org/obo/RO_0002602 [rdf-schema#label](../../el/rdf-schema#label.md) in approximate one to one relationship with + * http://purl.obolibrary.org/obo/RO_0002603 [rdf-schema#label](../../el/rdf-schema#label.md) is approximately equivalent to + * http://purl.obolibrary.org/obo/RO_0002604 [rdf-schema#label](../../el/rdf-schema#label.md) is opposite of + * http://purl.obolibrary.org/obo/RO_0002605 [rdf-schema#label](../../el/rdf-schema#label.md) is indistinguishable from + * http://purl.obolibrary.org/obo/RO_0002606 [rdf-schema#label](../../el/rdf-schema#label.md) is substance that treats + * http://purl.obolibrary.org/obo/RO_0002607 [rdf-schema#label](../../el/rdf-schema#label.md) is marker for + * http://purl.obolibrary.org/obo/RO_0002609 [rdf-schema#label](../../el/rdf-schema#label.md) related via dependence to + * http://purl.obolibrary.org/obo/RO_0002610 [rdf-schema#label](../../el/rdf-schema#label.md) correlated with + * http://purl.obolibrary.org/obo/RO_0003000 [rdf-schema#label](../../el/rdf-schema#label.md) produces + * http://purl.obolibrary.org/obo/RO_0003001 [rdf-schema#label](../../el/rdf-schema#label.md) produced by + * http://purl.obolibrary.org/obo/RO_0003002 [rdf-schema#label](../../el/rdf-schema#label.md) represses expression of + * http://purl.obolibrary.org/obo/RO_0003003 [rdf-schema#label](../../el/rdf-schema#label.md) increases expression of + * http://purl.obolibrary.org/obo/RO_0003301 [rdf-schema#label](../../el/rdf-schema#label.md) is model of + * http://purl.obolibrary.org/obo/RO_HOM0000000 [rdf-schema#label](../../el/rdf-schema#label.md) in similarity relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000001 [rdf-schema#label](../../el/rdf-schema#label.md) in homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000002 [rdf-schema#label](../../el/rdf-schema#label.md) in homoplasy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000003 [rdf-schema#label](../../el/rdf-schema#label.md) in homocracy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000004 [rdf-schema#label](../../el/rdf-schema#label.md) in convergence relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000005 [rdf-schema#label](../../el/rdf-schema#label.md) in parallelism relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000006 [rdf-schema#label](../../el/rdf-schema#label.md) in structural homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000007 [rdf-schema#label](../../el/rdf-schema#label.md) in historical homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000008 [rdf-schema#label](../../el/rdf-schema#label.md) in biological homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000009 [rdf-schema#label](../../el/rdf-schema#label.md) in reversal relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000010 [rdf-schema#label](../../el/rdf-schema#label.md) in syntenic homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000011 [rdf-schema#label](../../el/rdf-schema#label.md) in paralogy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000012 [rdf-schema#label](../../el/rdf-schema#label.md) in syntenic paralogy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000013 [rdf-schema#label](../../el/rdf-schema#label.md) in syntenic orthology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000014 [rdf-schema#label](../../el/rdf-schema#label.md) in partial homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000015 [rdf-schema#label](../../el/rdf-schema#label.md) in protein structural homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000016 [rdf-schema#label](../../el/rdf-schema#label.md) in non functional homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000017 [rdf-schema#label](../../el/rdf-schema#label.md) in orthology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000018 [rdf-schema#label](../../el/rdf-schema#label.md) in xenology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000019 [rdf-schema#label](../../el/rdf-schema#label.md) in 1 to 1 homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000020 [rdf-schema#label](../../el/rdf-schema#label.md) in 1 to 1 orthology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000022 [rdf-schema#label](../../el/rdf-schema#label.md) in ohnology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000023 [rdf-schema#label](../../el/rdf-schema#label.md) in in-paralogy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000024 [rdf-schema#label](../../el/rdf-schema#label.md) in out-paralogy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000025 [rdf-schema#label](../../el/rdf-schema#label.md) in pro-orthology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000026 [rdf-schema#label](../../el/rdf-schema#label.md) in semi-orthology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000027 [rdf-schema#label](../../el/rdf-schema#label.md) in serial homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000028 [rdf-schema#label](../../el/rdf-schema#label.md) in heterochronous homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000029 [rdf-schema#label](../../el/rdf-schema#label.md) in paedomorphorsis relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000030 [rdf-schema#label](../../el/rdf-schema#label.md) in peramorphosis relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000031 [rdf-schema#label](../../el/rdf-schema#label.md) in progenesis relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000032 [rdf-schema#label](../../el/rdf-schema#label.md) in neoteny relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000033 [rdf-schema#label](../../el/rdf-schema#label.md) in mimicry relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000034 [rdf-schema#label](../../el/rdf-schema#label.md) in 1 to many orthology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000036 [rdf-schema#label](../../el/rdf-schema#label.md) in many to many homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000037 [rdf-schema#label](../../el/rdf-schema#label.md) in 1 to many homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000042 [rdf-schema#label](../../el/rdf-schema#label.md) in apomorphy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000043 [rdf-schema#label](../../el/rdf-schema#label.md) in plesiomorphy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000044 [rdf-schema#label](../../el/rdf-schema#label.md) in deep homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000045 [rdf-schema#label](../../el/rdf-schema#label.md) in hemiplasy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000046 [rdf-schema#label](../../el/rdf-schema#label.md) in gametology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000047 [rdf-schema#label](../../el/rdf-schema#label.md) in chromosomal homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000048 [rdf-schema#label](../../el/rdf-schema#label.md) in many to many orthology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000049 [rdf-schema#label](../../el/rdf-schema#label.md) in within-species paralogy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000050 [rdf-schema#label](../../el/rdf-schema#label.md) in between-species paralogy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000051 [rdf-schema#label](../../el/rdf-schema#label.md) in postdisplacement relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000052 [rdf-schema#label](../../el/rdf-schema#label.md) in hypermorphosis relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000053 [rdf-schema#label](../../el/rdf-schema#label.md) in synology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000054 [rdf-schema#label](../../el/rdf-schema#label.md) in isoorthology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000055 [rdf-schema#label](../../el/rdf-schema#label.md) in tandem paralogy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000057 [rdf-schema#label](../../el/rdf-schema#label.md) in latent homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000058 [rdf-schema#label](../../el/rdf-schema#label.md) in syngeny relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000060 [rdf-schema#label](../../el/rdf-schema#label.md) in apparent orthology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000061 [rdf-schema#label](../../el/rdf-schema#label.md) in pseudoparalogy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000062 [rdf-schema#label](../../el/rdf-schema#label.md) in equivalogy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000063 [rdf-schema#label](../../el/rdf-schema#label.md) in interology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000065 [rdf-schema#label](../../el/rdf-schema#label.md) in functional equivalence relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000066 [rdf-schema#label](../../el/rdf-schema#label.md) in iterative homology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000068 [rdf-schema#label](../../el/rdf-schema#label.md) in paraxenology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000069 [rdf-schema#label](../../el/rdf-schema#label.md) in plerology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000071 [rdf-schema#label](../../el/rdf-schema#label.md) in homotopy relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000072 [rdf-schema#label](../../el/rdf-schema#label.md) in homeosis relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000073 [rdf-schema#label](../../el/rdf-schema#label.md) in homoeology relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000074 [rdf-schema#label](../../el/rdf-schema#label.md) in paramorphism relationship with + * http://purl.obolibrary.org/obo/RO_HOM0000075 [rdf-schema#label](../../el/rdf-schema#label.md) in regulogy relationship with + * http://purl.obolibrary.org/obo/ro/subsets#ro-eco [rdf-schema#label](../../el/rdf-schema#label.md) eco subset + * http://www.geneontology.org/formats/oboInOwl#ObsoleteClass [rdf-schema#label](../../el/rdf-schema#label.md) Obsolete Class + * http://www.geneontology.org/formats/oboInOwl#SubsetProperty [rdf-schema#label](../../el/rdf-schema#label.md) subset_property + * http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym [rdf-schema#label](../../el/rdf-schema#label.md) has_broad_synonym + * http://www.geneontology.org/formats/oboInOwl#hasDbXref [rdf-schema#label](../../el/rdf-schema#label.md) database_cross_reference + * http://www.geneontology.org/formats/oboInOwl#hasExactSynonym [rdf-schema#label](../../el/rdf-schema#label.md) has_exact_synonym + * http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion [rdf-schema#label](../../el/rdf-schema#label.md) has_obo_format_version + * http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym [rdf-schema#label](../../el/rdf-schema#label.md) has_related_synonym + * http://www.geneontology.org/formats/oboInOwl#inSubset [rdf-schema#label](../../el/rdf-schema#label.md) in_subset + * http://www.geneontology.org/formats/oboInOwl#shorthand [rdf-schema#label](../../el/rdf-schema#label.md) shorthand + +## External Comments + diff --git a/src/ontology/md/er/publisher.md b/src/ontology/md/er/publisher.md new file mode 100644 index 00000000..599141ee --- /dev/null +++ b/src/ontology/md/er/publisher.md @@ -0,0 +1,32 @@ + +## Class : null + + * *IRI* = http://purl.org/dc/elements/1.1/publisher + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + +## External Comments + diff --git a/src/ontology/md/et/oboInOwl#inSubset.md b/src/ontology/md/et/oboInOwl#inSubset.md new file mode 100644 index 00000000..f921df79 --- /dev/null +++ b/src/ontology/md/et/oboInOwl#inSubset.md @@ -0,0 +1,128 @@ + +## Class : in_subset + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#inSubset + * *Label* = in_subset + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = in_subset + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000062 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/BFO_0000063 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0001000 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0001001 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0001018 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0001019 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002007 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002008 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002011 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002081 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002082 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002083 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002084 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002086 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002088 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002089 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002090 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002091 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002092 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002093 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002131 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002151 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002162 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002163 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002180 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002200 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002201 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002215 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002218 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002222 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002223 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002224 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002229 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002230 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002231 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002232 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002233 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002234 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002303 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002321 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002322 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002352 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002353 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002371 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002376 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002377 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002378 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002380 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002381 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002382 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002383 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002434 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002437 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002438 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002439 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002440 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002441 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002442 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002443 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002444 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002445 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002446 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002453 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002454 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002455 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002456 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002457 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002458 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002459 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002460 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002469 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002470 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002471 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002472 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002473 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002479 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002505 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002507 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002508 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002509 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002553 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002554 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002555 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002556 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002557 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002558 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002569 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002570 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002571 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002572 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002573 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0002574 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0003000 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + * http://purl.obolibrary.org/obo/RO_0003001 [in_subset](../../et/oboInOwl#inSubset.md) http://purl.obolibrary.org/obo/ro/subsets#ro-eco + +## External Comments + diff --git a/src/ontology/md/ge/homepage.md b/src/ontology/md/ge/homepage.md new file mode 100644 index 00000000..49344773 --- /dev/null +++ b/src/ontology/md/ge/homepage.md @@ -0,0 +1,32 @@ + +## Class : null + + * *IRI* = http://xmlns.com/foaf/0.1/homepage + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + +## External Comments + diff --git a/src/ontology/md/ge/page.md b/src/ontology/md/ge/page.md new file mode 100644 index 00000000..e89a4a8d --- /dev/null +++ b/src/ontology/md/ge/page.md @@ -0,0 +1,46 @@ + +## Class : null + + * *IRI* = http://xmlns.com/foaf/0.1/page + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0001900 [page](../../ge/page.md) https://code.google.com/p/obo-relations/wiki/ROAndTime + * http://purl.obolibrary.org/obo/RO_0002163 [page](../../ge/page.md) https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + * http://purl.obolibrary.org/obo/RO_0002170 [page](../../ge/page.md) https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + * http://purl.obolibrary.org/obo/RO_0002170 [page](../../ge/page.md) https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + * http://purl.obolibrary.org/obo/RO_0002171 [page](../../ge/page.md) https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + * http://purl.obolibrary.org/obo/RO_0002176 [page](../../ge/page.md) https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + * http://purl.obolibrary.org/obo/RO_0002176 [page](../../ge/page.md) https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + * http://purl.obolibrary.org/obo/RO_0002375 [page](../../ge/page.md) https://github.com/obophenotype/uberon/issues/170 + * http://purl.obolibrary.org/obo/RO_0002416 [page](../../ge/page.md) https://code.google.com/p/obo-relations/wiki/ShortcutRelations + * http://purl.obolibrary.org/obo/RO_0002434 [page](../../ge/page.md) https://code.google.com/p/obo-relations/wiki/InteractionRelations + * http://purl.obolibrary.org/obo/RO_0002560 [page](../../ge/page.md) https://code.google.com/p/obo-relations/wiki/InteractionRelations + * http://purl.obolibrary.org/obo/RO_0002561 [page](../../ge/page.md) https://code.google.com/p/obo-relations/wiki/InteractionRelations + * http://purl.obolibrary.org/obo/RO_0002562 [page](../../ge/page.md) https://code.google.com/p/obo-relations/wiki/InteractionRelations + * http://purl.obolibrary.org/obo/RO_0002563 [page](../../ge/page.md) https://code.google.com/p/obo-relations/wiki/InteractionRelations + +## External Comments + diff --git a/src/ontology/md/id/oboInOwl#id.md b/src/ontology/md/id/oboInOwl#id.md new file mode 100644 index 00000000..22ee165f --- /dev/null +++ b/src/ontology/md/id/oboInOwl#id.md @@ -0,0 +1,32 @@ + +## Class : null + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#id + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + +## External Comments + diff --git a/src/ontology/md/index.md b/src/ontology/md/index.md new file mode 100644 index 00000000..db53f7f3 --- /dev/null +++ b/src/ontology/md/index.md @@ -0,0 +1,609 @@ + +## Ontology + + * *OID* = http://purl.obolibrary.org/obo/ro.owl + * *Version* = http://purl.obolibrary.org/obo/ro/releases/2015-07-08/ro.owl + +## Classes + + * [obsolete dependent continuant](BFO/05/BFO_0000005.md) + * [role](BFO/23/BFO_0000023.md) + * [synapse part](GO/56/GO_0044456.md) + * [environmental system](ENVO/54/ENVO_01000254.md) + * [cell part](CARO/14/CARO_0000014.md) + * [system](RO/77/RO_0002577.md) + * [connected anatomical system](CARO/11/CARO_0000011.md) + * [nucleus](GO/34/GO_0005634.md) + * [GO_0040011](GO/11/GO_0040011.md) + * [quality](BFO/19/BFO_0000019.md) + * [kinase activity](GO/01/GO_0016301.md) + * [realizable entity](BFO/17/BFO_0000017.md) + * [biome](ENVO/28/ENVO_00000428.md) + * [process](BFO/15/BFO_0000015.md) + * [quality](PATO/01/PATO_0000001.md) + * [immaterial anatomical entity](CARO/07/CARO_0000007.md) + * [material anatomical entity](CARO/06/CARO_0000006.md) + * [anatomical structure](CARO/03/CARO_0000003.md) + * [postsynaptic membrane](GO/11/GO_0045211.md) + * [habitat](ENVO/36/ENVO_00002036.md) + * [branchiness](PATO/09/PATO_0002009.md) + * [acquisition of nutrients from symbiont](GO/50/GO_0051850.md) + * [multicellular anatomical structure](CARO/00/CARO_0010000.md) + * [specifically dependent continuant](BFO/20/BFO_0000020.md) + * [dendrite](GO/25/GO_0030425.md) + * [independent continuant](BFO/04/BFO_0000004.md) + * [occurrent](BFO/03/BFO_0000003.md) + * [continuant](BFO/02/BFO_0000002.md) + * [membrane](GO/20/GO_0016020.md) + * [branched](PATO/02/PATO_0000402.md) + * [ubiquitin-protein ligase activity](GO/42/GO_0004842.md) + * [presynaptic membrane](GO/34/GO_0042734.md) + * [neuron](CL/40/CL_0000540.md) + * [transferase activity, transferring phosphorus-containing groups](GO/72/GO_0016772.md) + * [response to stimulus](GO/96/GO_0050896.md) + * [cell](CL/00/CL_0000000.md) + * [parasitism](GO/19/GO_0072519.md) + * [acid-amino acid ligase activity](GO/81/GO_0016881.md) + * [cell projection](GO/95/GO_0042995.md) + * [biological_process](GO/50/GO_0008150.md) + * [ligase activity, forming carbon-nitrogen bonds](GO/79/GO_0016879.md) + * [Obsolete Class](ss/oboInOwl#ObsoleteClass.md) + * [ligase activity](GO/74/GO_0016874.md) + * [neuron projection](GO/05/GO_0043005.md) + * [small conjugating protein ligase activity](GO/87/GO_0019787.md) + * [feeding behavior](GO/31/GO_0007631.md) + * [interspecies interaction between organisms](GO/19/GO_0044419.md) + * [morphology](PATO/51/PATO_0000051.md) + * [neuron projection bundle](CARO/01/CARO_0001001.md) + * [sequence bearer](RO/34/RO_0002534.md) + * [sequence atomic unit](RO/33/RO_0002533.md) + * [sequentially ordered entity](RO/32/RO_0002532.md) + * [material entity](BFO/40/BFO_0000040.md) + * [shape](PATO/52/PATO_0000052.md) + * [axon](GO/24/GO_0030424.md) + * [synapse](GO/02/GO_0045202.md) + * [physical object quality](PATO/41/PATO_0001241.md) + * [symbiosis, encompassing mutualism through parasitism](GO/03/GO_0044403.md) + * [immaterial entity](BFO/41/BFO_0000141.md) + * [function](BFO/34/BFO_0000034.md) + * [generically dependent continuant](BFO/31/BFO_0000031.md) + * [linear](PATO/99/PATO_0001199.md) + * [cell part](GO/64/GO_0044464.md) + * [molecular_function](GO/74/GO_0003674.md) + * [acquisition of nutrients from other organism during symbiotic interaction](GO/16/GO_0051816.md) + * [transferase activity](GO/40/GO_0016740.md) + * [catalytic activity](GO/24/GO_0003824.md) + * [structure](PATO/41/PATO_0000141.md) + * [multi-organism behavior](GO/05/GO_0051705.md) + * [multi-organism process](GO/04/GO_0051704.md) + * [interaction with symbiont](GO/02/GO_0051702.md) + * [behavior](GO/10/GO_0007610.md) + * [commensalism](GO/31/GO_0085031.md) + * [mutualism](GO/30/GO_0085030.md) + * [laminar](PATO/24/PATO_0002124.md) + * [multi-cell-part structure](CARO/00/CARO_0001000.md) + +## ObjectProperties + + * [ends](RO/29/RO_0002229.md) + * [develops in](RO/26/RO_0002226.md) + * [develops from part of](RO/25/RO_0002225.md) + * [starts with](RO/24/RO_0002224.md) + * [starts](RO/23/RO_0002223.md) + * [temporally related to](RO/22/RO_0002222.md) + * [surrounds](RO/21/RO_0002221.md) + * [adjacent to](RO/20/RO_0002220.md) + * [supplies](RO/78/RO_0002178.md) + * [attached to part of](RO/77/RO_0002177.md) + * [connects](RO/76/RO_0002176.md) + * [inheres in](RO/52/RO_0000052.md) + * [connected to](RO/70/RO_0002170.md) + * [determined by part of](RO/09/RO_0002509.md) + * [surrounded by](RO/19/RO_0002219.md) + * [has active participant](RO/18/RO_0002218.md) + * [actively participates in](RO/17/RO_0002217.md) + * [capable of part of](RO/16/RO_0002216.md) + * [capable of](RO/15/RO_0002215.md) + * [has prototype](RO/14/RO_0002214.md) + * [positively regulates](RO/13/RO_0002213.md) + * [negatively regulates](RO/12/RO_0002212.md) + * [regulates](RO/11/RO_0002211.md) + * [directly develops into](RO/10/RO_0002210.md) + * [concretizes](RO/59/RO_0000059.md) + * [is concretized as](RO/58/RO_0000058.md) + * [transcribed from](RO/10/RO_0002510.md) + * [participates in](RO/56/RO_0000056.md) + * [spatially disjoint from](RO/63/RO_0002163.md) + * [in taxon](RO/62/RO_0002162.md) + * [bearer of](RO/53/RO_0000053.md) + * [only in taxon](RO/60/RO_0002160.md) + * [directly develops from](RO/07/RO_0002207.md) + * [expressed in](RO/06/RO_0002206.md) + * [has gene product](RO/05/RO_0002205.md) + * [gene product of](RO/04/RO_0002204.md) + * [develops into](RO/03/RO_0002203.md) + * [develops from](RO/02/RO_0002202.md) + * [has part](BFO/51/BFO_0000051.md) + * [has part that occurs in](RO/79/RO_0002479.md) + * [shares ancestor with](RO/58/RO_0002158.md) + * [has derived by descendant](RO/57/RO_0002157.md) + * [derived by descent from](RO/56/RO_0002156.md) + * [in many to many orthology relationship with](RO/48/RO_HOM0000048.md) + * [in within-species paralogy relationship with](RO/49/RO_HOM0000049.md) + * [partially overlaps](RO/51/RO_0002151.md) + * [continuous with](RO/50/RO_0002150.md) + * [owl#topObjectProperty](ty/owl#topObjectProperty.md) + * [capable of inhibiting or preventing pathological process](RO/99/RO_0002599.md) + * [capable of positively regulating](RO/98/RO_0002598.md) + * [capable of negatively regulating](RO/97/RO_0002597.md) + * [capable of regulating](RO/96/RO_0002596.md) + * [causal relation between material entity and a process](RO/95/RO_0002595.md) + * [existence ends at point](RO/93/RO_0002593.md) + * [results in organization of](RO/92/RO_0002592.md) + * [results in remodeling of](RO/91/RO_0002591.md) + * [results in disassembly of](RO/90/RO_0002590.md) + * [in isoorthology relationship with](RO/54/RO_HOM0000054.md) + * [in tandem paralogy relationship with](RO/55/RO_HOM0000055.md) + * [obsolete preceded by](BFO/60/BFO_0000060.md) + * [in latent homology relationship with](RO/57/RO_HOM0000057.md) + * [in syngeny relationship with](RO/58/RO_HOM0000058.md) + * [derives from](RO/00/RO_0001000.md) + * [ends during](RO/93/RO_0002093.md) + * [happens during](RO/92/RO_0002092.md) + * [results in catabolism of](RO/89/RO_0002589.md) + * [results in assembly of](RO/88/RO_0002588.md) + * [results in synthesis of](RO/87/RO_0002587.md) + * [results in breakdown of](RO/86/RO_0002586.md) + * [results in closure of](RO/85/RO_0002585.md) + * [has part structure that is capable of](RO/84/RO_0002584.md) + * [existence starts at point](RO/83/RO_0002583.md) + * [in functional equivalence relationship with](RO/65/RO_HOM0000065.md) + * [in iterative homology relationship with](RO/66/RO_HOM0000066.md) + * [in plerology relationship with](RO/69/RO_HOM0000069.md) + * [innervates](RO/34/RO_0002134.md) + * [has fasciculating neuron projection](RO/32/RO_0002132.md) + * [overlaps](RO/31/RO_0002131.md) + * [has synaptic terminal in](RO/30/RO_0002130.md) + * [during which starts](RO/88/RO_0002088.md) + * [immediately preceded by](RO/87/RO_0002087.md) + * [ends after](RO/86/RO_0002086.md) + * [encompasses](RO/85/RO_0002085.md) + * [in non functional homology relationship with](RO/16/RO_HOM0000016.md) + * [before](RO/83/RO_0002083.md) + * [simultaneous with](RO/82/RO_0002082.md) + * [before or simultaneous with](RO/81/RO_0002081.md) + * [directly regulates](RO/78/RO_0002578.md) + * [skeleton of](RO/76/RO_0002576.md) + * [participates in a biotic-biotic interaction with](RO/74/RO_0002574.md) + * [has modifier](RO/73/RO_0002573.md) + * [luminal space of](RO/72/RO_0002572.md) + * [lumen of](RO/71/RO_0002571.md) + * [conduit for](RO/70/RO_0002570.md) + * [in paramorphism relationship with](RO/74/RO_HOM0000074.md) + * [dendrite synapsed in](RO/21/RO_0002121.md) + * [synapsed to](RO/20/RO_0002120.md) + * [has branching part](RO/69/RO_0002569.md) + * [has muscle antagonist](RO/68/RO_0002568.md) + * [biomechanically related to](RO/67/RO_0002567.md) + * [causally influences](RO/66/RO_0002566.md) + * [results in movement of](RO/65/RO_0002565.md) + * [molecular interaction relation helper property](RO/64/RO_0002564.md) + * [interaction relation helper property](RO/63/RO_0002563.md) + * [related via dependence to](RO/09/RO_0002609.md) + * [synapsed_by_via_type_III_bouton](RO/15/RO_0002115.md) + * [synapsed_via_type_III_bouton_to](RO/14/RO_0002114.md) + * [has presynaptic terminal in](RO/13/RO_0002113.md) + * [synapsed_by_via_type_Is_bouton](RO/12/RO_0002112.md) + * [releases neurotransmitter](RO/11/RO_0002111.md) + * [has postsynaptic terminal in](RO/10/RO_0002110.md) + * [is marker for](RO/07/RO_0002607.md) + * [is substance that treats](RO/06/RO_0002606.md) + * [in pro-orthology relationship with](RO/25/RO_HOM0000025.md) + * [in serial homology relationship with](RO/27/RO_HOM0000027.md) + * [causally influenced by](RO/59/RO_0002559.md) + * [has evidence](RO/58/RO_0002558.md) + * [has pathogen](RO/57/RO_0002557.md) + * [pathogen of](RO/56/RO_0002556.md) + * [allelopath of](RO/55/RO_0002555.md) + * [hyperparasitized by](RO/54/RO_0002554.md) + * [hyperparasite of](RO/53/RO_0002553.md) + * [results in ending of](RO/52/RO_0002552.md) + * [has skeleton](RO/51/RO_0002551.md) + * [starts before](RO/89/RO_0002089.md) + * [synapsed_by_via_type_Ib_bouton](RO/09/RO_0002109.md) + * [synapsed_by_via_type_II_bouton](RO/08/RO_0002108.md) + * [synapsed_via_type_II_bouton_to](RO/07/RO_0002107.md) + * [synapsed_via_type_Is_bouton_to](RO/06/RO_0002106.md) + * [synapsed_via_type_Ib_bouton_to](RO/05/RO_0002105.md) + * [has plasma membrane part](RO/04/RO_0002104.md) + * [synapsed by](RO/03/RO_0002103.md) + * [axon synapses in](RO/02/RO_0002102.md) + * [fasciculates with](RO/01/RO_0002101.md) + * [has soma location](RO/00/RO_0002100.md) + * [immediately precedes](RO/90/RO_0002090.md) + * [in regulogy relationship with](RO/75/RO_HOM0000075.md) + * [located in](RO/25/RO_0001025.md) + * [in homoeology relationship with](RO/73/RO_HOM0000073.md) + * [in homeosis relationship with](RO/72/RO_HOM0000072.md) + * [in homotopy relationship with](RO/71/RO_HOM0000071.md) + * [existence ends during or before](RO/97/RO_0002497.md) + * [existence starts during or after](RO/96/RO_0002496.md) + * [immediate transformation of](RO/95/RO_0002495.md) + * [transformation of](RO/94/RO_0002494.md) + * [existence ends with](RO/93/RO_0002493.md) + * [existence ends during](RO/92/RO_0002492.md) + * [existence starts and ends during](RO/91/RO_0002491.md) + * [existence overlaps](RO/90/RO_0002490.md) + * [in neoteny relationship with](RO/32/RO_HOM0000032.md) + * [in 1 to many orthology relationship with](RO/34/RO_HOM0000034.md) + * [in many to many homology relationship with](RO/36/RO_HOM0000036.md) + * [contains process](BFO/67/BFO_0000067.md) + * [occurs in](BFO/66/BFO_0000066.md) + * [in paraxenology relationship with](RO/68/RO_HOM0000068.md) + * [precedes](BFO/63/BFO_0000063.md) + * [preceded by](BFO/62/BFO_0000062.md) + * [in interology relationship with](RO/63/RO_HOM0000063.md) + * [in equivalogy relationship with](RO/62/RO_HOM0000062.md) + * [in pseudoparalogy relationship with](RO/61/RO_HOM0000061.md) + * [is immediately upstream of sequence of](RO/31/RO_0002531.md) + * [is immediately downstream of sequence of](RO/30/RO_0002530.md) + * [existence starts during](RO/88/RO_0002488.md) + * [relation between structure and stage](RO/87/RO_0002487.md) + * [sends output to](RO/86/RO_0002486.md) + * [receives input from](RO/85/RO_0002485.md) + * [is ubiquitination](RO/82/RO_0002482.md) + * [is kinase activity](RO/81/RO_0002481.md) + * [ubiquitinates](RO/80/RO_0002480.md) + * [serially homologous to](RO/59/RO_0002159.md) + * [has phenotype](RO/00/RO_0002200.md) + * [is downstream of sequence of](RO/29/RO_0002529.md) + * [is upstream of sequence of](RO/28/RO_0002528.md) + * [does not overlap sequence of](RO/27/RO_0002527.md) + * [overlaps sequence of](RO/26/RO_0002526.md) + * [is subsequence of](RO/25/RO_0002525.md) + * [part of](BFO/50/BFO_0000050.md) + * [is bound by sequence of](RO/23/RO_0002523.md) + * [bounds sequence of](RO/22/RO_0002522.md) + * [is sequentially aligned with](RO/21/RO_0002521.md) + * [is consecutive sequence of](RO/20/RO_0002520.md) + * [child nucleus of in male](RO/78/RO_0002478.md) + * [child nucleus of in hermaphrodite](RO/77/RO_0002477.md) + * [child nucleus of](RO/76/RO_0002476.md) + * [composed primarily of](RO/73/RO_0002473.md) + * [is evidence for](RO/72/RO_0002472.md) + * [is eaten by](RO/71/RO_0002471.md) + * [eats](RO/70/RO_0002470.md) + * [in apomorphy relationship with](RO/42/RO_HOM0000042.md) + * [in plesiomorphy relationship with](RO/43/RO_HOM0000043.md) + * [in deep homology relationship with](RO/44/RO_HOM0000044.md) + * [in hemiplasy relationship with](RO/45/RO_HOM0000045.md) + * [in gametology relationship with](RO/46/RO_HOM0000046.md) + * [in chromosomal homology relationship with](RO/47/RO_HOM0000047.md) + * [is end sequence of](RO/19/RO_0002519.md) + * [has end sequence](RO/18/RO_0002518.md) + * [is start sequence of](RO/17/RO_0002517.md) + * [has start sequence](RO/16/RO_0002516.md) + * [sequentially adjacent to](RO/15/RO_0002515.md) + * [sequentially related to](RO/14/RO_0002514.md) + * [ribosomally translates to](RO/13/RO_0002513.md) + * [ribosomal translation of](RO/12/RO_0002512.md) + * [transcribed to](RO/11/RO_0002511.md) + * [provides nutrients for](RO/69/RO_0002469.md) + * [is parasitism](RO/68/RO_0002468.md) + * [is mutualism](RO/67/RO_0002467.md) + * [is commensalism](RO/66/RO_0002466.md) + * [is symbiosis](RO/65/RO_0002465.md) + * [helper property](RO/64/RO_0002464.md) + * [target participant in](RO/63/RO_0002463.md) + * [subject participant in](RO/62/RO_0002462.md) + * [partner in](RO/61/RO_0002461.md) + * [has vector](RO/60/RO_0002460.md) + * [realized in](BFO/54/BFO_0000054.md) + * [realizes](BFO/55/BFO_0000055.md) + * [drains](RO/79/RO_0002179.md) + * [has subsequence](RO/24/RO_0002524.md) + * [regulates transport of](RO/11/RO_0002011.md) + * [regulates in other organism](RO/10/RO_0002010.md) + * [determined by](RO/07/RO_0002507.md) + * [causal relation between material entities](RO/06/RO_0002506.md) + * [has intermediate](RO/05/RO_0002505.md) + * [in mimicry relationship with](RO/33/RO_HOM0000033.md) + * [towards](RO/03/RO_0002503.md) + * [depends on](RO/02/RO_0002502.md) + * [causal relation between processes](RO/01/RO_0002501.md) + * [is vector for](RO/59/RO_0002459.md) + * [preyed upon by](RO/58/RO_0002458.md) + * [acquires nutrients from](RO/57/RO_0002457.md) + * [pollinated by](RO/56/RO_0002456.md) + * [pollinates](RO/55/RO_0002455.md) + * [has host](RO/54/RO_0002454.md) + * [host of](RO/53/RO_0002453.md) + * [has symptom](RO/52/RO_0002452.md) + * [transmitted by](RO/51/RO_0002451.md) + * [molecularly increases activity of](RO/50/RO_0002450.md) + * [in hypermorphosis relationship with](RO/52/RO_HOM0000052.md) + * [in synology relationship with](RO/53/RO_HOM0000053.md) + * [cell expresses](RO/09/RO_0002009.md) + * [coincident with](RO/08/RO_0002008.md) + * [bounding layer of](RO/07/RO_0002007.md) + * [has synaptic terminal of](RO/06/RO_0002006.md) + * [innervated_by](RO/05/RO_0002005.md) + * [tracheates](RO/04/RO_0002004.md) + * [electrically_synapsed_to](RO/03/RO_0002003.md) + * [has 2D boundary](RO/02/RO_0002002.md) + * [aligned with](RO/01/RO_0002001.md) + * [2D boundary of](RO/00/RO_0002000.md) + * [in semi-orthology relationship with](RO/26/RO_HOM0000026.md) + * [is model of](RO/01/RO_0003301.md) + * [in out-paralogy relationship with](RO/24/RO_HOM0000024.md) + * [in in-paralogy relationship with](RO/23/RO_HOM0000023.md) + * [in ohnology relationship with](RO/22/RO_HOM0000022.md) + * [in 1 to 1 orthology relationship with](RO/20/RO_HOM0000020.md) + * [molecularly decreases activity of](RO/49/RO_0002449.md) + * [molecularly controls](RO/48/RO_0002448.md) + * [phosphorylates](RO/47/RO_0002447.md) + * [participates in a abiotic-biotic interaction with](RO/46/RO_0002446.md) + * [parasitized by](RO/45/RO_0002445.md) + * [parasite of](RO/44/RO_0002444.md) + * [interacts with via parasite-host interaction](RO/43/RO_0002443.md) + * [mutualistically interacts with](RO/42/RO_0002442.md) + * [commensually interacts with](RO/41/RO_0002441.md) + * [symbiotically interacts with](RO/40/RO_0002440.md) + * [produced by](RO/01/RO_0003001.md) + * [represses expression of](RO/02/RO_0003002.md) + * [increases expression of](RO/03/RO_0003003.md) + * [in paedomorphorsis relationship with](RO/29/RO_HOM0000029.md) + * [in 1 to 1 homology relationship with](RO/19/RO_HOM0000019.md) + * [in xenology relationship with](RO/18/RO_HOM0000018.md) + * [in orthology relationship with](RO/17/RO_HOM0000017.md) + * [has participant](RO/57/RO_0000057.md) + * [in protein structural homology relationship with](RO/15/RO_HOM0000015.md) + * [in partial homology relationship with](RO/14/RO_HOM0000014.md) + * [in syntenic orthology relationship with](RO/13/RO_HOM0000013.md) + * [in syntenic paralogy relationship with](RO/12/RO_HOM0000012.md) + * [in paralogy relationship with](RO/11/RO_HOM0000011.md) + * [downstream in neural circuit with](RO/02/RO_0000302.md) + * [preys on](RO/39/RO_0002439.md) + * [trophically interacts with](RO/38/RO_0002438.md) + * [biotically interacts with](RO/37/RO_0002437.md) + * [molecularly interacts with](RO/36/RO_0002436.md) + * [genetically interacts with](RO/35/RO_0002435.md) + * [interacts with](RO/34/RO_0002434.md) + * [contributes to morphology of](RO/33/RO_0002433.md) + * [enables activity in](RO/32/RO_0002432.md) + * [involved in or regulates](RO/31/RO_0002431.md) + * [involved in negative regulation of](RO/30/RO_0002430.md) + * [has potential to directly develop into](RO/88/RO_0002388.md) + * [has potential to develop into](RO/87/RO_0002387.md) + * [has potential to developmentally induce](RO/86/RO_0002386.md) + * [has potential to developmentally contribute to](RO/85/RO_0002385.md) + * [has developmental potential involving](RO/84/RO_0002384.md) + * [proper tributary of](RO/83/RO_0002383.md) + * [proper distributary of](RO/82/RO_0002382.md) + * [main stem of](RO/81/RO_0002381.md) + * [branching part of](RO/80/RO_0002380.md) + * [in reversal relationship with](RO/09/RO_HOM0000009.md) + * [in biological homology relationship with](RO/08/RO_HOM0000008.md) + * [in historical homology relationship with](RO/07/RO_HOM0000007.md) + * [in structural homology relationship with](RO/06/RO_HOM0000006.md) + * [in parallelism relationship with](RO/05/RO_HOM0000005.md) + * [in convergence relationship with](RO/04/RO_HOM0000004.md) + * [in homocracy relationship with](RO/03/RO_HOM0000003.md) + * [in homoplasy relationship with](RO/02/RO_HOM0000002.md) + * [in homology relationship with](RO/01/RO_HOM0000001.md) + * [in similarity relationship with](RO/00/RO_HOM0000000.md) + * [involved in positive regulation of](RO/29/RO_0002429.md) + * [involved in regulation of](RO/28/RO_0002428.md) + * [causally downstream of or within](RO/27/RO_0002427.md) + * [differs in attribute](RO/26/RO_0002426.md) + * [differs in attribute of](RO/25/RO_0002425.md) + * [differs in](RO/24/RO_0002424.md) + * [spatially coextensive with](RO/79/RO_0002379.md) + * [anabranch of](RO/78/RO_0002378.md) + * [distributary of](RO/77/RO_0002377.md) + * [tributary of](RO/76/RO_0002376.md) + * [in branching relationship with](RO/75/RO_0002375.md) + * [has fused element](RO/74/RO_0002374.md) + * [has muscle insertion](RO/73/RO_0002373.md) + * [has muscle origin](RO/72/RO_0002372.md) + * [attached to](RO/71/RO_0002371.md) + * [in progenesis relationship with](RO/31/RO_HOM0000031.md) + * [starts during](RO/91/RO_0002091.md) + * [causally upstream of or within](RO/18/RO_0002418.md) + * [transitively provides input for](RO/14/RO_0002414.md) + * [directly provides input for](RO/13/RO_0002413.md) + * [immediately causally upstream of](RO/12/RO_0002412.md) + * [causally upstream of](RO/11/RO_0002411.md) + * [causally related to](RO/10/RO_0002410.md) + * [upstream in neural circuit with](RO/01/RO_0000301.md) + * [in neural circuit with](RO/00/RO_0000300.md) + * [has dendrite location](RO/60/RO_0002360.md) + * [indirectly inhibits](RO/09/RO_0002409.md) + * [directly inhibits](RO/08/RO_0002408.md) + * [indirectly activates](RO/07/RO_0002407.md) + * [directly activates](RO/06/RO_0002406.md) + * [immediately causally downstream of](RO/05/RO_0002405.md) + * [causally downstream of](RO/04/RO_0002404.md) + * [obsolete has indirect output](RO/03/RO_0002403.md) + * [obsolete has direct output](RO/02/RO_0002402.md) + * [obsolete has indirect input](RO/01/RO_0002401.md) + * [has direct input](RO/00/RO_0002400.md) + * [results in developmental induction of](RO/57/RO_0002357.md) + * [results in specification of](RO/56/RO_0002356.md) + * [results in structural organization of](RO/55/RO_0002355.md) + * [formed as result of](RO/54/RO_0002354.md) + * [output of](RO/53/RO_0002353.md) + * [input of](RO/52/RO_0002352.md) + * [has member](RO/51/RO_0002351.md) + * [member of](RO/50/RO_0002350.md) + * [results in determination of](RO/49/RO_0002349.md) + * [results in commitment to](RO/48/RO_0002348.md) + * [exports](RO/45/RO_0002345.md) + * [results in transport to from or in](RO/44/RO_0002344.md) + * [results in growth of](RO/43/RO_0002343.md) + * [results in transport across](RO/42/RO_0002342.md) + * [results in transport along](RO/41/RO_0002341.md) + * [imports](RO/40/RO_0002340.md) + * [results in morphogenesis of](RO/98/RO_0002298.md) + * [results in formation of](RO/97/RO_0002297.md) + * [results in development of](RO/96/RO_0002296.md) + * [results in developmental progression of](RO/95/RO_0002295.md) + * [phenotype of](RO/01/RO_0002201.md) + * [ubiquitously expresses](RO/93/RO_0002293.md) + * [expresses](RO/92/RO_0002292.md) + * [ubiquitously expressed in](RO/91/RO_0002291.md) + * [existence starts with](RO/89/RO_0002489.md) + * [determines](RO/08/RO_0002508.md) + * [results in maturation of](RO/99/RO_0002299.md) + * [capable of upregulating or causing pathological process](RO/00/RO_0002600.md) + * [has target end location](RO/39/RO_0002339.md) + * [has target start location](RO/38/RO_0002338.md) + * [related via localization to](RO/37/RO_0002337.md) + * [positively regulated by](RO/36/RO_0002336.md) + * [negatively regulated by](RO/35/RO_0002335.md) + * [regulated by](RO/34/RO_0002334.md) + * [enabled by](RO/33/RO_0002333.md) + * [regulates levels of](RO/32/RO_0002332.md) + * [involved in](RO/31/RO_0002331.md) + * [genomically related to](RO/30/RO_0002330.md) + * [part of developmental precursor of](RO/87/RO_0002287.md) + * [developmentally succeeded by](RO/86/RO_0002286.md) + * [developmentally replaces](RO/85/RO_0002285.md) + * [in heterochronous homology relationship with](RO/28/RO_HOM0000028.md) + * [correlated with](RO/10/RO_0002610.md) + * [part of structure that is capable of](RO/29/RO_0002329.md) + * [functionally related to](RO/28/RO_0002328.md) + * [enables](RO/27/RO_0002327.md) + * [contributes to](RO/26/RO_0002326.md) + * [colocalizes with](RO/25/RO_0002325.md) + * [developmentally related to](RO/24/RO_0002324.md) + * [mereotopologically related to](RO/23/RO_0002323.md) + * [confers advantage in](RO/22/RO_0002322.md) + * [ecologically related to](RO/21/RO_0002321.md) + * [evolutionarily related to](RO/20/RO_0002320.md) + * [during which ends](RO/84/RO_0002084.md) + * [produces](RO/00/RO_0003000.md) + * [contains](RO/19/RO_0001019.md) + * [contained in](RO/18/RO_0001018.md) + * [location of](RO/15/RO_0001015.md) + * [results in acquisition of features of](RO/15/RO_0002315.md) + * [inheres in part of](RO/14/RO_0002314.md) + * [transports or maintains localization of](RO/13/RO_0002313.md) + * [evolutionary variant of](RO/12/RO_0002312.md) + * [in between-species paralogy relationship with](RO/50/RO_HOM0000050.md) + * [in postdisplacement relationship with](RO/51/RO_HOM0000051.md) + * [derives into](RO/01/RO_0001001.md) + * [has habitat](RO/03/RO_0002303.md) + * [results in developmental regression of](RO/01/RO_0002301.md) + * [results in disappearance of](RO/00/RO_0002300.md) + * [developmentally preceded by](RO/58/RO_0002258.md) + * [developmentally induces](RO/57/RO_0002257.md) + * [developmentally induced by](RO/56/RO_0002256.md) + * [developmentally contributes to](RO/55/RO_0002255.md) + * [has developmental contribution from](RO/54/RO_0002254.md) + * [in peramorphosis relationship with](RO/30/RO_HOM0000030.md) + * [in 1 to many homology relationship with](RO/37/RO_HOM0000037.md) + * [has role](RO/87/RO_0000087.md) + * [has quality](RO/86/RO_0000086.md) + * [has function](RO/85/RO_0000085.md) + * [role of](RO/81/RO_0000081.md) + * [quality of](RO/80/RO_0000080.md) + * [in apparent orthology relationship with](RO/60/RO_HOM0000060.md) + * [in syntenic homology relationship with](RO/10/RO_HOM0000010.md) + * [has output](RO/34/RO_0002234.md) + * [has input](RO/33/RO_0002233.md) + * [has end location](RO/32/RO_0002232.md) + * [has start location](RO/31/RO_0002231.md) + * [ends with](RO/30/RO_0002230.md) + * [function of](RO/79/RO_0000079.md) + * [has component](RO/80/RO_0002180.md) + +## AnnotationProperties + + * [always present in taxon](RO/04/RO_0002504.md) + * [end, days post coitum](RO/48/RO_0002548.md) + * [is relational form of a class](RO/94/RO_0002594.md) + * [start, weeks post birth](RO/49/RO_0002549.md) + * [has developmental stage marker](RO/46/RO_0002546.md) + * [start, days post coitum](RO/47/RO_0002547.md) + * [description](on/description.md) + * [eco subset](co/subsets#ro-eco.md) + * [end, weeks post birth](RO/50/RO_0002550.md) + * [contributor](or/contributor.md) + * [page](ge/page.md) + * [database_cross_reference](ef/oboInOwl#hasDbXref.md) + * [curator note](IAO/32/IAO_0000232.md) + * [OBO foundry unique label](IAO/89/IAO_0000589.md) + * [subset_property](ty/oboInOwl#SubsetProperty.md) + * [creator](or/creator.md) + * [ambiguous for taxon](RO/73/RO_0002173.md) + * [dubious for taxon](RO/74/RO_0002174.md) + * [mutually spatially disjoint with](RO/71/RO_0002171.md) + * [taxonomic class assertion](RO/72/RO_0002172.md) + * [annotation property cardinality](RO/19/RO_0002419.md) + * [present in taxon](RO/75/RO_0002175.md) + * [has_exact_synonym](ym/oboInOwl#hasExactSynonym.md) + * [owl#deprecated](ed/owl#deprecated.md) + * [rdf-schema#comment](nt/rdf-schema#comment.md) + * [logical macro assertion](RO/16/RO_0002416.md) + * [is symmetric relational form of process class](RO/61/RO_0002561.md) + * [logical macro assertion on a property](RO/21/RO_0002421.md) + * [is asymmetric relational form of process class](RO/60/RO_0002560.md) + * [logical macro assertion on an object property](RO/22/RO_0002422.md) + * [logical macro assertion on an annotation property](RO/23/RO_0002423.md) + * [is relational form of process class](RO/62/RO_0002562.md) + * [rdf-schema#isDefinedBy](By/rdf-schema#isDefinedBy.md) + * [temporal interpretation](RO/00/RO_0001900.md) + * [logical macro assertion on a class](RO/20/RO_0002420.md) + * [elucidation](IAO/00/IAO_0000600.md) + * [title](le/title.md) + * [has_broad_synonym](ym/oboInOwl#hasBroadSynonym.md) + * [never in taxon](RO/61/RO_0002161.md) + * [dispositional interpretation](RO/74/RO_0002474.md) + * [has no connections with](RO/75/RO_0002475.md) + * [homepage](ge/homepage.md) + * [shorthand](nd/oboInOwl#shorthand.md) + * [in_subset](et/oboInOwl#inSubset.md) + * [has_obo_format_version](on/oboInOwl#hasOBOFormatVersion.md) + * [definition](IAO/15/IAO_0000115.md) + * [expand expression to](IAO/24/IAO_0000424.md) + * [editor note](IAO/16/IAO_0000116.md) + * [has curation status](IAO/14/IAO_0000114.md) + * [is direct form of](RO/75/RO_0002575.md) + * [definition source](IAO/19/IAO_0000119.md) + * [term editor](IAO/17/IAO_0000117.md) + * [first order logic expression](IAO/26/IAO_0000426.md) + * [alternative term](IAO/18/IAO_0000118.md) + * [expand assertion to](IAO/25/IAO_0000425.md) + * [source](ce/source.md) + * [editor preferred term](IAO/11/IAO_0000111.md) + * [example of usage](IAO/12/IAO_0000112.md) + * [oboInOwl#id](id/oboInOwl#id.md) + * [start, days post fertilization](RO/39/RO_0002539.md) + * [inherited annotation property](RO/83/RO_0002483.md) + * [publisher](er/publisher.md) + * [citesAsAuthority](ty/citesAsAuthority.md) + * [curator guidance link](RO/84/RO_0002484.md) + * [measurement property has unit](RO/36/RO_0002536.md) + * [temporal logical macro assertion on a class](RO/35/RO_0002535.md) + * [has end time value](RO/38/RO_0002538.md) + * [has start time value](RO/37/RO_0002537.md) + * [rdf-schema#label](el/rdf-schema#label.md) + * [is indirect form of](RO/79/RO_0002579.md) + * [rdf-schema#seeAlso](so/rdf-schema#seeAlso.md) + * [has_related_synonym](ym/oboInOwl#hasRelatedSynonym.md) + * [imported from](IAO/12/IAO_0000412.md) + * [is a defining property chain axiom where second argument is reflexive](RO/82/RO_0002582.md) + * [logical macro assertion involving identity](RO/01/RO_0002601.md) + * [end, years post birth](RO/42/RO_0002542.md) + * [in approximate one to one relationship with](RO/02/RO_0002602.md) + * [start, months post birth](RO/43/RO_0002543.md) + * [is approximately equivalent to](RO/03/RO_0002603.md) + * [is a defining property chain axiom](RO/81/RO_0002581.md) + * [end, months post birth](RO/44/RO_0002544.md) + * [is opposite of](RO/04/RO_0002604.md) + * [logical macro assertion on an axiom](RO/80/RO_0002580.md) + * [month of gestation](RO/45/RO_0002545.md) + * [is indistinguishable from](RO/05/RO_0002605.md) + * [end, days post fertilization](RO/40/RO_0002540.md) + * [start, years post birth](RO/41/RO_0002541.md) diff --git a/src/ontology/md/le/title.md b/src/ontology/md/le/title.md new file mode 100644 index 00000000..4b1d4fca --- /dev/null +++ b/src/ontology/md/le/title.md @@ -0,0 +1,32 @@ + +## Class : null + + * *IRI* = http://purl.org/dc/elements/1.1/title + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + +## External Comments + diff --git a/src/ontology/md/nd/oboInOwl#shorthand.md b/src/ontology/md/nd/oboInOwl#shorthand.md new file mode 100644 index 00000000..0cdf7bf0 --- /dev/null +++ b/src/ontology/md/nd/oboInOwl#shorthand.md @@ -0,0 +1,41 @@ + +## Class : shorthand + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#shorthand + * *Label* = shorthand + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = shorthand + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002295 [shorthand](../../nd/oboInOwl#shorthand.md) results_in_developmental_progression_of + * http://purl.obolibrary.org/obo/RO_0002296 [shorthand](../../nd/oboInOwl#shorthand.md) results_in_development_of + * http://purl.obolibrary.org/obo/RO_0002297 [shorthand](../../nd/oboInOwl#shorthand.md) results_in_formation_of + * http://purl.obolibrary.org/obo/RO_0002298 [shorthand](../../nd/oboInOwl#shorthand.md) results_in_morphogenesis_of + * http://purl.obolibrary.org/obo/RO_0002299 [shorthand](../../nd/oboInOwl#shorthand.md) results_in_maturation_of + * http://purl.obolibrary.org/obo/RO_0002300 [shorthand](../../nd/oboInOwl#shorthand.md) results_in_disappearance_of + * http://purl.obolibrary.org/obo/RO_0002315 [shorthand](../../nd/oboInOwl#shorthand.md) results_in_acquisition_of_features_of + +## External Comments + diff --git a/src/ontology/md/nt/rdf-schema#comment.md b/src/ontology/md/nt/rdf-schema#comment.md new file mode 100644 index 00000000..f0a80e52 --- /dev/null +++ b/src/ontology/md/nt/rdf-schema#comment.md @@ -0,0 +1,110 @@ + +## Class : null + + * *IRI* = http://www.w3.org/2000/01/rdf-schema#comment + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * http://purl.obolibrary.org/obo/BFO_0000054 [rdf-schema#comment](../../nt/rdf-schema#comment.md) 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 + * http://purl.obolibrary.org/obo/BFO_0000055 [rdf-schema#comment](../../nt/rdf-schema#comment.md) 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 + * http://purl.obolibrary.org/obo/BFO_0000060 [rdf-schema#comment](../../nt/rdf-schema#comment.md) accidentally included in BFO 1.2 proposal + - should have been BFO_0000062 + * http://purl.obolibrary.org/obo/BFO_0000066 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + * http://purl.obolibrary.org/obo/BFO_0000067 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + * http://purl.obolibrary.org/obo/RO_0002007 [rdf-schema#comment](../../nt/rdf-schema#comment.md) A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + * http://purl.obolibrary.org/obo/RO_0002008 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + * http://purl.obolibrary.org/obo/RO_0002081 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Primitive instance level timing relation between events + * http://purl.obolibrary.org/obo/RO_0002082 [rdf-schema#comment](../../nt/rdf-schema#comment.md) t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + * http://purl.obolibrary.org/obo/RO_0002083 [rdf-schema#comment](../../nt/rdf-schema#comment.md) t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + * http://purl.obolibrary.org/obo/RO_0002084 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + * http://purl.obolibrary.org/obo/RO_0002085 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + * http://purl.obolibrary.org/obo/RO_0002086 [rdf-schema#comment](../../nt/rdf-schema#comment.md) X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + * http://purl.obolibrary.org/obo/RO_0002087 [rdf-schema#comment](../../nt/rdf-schema#comment.md) X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + * http://purl.obolibrary.org/obo/RO_0002088 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + * http://purl.obolibrary.org/obo/RO_0002090 [rdf-schema#comment](../../nt/rdf-schema#comment.md) X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + * http://purl.obolibrary.org/obo/RO_0002091 [rdf-schema#comment](../../nt/rdf-schema#comment.md) X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + * http://purl.obolibrary.org/obo/RO_0002092 [rdf-schema#comment](../../nt/rdf-schema#comment.md) X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + * http://purl.obolibrary.org/obo/RO_0002093 [rdf-schema#comment](../../nt/rdf-schema#comment.md) X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + * http://purl.obolibrary.org/obo/RO_0002105 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + * http://purl.obolibrary.org/obo/RO_0002106 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + * http://purl.obolibrary.org/obo/RO_0002107 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + * http://purl.obolibrary.org/obo/RO_0002108 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + * http://purl.obolibrary.org/obo/RO_0002109 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + * http://purl.obolibrary.org/obo/RO_0002112 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + * http://purl.obolibrary.org/obo/RO_0002114 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + * http://purl.obolibrary.org/obo/RO_0002115 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + * http://purl.obolibrary.org/obo/RO_0002120 [rdf-schema#comment](../../nt/rdf-schema#comment.md) N1 synapsed_to some N2 +Expands to: +N1 SubclassOf ( + has_part some ( + ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( + ‘synapse ; GO:0045202’ that has_part some ( + ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) + * http://purl.obolibrary.org/obo/RO_0002158 [rdf-schema#comment](../../nt/rdf-schema#comment.md) VBO calls this homologous_to + * http://purl.obolibrary.org/obo/RO_0002162 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Connects a biological entity to its taxon of origin. + * http://purl.obolibrary.org/obo/RO_0002174 [rdf-schema#comment](../../nt/rdf-schema#comment.md) This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost + * http://purl.obolibrary.org/obo/RO_0002202 [rdf-schema#comment](../../nt/rdf-schema#comment.md) This is the transitive form of the develops from relation + * http://purl.obolibrary.org/obo/RO_0002207 [rdf-schema#comment](../../nt/rdf-schema#comment.md) TODO - add child relations from DOS + * http://purl.obolibrary.org/obo/RO_0002222 [rdf-schema#comment](../../nt/rdf-schema#comment.md) A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + * http://purl.obolibrary.org/obo/RO_0002258 [rdf-schema#comment](../../nt/rdf-schema#comment.md) This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + * http://purl.obolibrary.org/obo/RO_0002374 [rdf-schema#comment](../../nt/rdf-schema#comment.md) A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. + * http://purl.obolibrary.org/obo/RO_0002401 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + * http://purl.obolibrary.org/obo/RO_0002403 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + * http://purl.obolibrary.org/obo/RO_0002424 [rdf-schema#comment](../../nt/rdf-schema#comment.md) This is an exploratory relation + * http://purl.obolibrary.org/obo/RO_0002490 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * http://purl.obolibrary.org/obo/RO_0002491 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * http://purl.obolibrary.org/obo/RO_0002492 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * http://purl.obolibrary.org/obo/RO_0002493 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * http://purl.obolibrary.org/obo/RO_0002496 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * http://purl.obolibrary.org/obo/RO_0002497 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + * http://purl.obolibrary.org/obo/RO_0002558 [rdf-schema#comment](../../nt/rdf-schema#comment.md) x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. + * http://purl.obolibrary.org/obo/RO_0002599 [alternative term](../../IAO/18/IAO_0000118.md) treats + * http://purl.obolibrary.org/obo/RO_0003000 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + * http://purl.obolibrary.org/obo/RO_0003301 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + * http://purl.obolibrary.org/obo/RO_HOM0000001 [rdf-schema#comment](../../nt/rdf-schema#comment.md) This broad definition encompasses all the working definitions proposed so far in the literature. + * http://purl.obolibrary.org/obo/RO_HOM0000003 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + * http://purl.obolibrary.org/obo/RO_HOM0000004 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Convergence usually implies a notion of adaptation. + * http://purl.obolibrary.org/obo/RO_HOM0000005 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + * http://purl.obolibrary.org/obo/RO_HOM0000008 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + * http://purl.obolibrary.org/obo/RO_HOM0000017 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The term is sometimes also used for anatomical structures. + * http://purl.obolibrary.org/obo/RO_HOM0000018 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + * http://purl.obolibrary.org/obo/RO_HOM0000026 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The converse of pro-orthologous. + * http://purl.obolibrary.org/obo/RO_HOM0000043 [rdf-schema#comment](../../nt/rdf-schema#comment.md) This term is usually contrasted to apomorphy. + * http://purl.obolibrary.org/obo/RO_HOM0000044 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Used for structures in distantly related taxa. + * http://purl.obolibrary.org/obo/RO_HOM0000050 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The genes have diverged before a speciation event. + * http://purl.obolibrary.org/obo/RO_HOM0000057 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Used for structures in closely related taxa. + * http://purl.obolibrary.org/obo/RO_HOM0000058 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + * http://purl.obolibrary.org/obo/RO_HOM0000060 [rdf-schema#comment](../../nt/rdf-schema#comment.md) The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + * http://purl.obolibrary.org/obo/RO_HOM0000061 [rdf-schema#comment](../../nt/rdf-schema#comment.md) These genes may come out as paralogs in a single-genome analysis. + * http://purl.obolibrary.org/obo/RO_HOM0000062 [rdf-schema#comment](../../nt/rdf-schema#comment.md) This may include examples of orthology, paralogy and xenology. + * http://purl.obolibrary.org/obo/RO_HOM0000069 [rdf-schema#comment](../../nt/rdf-schema#comment.md) This phenomenon is usually due to gene conversion process. + * http://purl.obolibrary.org/obo/RO_HOM0000071 [rdf-schema#comment](../../nt/rdf-schema#comment.md) Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + * http://purl.obolibrary.org/obo/RO_HOM0000073 [rdf-schema#comment](../../nt/rdf-schema#comment.md) On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + * http://www.w3.org/2000/01/rdf-schema#isDefinedBy [OBO foundry unique label](../../IAO/89/IAO_0000589.md) is defined by + +## External Comments + diff --git a/src/ontology/md/on/description.md b/src/ontology/md/on/description.md new file mode 100644 index 00000000..888ed05e --- /dev/null +++ b/src/ontology/md/on/description.md @@ -0,0 +1,38 @@ + +## Class : null + + * *IRI* = http://purl.org/dc/elements/1.1/description + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002009 [description](../../on/description.md) x 'cell expresses' y iff: +cell(x) +AND gene(y) +AND exists some 'transcription, DNA templated (GO_0006351)'(t) +AND t occurs_in x +AND t has_input y + +## External Comments + diff --git a/src/ontology/md/on/oboInOwl#hasOBOFormatVersion.md b/src/ontology/md/on/oboInOwl#hasOBOFormatVersion.md new file mode 100644 index 00000000..31355d13 --- /dev/null +++ b/src/ontology/md/on/oboInOwl#hasOBOFormatVersion.md @@ -0,0 +1,34 @@ + +## Class : has_obo_format_version + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion + * *Label* = has_obo_format_version + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has_obo_format_version + +## Usage + + * - + +## External Comments + diff --git a/src/ontology/md/or/contributor.md b/src/ontology/md/or/contributor.md new file mode 100644 index 00000000..d2b77605 --- /dev/null +++ b/src/ontology/md/or/contributor.md @@ -0,0 +1,33 @@ + +## Class : null + + * *IRI* = http://purl.org/dc/elements/1.1/contributor + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002327 [rdf-schema#label](../../el/rdf-schema#label.md) enables + +## External Comments + diff --git a/src/ontology/md/or/creator.md b/src/ontology/md/or/creator.md new file mode 100644 index 00000000..d403d5c1 --- /dev/null +++ b/src/ontology/md/or/creator.md @@ -0,0 +1,102 @@ + +## Class : null + + * *IRI* = http://purl.org/dc/elements/1.1/creator + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002325 [creator](../../or/creator.md) Gene Ontology Consortium + * http://purl.obolibrary.org/obo/RO_0002507 [creator](../../or/creator.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002507 [creator](../../or/creator.md) Pier Buttigieg + * http://purl.obolibrary.org/obo/RO_0002575 [creator](../../or/creator.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_0002579 [creator](../../or/creator.md) Chris Mungall + * http://purl.obolibrary.org/obo/RO_HOM0000000 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000001 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000002 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000003 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000004 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000005 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000006 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000007 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000008 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000009 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000010 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000011 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000012 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000013 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000014 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000015 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000016 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000017 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000018 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000019 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000020 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000022 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000023 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000024 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000025 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000026 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000027 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000028 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000029 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000030 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000031 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000032 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000033 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000034 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000036 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000037 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000042 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000043 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000044 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000045 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000046 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000047 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000048 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000049 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000050 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000051 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000052 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000053 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000054 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000055 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000057 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000058 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000060 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000061 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000062 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000063 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000065 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000066 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000068 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000069 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000071 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000072 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000073 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000074 [creator](../../or/creator.md) http://bgee.unil.ch + * http://purl.obolibrary.org/obo/RO_HOM0000075 [creator](../../or/creator.md) http://bgee.unil.ch + +## External Comments + diff --git a/src/ontology/md/so/rdf-schema#seeAlso.md b/src/ontology/md/so/rdf-schema#seeAlso.md new file mode 100644 index 00000000..9194a4ca --- /dev/null +++ b/src/ontology/md/so/rdf-schema#seeAlso.md @@ -0,0 +1,139 @@ + +## Class : null + + * *IRI* = http://www.w3.org/2000/01/rdf-schema#seeAlso + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * http://purl.obolibrary.org/obo/BFO_0000050 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections + * http://purl.obolibrary.org/obo/BFO_0000050 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://ontologydesignpatterns.org/wiki/Submissions:PartOf + * http://purl.obolibrary.org/obo/BFO_0000050 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://www.obofoundry.org/ro/#OBO_REL:part_of + * http://purl.obolibrary.org/obo/RO_0002150 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) FMA:85972 + * http://purl.obolibrary.org/obo/RO_0002160 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) https://github.com/obophenotype/uberon/wiki/Taxon-constraints + * http://purl.obolibrary.org/obo/RO_0002161 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) https://github.com/obophenotype/uberon/wiki/Taxon-constraints + * http://purl.obolibrary.org/obo/RO_0002162 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) https://github.com/obophenotype/uberon/wiki/Taxon-constraints + * http://purl.obolibrary.org/obo/RO_0002171 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/RO_0002163 + * http://purl.obolibrary.org/obo/RO_0002172 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) https://github.com/obophenotype/uberon/wiki/Taxon-constraints + * http://purl.obolibrary.org/obo/RO_0002173 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) https://github.com/obophenotype/uberon/wiki/Taxon-constraints + * http://purl.obolibrary.org/obo/RO_0002174 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) https://github.com/obophenotype/uberon/wiki/Taxon-constraints + * http://purl.obolibrary.org/obo/RO_0002175 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) https://github.com/obophenotype/uberon/wiki/Taxon-constraints + * http://purl.obolibrary.org/obo/RO_0002180 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://ontologydesignpatterns.org/wiki/Submissions:Componency + * http://purl.obolibrary.org/obo/RO_0002295 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://wiki.geneontology.org/index.php/Ontology_extensions + * http://purl.obolibrary.org/obo/RO_0002372 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://dbpedia.org/property/origin + * http://purl.obolibrary.org/obo/RO_0002373 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://dbpedia.org/property/insertion + * http://purl.obolibrary.org/obo/RO_0002376 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://dbpedia.org/ontology/drainsTo + * http://purl.obolibrary.org/obo/RO_0002376 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://en.wikipedia.org/wiki/Tributary + * http://purl.obolibrary.org/obo/RO_0002380 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) FMA:85994 + * http://purl.obolibrary.org/obo/RO_0002424 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions + * http://purl.obolibrary.org/obo/RO_0002434 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/MI_0914 + * http://purl.obolibrary.org/obo/RO_0002435 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/ECO_0000316 + * http://purl.obolibrary.org/obo/RO_0002435 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/MI_0208 + * http://purl.obolibrary.org/obo/RO_0002436 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/ECO_0000353 + * http://purl.obolibrary.org/obo/RO_0002436 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/MI_0915 + * http://purl.obolibrary.org/obo/RO_0002437 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 + * http://purl.obolibrary.org/obo/RO_0002437 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://eol.org/schema/terms/interactsWith + * http://purl.obolibrary.org/obo/RO_0002438 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 + * http://purl.obolibrary.org/obo/RO_0002439 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://eol.org/schema/terms/preysUpon + * http://purl.obolibrary.org/obo/RO_0002444 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://eol.org/schema/terms/parasitizes + * http://purl.obolibrary.org/obo/RO_0002445 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://eol.org/schema/terms/hasParasite + * http://purl.obolibrary.org/obo/RO_0002446 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 + * http://purl.obolibrary.org/obo/RO_0002454 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://eol.org/schema/terms/hasHost + * http://purl.obolibrary.org/obo/RO_0002455 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://eol.org/schema/terms/pollinates + * http://purl.obolibrary.org/obo/RO_0002456 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://eol.org/schema/terms/hasPollinator + * http://purl.obolibrary.org/obo/RO_0002458 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://eol.org/schema/terms/HasPredator + * http://purl.obolibrary.org/obo/RO_0002458 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://polytraits.lifewatchgreece.eu/terms/PRED + * http://purl.obolibrary.org/obo/RO_0002502 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/BFO_0000169 + * http://purl.obolibrary.org/obo/RO_0002555 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://eol.org/schema/terms/allelopathyYes + * http://purl.obolibrary.org/obo/RO_0002555 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y + * http://purl.obolibrary.org/obo/RO_0002563 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 + * http://purl.obolibrary.org/obo/RO_0002574 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 + * http://purl.obolibrary.org/obo/RO_0002606 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) https://code.google.com/p/obo-relations/issues/detail?id=46 + * http://purl.obolibrary.org/obo/RO_HOM0000000 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000000 + * http://purl.obolibrary.org/obo/RO_HOM0000001 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000001 + * http://purl.obolibrary.org/obo/RO_HOM0000002 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000002 + * http://purl.obolibrary.org/obo/RO_HOM0000003 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000003 + * http://purl.obolibrary.org/obo/RO_HOM0000004 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000004 + * http://purl.obolibrary.org/obo/RO_HOM0000005 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000005 + * http://purl.obolibrary.org/obo/RO_HOM0000006 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000006 + * http://purl.obolibrary.org/obo/RO_HOM0000007 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000007 + * http://purl.obolibrary.org/obo/RO_HOM0000008 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000008 + * http://purl.obolibrary.org/obo/RO_HOM0000009 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000009 + * http://purl.obolibrary.org/obo/RO_HOM0000010 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000010 + * http://purl.obolibrary.org/obo/RO_HOM0000011 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000011 + * http://purl.obolibrary.org/obo/RO_HOM0000012 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000012 + * http://purl.obolibrary.org/obo/RO_HOM0000013 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000013 + * http://purl.obolibrary.org/obo/RO_HOM0000014 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000014 + * http://purl.obolibrary.org/obo/RO_HOM0000015 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000015 + * http://purl.obolibrary.org/obo/RO_HOM0000016 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000016 + * http://purl.obolibrary.org/obo/RO_HOM0000017 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000017 + * http://purl.obolibrary.org/obo/RO_HOM0000018 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000018 + * http://purl.obolibrary.org/obo/RO_HOM0000019 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000019 + * http://purl.obolibrary.org/obo/RO_HOM0000020 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000020 + * http://purl.obolibrary.org/obo/RO_HOM0000022 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000022 + * http://purl.obolibrary.org/obo/RO_HOM0000023 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000023 + * http://purl.obolibrary.org/obo/RO_HOM0000024 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000024 + * http://purl.obolibrary.org/obo/RO_HOM0000025 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000025 + * http://purl.obolibrary.org/obo/RO_HOM0000026 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000026 + * http://purl.obolibrary.org/obo/RO_HOM0000027 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000027 + * http://purl.obolibrary.org/obo/RO_HOM0000028 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000028 + * http://purl.obolibrary.org/obo/RO_HOM0000029 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000029 + * http://purl.obolibrary.org/obo/RO_HOM0000030 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000030 + * http://purl.obolibrary.org/obo/RO_HOM0000031 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000031 + * http://purl.obolibrary.org/obo/RO_HOM0000032 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000032 + * http://purl.obolibrary.org/obo/RO_HOM0000033 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000033 + * http://purl.obolibrary.org/obo/RO_HOM0000034 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000034 + * http://purl.obolibrary.org/obo/RO_HOM0000036 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000036 + * http://purl.obolibrary.org/obo/RO_HOM0000037 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000037 + * http://purl.obolibrary.org/obo/RO_HOM0000042 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000042 + * http://purl.obolibrary.org/obo/RO_HOM0000043 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000043 + * http://purl.obolibrary.org/obo/RO_HOM0000044 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000044 + * http://purl.obolibrary.org/obo/RO_HOM0000045 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000045 + * http://purl.obolibrary.org/obo/RO_HOM0000046 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000046 + * http://purl.obolibrary.org/obo/RO_HOM0000047 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000047 + * http://purl.obolibrary.org/obo/RO_HOM0000048 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000048 + * http://purl.obolibrary.org/obo/RO_HOM0000049 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000049 + * http://purl.obolibrary.org/obo/RO_HOM0000050 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000050 + * http://purl.obolibrary.org/obo/RO_HOM0000051 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000051 + * http://purl.obolibrary.org/obo/RO_HOM0000052 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000052 + * http://purl.obolibrary.org/obo/RO_HOM0000053 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000053 + * http://purl.obolibrary.org/obo/RO_HOM0000054 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000054 + * http://purl.obolibrary.org/obo/RO_HOM0000055 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000055 + * http://purl.obolibrary.org/obo/RO_HOM0000057 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000057 + * http://purl.obolibrary.org/obo/RO_HOM0000058 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000058 + * http://purl.obolibrary.org/obo/RO_HOM0000060 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000060 + * http://purl.obolibrary.org/obo/RO_HOM0000061 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000061 + * http://purl.obolibrary.org/obo/RO_HOM0000062 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000062 + * http://purl.obolibrary.org/obo/RO_HOM0000063 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000063 + * http://purl.obolibrary.org/obo/RO_HOM0000065 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000065 + * http://purl.obolibrary.org/obo/RO_HOM0000066 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000066 + * http://purl.obolibrary.org/obo/RO_HOM0000068 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000068 + * http://purl.obolibrary.org/obo/RO_HOM0000069 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000069 + * http://purl.obolibrary.org/obo/RO_HOM0000071 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000071 + * http://purl.obolibrary.org/obo/RO_HOM0000072 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000072 + * http://purl.obolibrary.org/obo/RO_HOM0000073 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000073 + * http://purl.obolibrary.org/obo/RO_HOM0000074 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000074 + * http://purl.obolibrary.org/obo/RO_HOM0000075 [rdf-schema#seeAlso](../../so/rdf-schema#seeAlso.md) http://purl.obolibrary.org/obo/HOM_0000075 + +## External Comments + diff --git a/src/ontology/md/ss/oboInOwl#ObsoleteClass.md b/src/ontology/md/ss/oboInOwl#ObsoleteClass.md new file mode 100644 index 00000000..e53d97ae --- /dev/null +++ b/src/ontology/md/ss/oboInOwl#ObsoleteClass.md @@ -0,0 +1,35 @@ + +## Class : Obsolete Class + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#ObsoleteClass + * *Label* = Obsolete Class + +## Synonyms + + +## Cross-references + + +## Subsets + + +## Superclasses + + +## Equivalencies + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = Obsolete Class + +## Usage + + * - + * [obsolete dependent continuant](../../BFO/05/BFO_0000005.md) SubClassOf [Obsolete Class](../../ss/oboInOwl#ObsoleteClass.md) + +## External Comments + diff --git a/src/ontology/md/ty/citesAsAuthority.md b/src/ontology/md/ty/citesAsAuthority.md new file mode 100644 index 00000000..0c8fe20c --- /dev/null +++ b/src/ontology/md/ty/citesAsAuthority.md @@ -0,0 +1,72 @@ + +## Class : null + + * *IRI* = http://purl.org/spar/cito/citesAsAuthority + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0000300 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0000301 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0000302 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002003 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002005 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002101 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002102 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002103 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002105 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002106 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002108 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002109 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002110 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002112 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002113 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002114 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002115 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002120 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002121 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002130 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002132 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002134 [citesAsAuthority](../../ty/citesAsAuthority.md) http://www.ncbi.nlm.nih.gov/pubmed/22402613 + * http://purl.obolibrary.org/obo/RO_0002514 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002515 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002516 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002517 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002518 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002519 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002520 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002521 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002522 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002523 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002524 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002525 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002526 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002527 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002528 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002529 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002530 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + * http://purl.obolibrary.org/obo/RO_0002531 [citesAsAuthority](../../ty/citesAsAuthority.md) http://biorxiv.org/content/early/2014/06/27/006650.abstract + +## External Comments + diff --git a/src/ontology/md/ty/oboInOwl#SubsetProperty.md b/src/ontology/md/ty/oboInOwl#SubsetProperty.md new file mode 100644 index 00000000..fd23da42 --- /dev/null +++ b/src/ontology/md/ty/oboInOwl#SubsetProperty.md @@ -0,0 +1,36 @@ + +## Class : subset_property + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#SubsetProperty + * *Label* = subset_property + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + * [eco subset](../../co/subsets#ro-eco.md) + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = subset_property + +## Usage + + * - + * SubAnnotationPropertyOf( ) + +## External Comments + diff --git a/src/ontology/md/ty/owl#topObjectProperty.md b/src/ontology/md/ty/owl#topObjectProperty.md new file mode 100644 index 00000000..bb4c9be7 --- /dev/null +++ b/src/ontology/md/ty/owl#topObjectProperty.md @@ -0,0 +1,36 @@ + +## Class : null + + * *IRI* = http://www.w3.org/2002/07/owl#topObjectProperty + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + +## Usage + + * - + * [has phenotype](../../RO/00/RO_0002200.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + * [innervates](../../RO/34/RO_0002134.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + * [phenotype of](../../RO/01/RO_0002201.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + * [releases neurotransmitter](../../RO/11/RO_0002111.md) SubPropertyOf [owl#topObjectProperty](../../ty/owl#topObjectProperty.md) + +## External Comments + diff --git a/src/ontology/md/ym/oboInOwl#hasBroadSynonym.md b/src/ontology/md/ym/oboInOwl#hasBroadSynonym.md new file mode 100644 index 00000000..c17a7660 --- /dev/null +++ b/src/ontology/md/ym/oboInOwl#hasBroadSynonym.md @@ -0,0 +1,36 @@ + +## Class : has_broad_synonym + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym + * *Label* = has_broad_synonym + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has_broad_synonym + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_HOM0000007 [has_broad_synonym](../../ym/oboInOwl#hasBroadSynonym.md) homology + * http://purl.obolibrary.org/obo/RO_HOM0000016 [has_broad_synonym](../../ym/oboInOwl#hasBroadSynonym.md) pseudogene + +## External Comments + diff --git a/src/ontology/md/ym/oboInOwl#hasExactSynonym.md b/src/ontology/md/ym/oboInOwl#hasExactSynonym.md new file mode 100644 index 00000000..c53e083e --- /dev/null +++ b/src/ontology/md/ym/oboInOwl#hasExactSynonym.md @@ -0,0 +1,129 @@ + +## Class : has_exact_synonym + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#hasExactSynonym + * *Label* = has_exact_synonym + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has_exact_synonym + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002434 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) in pairwise interaction with + * http://purl.obolibrary.org/obo/RO_HOM0000000 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) sameness + * http://purl.obolibrary.org/obo/RO_HOM0000000 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) similar to + * http://purl.obolibrary.org/obo/RO_HOM0000001 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000002 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) homoplasous to + * http://purl.obolibrary.org/obo/RO_HOM0000003 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) homocracous to + * http://purl.obolibrary.org/obo/RO_HOM0000005 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) parallel evolution + * http://purl.obolibrary.org/obo/RO_HOM0000006 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) structural homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000007 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) cladistic homology + * http://purl.obolibrary.org/obo/RO_HOM0000007 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) historical homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000007 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) phylogenetic homology + * http://purl.obolibrary.org/obo/RO_HOM0000007 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) taxic homology + * http://purl.obolibrary.org/obo/RO_HOM0000008 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) biological homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000009 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) atavism + * http://purl.obolibrary.org/obo/RO_HOM0000009 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) rudiment + * http://purl.obolibrary.org/obo/RO_HOM0000010 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) syntenic homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000011 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) paralogous to + * http://purl.obolibrary.org/obo/RO_HOM0000012 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) syntenic paralogous to + * http://purl.obolibrary.org/obo/RO_HOM0000013 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) syntenic orthologous to + * http://purl.obolibrary.org/obo/RO_HOM0000014 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) fractional homology + * http://purl.obolibrary.org/obo/RO_HOM0000014 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) partial homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000014 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) segmental homology + * http://purl.obolibrary.org/obo/RO_HOM0000015 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) protein structural homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000016 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) non functional homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000017 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) orthologous to + * http://purl.obolibrary.org/obo/RO_HOM0000018 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) xenologous to + * http://purl.obolibrary.org/obo/RO_HOM0000019 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) 1 to 1 homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000019 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) 1:1 homology + * http://purl.obolibrary.org/obo/RO_HOM0000019 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) one-to-one homology + * http://purl.obolibrary.org/obo/RO_HOM0000020 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) 1 to 1 orthologous to + * http://purl.obolibrary.org/obo/RO_HOM0000020 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) 1:1 orthology + * http://purl.obolibrary.org/obo/RO_HOM0000020 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) one-to-one orthology + * http://purl.obolibrary.org/obo/RO_HOM0000022 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) ohnologous to + * http://purl.obolibrary.org/obo/RO_HOM0000023 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) in-paralogous to + * http://purl.obolibrary.org/obo/RO_HOM0000023 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) inparalogy + * http://purl.obolibrary.org/obo/RO_HOM0000023 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) symparalogy + * http://purl.obolibrary.org/obo/RO_HOM0000024 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) alloparalogy + * http://purl.obolibrary.org/obo/RO_HOM0000024 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) out-paralogous to + * http://purl.obolibrary.org/obo/RO_HOM0000024 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) outparalogy + * http://purl.obolibrary.org/obo/RO_HOM0000025 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) pro-orthologous to + * http://purl.obolibrary.org/obo/RO_HOM0000026 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) semi-orthologous to + * http://purl.obolibrary.org/obo/RO_HOM0000027 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) serial homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000028 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) heterochronous homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000028 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) heterochrony + * http://purl.obolibrary.org/obo/RO_HOM0000029 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) juvenification + * http://purl.obolibrary.org/obo/RO_HOM0000029 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) pedomorphosis + * http://purl.obolibrary.org/obo/RO_HOM0000032 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) juvenilization + * http://purl.obolibrary.org/obo/RO_HOM0000032 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) neotenous to + * http://purl.obolibrary.org/obo/RO_HOM0000033 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) mimicrous to + * http://purl.obolibrary.org/obo/RO_HOM0000034 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) 1 to many orthologous to + * http://purl.obolibrary.org/obo/RO_HOM0000034 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) 1:many orthology + * http://purl.obolibrary.org/obo/RO_HOM0000034 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) one-to-many orthology + * http://purl.obolibrary.org/obo/RO_HOM0000036 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) many to many homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000036 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) many-to-many homology + * http://purl.obolibrary.org/obo/RO_HOM0000036 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) many:many homology + * http://purl.obolibrary.org/obo/RO_HOM0000037 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) 1 to many homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000037 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) one-to-many homology + * http://purl.obolibrary.org/obo/RO_HOM0000042 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) apomorphous to + * http://purl.obolibrary.org/obo/RO_HOM0000043 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) plesiomorphous to + * http://purl.obolibrary.org/obo/RO_HOM0000044 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) deep genetic homology + * http://purl.obolibrary.org/obo/RO_HOM0000044 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) deep homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000045 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) hemiplasous to + * http://purl.obolibrary.org/obo/RO_HOM0000046 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) gametologous to + * http://purl.obolibrary.org/obo/RO_HOM0000047 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) chromosomal homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000048 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) many to many orthologous to + * http://purl.obolibrary.org/obo/RO_HOM0000048 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) many-to-many orthology + * http://purl.obolibrary.org/obo/RO_HOM0000048 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) many:many orthology + * http://purl.obolibrary.org/obo/RO_HOM0000048 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) trans-orthology + * http://purl.obolibrary.org/obo/RO_HOM0000049 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) within-species paralogous to + * http://purl.obolibrary.org/obo/RO_HOM0000050 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) between-species paralogous to + * http://purl.obolibrary.org/obo/RO_HOM0000051 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) post-displacement + * http://purl.obolibrary.org/obo/RO_HOM0000053 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) synologous to + * http://purl.obolibrary.org/obo/RO_HOM0000054 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) isoorthologous to + * http://purl.obolibrary.org/obo/RO_HOM0000055 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) tandem paralogous to + * http://purl.obolibrary.org/obo/RO_HOM0000057 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) apomorphic tendency + * http://purl.obolibrary.org/obo/RO_HOM0000057 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) cryptic homology + * http://purl.obolibrary.org/obo/RO_HOM0000057 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) latent homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000057 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) underlying synapomorphy + * http://purl.obolibrary.org/obo/RO_HOM0000058 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) generative homology + * http://purl.obolibrary.org/obo/RO_HOM0000058 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) syngenous to + * http://purl.obolibrary.org/obo/RO_HOM0000060 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) 1:1 paralogy + * http://purl.obolibrary.org/obo/RO_HOM0000060 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) apparent 1:1 orthology + * http://purl.obolibrary.org/obo/RO_HOM0000060 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) apparent orthologous to + * http://purl.obolibrary.org/obo/RO_HOM0000060 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) pseudoorthology + * http://purl.obolibrary.org/obo/RO_HOM0000061 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) pseudoparalogous to + * http://purl.obolibrary.org/obo/RO_HOM0000062 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) equivalogous to + * http://purl.obolibrary.org/obo/RO_HOM0000063 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) interologous to + * http://purl.obolibrary.org/obo/RO_HOM0000066 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) iterative homologous to + * http://purl.obolibrary.org/obo/RO_HOM0000068 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) duplicate xenology + * http://purl.obolibrary.org/obo/RO_HOM0000068 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) multiple xenology + * http://purl.obolibrary.org/obo/RO_HOM0000068 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) paraxenologous to + * http://purl.obolibrary.org/obo/RO_HOM0000069 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) plerologous to + * http://purl.obolibrary.org/obo/RO_HOM0000071 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) homotopous to + * http://purl.obolibrary.org/obo/RO_HOM0000073 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) homoeologous to + * http://purl.obolibrary.org/obo/RO_HOM0000075 [has_exact_synonym](../../ym/oboInOwl#hasExactSynonym.md) regulogous to + +## External Comments + diff --git a/src/ontology/md/ym/oboInOwl#hasRelatedSynonym.md b/src/ontology/md/ym/oboInOwl#hasRelatedSynonym.md new file mode 100644 index 00000000..73872734 --- /dev/null +++ b/src/ontology/md/ym/oboInOwl#hasRelatedSynonym.md @@ -0,0 +1,71 @@ + +## Class : has_related_synonym + + * *IRI* = http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym + * *Label* = has_related_synonym + +## Synonyms + + +## Cross-references + + +## Subsets + + +## SuperProperties + + +## SubProperties + + +## Other Logical Axioms + + +## Other Annotations + + * *[rdf-schema#label](../../el/rdf-schema#label.md)* = has_related_synonym + +## Usage + + * - + * http://purl.obolibrary.org/obo/RO_0002446 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) semibiotically interacts with + * http://purl.obolibrary.org/obo/RO_0002553 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) hyperparasitoid of + * http://purl.obolibrary.org/obo/RO_0002554 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) hyperparasitoidized by + * http://purl.obolibrary.org/obo/RO_HOM0000000 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) correspondence + * http://purl.obolibrary.org/obo/RO_HOM0000000 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) resemblance + * http://purl.obolibrary.org/obo/RO_HOM0000002 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) analogy + * http://purl.obolibrary.org/obo/RO_HOM0000004 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) analogy + * http://purl.obolibrary.org/obo/RO_HOM0000006 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) idealistic homology + * http://purl.obolibrary.org/obo/RO_HOM0000007 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) true homology + * http://purl.obolibrary.org/obo/RO_HOM0000008 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) transformational homology + * http://purl.obolibrary.org/obo/RO_HOM0000009 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) reversion + * http://purl.obolibrary.org/obo/RO_HOM0000010 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) synteny + * http://purl.obolibrary.org/obo/RO_HOM0000012 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) duplicon + * http://purl.obolibrary.org/obo/RO_HOM0000012 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) paralogon + * http://purl.obolibrary.org/obo/RO_HOM0000014 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) mixed homology + * http://purl.obolibrary.org/obo/RO_HOM0000014 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) modular homology + * http://purl.obolibrary.org/obo/RO_HOM0000014 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) partial correspondence + * http://purl.obolibrary.org/obo/RO_HOM0000014 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) percent homology + * http://purl.obolibrary.org/obo/RO_HOM0000022 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) homoeology + * http://purl.obolibrary.org/obo/RO_HOM0000027 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) homonomy + * http://purl.obolibrary.org/obo/RO_HOM0000034 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) co-orthology + * http://purl.obolibrary.org/obo/RO_HOM0000034 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) many to 1 orthology + * http://purl.obolibrary.org/obo/RO_HOM0000037 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) 1:many homology + * http://purl.obolibrary.org/obo/RO_HOM0000042 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) synapomorphy + * http://purl.obolibrary.org/obo/RO_HOM0000043 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) symplesiomorphy + * http://purl.obolibrary.org/obo/RO_HOM0000044 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) generative homology + * http://purl.obolibrary.org/obo/RO_HOM0000044 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) homoiology + * http://purl.obolibrary.org/obo/RO_HOM0000048 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) co-orthology + * http://purl.obolibrary.org/obo/RO_HOM0000048 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) trans-homology + * http://purl.obolibrary.org/obo/RO_HOM0000055 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) iterative paralogy + * http://purl.obolibrary.org/obo/RO_HOM0000055 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) serial paralogy + * http://purl.obolibrary.org/obo/RO_HOM0000057 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) homoiology + * http://purl.obolibrary.org/obo/RO_HOM0000057 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) homoplastic tendency + * http://purl.obolibrary.org/obo/RO_HOM0000057 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) re-awakening + * http://purl.obolibrary.org/obo/RO_HOM0000065 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) functional similarity + * http://purl.obolibrary.org/obo/RO_HOM0000072 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) heterotopy + * http://purl.obolibrary.org/obo/RO_HOM0000074 [has_related_synonym](../../ym/oboInOwl#hasRelatedSynonym.md) axis paramorphism + +## External Comments + diff --git a/src/ontology/ro.owl b/src/ontology/ro.owl index 91e97be3..cd311b2f 100644 --- a/src/ontology/ro.owl +++ b/src/ontology/ro.owl @@ -24,7 +24,7 @@ - + @@ -2462,7 +2462,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has input - p has input c if either: p has direct input c or p has indirect input c. See subrelations for definitions. + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes Chris Mungall @@ -2481,8 +2481,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has output Chris Mungall + p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. produces - p has direct input c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of c. @@ -4988,7 +4988,7 @@ the a supports either the existence of b, or the truth value of b. - + @@ -4999,12 +4999,12 @@ the a supports either the existence of b, or the truth value of b. - + - + @@ -6092,6 +6092,18 @@ the a supports either the existence of b, or the truth value of b. + + + is model of + Matthew Brush + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. + To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? + + + + @@ -6637,8 +6649,8 @@ the a supports either the existence of b, or the truth value of b.is defined by - is defined by This is an experimental annotation + is defined by