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zHHwH76U125#>M63mhF#1aU;;cL1m@KZB}AcnkshrWyxe8aY({KL#w}E+@M=~_&E%< zd4B{AQsgLr+S}TmS4B`rtOAHYD6qPVZHlIE_l0?zah6@!+3!~p$|k~jmY@UfD+`N@ z2`5kDtsaev+RNp+2S7&!9E?OFK^k)92FqQReVSrxp#}eIKwgdrLw;Dua49^{y>d+! z<>4-8RK%w%J z{O8g@sm0&1_;D>T(T3l(;4g9I^KJ9m`!GNWC*a%PG%2&bb$@fPyQygq0{?&k2-&y| ziya-BJ=Uf)+)3Dl2tm<%co+dVy)WKAd6Bdt#c3yK z2s8Ex2uQ$`1Q_zPG?mKv&=Uatmkj*0P>X15uiPDyZC2wSh)*{&llSsIEyL|=E-z?x zt_KBHsP8^tx5;dS@XZ7PM`lsO224kwbB|E)pgn}PtXiFrkYI6H<1SU7cA7r%y#D_H z77#1*_Y6UKf%A?oOM1E*Q$vZk%rv0_M;jX!O*2>Fn=E&_iZZ?qouWd?pAZk)zUeM2 Utlga5g`Wu5uRWZuIj~Ou34#umSpWb4 literal 0 HcmV?d00001 diff --git a/_sources/datamodels/association/aggregator_knowledge_source.md.txt b/_sources/datamodels/association/aggregator_knowledge_source.md.txt index fc2d72514..ee7548ad9 100644 --- a/_sources/datamodels/association/aggregator_knowledge_source.md.txt +++ b/_sources/datamodels/association/aggregator_knowledge_source.md.txt @@ -21,10 +21,10 @@ URI: [biolink:aggregator_knowledge_source](https://w3id.org/biolink/vocab/aggreg | Name | Description | Modifies Slot | | --- | --- | --- | -| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | -| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no | +| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | +| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no | diff --git a/_sources/datamodels/association/comments.md.txt b/_sources/datamodels/association/comments.md.txt index 103a87bfb..a8fcd9f0b 100644 --- a/_sources/datamodels/association/comments.md.txt +++ b/_sources/datamodels/association/comments.md.txt @@ -21,9 +21,9 @@ URI: [rdfs:comment](rdfs:comment) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/evidence_type.md.txt b/_sources/datamodels/association/evidence_type.md.txt index 5d95cf196..0108a34a3 100644 --- a/_sources/datamodels/association/evidence_type.md.txt +++ b/_sources/datamodels/association/evidence_type.md.txt @@ -21,9 +21,9 @@ URI: [ontoassoc:evidence_type](https://w3id.org/oak/association/evidence_type) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/negated.md.txt b/_sources/datamodels/association/negated.md.txt index 95b321a31..ecb1441a7 100644 --- a/_sources/datamodels/association/negated.md.txt +++ b/_sources/datamodels/association/negated.md.txt @@ -21,9 +21,9 @@ URI: [ontoassoc:negated](https://w3id.org/oak/association/negated) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | yes | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | yes | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/object.md.txt b/_sources/datamodels/association/object.md.txt index 37c7c8527..c09803c27 100644 --- a/_sources/datamodels/association/object.md.txt +++ b/_sources/datamodels/association/object.md.txt @@ -29,10 +29,10 @@ URI: [rdf:object](rdf:object) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | -| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | +| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/object_closure.md.txt b/_sources/datamodels/association/object_closure.md.txt index fe593fb9e..a1da50b6c 100644 --- a/_sources/datamodels/association/object_closure.md.txt +++ b/_sources/datamodels/association/object_closure.md.txt @@ -21,9 +21,9 @@ URI: [ontoassoc:object_closure](https://w3id.org/oak/association/object_closure) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/object_closure_label.md.txt b/_sources/datamodels/association/object_closure_label.md.txt index d50d866bf..952bd1d84 100644 --- a/_sources/datamodels/association/object_closure_label.md.txt +++ b/_sources/datamodels/association/object_closure_label.md.txt @@ -21,9 +21,9 @@ URI: [ontoassoc:object_closure_label](https://w3id.org/oak/association/object_cl | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/object_label.md.txt b/_sources/datamodels/association/object_label.md.txt index 28a986125..f8edea4b6 100644 --- a/_sources/datamodels/association/object_label.md.txt +++ b/_sources/datamodels/association/object_label.md.txt @@ -25,9 +25,9 @@ URI: [sssom:object_label](https://w3id.org/sssom/object_label) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/predicate.md.txt b/_sources/datamodels/association/predicate.md.txt index 8ca10884f..6b23fd9c1 100644 --- a/_sources/datamodels/association/predicate.md.txt +++ b/_sources/datamodels/association/predicate.md.txt @@ -27,10 +27,10 @@ URI: [rdf:predicate](rdf:predicate) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | -| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | +| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/predicate_label.md.txt b/_sources/datamodels/association/predicate_label.md.txt index 2947fd9d5..0b96eb81f 100644 --- a/_sources/datamodels/association/predicate_label.md.txt +++ b/_sources/datamodels/association/predicate_label.md.txt @@ -25,9 +25,9 @@ URI: [sssom:predicate_label](https://w3id.org/sssom/predicate_label) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/primary_knowledge_source.md.txt b/_sources/datamodels/association/primary_knowledge_source.md.txt index 44cf0b581..4334eaf99 100644 --- a/_sources/datamodels/association/primary_knowledge_source.md.txt +++ b/_sources/datamodels/association/primary_knowledge_source.md.txt @@ -21,10 +21,10 @@ URI: [biolink:primary_knowledge_source](https://w3id.org/biolink/vocab/primary_k | Name | Description | Modifies Slot | | --- | --- | --- | -| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | -| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no | +| [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | +| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no | diff --git a/_sources/datamodels/association/property_values.md.txt b/_sources/datamodels/association/property_values.md.txt index ebcbc9b83..ffb6fe918 100644 --- a/_sources/datamodels/association/property_values.md.txt +++ b/_sources/datamodels/association/property_values.md.txt @@ -21,9 +21,9 @@ URI: [ontoassoc:property_values](https://w3id.org/oak/association/property_value | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/publications.md.txt b/_sources/datamodels/association/publications.md.txt index 42f7b67fe..d6ea8f888 100644 --- a/_sources/datamodels/association/publications.md.txt +++ b/_sources/datamodels/association/publications.md.txt @@ -21,10 +21,10 @@ URI: [biolink:publications](https://w3id.org/biolink/vocab/publications) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | -| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no | +| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/subject.md.txt b/_sources/datamodels/association/subject.md.txt index 09411481c..9cc23e852 100644 --- a/_sources/datamodels/association/subject.md.txt +++ b/_sources/datamodels/association/subject.md.txt @@ -21,10 +21,10 @@ URI: [rdf:subject](rdf:subject) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | -| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no | +| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/subject_closure.md.txt b/_sources/datamodels/association/subject_closure.md.txt index f37f9077a..59c9ee0b6 100644 --- a/_sources/datamodels/association/subject_closure.md.txt +++ b/_sources/datamodels/association/subject_closure.md.txt @@ -21,9 +21,9 @@ URI: [ontoassoc:subject_closure](https://w3id.org/oak/association/subject_closur | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/subject_closure_label.md.txt b/_sources/datamodels/association/subject_closure_label.md.txt index ffaadccd4..9fa9e1c1e 100644 --- a/_sources/datamodels/association/subject_closure_label.md.txt +++ b/_sources/datamodels/association/subject_closure_label.md.txt @@ -21,9 +21,9 @@ URI: [ontoassoc:subject_closure_label](https://w3id.org/oak/association/subject_ | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/subject_label.md.txt b/_sources/datamodels/association/subject_label.md.txt index ec40dd98a..baa96ab5e 100644 --- a/_sources/datamodels/association/subject_label.md.txt +++ b/_sources/datamodels/association/subject_label.md.txt @@ -25,9 +25,9 @@ URI: [sssom:subject_label](https://w3id.org/sssom/subject_label) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/association/supporting_objects.md.txt b/_sources/datamodels/association/supporting_objects.md.txt index 67ca9cb9d..580b3577f 100644 --- a/_sources/datamodels/association/supporting_objects.md.txt +++ b/_sources/datamodels/association/supporting_objects.md.txt @@ -21,9 +21,9 @@ URI: [ontoassoc:supporting_objects](https://w3id.org/oak/association/supporting_ | Name | Description | Modifies Slot | | --- | --- | --- | -| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | | [NegatedAssociation](NegatedAssociation.md) | A negated association between a thing (subject) and another thing (object) | no | | [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no | +| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no | diff --git a/_sources/datamodels/item-list/description.md.txt b/_sources/datamodels/item-list/description.md.txt index 58958d683..c02518245 100644 --- a/_sources/datamodels/item-list/description.md.txt +++ b/_sources/datamodels/item-list/description.md.txt @@ -16,8 +16,8 @@ URI: [itemList:description](https://w3id.org/linkml/item-list/description) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ItemList](ItemList.md) | a list of entities plus metadata | no | | [Thing](Thing.md) | | no | +| [ItemList](ItemList.md) | a list of entities plus metadata | no | diff --git a/_sources/datamodels/item-list/id.md.txt b/_sources/datamodels/item-list/id.md.txt index 3a370cc41..5d63d422f 100644 --- a/_sources/datamodels/item-list/id.md.txt +++ b/_sources/datamodels/item-list/id.md.txt @@ -16,8 +16,8 @@ URI: [itemList:id](https://w3id.org/linkml/item-list/id) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ItemList](ItemList.md) | a list of entities plus metadata | no | | [Thing](Thing.md) | | no | +| [ItemList](ItemList.md) | a list of entities plus metadata | no | diff --git a/_sources/datamodels/item-list/name.md.txt b/_sources/datamodels/item-list/name.md.txt index ce080a242..ac4ddc6e6 100644 --- a/_sources/datamodels/item-list/name.md.txt +++ b/_sources/datamodels/item-list/name.md.txt @@ -16,8 +16,8 @@ URI: [itemList:name](https://w3id.org/linkml/item-list/name) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ItemList](ItemList.md) | a list of entities plus metadata | no | | [Thing](Thing.md) | | no | +| [ItemList](ItemList.md) | a list of entities plus metadata | no | diff --git a/_sources/datamodels/mapping-rules/description.md.txt b/_sources/datamodels/mapping-rules/description.md.txt index fae46f765..2870f8a2f 100644 --- a/_sources/datamodels/mapping-rules/description.md.txt +++ b/_sources/datamodels/mapping-rules/description.md.txt @@ -16,8 +16,8 @@ URI: [mappingrules:description](https://w3id.org/oak/mapping-rules-datamodel/des | Name | Description | Modifies Slot | | --- | --- | --- | -| [Synonymizer](Synonymizer.md) | Specification of a rule for generating a synonym or alternate lexical element | no | | [MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no | +| [Synonymizer](Synonymizer.md) | Specification of a rule for generating a synonym or alternate lexical element | no | diff --git a/_sources/datamodels/mapping-rules/prefix.md.txt b/_sources/datamodels/mapping-rules/prefix.md.txt index 5be51fbc0..cf5dc00cd 100644 --- a/_sources/datamodels/mapping-rules/prefix.md.txt +++ b/_sources/datamodels/mapping-rules/prefix.md.txt @@ -17,8 +17,8 @@ URI: [mappingrules:prefix](https://w3id.org/oak/mapping-rules-datamodel/prefix) | Name | Description | Modifies Slot | | --- | --- | --- | | [Test](Test.md) | A unit test for a rule, specifies an intended output for an input | no | -| [Synonymizer](Synonymizer.md) | Specification of a rule for generating a synonym or alternate lexical element | no | | [RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no | +| [Synonymizer](Synonymizer.md) | Specification of a rule for generating a synonym or alternate lexical element | no | diff --git a/_sources/datamodels/mapping-rules/rules.md.txt b/_sources/datamodels/mapping-rules/rules.md.txt index 1b068045d..dc695747f 100644 --- a/_sources/datamodels/mapping-rules/rules.md.txt +++ b/_sources/datamodels/mapping-rules/rules.md.txt @@ -16,8 +16,8 @@ URI: [mappingrules:rules](https://w3id.org/oak/mapping-rules-datamodel/rules) | Name | Description | Modifies Slot | | --- | --- | --- | -| [MappingRuleCollection](MappingRuleCollection.md) | A collection of mapping rules | no | | [RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no | +| [MappingRuleCollection](MappingRuleCollection.md) | A collection of mapping rules | no | diff --git a/_sources/datamodels/obograph/id.md.txt b/_sources/datamodels/obograph/id.md.txt index 7b3834f53..76ef7e43c 100644 --- a/_sources/datamodels/obograph/id.md.txt +++ b/_sources/datamodels/obograph/id.md.txt @@ -21,9 +21,9 @@ URI: [obographs:id](https://github.com/geneontology/obographs/id) | Name | Description | Modifies Slot | | --- | --- | --- | +| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | | [Node](Node.md) | A node is a class, property, or other entity in an ontology | no | | [SubsetDefinition](SubsetDefinition.md) | | no | -| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | | [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no | diff --git a/_sources/datamodels/obograph/lang.md.txt b/_sources/datamodels/obograph/lang.md.txt index 318dac109..134e96d99 100644 --- a/_sources/datamodels/obograph/lang.md.txt +++ b/_sources/datamodels/obograph/lang.md.txt @@ -21,11 +21,11 @@ URI: [obographs:lang](https://github.com/geneontology/obographs/lang) | Name | Description | Modifies Slot | | --- | --- | --- | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | -| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | | [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | | [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | diff --git a/_sources/datamodels/obograph/lbl.md.txt b/_sources/datamodels/obograph/lbl.md.txt index 065f83a47..b6c6d5c1a 100644 --- a/_sources/datamodels/obograph/lbl.md.txt +++ b/_sources/datamodels/obograph/lbl.md.txt @@ -21,9 +21,9 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label) | Name | Description | Modifies Slot | | --- | --- | --- | +| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | | [Node](Node.md) | A node is a class, property, or other entity in an ontology | no | | [SubsetDefinition](SubsetDefinition.md) | | no | -| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | | [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no | diff --git a/_sources/datamodels/obograph/meta.md.txt b/_sources/datamodels/obograph/meta.md.txt index b73cbb638..dd5dd6342 100644 --- a/_sources/datamodels/obograph/meta.md.txt +++ b/_sources/datamodels/obograph/meta.md.txt @@ -21,21 +21,21 @@ URI: [obographs:meta](https://github.com/geneontology/obographs/meta) | Name | Description | Modifies Slot | | --- | --- | --- | +| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no | +| [PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no | +| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no | +| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | +| [EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no | | [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | | [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | -| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no | -| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | +| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | | [Node](Node.md) | A node is a class, property, or other entity in an ontology | no | -| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | -| [LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no | | [Axiom](Axiom.md) | A generic grouping for any OWL axiom or group of axioms that is not captured ... | no | -| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no | | [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no | -| [EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no | -| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no | -| [PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no | -| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | +| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no | diff --git a/_sources/datamodels/obograph/pred.md.txt b/_sources/datamodels/obograph/pred.md.txt index 1b6f63d91..808182811 100644 --- a/_sources/datamodels/obograph/pred.md.txt +++ b/_sources/datamodels/obograph/pred.md.txt @@ -21,13 +21,13 @@ URI: [rdf:predicate](http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate) | Name | Description | Modifies Slot | | --- | --- | --- | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | -| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no | +| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | | [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes | +| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | +| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | | [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no | | [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | -| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | -| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | diff --git a/_sources/datamodels/obograph/prefixes.md.txt b/_sources/datamodels/obograph/prefixes.md.txt index 53707aed8..09d8fdf1d 100644 --- a/_sources/datamodels/obograph/prefixes.md.txt +++ b/_sources/datamodels/obograph/prefixes.md.txt @@ -21,8 +21,8 @@ URI: [sh:declare](https://w3id.org/shacl/declare) | Name | Description | Modifies Slot | | --- | --- | --- | -| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no | | [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | +| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no | diff --git a/_sources/datamodels/obograph/val.md.txt b/_sources/datamodels/obograph/val.md.txt index e810c9eea..abbd8de5f 100644 --- a/_sources/datamodels/obograph/val.md.txt +++ b/_sources/datamodels/obograph/val.md.txt @@ -21,11 +21,11 @@ URI: [rdf:object](http://www.w3.org/1999/02/22-rdf-syntax-ns#object) | Name | Description | Modifies Slot | | --- | --- | --- | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes | -| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | yes | | [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes | | [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | yes | diff --git a/_sources/datamodels/obograph/valType.md.txt b/_sources/datamodels/obograph/valType.md.txt index 00394089a..4462f2186 100644 --- a/_sources/datamodels/obograph/valType.md.txt +++ b/_sources/datamodels/obograph/valType.md.txt @@ -21,11 +21,11 @@ URI: [obographs:valType](https://github.com/geneontology/obographs/valType) | Name | Description | Modifies Slot | | --- | --- | --- | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | -| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | | [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | | [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | diff --git a/_sources/datamodels/obograph/xrefs.md.txt b/_sources/datamodels/obograph/xrefs.md.txt index b2a52e736..8e7772ef3 100644 --- a/_sources/datamodels/obograph/xrefs.md.txt +++ b/_sources/datamodels/obograph/xrefs.md.txt @@ -21,12 +21,12 @@ URI: [obographs:xrefs](https://github.com/geneontology/obographs/xrefs) | Name | Description | Modifies Slot | | --- | --- | --- | +| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | | [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | yes | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes | | [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | -| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes | | [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | diff --git a/_sources/datamodels/ontology-metadata/IEDB_alternative_term.md.txt b/_sources/datamodels/ontology-metadata/IEDB_alternative_term.md.txt index 99ff9c487..7e3da62d1 100644 --- a/_sources/datamodels/ontology-metadata/IEDB_alternative_term.md.txt +++ b/_sources/datamodels/ontology-metadata/IEDB_alternative_term.md.txt @@ -21,18 +21,18 @@ URI: [OBI:9991118](http://purl.obolibrary.org/obo/OBI_9991118) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/ISA_alternative_term.md.txt b/_sources/datamodels/ontology-metadata/ISA_alternative_term.md.txt index cd84f260e..9d6742db1 100644 --- a/_sources/datamodels/ontology-metadata/ISA_alternative_term.md.txt +++ b/_sources/datamodels/ontology-metadata/ISA_alternative_term.md.txt @@ -21,18 +21,18 @@ URI: [OBI:0001847](http://purl.obolibrary.org/obo/OBI_0001847) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/OBO_foundry_unique_label.md.txt b/_sources/datamodels/ontology-metadata/OBO_foundry_unique_label.md.txt index 643f920a4..6ca150297 100644 --- a/_sources/datamodels/ontology-metadata/OBO_foundry_unique_label.md.txt +++ b/_sources/datamodels/ontology-metadata/OBO_foundry_unique_label.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000589](http://purl.obolibrary.org/obo/IAO_0000589) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/alternative_term.md.txt b/_sources/datamodels/ontology-metadata/alternative_term.md.txt index 9c78cbc28..5ab7cabda 100644 --- a/_sources/datamodels/ontology-metadata/alternative_term.md.txt +++ b/_sources/datamodels/ontology-metadata/alternative_term.md.txt @@ -25,18 +25,18 @@ URI: [IAO:0000118](http://purl.obolibrary.org/obo/IAO_0000118) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/broadMatch.md.txt b/_sources/datamodels/ontology-metadata/broadMatch.md.txt index 8279ba175..ef8aa0759 100644 --- a/_sources/datamodels/ontology-metadata/broadMatch.md.txt +++ b/_sources/datamodels/ontology-metadata/broadMatch.md.txt @@ -21,18 +21,18 @@ URI: [skos:broadMatch](http://www.w3.org/2004/02/skos/core#broadMatch) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | yes | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | yes | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | yes | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/category.md.txt b/_sources/datamodels/ontology-metadata/category.md.txt index d53a1579b..1ac32c2c5 100644 --- a/_sources/datamodels/ontology-metadata/category.md.txt +++ b/_sources/datamodels/ontology-metadata/category.md.txt @@ -21,18 +21,18 @@ URI: [biolink:category](https://w3id.org/biolink/vocab/category) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [HasCategory](HasCategory.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/closeMatch.md.txt b/_sources/datamodels/ontology-metadata/closeMatch.md.txt index 21a6e3ad9..0c42d6ab3 100644 --- a/_sources/datamodels/ontology-metadata/closeMatch.md.txt +++ b/_sources/datamodels/ontology-metadata/closeMatch.md.txt @@ -21,18 +21,18 @@ URI: [skos:closeMatch](http://www.w3.org/2004/02/skos/core#closeMatch) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | yes | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | yes | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | yes | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/comment.md.txt b/_sources/datamodels/ontology-metadata/comment.md.txt index 942f759df..9c04ba804 100644 --- a/_sources/datamodels/ontology-metadata/comment.md.txt +++ b/_sources/datamodels/ontology-metadata/comment.md.txt @@ -21,20 +21,20 @@ URI: [rdfs:comment](http://www.w3.org/2000/01/rdf-schema#comment) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | -| [Property](Property.md) | | no | -| [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HasUserInformation](HasUserInformation.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/conformsTo.md.txt b/_sources/datamodels/ontology-metadata/conformsTo.md.txt index bb7b430c7..03c858cd2 100644 --- a/_sources/datamodels/ontology-metadata/conformsTo.md.txt +++ b/_sources/datamodels/ontology-metadata/conformsTo.md.txt @@ -21,18 +21,18 @@ URI: [dcterms:conformsTo](http://purl.org/dc/terms/conformsTo) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [HasCategory](HasCategory.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/consider.md.txt b/_sources/datamodels/ontology-metadata/consider.md.txt index 2c4977080..0f9ccab7e 100644 --- a/_sources/datamodels/ontology-metadata/consider.md.txt +++ b/_sources/datamodels/ontology-metadata/consider.md.txt @@ -21,18 +21,18 @@ URI: [oio:consider](http://www.geneontology.org/formats/oboInOwl#consider) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/contributor.md.txt b/_sources/datamodels/ontology-metadata/contributor.md.txt index 7b24a55e0..16abfae49 100644 --- a/_sources/datamodels/ontology-metadata/contributor.md.txt +++ b/_sources/datamodels/ontology-metadata/contributor.md.txt @@ -21,18 +21,18 @@ URI: [dcterms:contributor](http://purl.org/dc/terms/contributor) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/created.md.txt b/_sources/datamodels/ontology-metadata/created.md.txt index d04bf6fed..ece805c44 100644 --- a/_sources/datamodels/ontology-metadata/created.md.txt +++ b/_sources/datamodels/ontology-metadata/created.md.txt @@ -26,19 +26,19 @@ URI: [dcterms:created](http://purl.org/dc/terms/created) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/created_by.md.txt b/_sources/datamodels/ontology-metadata/created_by.md.txt index e745d9ab3..5e9010dbd 100644 --- a/_sources/datamodels/ontology-metadata/created_by.md.txt +++ b/_sources/datamodels/ontology-metadata/created_by.md.txt @@ -21,19 +21,19 @@ URI: [oio:created_by](http://www.geneontology.org/formats/oboInOwl#created_by) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/creation_date.md.txt b/_sources/datamodels/ontology-metadata/creation_date.md.txt index 306768094..29c7b50fc 100644 --- a/_sources/datamodels/ontology-metadata/creation_date.md.txt +++ b/_sources/datamodels/ontology-metadata/creation_date.md.txt @@ -21,18 +21,18 @@ URI: [oio:creation_date](http://www.geneontology.org/formats/oboInOwl#creation_d | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/creator.md.txt b/_sources/datamodels/ontology-metadata/creator.md.txt index 6cbde240c..9f921cb1a 100644 --- a/_sources/datamodels/ontology-metadata/creator.md.txt +++ b/_sources/datamodels/ontology-metadata/creator.md.txt @@ -21,19 +21,19 @@ URI: [dcterms:creator](http://purl.org/dc/terms/creator) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/curator_note.md.txt b/_sources/datamodels/ontology-metadata/curator_note.md.txt index 02e9a7d0c..339e6ea56 100644 --- a/_sources/datamodels/ontology-metadata/curator_note.md.txt +++ b/_sources/datamodels/ontology-metadata/curator_note.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000232](http://purl.obolibrary.org/obo/IAO_0000232) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/database_cross_reference.md.txt b/_sources/datamodels/ontology-metadata/database_cross_reference.md.txt index 6310ca3d7..e033aa969 100644 --- a/_sources/datamodels/ontology-metadata/database_cross_reference.md.txt +++ b/_sources/datamodels/ontology-metadata/database_cross_reference.md.txt @@ -21,19 +21,19 @@ URI: [oio:hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | yes | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | yes | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/date.md.txt b/_sources/datamodels/ontology-metadata/date.md.txt index ffe404f92..d62a008ee 100644 --- a/_sources/datamodels/ontology-metadata/date.md.txt +++ b/_sources/datamodels/ontology-metadata/date.md.txt @@ -26,18 +26,18 @@ URI: [dcterms:date](http://purl.org/dc/terms/date) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/definition.md.txt b/_sources/datamodels/ontology-metadata/definition.md.txt index d96988b8a..cda00c955 100644 --- a/_sources/datamodels/ontology-metadata/definition.md.txt +++ b/_sources/datamodels/ontology-metadata/definition.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000115](http://purl.obolibrary.org/obo/IAO_0000115) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | yes | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | yes | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [HasMinimalMetadata](HasMinimalMetadata.md) | Absolute minimum metadata model | no | -| [Property](Property.md) | | yes | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/definition_source.md.txt b/_sources/datamodels/ontology-metadata/definition_source.md.txt index deca2b6fa..55d8258d7 100644 --- a/_sources/datamodels/ontology-metadata/definition_source.md.txt +++ b/_sources/datamodels/ontology-metadata/definition_source.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000119](http://purl.obolibrary.org/obo/IAO_0000119) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/depicted_by.md.txt b/_sources/datamodels/ontology-metadata/depicted_by.md.txt index 7394ba03f..004cfec45 100644 --- a/_sources/datamodels/ontology-metadata/depicted_by.md.txt +++ b/_sources/datamodels/ontology-metadata/depicted_by.md.txt @@ -21,18 +21,18 @@ URI: [foaf:depicted_by](http://xmlns.com/foaf/0.1/depicted_by) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/deprecated.md.txt b/_sources/datamodels/ontology-metadata/deprecated.md.txt index e9c411cf1..663eebdff 100644 --- a/_sources/datamodels/ontology-metadata/deprecated.md.txt +++ b/_sources/datamodels/ontology-metadata/deprecated.md.txt @@ -21,18 +21,18 @@ URI: [owl:deprecated](http://www.w3.org/2002/07/owl#deprecated) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/disjointWith.md.txt b/_sources/datamodels/ontology-metadata/disjointWith.md.txt index 01ff46175..c9ea1aee2 100644 --- a/_sources/datamodels/ontology-metadata/disjointWith.md.txt +++ b/_sources/datamodels/ontology-metadata/disjointWith.md.txt @@ -21,12 +21,12 @@ URI: [owl:disjointWith](http://www.w3.org/2002/07/owl#disjointWith) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Class](Class.md) | | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [ClassExpression](ClassExpression.md) | | no | | [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Restriction](Restriction.md) | | no | | [PropertyExpression](PropertyExpression.md) | | no | +| [ClassExpression](ClassExpression.md) | | no | +| [Restriction](Restriction.md) | | no | +| [Class](Class.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/_sources/datamodels/ontology-metadata/domain.md.txt b/_sources/datamodels/ontology-metadata/domain.md.txt index b573af9bb..a937e2a5f 100644 --- a/_sources/datamodels/ontology-metadata/domain.md.txt +++ b/_sources/datamodels/ontology-metadata/domain.md.txt @@ -21,11 +21,11 @@ URI: [rdfs:domain](http://www.w3.org/2000/01/rdf-schema#domain) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/_sources/datamodels/ontology-metadata/editor_note.md.txt b/_sources/datamodels/ontology-metadata/editor_note.md.txt index 2fdd161b3..2f3a7f0d6 100644 --- a/_sources/datamodels/ontology-metadata/editor_note.md.txt +++ b/_sources/datamodels/ontology-metadata/editor_note.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000116](http://purl.obolibrary.org/obo/IAO_0000116) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/editor_preferred_term.md.txt b/_sources/datamodels/ontology-metadata/editor_preferred_term.md.txt index 8b02292d8..2820a3dd4 100644 --- a/_sources/datamodels/ontology-metadata/editor_preferred_term.md.txt +++ b/_sources/datamodels/ontology-metadata/editor_preferred_term.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000111](http://purl.obolibrary.org/obo/IAO_0000111) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/exactMatch.md.txt b/_sources/datamodels/ontology-metadata/exactMatch.md.txt index b643993ab..75429d24c 100644 --- a/_sources/datamodels/ontology-metadata/exactMatch.md.txt +++ b/_sources/datamodels/ontology-metadata/exactMatch.md.txt @@ -21,18 +21,18 @@ URI: [skos:exactMatch](http://www.w3.org/2004/02/skos/core#exactMatch) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | yes | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | yes | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | yes | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/example_of_usage.md.txt b/_sources/datamodels/ontology-metadata/example_of_usage.md.txt index 3f0f79f01..5ca0003eb 100644 --- a/_sources/datamodels/ontology-metadata/example_of_usage.md.txt +++ b/_sources/datamodels/ontology-metadata/example_of_usage.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000112](http://purl.obolibrary.org/obo/IAO_0000112) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/excluded_from_QC_check.md.txt b/_sources/datamodels/ontology-metadata/excluded_from_QC_check.md.txt index ef71d3667..ea65adff8 100644 --- a/_sources/datamodels/ontology-metadata/excluded_from_QC_check.md.txt +++ b/_sources/datamodels/ontology-metadata/excluded_from_QC_check.md.txt @@ -21,18 +21,18 @@ URI: [omoschema:excluded_from_QC_check](https://w3id.org/oak/ontology-metadata/e | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/excluded_subClassOf.md.txt b/_sources/datamodels/ontology-metadata/excluded_subClassOf.md.txt index bebe788e8..883b6604b 100644 --- a/_sources/datamodels/ontology-metadata/excluded_subClassOf.md.txt +++ b/_sources/datamodels/ontology-metadata/excluded_subClassOf.md.txt @@ -21,18 +21,18 @@ URI: [omoschema:excluded_subClassOf](https://w3id.org/oak/ontology-metadata/excl | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/excluded_synonym.md.txt b/_sources/datamodels/ontology-metadata/excluded_synonym.md.txt index 499fbdccc..e64e5cbcc 100644 --- a/_sources/datamodels/ontology-metadata/excluded_synonym.md.txt +++ b/_sources/datamodels/ontology-metadata/excluded_synonym.md.txt @@ -21,18 +21,18 @@ URI: [omoschema:excluded_synonym](https://w3id.org/oak/ontology-metadata/exclude | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/has_alternative_id.md.txt b/_sources/datamodels/ontology-metadata/has_alternative_id.md.txt index f67f9ac0f..a1d3cbad8 100644 --- a/_sources/datamodels/ontology-metadata/has_alternative_id.md.txt +++ b/_sources/datamodels/ontology-metadata/has_alternative_id.md.txt @@ -26,18 +26,18 @@ URI: [oio:hasAlternativeId](http://www.geneontology.org/formats/oboInOwl#hasAlte | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/has_broad_synonym.md.txt b/_sources/datamodels/ontology-metadata/has_broad_synonym.md.txt index d0c047028..2cc0e6c76 100644 --- a/_sources/datamodels/ontology-metadata/has_broad_synonym.md.txt +++ b/_sources/datamodels/ontology-metadata/has_broad_synonym.md.txt @@ -22,18 +22,18 @@ URI: [oio:hasBroadSynonym](http://www.geneontology.org/formats/oboInOwl#hasBroad | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/has_curation_status.md.txt b/_sources/datamodels/ontology-metadata/has_curation_status.md.txt index d8b28ce70..c254a613f 100644 --- a/_sources/datamodels/ontology-metadata/has_curation_status.md.txt +++ b/_sources/datamodels/ontology-metadata/has_curation_status.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000114](http://purl.obolibrary.org/obo/IAO_0000114) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/has_exact_synonym.md.txt b/_sources/datamodels/ontology-metadata/has_exact_synonym.md.txt index 18db98321..2bff7b21b 100644 --- a/_sources/datamodels/ontology-metadata/has_exact_synonym.md.txt +++ b/_sources/datamodels/ontology-metadata/has_exact_synonym.md.txt @@ -22,19 +22,19 @@ URI: [oio:hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExact | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/has_narrow_synonym.md.txt b/_sources/datamodels/ontology-metadata/has_narrow_synonym.md.txt index 2b5a78794..bb5143c28 100644 --- a/_sources/datamodels/ontology-metadata/has_narrow_synonym.md.txt +++ b/_sources/datamodels/ontology-metadata/has_narrow_synonym.md.txt @@ -22,18 +22,18 @@ URI: [oio:hasNarrowSynonym](http://www.geneontology.org/formats/oboInOwl#hasNarr | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/has_obo_namespace.md.txt b/_sources/datamodels/ontology-metadata/has_obo_namespace.md.txt index 2076712b2..1463670ef 100644 --- a/_sources/datamodels/ontology-metadata/has_obo_namespace.md.txt +++ b/_sources/datamodels/ontology-metadata/has_obo_namespace.md.txt @@ -16,18 +16,18 @@ URI: [oio:hasOBONamespace](http://www.geneontology.org/formats/oboInOwl#hasOBONa | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [HasCategory](HasCategory.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/has_obsolescence_reason.md.txt b/_sources/datamodels/ontology-metadata/has_obsolescence_reason.md.txt index 352584f5c..365618de2 100644 --- a/_sources/datamodels/ontology-metadata/has_obsolescence_reason.md.txt +++ b/_sources/datamodels/ontology-metadata/has_obsolescence_reason.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000231](http://purl.obolibrary.org/obo/IAO_0000231) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/has_related_synonym.md.txt b/_sources/datamodels/ontology-metadata/has_related_synonym.md.txt index 3776ccd1b..a1ca98121 100644 --- a/_sources/datamodels/ontology-metadata/has_related_synonym.md.txt +++ b/_sources/datamodels/ontology-metadata/has_related_synonym.md.txt @@ -16,18 +16,18 @@ URI: [oio:hasRelatedSynonym](http://www.geneontology.org/formats/oboInOwl#hasRel | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/id.md.txt b/_sources/datamodels/ontology-metadata/id.md.txt index 92c0d849c..d9f6d6738 100644 --- a/_sources/datamodels/ontology-metadata/id.md.txt +++ b/_sources/datamodels/ontology-metadata/id.md.txt @@ -26,19 +26,19 @@ URI: [omoschema:id](https://w3id.org/oak/ontology-metadata/id) | Name | Description | Modifies Slot | | --- | --- | --- | +| [NamedObject](NamedObject.md) | Anything with an IRI | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | yes | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | yes | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedObject](NamedObject.md) | Anything with an IRI | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | yes | diff --git a/_sources/datamodels/ontology-metadata/image.md.txt b/_sources/datamodels/ontology-metadata/image.md.txt index 300abb335..86f468bad 100644 --- a/_sources/datamodels/ontology-metadata/image.md.txt +++ b/_sources/datamodels/ontology-metadata/image.md.txt @@ -21,18 +21,18 @@ URI: [sdo:image](http://schema.org/image) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/imported_from.md.txt b/_sources/datamodels/ontology-metadata/imported_from.md.txt index 4faa4311d..defeab245 100644 --- a/_sources/datamodels/ontology-metadata/imported_from.md.txt +++ b/_sources/datamodels/ontology-metadata/imported_from.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000412](http://purl.obolibrary.org/obo/IAO_0000412) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/in_subset.md.txt b/_sources/datamodels/ontology-metadata/in_subset.md.txt index a556a5f24..630a77304 100644 --- a/_sources/datamodels/ontology-metadata/in_subset.md.txt +++ b/_sources/datamodels/ontology-metadata/in_subset.md.txt @@ -21,18 +21,18 @@ URI: [oio:inSubset](http://www.geneontology.org/formats/oboInOwl#inSubset) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [HasCategory](HasCategory.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/isDefinedBy.md.txt b/_sources/datamodels/ontology-metadata/isDefinedBy.md.txt index 7b5f12af9..d8b0d0119 100644 --- a/_sources/datamodels/ontology-metadata/isDefinedBy.md.txt +++ b/_sources/datamodels/ontology-metadata/isDefinedBy.md.txt @@ -16,18 +16,18 @@ URI: [rdfs:isDefinedBy](http://www.w3.org/2000/01/rdf-schema#isDefinedBy) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/is_class_level.md.txt b/_sources/datamodels/ontology-metadata/is_class_level.md.txt index ba17ee809..272500536 100644 --- a/_sources/datamodels/ontology-metadata/is_class_level.md.txt +++ b/_sources/datamodels/ontology-metadata/is_class_level.md.txt @@ -16,11 +16,11 @@ URI: [oio:is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_ | Name | Description | Modifies Slot | | --- | --- | --- | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/_sources/datamodels/ontology-metadata/is_metadata_tag.md.txt b/_sources/datamodels/ontology-metadata/is_metadata_tag.md.txt index b86998bf7..7261f28ba 100644 --- a/_sources/datamodels/ontology-metadata/is_metadata_tag.md.txt +++ b/_sources/datamodels/ontology-metadata/is_metadata_tag.md.txt @@ -16,11 +16,11 @@ URI: [oio:is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metad | Name | Description | Modifies Slot | | --- | --- | --- | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/_sources/datamodels/ontology-metadata/label.md.txt b/_sources/datamodels/ontology-metadata/label.md.txt index aab579974..3b9c100d3 100644 --- a/_sources/datamodels/ontology-metadata/label.md.txt +++ b/_sources/datamodels/ontology-metadata/label.md.txt @@ -21,19 +21,19 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | yes | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | yes | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [HasMinimalMetadata](HasMinimalMetadata.md) | Absolute minimum metadata model | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | -| [Property](Property.md) | | yes | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/narrowMatch.md.txt b/_sources/datamodels/ontology-metadata/narrowMatch.md.txt index 484b4d313..e2d818aee 100644 --- a/_sources/datamodels/ontology-metadata/narrowMatch.md.txt +++ b/_sources/datamodels/ontology-metadata/narrowMatch.md.txt @@ -21,18 +21,18 @@ URI: [skos:narrowMatch](http://www.w3.org/2004/02/skos/core#narrowMatch) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | yes | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | yes | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | yes | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/ontology_term_requester.md.txt b/_sources/datamodels/ontology-metadata/ontology_term_requester.md.txt index 69b0bc5cf..412a513e4 100644 --- a/_sources/datamodels/ontology-metadata/ontology_term_requester.md.txt +++ b/_sources/datamodels/ontology-metadata/ontology_term_requester.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000234](http://purl.obolibrary.org/obo/IAO_0000234) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/page.md.txt b/_sources/datamodels/ontology-metadata/page.md.txt index 65fe63dbd..a0f04f245 100644 --- a/_sources/datamodels/ontology-metadata/page.md.txt +++ b/_sources/datamodels/ontology-metadata/page.md.txt @@ -21,18 +21,18 @@ URI: [foaf:page](http://xmlns.com/foaf/0.1/page) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/range.md.txt b/_sources/datamodels/ontology-metadata/range.md.txt index 9c3574f89..92abc8765 100644 --- a/_sources/datamodels/ontology-metadata/range.md.txt +++ b/_sources/datamodels/ontology-metadata/range.md.txt @@ -21,11 +21,11 @@ URI: [rdfs:range](http://www.w3.org/2000/01/rdf-schema#range) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/_sources/datamodels/ontology-metadata/seeAlso.md.txt b/_sources/datamodels/ontology-metadata/seeAlso.md.txt index 86f601489..d7e8b3959 100644 --- a/_sources/datamodels/ontology-metadata/seeAlso.md.txt +++ b/_sources/datamodels/ontology-metadata/seeAlso.md.txt @@ -16,19 +16,19 @@ URI: [rdfs:seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/shorthand.md.txt b/_sources/datamodels/ontology-metadata/shorthand.md.txt index 7d5adf07e..5016fd3b4 100644 --- a/_sources/datamodels/ontology-metadata/shorthand.md.txt +++ b/_sources/datamodels/ontology-metadata/shorthand.md.txt @@ -16,10 +16,10 @@ URI: [oio:shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/_sources/datamodels/ontology-metadata/should_conform_to.md.txt b/_sources/datamodels/ontology-metadata/should_conform_to.md.txt index 646f83627..d1bae1035 100644 --- a/_sources/datamodels/ontology-metadata/should_conform_to.md.txt +++ b/_sources/datamodels/ontology-metadata/should_conform_to.md.txt @@ -21,18 +21,18 @@ URI: [omoschema:should_conform_to](https://w3id.org/oak/ontology-metadata/should | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/term_editor.md.txt b/_sources/datamodels/ontology-metadata/term_editor.md.txt index b61f241cc..ca1a7f2e8 100644 --- a/_sources/datamodels/ontology-metadata/term_editor.md.txt +++ b/_sources/datamodels/ontology-metadata/term_editor.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000117](http://purl.obolibrary.org/obo/IAO_0000117) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/term_replaced_by.md.txt b/_sources/datamodels/ontology-metadata/term_replaced_by.md.txt index 8648f9228..4e054b2c5 100644 --- a/_sources/datamodels/ontology-metadata/term_replaced_by.md.txt +++ b/_sources/datamodels/ontology-metadata/term_replaced_by.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0100001](http://purl.obolibrary.org/obo/IAO_0100001) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/term_tracker_item.md.txt b/_sources/datamodels/ontology-metadata/term_tracker_item.md.txt index d29df3596..ae7bce31e 100644 --- a/_sources/datamodels/ontology-metadata/term_tracker_item.md.txt +++ b/_sources/datamodels/ontology-metadata/term_tracker_item.md.txt @@ -21,18 +21,18 @@ URI: [IAO:0000233](http://purl.obolibrary.org/obo/IAO_0000233) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/ontology-metadata/type.md.txt b/_sources/datamodels/ontology-metadata/type.md.txt index 9a3807adc..f131efe34 100644 --- a/_sources/datamodels/ontology-metadata/type.md.txt +++ b/_sources/datamodels/ontology-metadata/type.md.txt @@ -21,20 +21,20 @@ URI: [rdf:type](http://www.w3.org/1999/02/22-rdf-syntax-ns#type) | Name | Description | Modifies Slot | | --- | --- | --- | +| [NamedObject](NamedObject.md) | Anything with an IRI | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Thing](Thing.md) | | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Thing](Thing.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedObject](NamedObject.md) | Anything with an IRI | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/_sources/datamodels/summary-statistics/agents.md.txt b/_sources/datamodels/summary-statistics/agents.md.txt index aa492661a..d51dbc70f 100644 --- a/_sources/datamodels/summary-statistics/agents.md.txt +++ b/_sources/datamodels/summary-statistics/agents.md.txt @@ -21,9 +21,9 @@ URI: [summary_statistics:agents](https://w3id.org/oaklib/summary_statistics.agen | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | | [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | +| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | diff --git a/_sources/datamodels/summary-statistics/compared_with.md.txt b/_sources/datamodels/summary-statistics/compared_with.md.txt index 038302f2c..662a82f23 100644 --- a/_sources/datamodels/summary-statistics/compared_with.md.txt +++ b/_sources/datamodels/summary-statistics/compared_with.md.txt @@ -21,9 +21,9 @@ URI: [summary_statistics:compared_with](https://w3id.org/oaklib/summary_statisti | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | | [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | +| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | diff --git a/_sources/datamodels/summary-statistics/facet.md.txt b/_sources/datamodels/summary-statistics/facet.md.txt index bc3f4e4fc..f8e97e1c3 100644 --- a/_sources/datamodels/summary-statistics/facet.md.txt +++ b/_sources/datamodels/summary-statistics/facet.md.txt @@ -16,8 +16,8 @@ URI: [summary_statistics:facet](https://w3id.org/oaklib/summary_statistics.facet | Name | Description | Modifies Slot | | --- | --- | --- | -| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no | | [ChangeTypeStatistic](ChangeTypeStatistic.md) | statistics for a particular kind of diff | no | +| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no | diff --git a/_sources/datamodels/summary-statistics/filtered_count.md.txt b/_sources/datamodels/summary-statistics/filtered_count.md.txt index a6467f518..db4e278e2 100644 --- a/_sources/datamodels/summary-statistics/filtered_count.md.txt +++ b/_sources/datamodels/summary-statistics/filtered_count.md.txt @@ -16,8 +16,8 @@ URI: [summary_statistics:filtered_count](https://w3id.org/oaklib/summary_statist | Name | Description | Modifies Slot | | --- | --- | --- | -| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no | | [ChangeTypeStatistic](ChangeTypeStatistic.md) | statistics for a particular kind of diff | no | +| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no | diff --git a/_sources/datamodels/summary-statistics/id.md.txt b/_sources/datamodels/summary-statistics/id.md.txt index 630cf5fd5..406a141b0 100644 --- a/_sources/datamodels/summary-statistics/id.md.txt +++ b/_sources/datamodels/summary-statistics/id.md.txt @@ -16,12 +16,12 @@ URI: [summary_statistics:id](https://w3id.org/oaklib/summary_statistics.id) | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | -| [ContributorRole](ContributorRole.md) | A role that a contributor can have | no | | [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | -| [Ontology](Ontology.md) | An ontology | no | +| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | | [Agent](Agent.md) | An agent | no | +| [Ontology](Ontology.md) | An ontology | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | +| [ContributorRole](ContributorRole.md) | A role that a contributor can have | no | diff --git a/_sources/datamodels/summary-statistics/ontologies.md.txt b/_sources/datamodels/summary-statistics/ontologies.md.txt index 1a6515a33..0b45b44e7 100644 --- a/_sources/datamodels/summary-statistics/ontologies.md.txt +++ b/_sources/datamodels/summary-statistics/ontologies.md.txt @@ -21,9 +21,9 @@ URI: [summary_statistics:ontologies](https://w3id.org/oaklib/summary_statistics. | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | | [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | +| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | diff --git a/_sources/datamodels/summary-statistics/was_generated_by.md.txt b/_sources/datamodels/summary-statistics/was_generated_by.md.txt index 144936119..6ce702663 100644 --- a/_sources/datamodels/summary-statistics/was_generated_by.md.txt +++ b/_sources/datamodels/summary-statistics/was_generated_by.md.txt @@ -21,9 +21,9 @@ URI: [summary_statistics:was_generated_by](https://w3id.org/oaklib/summary_stati | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | | [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | +| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | diff --git a/_sources/datamodels/taxon-constraints/id.md.txt b/_sources/datamodels/taxon-constraints/id.md.txt index b31598f1d..b7738b1ad 100644 --- a/_sources/datamodels/taxon-constraints/id.md.txt +++ b/_sources/datamodels/taxon-constraints/id.md.txt @@ -21,10 +21,10 @@ URI: [tc:id](https://w3id.org/linkml/taxon_constraints/id) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no | | [Term](Term.md) | An ontology term | no | | [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no | | [Taxon](Taxon.md) | A term that represents a taxonomic group, may be at species level of a higher... | no | +| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no | diff --git a/_sources/datamodels/taxon-constraints/label.md.txt b/_sources/datamodels/taxon-constraints/label.md.txt index 440b35870..7546fd9dc 100644 --- a/_sources/datamodels/taxon-constraints/label.md.txt +++ b/_sources/datamodels/taxon-constraints/label.md.txt @@ -21,10 +21,10 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no | | [Term](Term.md) | An ontology term | no | | [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no | | [Taxon](Taxon.md) | A term that represents a taxonomic group, may be at species level of a higher... | no | +| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no | diff --git a/_sources/datamodels/text-annotator/matches_whole_text.md.txt b/_sources/datamodels/text-annotator/matches_whole_text.md.txt index efb807866..5e009d3f7 100644 --- a/_sources/datamodels/text-annotator/matches_whole_text.md.txt +++ b/_sources/datamodels/text-annotator/matches_whole_text.md.txt @@ -16,8 +16,8 @@ URI: [ann:matches_whole_text](https://w3id.org/linkml/text_annotator/matches_who | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no | | [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | +| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no | diff --git a/_sources/datamodels/text-annotator/subject_end.md.txt b/_sources/datamodels/text-annotator/subject_end.md.txt index d161bde14..20c0707b2 100644 --- a/_sources/datamodels/text-annotator/subject_end.md.txt +++ b/_sources/datamodels/text-annotator/subject_end.md.txt @@ -16,8 +16,8 @@ URI: [ann:subject_end](https://w3id.org/linkml/text_annotator/subject_end) | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/_sources/datamodels/text-annotator/subject_label.md.txt b/_sources/datamodels/text-annotator/subject_label.md.txt index 58117545c..ab71b81bd 100644 --- a/_sources/datamodels/text-annotator/subject_label.md.txt +++ b/_sources/datamodels/text-annotator/subject_label.md.txt @@ -21,8 +21,8 @@ URI: [ann:subject_label](https://w3id.org/linkml/text_annotator/subject_label) | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/_sources/datamodels/text-annotator/subject_source.md.txt b/_sources/datamodels/text-annotator/subject_source.md.txt index be42b1ff3..a483bfe2d 100644 --- a/_sources/datamodels/text-annotator/subject_source.md.txt +++ b/_sources/datamodels/text-annotator/subject_source.md.txt @@ -16,8 +16,8 @@ URI: [sssom:subject_source](http://w3id.org/sssom/subject_source) | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/_sources/datamodels/text-annotator/subject_start.md.txt b/_sources/datamodels/text-annotator/subject_start.md.txt index 46c36d570..b65647c1f 100644 --- a/_sources/datamodels/text-annotator/subject_start.md.txt +++ b/_sources/datamodels/text-annotator/subject_start.md.txt @@ -16,8 +16,8 @@ URI: [ann:subject_start](https://w3id.org/linkml/text_annotator/subject_start) | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/_sources/datamodels/text-annotator/subject_text_id.md.txt b/_sources/datamodels/text-annotator/subject_text_id.md.txt index 37a81887b..6ac072152 100644 --- a/_sources/datamodels/text-annotator/subject_text_id.md.txt +++ b/_sources/datamodels/text-annotator/subject_text_id.md.txt @@ -16,8 +16,8 @@ URI: [ann:subject_text_id](https://w3id.org/linkml/text_annotator/subject_text_i | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/_sources/datamodels/validation/info.md.txt b/_sources/datamodels/validation/info.md.txt index 1910dc182..48a4a2da3 100644 --- a/_sources/datamodels/validation/info.md.txt +++ b/_sources/datamodels/validation/info.md.txt @@ -22,9 +22,9 @@ URI: [sh:resultMessage](http://www.w3.org/ns/shacl#resultMessage) | Name | Description | Modifies Slot | | --- | --- | --- | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | -| [RepairOperation](RepairOperation.md) | The result of performing an individual repair | no | | [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | +| [RepairOperation](RepairOperation.md) | The result of performing an individual repair | no | | [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/_sources/datamodels/validation/instantiates.md.txt b/_sources/datamodels/validation/instantiates.md.txt index ca2ffcee6..3a5e8c295 100644 --- a/_sources/datamodels/validation/instantiates.md.txt +++ b/_sources/datamodels/validation/instantiates.md.txt @@ -21,9 +21,9 @@ URI: [vm:instantiates](https://w3id.org/linkml/validation-model/instantiates) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/_sources/datamodels/validation/object.md.txt b/_sources/datamodels/validation/object.md.txt index 16fac1880..2e3592269 100644 --- a/_sources/datamodels/validation/object.md.txt +++ b/_sources/datamodels/validation/object.md.txt @@ -16,9 +16,9 @@ URI: [sh:value](http://www.w3.org/ns/shacl#value) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/_sources/datamodels/validation/object_str.md.txt b/_sources/datamodels/validation/object_str.md.txt index 4420d0363..840d518ef 100644 --- a/_sources/datamodels/validation/object_str.md.txt +++ b/_sources/datamodels/validation/object_str.md.txt @@ -16,9 +16,9 @@ URI: [vm:object_str](https://w3id.org/linkml/validation-model/object_str) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/_sources/datamodels/validation/predicate.md.txt b/_sources/datamodels/validation/predicate.md.txt index d89de45b9..3f80dcdd1 100644 --- a/_sources/datamodels/validation/predicate.md.txt +++ b/_sources/datamodels/validation/predicate.md.txt @@ -21,9 +21,9 @@ URI: [vm:predicate](https://w3id.org/linkml/validation-model/predicate) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/_sources/datamodels/validation/results.md.txt b/_sources/datamodels/validation/results.md.txt index 8693bd211..af5b91fe3 100644 --- a/_sources/datamodels/validation/results.md.txt +++ b/_sources/datamodels/validation/results.md.txt @@ -21,9 +21,9 @@ URI: [sh:result](http://www.w3.org/ns/shacl#result) | Name | Description | Modifies Slot | | --- | --- | --- | -| [RepairReport](RepairReport.md) | A report that consists of repair operation results | yes | | [ValidationReport](ValidationReport.md) | A report that consists of validation results | yes | | [Report](Report.md) | A report object that is a holder to multiple report results | no | +| [RepairReport](RepairReport.md) | A report that consists of repair operation results | yes | diff --git a/_sources/datamodels/validation/severity.md.txt b/_sources/datamodels/validation/severity.md.txt index 2afbdc29e..6e6889306 100644 --- a/_sources/datamodels/validation/severity.md.txt +++ b/_sources/datamodels/validation/severity.md.txt @@ -21,10 +21,10 @@ URI: [sh:resultSeverity](http://www.w3.org/ns/shacl#resultSeverity) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | | [TypeSeverityKeyValue](TypeSeverityKeyValue.md) | key-value pair that maps a validation result type to a severity setting, for ... | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/_sources/datamodels/validation/source.md.txt b/_sources/datamodels/validation/source.md.txt index 64609f55d..0902c4d63 100644 --- a/_sources/datamodels/validation/source.md.txt +++ b/_sources/datamodels/validation/source.md.txt @@ -16,9 +16,9 @@ URI: [vm:source](https://w3id.org/linkml/validation-model/source) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/_sources/datamodels/validation/subject.md.txt b/_sources/datamodels/validation/subject.md.txt index e4af7da44..cdbab69a6 100644 --- a/_sources/datamodels/validation/subject.md.txt +++ b/_sources/datamodels/validation/subject.md.txt @@ -21,9 +21,9 @@ URI: [sh:focusNode](http://www.w3.org/ns/shacl#focusNode) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/_sources/datamodels/validation/type.md.txt b/_sources/datamodels/validation/type.md.txt index 4f005ecf2..d1d7d06df 100644 --- a/_sources/datamodels/validation/type.md.txt +++ b/_sources/datamodels/validation/type.md.txt @@ -21,10 +21,10 @@ URI: [sh:sourceConstraintComponent](http://www.w3.org/ns/shacl#sourceConstraintC | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | | [TypeSeverityKeyValue](TypeSeverityKeyValue.md) | key-value pair that maps a validation result type to a severity setting, for ... | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/_sources/guide/similarity.rst.txt b/_sources/guide/similarity.rst.txt index cf50d35ce..872208d12 100644 --- a/_sources/guide/similarity.rst.txt +++ b/_sources/guide/similarity.rst.txt @@ -10,7 +10,6 @@ A common use case for ontologies is to compute :term:`Similarity` between :term: or between :term:`Terms `, based on properties of the ontology. For example, when comparing two terms, we may want to score terms that are closer together in the ontology :term:`Graph` as more similar. Other measures of similarity may be on frequency of usage of terms, -or on vector :term:`Embeddings ` of terms. If :term:`Entities ` are annotated/associated with terms, we can also compute similarity between these based on the aggregate set of terms they are annotated with. The canonical use @@ -42,13 +41,73 @@ between two sets: where :math:`A` and :math:`B` are sets. -When applied to pairs of ontology terms, the sets are typically the :term:`Reflexive` :term:`Ancestors` +For example given two sets ``{banana, apple, orange}`` and ``{apple, orange, pear}``, the intersection of these +two sets is ``{apple, orange}`` (size 2) and the union is ``{banana, apple, orange, pear}`` (size 4). The Jaccard similarity +is therefore: + +.. math:: + + J = \frac{2}{4} = 0.5 + +Jaccard Similarity of ontology terms +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +When applied to pairs of ontology :term:`Terms `, the sets are typically the :term:`Reflexive` :term:`Ancestors` of the terms of interest. Like all OAK graph operations, the choice of :term:`Predicates` used is important. - Phenotype ontologies typically compute this using :term:`SubClassOf` links only - Ontologies such as GO, Uberon, and ENVO typically use :term:`SubClassOf` and :term:`PartOf` links +For example, given an ontology of vehicles with the following structure: + +.. code-block:: none + + Car is-a Vehicle + Car has-part Engine is_a Part + Car has-part Wheel is_a Part + Car has-part Door is_a Part + Engine has-part Piston is_a Part + Car has-part Seat is_a Part + Bicycle is-a Vehicle + Bicycle has-part Wheel is_a Part + Bicycle has-part Handlebar is_a Part + Bicycle has-part Seat is_a Part + +Visualized as: + +.. figure:: ./images/vehicles.png + :alt: Vehicle ontology + + Vehicle ontology + +If we follow predicates ``{is-a, has-part}`` (both of which are reflexive), then we have reflexive ancestors: + +- Car: {Car, Vehicle, Engine, Wheel, Door, Piston, Seat, Part} +- Bicycle: {Bicycle, Vehicle, Wheel, Handlebar, Seat, Part} + +- Intersection: {Vehicle, Wheel, Seat, Part} +- Union: {Car, Vehicle, Engine, Wheel, Door, Piston, Seat, Bicycle, Handlebar, Part} + +The same ontology with the :term:`Most Recent Common Ancestor` terms of Car and Bicycle highlighted: + +.. figure:: ./images/vehicles-mrca.png + :alt: Vehicle ontology with MRCAs + + Vehicle ontology with MRCAs + +Jaccard similarity between Car and Bicycle would be: + +.. math:: + + J = \frac{4}{10} = 0.4 + +You can test this by running: + +.. code-block:: bash + + runoak -i simpleobo:tests/input/vehicles.obo similarity Car @ Bicycle + Information Content ^^^^^^^^^^^^^^^^^^^ @@ -64,7 +123,9 @@ where :math:`P(t)` is the probability of the term in the corpus. There are two w - Using the ontology as the corpus - Using :term:`Associations ` between entities and terms as the corpus -In both cases the ontology graph is used. +In both cases the whole ontology :term:`Graph` is used. This means that a :term:`Descendant` term +will always have IC that is equal to or greater than its :term:`Ancestor` term (over some specified +set of predicates). When the ontology is used as the corpus, the probability of a term is computed as the number of descendants of a term (reflexive) divided by the total number of terms in the ontology: @@ -73,6 +134,14 @@ descendants of a term (reflexive) divided by the total number of terms in the on P(t) = \frac{|Desc*(t)|}{|T|} +You can see this via + +.. code-block:: bash + + runoak -i simpleobo:tests/input/vehicles.obo similarity Car @ Bicycle + +When we consider all relationships, there are multiple MRCAs (see figure above). These are tied with an IC of 1.29. + When associations are used, the probability of a term is computed as the number of entities associated with a term (directly or indirectly) divided by the total number of entities: @@ -93,19 +162,82 @@ specifying the associations themselves: .. code-block:: bash - runoak -g phenotype.hpoa -G hpoa -i sqlite:obo:hp information-content -p i --use-associations i^HP: + runoak -g phenotype.hpoa -G hpoa -i sqlite:obo:hp information-content -p i --use-associations i^HP: -o hp.ics.tsv + +Here we save to a file ``hp.ics.tsv`` IC can be used to score the :term:`Most Recent Common Ancestor` (MRCAs) of two terms; also known as Resnik similarity. +We can compare scores using native ontology ICs and ICs using annotations as a corpus + +.. code-block:: bash + + runoak -i sqlite:obo:hp similarity -p i HP:0000015 @ HP:0000017 + +Gives an IC of 9.02 for the MRCA of Bladder diverticulum and Nocturia. + +.. code-block:: yaml + + subject_id: HP:0000015 + subject_label: Bladder diverticulum + object_id: HP:0000017 + object_label: Nocturia + ancestor_id: HP:0000014 + ancestor_label: Abnormality of the bladder + ancestor_information_content: 9.020517017340513 + jaccard_similarity: 0.6 + phenodigm_score: 2.3264372354319613 + +We can plug in the association corpus based IC table using the ``--information-content-file`` option: + +.. code-block:: bash + + runoak -i sqlite:obo:hp similarity -p i --information-content-file hp.ics.tsv HP:0000015 @ HP:0000017 + +This will give a lower IC: + +.. code-block:: yaml + + subject_id: HP:0000015 + subject_label: Bladder diverticulum + object_id: HP:0000017 + object_label: Nocturia + ancestor_id: HP:0000014 + ancestor_label: Abnormality of the bladder + ancestor_information_content: 3.042673785507031 + jaccard_similarity: 0.6 + phenodigm_score: 1.3511492409442485 + +The higher IC for pure ontology corpus reflects a bias in depth in the ontology. + +Ensemble Scoring of term pairs +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +We can compute ensemble scores by combining existing scores. For example, the **Phenodigm score** combines +Jaccard similarity and Resnik similarity. + +See the `Phenodigm paper `_ for details. + +Other similarity measures +^^^^^^^^^^^^^^^^^^^^^^^^^ + +Other potential similarity measures include: + +- Phenologs +- Embedding-based methods + + * KGE embeddings, e.g. GRAPE + * Text embeddings, e.g. using OpenAI text-ada-002 + Aggregate measures for comparing entities ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Computing similarity between terms (classes) is relatively easy. But in general users want to compare -*entities* such as genes. Here we broadly have two approaches: +Computing similarity between terms (classes) is relatively easy. But in general, users want to compare +*entities* such as genes. Here we have two broad approaches: -- Knowledge Graph (KG): treat the entities as nodes in the graph and use the standard ontology methods above -- Aggregate Statistics +- Knowledge Graph (KG): treat the **entities as nodes/terms in the graph** and use the standard ontology methods above +- Aggregate Statistics (e.g. Best Match Average) With the KG approach the entities typically become leaf nodes in the graph, and we compare using standard graph methods where both association predicates (e.g. has-phenotype) and ontology predicates (e.g. is-a and part-of) @@ -126,7 +258,7 @@ for the IC of the MRCA this would be: However, this doesn't take into account all the other associations for each entity. -A more common aggregate statistic is Best Match Average (BMA), which is the average of the maximum +A more common aggregate statistic is **Best Match Average** (BMA), which is the average of the maximum pairwise similarity between each term in the first profile and the second profile: .. math:: @@ -135,6 +267,13 @@ pairwise similarity between each term in the first profile and the second profil Currently this is the default used in OAK. +This is illustrated in this figure: + +.. figure:: https://www.ncbi.nlm.nih.gov/pmc/articles/instance/3649640/bin/bat025f1p.jpg + :alt: + + Aggregate statistics, from the Phenodigm paper. + To compare two profiles in OAK you can use the ``termset-similarity`` command, passing in each profile, separated by ``@``: @@ -216,6 +355,10 @@ Data Model See the `Similarity data model `_ for details of the data model. +Companion Notebooks +------------------- + +See the notebook for the `termset-similarity Command Applicable Classes

Association

-

A generic association between a thing (subject) and another thing (object)

+

PositiveOrNegativeAssociation

+

no

-

PositiveOrNegativeAssociation

-

+

ParserConfiguration

+

Settings that determine behavior when parsing associations

no

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

ParserConfiguration

-

Settings that determine behavior when parsing associations

+

Association

+

A generic association between a thing (subject) and another thing (object)

no

AssociationChange

diff --git a/datamodels/association/comments.html b/datamodels/association/comments.html index e6cbafb76..b7e3d882d 100644 --- a/datamodels/association/comments.html +++ b/datamodels/association/comments.html @@ -98,18 +98,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/evidence_type.html b/datamodels/association/evidence_type.html index aebfecbb4..9354ef908 100644 --- a/datamodels/association/evidence_type.html +++ b/datamodels/association/evidence_type.html @@ -98,18 +98,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/negated.html b/datamodels/association/negated.html index 1f9c0a013..0aa522beb 100644 --- a/datamodels/association/negated.html +++ b/datamodels/association/negated.html @@ -98,18 +98,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

yes

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

yes

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/object.html b/datamodels/association/object.html index 70939247b..b326a60fe 100644 --- a/datamodels/association/object.html +++ b/datamodels/association/object.html @@ -110,20 +110,20 @@

Applicable Classes

PositiveOrNegativeAssociation

-

+

NegatedAssociation

+

A negated association between a thing (subject) and another thing (object)

no

Association

A generic association between a thing (subject) and another thing (object)

no

-

NegatedAssociation

-

A negated association between a thing (subject) and another thing (object)

+

PropertyValue

+

A generic tag-value that can be associated with an association

no

-

PropertyValue

-

A generic tag-value that can be associated with an association

+

PositiveOrNegativeAssociation

+

no

diff --git a/datamodels/association/object_closure.html b/datamodels/association/object_closure.html index e45d13c44..b53c02cdd 100644 --- a/datamodels/association/object_closure.html +++ b/datamodels/association/object_closure.html @@ -98,18 +98,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/object_closure_label.html b/datamodels/association/object_closure_label.html index 393017c79..405845ec2 100644 --- a/datamodels/association/object_closure_label.html +++ b/datamodels/association/object_closure_label.html @@ -98,18 +98,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/object_label.html b/datamodels/association/object_label.html index 38ec0faa4..8b83fb8aa 100644 --- a/datamodels/association/object_label.html +++ b/datamodels/association/object_label.html @@ -103,18 +103,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/predicate.html b/datamodels/association/predicate.html index 302330bf8..42b62db90 100644 --- a/datamodels/association/predicate.html +++ b/datamodels/association/predicate.html @@ -108,20 +108,20 @@

Applicable Classes

PositiveOrNegativeAssociation

-

+

NegatedAssociation

+

A negated association between a thing (subject) and another thing (object)

no

Association

A generic association between a thing (subject) and another thing (object)

no

-

NegatedAssociation

-

A negated association between a thing (subject) and another thing (object)

+

PropertyValue

+

A generic tag-value that can be associated with an association

no

-

PropertyValue

-

A generic tag-value that can be associated with an association

+

PositiveOrNegativeAssociation

+

no

diff --git a/datamodels/association/predicate_label.html b/datamodels/association/predicate_label.html index 3ccda38a0..fb445fd85 100644 --- a/datamodels/association/predicate_label.html +++ b/datamodels/association/predicate_label.html @@ -103,18 +103,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/primary_knowledge_source.html b/datamodels/association/primary_knowledge_source.html index bdd9801ea..6ce1a3812 100644 --- a/datamodels/association/primary_knowledge_source.html +++ b/datamodels/association/primary_knowledge_source.html @@ -98,20 +98,20 @@

Applicable Classes

Association

-

A generic association between a thing (subject) and another thing (object)

+

PositiveOrNegativeAssociation

+

no

-

PositiveOrNegativeAssociation

-

+

ParserConfiguration

+

Settings that determine behavior when parsing associations

no

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

ParserConfiguration

-

Settings that determine behavior when parsing associations

+

Association

+

A generic association between a thing (subject) and another thing (object)

no

AssociationChange

diff --git a/datamodels/association/property_values.html b/datamodels/association/property_values.html index 87943a7fa..526d41212 100644 --- a/datamodels/association/property_values.html +++ b/datamodels/association/property_values.html @@ -98,18 +98,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/publications.html b/datamodels/association/publications.html index f9f32ea6b..157e15c33 100644 --- a/datamodels/association/publications.html +++ b/datamodels/association/publications.html @@ -98,14 +98,6 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

Association

-

A generic association between a thing (subject) and another thing (object)

-

no

-

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

@@ -114,6 +106,14 @@

Applicable Classes

Association

+

A generic association between a thing (subject) and another thing (object)

+

no

+ +

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/subject.html b/datamodels/association/subject.html index 36ac50adf..38a2dd6ff 100644 --- a/datamodels/association/subject.html +++ b/datamodels/association/subject.html @@ -98,14 +98,6 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

Association

-

A generic association between a thing (subject) and another thing (object)

-

no

-

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

@@ -114,6 +106,14 @@

Applicable Classes

Association

+

A generic association between a thing (subject) and another thing (object)

+

no

+ +

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/subject_closure.html b/datamodels/association/subject_closure.html index 2434d204b..1ed794c3c 100644 --- a/datamodels/association/subject_closure.html +++ b/datamodels/association/subject_closure.html @@ -98,18 +98,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/subject_closure_label.html b/datamodels/association/subject_closure_label.html index bbfe21b0b..6a52723c6 100644 --- a/datamodels/association/subject_closure_label.html +++ b/datamodels/association/subject_closure_label.html @@ -98,18 +98,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/subject_label.html b/datamodels/association/subject_label.html index aa4a3dd98..3faa1630c 100644 --- a/datamodels/association/subject_label.html +++ b/datamodels/association/subject_label.html @@ -103,18 +103,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/association/supporting_objects.html b/datamodels/association/supporting_objects.html index 395e42425..a2f4836ab 100644 --- a/datamodels/association/supporting_objects.html +++ b/datamodels/association/supporting_objects.html @@ -98,18 +98,18 @@

Applicable Classes

PositiveOrNegativeAssociation

-

-

no

- -

NegatedAssociation

+

NegatedAssociation

A negated association between a thing (subject) and another thing (object)

no

-

Association

+

Association

A generic association between a thing (subject) and another thing (object)

no

+

PositiveOrNegativeAssociation

+

+

no

+ diff --git a/datamodels/item-list/description.html b/datamodels/item-list/description.html index 51d8259eb..1d7852e16 100644 --- a/datamodels/item-list/description.html +++ b/datamodels/item-list/description.html @@ -97,12 +97,12 @@

Applicable Classes

ItemList

-

a list of entities plus metadata

+

Thing

+

no

-

Thing

-

+

ItemList

+

a list of entities plus metadata

no

diff --git a/datamodels/item-list/id.html b/datamodels/item-list/id.html index eea318b7e..94fea38ea 100644 --- a/datamodels/item-list/id.html +++ b/datamodels/item-list/id.html @@ -97,12 +97,12 @@

Applicable Classes

ItemList

-

a list of entities plus metadata

+

Thing

+

no

-

Thing

-

+

ItemList

+

a list of entities plus metadata

no

diff --git a/datamodels/item-list/name.html b/datamodels/item-list/name.html index 0481e7379..5f0e81f43 100644 --- a/datamodels/item-list/name.html +++ b/datamodels/item-list/name.html @@ -97,12 +97,12 @@

Applicable Classes

ItemList

-

a list of entities plus metadata

+

Thing

+

no

-

Thing

-

+

ItemList

+

a list of entities plus metadata

no

diff --git a/datamodels/mapping-rules/description.html b/datamodels/mapping-rules/description.html index b648a11ed..0c6bced59 100644 --- a/datamodels/mapping-rules/description.html +++ b/datamodels/mapping-rules/description.html @@ -97,12 +97,12 @@

Applicable Classes

Synonymizer

-

Specification of a rule for generating a synonym or alternate lexical element

+

MappingRule

+

An individual mapping rule, if preconditions match the postconditions are app…

no

-

MappingRule

-

An individual mapping rule, if preconditions match the postconditions are app…

+

Synonymizer

+

Specification of a rule for generating a synonym or alternate lexical element

no

diff --git a/datamodels/mapping-rules/prefix.html b/datamodels/mapping-rules/prefix.html index 9e4754698..9afbabaeb 100644 --- a/datamodels/mapping-rules/prefix.html +++ b/datamodels/mapping-rules/prefix.html @@ -101,12 +101,12 @@

Applicable Classes

Synonymizer

-

Specification of a rule for generating a synonym or alternate lexical element

+

RuleSet

+

A set of rules for generating synonyms or alternate lexical elements

no

-

RuleSet

-

A set of rules for generating synonyms or alternate lexical elements

+

Synonymizer

+

Specification of a rule for generating a synonym or alternate lexical element

no

diff --git a/datamodels/mapping-rules/rules.html b/datamodels/mapping-rules/rules.html index fc8eaf9c0..87e8f7260 100644 --- a/datamodels/mapping-rules/rules.html +++ b/datamodels/mapping-rules/rules.html @@ -97,12 +97,12 @@

Applicable Classes

MappingRuleCollection

-

A collection of mapping rules

+

RuleSet

+

A set of rules for generating synonyms or alternate lexical elements

no

-

RuleSet

-

A set of rules for generating synonyms or alternate lexical elements

+

MappingRuleCollection

+

A collection of mapping rules

no

diff --git a/datamodels/obograph/id.html b/datamodels/obograph/id.html index 987916a85..4e7598fc2 100644 --- a/datamodels/obograph/id.html +++ b/datamodels/obograph/id.html @@ -98,16 +98,16 @@

Applicable Classes

Node

-

A node is a class, property, or other entity in an ontology

+

Graph

+

A graph is a collection of nodes and edges and other axioms that represents a…

no

-

SubsetDefinition

-

+

Node

+

A node is a class, property, or other entity in an ontology

no

-

Graph

-

A graph is a collection of nodes and edges and other axioms that represents a…

+

SubsetDefinition

+

no

SynonymTypeDefinition

diff --git a/datamodels/obograph/lang.html b/datamodels/obograph/lang.html index 40770a343..5c81ab022 100644 --- a/datamodels/obograph/lang.html +++ b/datamodels/obograph/lang.html @@ -98,24 +98,24 @@

Applicable Classes

DefinitionPropertyValue

-

A property value that represents an assertion about the textual definition of…

+

PropertyValue

+

A generic grouping for the different kinds of key-value associations on objec…

no

SynonymPropertyValue

A property value that represents an assertion about a synonym of an entity

no

-

XrefPropertyValue

-

A property value that represents an assertion about an external reference to …

+

DefinitionPropertyValue

+

A property value that represents an assertion about the textual definition of…

no

-

PropertyValue

-

A generic grouping for the different kinds of key-value associations on objec…

+

BasicPropertyValue

+

A property value that represents an assertion about an entity that is not a d…

no

-

BasicPropertyValue

-

A property value that represents an assertion about an entity that is not a d…

+

XrefPropertyValue

+

A property value that represents an assertion about an external reference to …

no

diff --git a/datamodels/obograph/lbl.html b/datamodels/obograph/lbl.html index c9e8c92bd..505ccd67d 100644 --- a/datamodels/obograph/lbl.html +++ b/datamodels/obograph/lbl.html @@ -98,16 +98,16 @@

Applicable Classes

Node

-

A node is a class, property, or other entity in an ontology

+

Graph

+

A graph is a collection of nodes and edges and other axioms that represents a…

no

-

SubsetDefinition

-

+

Node

+

A node is a class, property, or other entity in an ontology

no

-

Graph

-

A graph is a collection of nodes and edges and other axioms that represents a…

+

SubsetDefinition

+

no

SynonymTypeDefinition

diff --git a/datamodels/obograph/meta.html b/datamodels/obograph/meta.html index 29b7422c2..4e44df468 100644 --- a/datamodels/obograph/meta.html +++ b/datamodels/obograph/meta.html @@ -98,64 +98,64 @@

Applicable Classes

DefinitionPropertyValue

-

A property value that represents an assertion about the textual definition of…

+

PropertyValue

+

A generic grouping for the different kinds of key-value associations on objec…

no

-

Graph

-

A graph is a collection of nodes and edges and other axioms that represents a…

+

LogicalDefinitionAxiom

+

An axiom that defines a class in terms of a genus or set of genus classes and…

no

-

DomainRangeAxiom

-

This groups potentially multiple axioms that constrain the usage of a propert…

+

PropertyChainAxiom

+

An axiom that represents an OWL property chain, e

no

-

SynonymPropertyValue

+

GraphDocument

+

A graph document is a collection of graphs together with a set of prefixes th…

+

no

+ +

SynonymPropertyValue

A property value that represents an assertion about a synonym of an entity

no

-

Node

-

A node is a class, property, or other entity in an ontology

+

EquivalentNodesSet

+

A clique of nodes that are all mutually equivalent

no

-

Edge

-

An edge is a simple typed relationship between two nodes

+

DefinitionPropertyValue

+

A property value that represents an assertion about the textual definition of…

no

-

XrefPropertyValue

-

A property value that represents an assertion about an external reference to …

+

Graph

+

A graph is a collection of nodes and edges and other axioms that represents a…

no

-

LogicalDefinitionAxiom

-

An axiom that defines a class in terms of a genus or set of genus classes and…

+

BasicPropertyValue

+

A property value that represents an assertion about an entity that is not a d…

+

no

+ +

Node

+

A node is a class, property, or other entity in an ontology

no

Axiom

A generic grouping for any OWL axiom or group of axioms that is not captured …

no

-

PropertyValue

-

A generic grouping for the different kinds of key-value associations on objec…

+

Edge

+

An edge is a simple typed relationship between two nodes

no

DisjointClassExpressionsAxiom

An axiom that defines a set of classes or class expressions as being mutually…

no

-

EquivalentNodesSet

-

A clique of nodes that are all mutually equivalent

-

no

- -

GraphDocument

-

A graph document is a collection of graphs together with a set of prefixes th…

-

no

- -

PropertyChainAxiom

-

An axiom that represents an OWL property chain, e

+

XrefPropertyValue

+

A property value that represents an assertion about an external reference to …

no

-

BasicPropertyValue

-

A property value that represents an assertion about an entity that is not a d…

+

DomainRangeAxiom

+

This groups potentially multiple axioms that constrain the usage of a propert…

no

diff --git a/datamodels/obograph/pred.html b/datamodels/obograph/pred.html index 3911c5df1..6d31b3a4c 100644 --- a/datamodels/obograph/pred.html +++ b/datamodels/obograph/pred.html @@ -98,17 +98,25 @@

Applicable Classes

DefinitionPropertyValue

-

A property value that represents an assertion about the textual definition of…

+

PropertyValue

+

A generic grouping for the different kinds of key-value associations on objec…

no

-

SynonymTypeDefinition

+

SynonymPropertyValue

+

A property value that represents an assertion about a synonym of an entity

+

yes

+ +

SynonymTypeDefinition

no

-

SynonymPropertyValue

-

A property value that represents an assertion about a synonym of an entity

-

yes

+

DefinitionPropertyValue

+

A property value that represents an assertion about the textual definition of…

+

no

+ +

BasicPropertyValue

+

A property value that represents an assertion about an entity that is not a d…

+

no

Edge

An edge is a simple typed relationship between two nodes

@@ -118,14 +126,6 @@

Applicable Classes

PropertyValue

-

A generic grouping for the different kinds of key-value associations on objec…

-

no

- -

BasicPropertyValue

-

A property value that represents an assertion about an entity that is not a d…

-

no

- diff --git a/datamodels/obograph/prefixes.html b/datamodels/obograph/prefixes.html index e83eda87f..25fd9a9ed 100644 --- a/datamodels/obograph/prefixes.html +++ b/datamodels/obograph/prefixes.html @@ -98,12 +98,12 @@

Applicable Classes

GraphDocument

-

A graph document is a collection of graphs together with a set of prefixes th…

+

Graph

+

A graph is a collection of nodes and edges and other axioms that represents a…

no

-

Graph

-

A graph is a collection of nodes and edges and other axioms that represents a…

+

GraphDocument

+

A graph document is a collection of graphs together with a set of prefixes th…

no

diff --git a/datamodels/obograph/val.html b/datamodels/obograph/val.html index ade75e26e..0ffe82662 100644 --- a/datamodels/obograph/val.html +++ b/datamodels/obograph/val.html @@ -98,26 +98,26 @@

Applicable Classes

DefinitionPropertyValue

-

A property value that represents an assertion about the textual definition of…

-

yes

+

PropertyValue

+

A generic grouping for the different kinds of key-value associations on objec…

+

no

SynonymPropertyValue

A property value that represents an assertion about a synonym of an entity

yes

-

XrefPropertyValue

-

A property value that represents an assertion about an external reference to …

+

DefinitionPropertyValue

+

A property value that represents an assertion about the textual definition of…

yes

-

PropertyValue

-

A generic grouping for the different kinds of key-value associations on objec…

-

no

- -

BasicPropertyValue

+

BasicPropertyValue

A property value that represents an assertion about an entity that is not a d…

no

+

XrefPropertyValue

+

A property value that represents an assertion about an external reference to …

+

yes

+ diff --git a/datamodels/obograph/valType.html b/datamodels/obograph/valType.html index 01f468924..103212626 100644 --- a/datamodels/obograph/valType.html +++ b/datamodels/obograph/valType.html @@ -98,24 +98,24 @@

Applicable Classes

DefinitionPropertyValue

-

A property value that represents an assertion about the textual definition of…

+

PropertyValue

+

A generic grouping for the different kinds of key-value associations on objec…

no

SynonymPropertyValue

A property value that represents an assertion about a synonym of an entity

no

-

XrefPropertyValue

-

A property value that represents an assertion about an external reference to …

+

DefinitionPropertyValue

+

A property value that represents an assertion about the textual definition of…

no

-

PropertyValue

-

A generic grouping for the different kinds of key-value associations on objec…

+

BasicPropertyValue

+

A property value that represents an assertion about an entity that is not a d…

no

-

BasicPropertyValue

-

A property value that represents an assertion about an entity that is not a d…

+

XrefPropertyValue

+

A property value that represents an assertion about an external reference to …

no

diff --git a/datamodels/obograph/xrefs.html b/datamodels/obograph/xrefs.html index 684a3ed5b..459c5bc42 100644 --- a/datamodels/obograph/xrefs.html +++ b/datamodels/obograph/xrefs.html @@ -98,30 +98,30 @@

Applicable Classes

Meta

+

PropertyValue

+

A generic grouping for the different kinds of key-value associations on objec…

+

no

+ +

Meta

A collection of annotations on an entity or ontology or edge or axiom

yes

+

SynonymPropertyValue

+

A property value that represents an assertion about a synonym of an entity

+

no

+

DefinitionPropertyValue

A property value that represents an assertion about the textual definition of…

yes

-

SynonymPropertyValue

-

A property value that represents an assertion about a synonym of an entity

+

BasicPropertyValue

+

A property value that represents an assertion about an entity that is not a d…

no

XrefPropertyValue

A property value that represents an assertion about an external reference to …

no

-

PropertyValue

-

A generic grouping for the different kinds of key-value associations on objec…

-

no

- -

BasicPropertyValue

-

A property value that represents an assertion about an entity that is not a d…

-

no

- diff --git a/datamodels/ontology-metadata/IEDB_alternative_term.html b/datamodels/ontology-metadata/IEDB_alternative_term.html index e6a98e8fe..d96220125 100644 --- a/datamodels/ontology-metadata/IEDB_alternative_term.html +++ b/datamodels/ontology-metadata/IEDB_alternative_term.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

HasSynonyms

+

a mixin for a class whose members can have synonyms

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

HasSynonyms

-

a mixin for a class whose members can have synonyms

+

Class

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/ISA_alternative_term.html b/datamodels/ontology-metadata/ISA_alternative_term.html index f31ffb917..b47af5cd4 100644 --- a/datamodels/ontology-metadata/ISA_alternative_term.html +++ b/datamodels/ontology-metadata/ISA_alternative_term.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

HasSynonyms

+

a mixin for a class whose members can have synonyms

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

HasSynonyms

-

a mixin for a class whose members can have synonyms

+

Class

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/OBO_foundry_unique_label.html b/datamodels/ontology-metadata/OBO_foundry_unique_label.html index b33c8cd15..9a914d2c1 100644 --- a/datamodels/ontology-metadata/OBO_foundry_unique_label.html +++ b/datamodels/ontology-metadata/OBO_foundry_unique_label.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

HasSynonyms

+

a mixin for a class whose members can have synonyms

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

HasSynonyms

-

a mixin for a class whose members can have synonyms

+

Class

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/alternative_term.html b/datamodels/ontology-metadata/alternative_term.html index 1364ff514..0d6f7a56f 100644 --- a/datamodels/ontology-metadata/alternative_term.html +++ b/datamodels/ontology-metadata/alternative_term.html @@ -110,52 +110,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

HasSynonyms

+

a mixin for a class whose members can have synonyms

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

HasSynonyms

-

a mixin for a class whose members can have synonyms

+

Class

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/broadMatch.html b/datamodels/ontology-metadata/broadMatch.html index 2ca4a4740..328d98cd9 100644 --- a/datamodels/ontology-metadata/broadMatch.html +++ b/datamodels/ontology-metadata/broadMatch.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

yes

-

Image

+

HasMappings

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

+

no

+ +

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

yes

-

HasMappings

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

-

no

- -

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/category.html b/datamodels/ontology-metadata/category.html index af3b1cf67..73d57f2df 100644 --- a/datamodels/ontology-metadata/category.html +++ b/datamodels/ontology-metadata/category.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

HasCategory

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

Subset

-

A collection of terms grouped for some purpose

+

Class

+

no

-

Property

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

HasCategory

+

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/closeMatch.html b/datamodels/ontology-metadata/closeMatch.html index 6ec62f1d5..d57a0eccd 100644 --- a/datamodels/ontology-metadata/closeMatch.html +++ b/datamodels/ontology-metadata/closeMatch.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

yes

-

Image

+

HasMappings

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

+

no

+ +

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

yes

-

HasMappings

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

-

no

- -

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/comment.html b/datamodels/ontology-metadata/comment.html index 536c53e85..32f532960 100644 --- a/datamodels/ontology-metadata/comment.html +++ b/datamodels/ontology-metadata/comment.html @@ -106,60 +106,60 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Axiom

+

A logical or non-logical statement

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Axiom

-

A logical or non-logical statement

+

Subset

+

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

HasUserInformation

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

Ontology

+

An OWL ontology

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

HasUserInformation

+

no

-

Ontology

-

An OWL ontology

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/conformsTo.html b/datamodels/ontology-metadata/conformsTo.html index cba35945d..6526c17f8 100644 --- a/datamodels/ontology-metadata/conformsTo.html +++ b/datamodels/ontology-metadata/conformsTo.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

HasCategory

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

Subset

-

A collection of terms grouped for some purpose

+

Class

+

no

-

Property

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

HasCategory

+

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/consider.html b/datamodels/ontology-metadata/consider.html index e0c1bb0d1..ebb59fb28 100644 --- a/datamodels/ontology-metadata/consider.html +++ b/datamodels/ontology-metadata/consider.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

HasLifeCycle

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Image

+

HasLifeCycle

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/contributor.html b/datamodels/ontology-metadata/contributor.html index cb7b59b1c..54643d68f 100644 --- a/datamodels/ontology-metadata/contributor.html +++ b/datamodels/ontology-metadata/contributor.html @@ -106,52 +106,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/created.html b/datamodels/ontology-metadata/created.html index 3fcc9c72c..aa644a2ff 100644 --- a/datamodels/ontology-metadata/created.html +++ b/datamodels/ontology-metadata/created.html @@ -107,56 +107,56 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

Ontology

+

An OWL ontology

no

-

Ontology

-

An OWL ontology

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/created_by.html b/datamodels/ontology-metadata/created_by.html index ffc3c409d..5c0749eee 100644 --- a/datamodels/ontology-metadata/created_by.html +++ b/datamodels/ontology-metadata/created_by.html @@ -106,56 +106,56 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Axiom

+

A logical or non-logical statement

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Axiom

-

A logical or non-logical statement

+

Subset

+

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/creation_date.html b/datamodels/ontology-metadata/creation_date.html index 0a56dea49..d710ddfc9 100644 --- a/datamodels/ontology-metadata/creation_date.html +++ b/datamodels/ontology-metadata/creation_date.html @@ -106,52 +106,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/creator.html b/datamodels/ontology-metadata/creator.html index d778903ff..02b0e4357 100644 --- a/datamodels/ontology-metadata/creator.html +++ b/datamodels/ontology-metadata/creator.html @@ -106,56 +106,56 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

Ontology

+

An OWL ontology

no

-

Ontology

-

An OWL ontology

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/curator_note.html b/datamodels/ontology-metadata/curator_note.html index 14b9cfead..52bcf8e4e 100644 --- a/datamodels/ontology-metadata/curator_note.html +++ b/datamodels/ontology-metadata/curator_note.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

HasUserInformation

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

HasUserInformation

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/database_cross_reference.html b/datamodels/ontology-metadata/database_cross_reference.html index ea9b7e04b..d7be0881a 100644 --- a/datamodels/ontology-metadata/database_cross_reference.html +++ b/datamodels/ontology-metadata/database_cross_reference.html @@ -106,56 +106,56 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

+

HasMappings

no

-

HomoSapiens

-

An individual human being

-

no

- -

ObjectProperty

-

A property that connects two objects in logical axioms

-

no

-

AnnotationProperty

A property used in non-logical axioms

no

-

Subset

-

A collection of terms grouped for some purpose

+

Agent

+

+

no

+ +

NamedIndividual

+

An instance that has a IRI

no

-

Axiom

+

Axiom

A logical or non-logical statement

yes

-

Property

-

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

+

no

+ +

Subset

+

A collection of terms grouped for some purpose

no

-

HasMappings

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/date.html b/datamodels/ontology-metadata/date.html index 07c3d7cfb..03b807d09 100644 --- a/datamodels/ontology-metadata/date.html +++ b/datamodels/ontology-metadata/date.html @@ -107,52 +107,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/definition.html b/datamodels/ontology-metadata/definition.html index 58e67ce2b..cadaa16a7 100644 --- a/datamodels/ontology-metadata/definition.html +++ b/datamodels/ontology-metadata/definition.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

yes

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

HasMinimalMetadata

-

Absolute minimum metadata model

-

no

- -

Property

+

Class

yes

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

HasMinimalMetadata

+

Absolute minimum metadata model

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

ObjectProperty

+

A property that connects two objects in logical axioms

+

no

+ +

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/definition_source.html b/datamodels/ontology-metadata/definition_source.html index ef7adb98a..1c78e3b42 100644 --- a/datamodels/ontology-metadata/definition_source.html +++ b/datamodels/ontology-metadata/definition_source.html @@ -106,52 +106,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/depicted_by.html b/datamodels/ontology-metadata/depicted_by.html index b54a2dfe9..0341d7453 100644 --- a/datamodels/ontology-metadata/depicted_by.html +++ b/datamodels/ontology-metadata/depicted_by.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

HasUserInformation

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

HasUserInformation

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/deprecated.html b/datamodels/ontology-metadata/deprecated.html index 568b07b3b..74bdb3838 100644 --- a/datamodels/ontology-metadata/deprecated.html +++ b/datamodels/ontology-metadata/deprecated.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

HasLifeCycle

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Image

+

HasLifeCycle

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/disjointWith.html b/datamodels/ontology-metadata/disjointWith.html index dd9c5bc6e..b5ca6d961 100644 --- a/datamodels/ontology-metadata/disjointWith.html +++ b/datamodels/ontology-metadata/disjointWith.html @@ -106,28 +106,28 @@

Applicable Classes

Class

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

PropertyExpression

+

no

ClassExpression

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

Restriction

+

no

-

Restriction

+

Class

no

-

PropertyExpression

-

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

diff --git a/datamodels/ontology-metadata/domain.html b/datamodels/ontology-metadata/domain.html index c4410005e..0ecb2a65b 100644 --- a/datamodels/ontology-metadata/domain.html +++ b/datamodels/ontology-metadata/domain.html @@ -106,24 +106,24 @@

Applicable Classes

ObjectProperty

-

A property that connects two objects in logical axioms

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Property

+

no

-

Subset

-

A collection of terms grouped for some purpose

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

diff --git a/datamodels/ontology-metadata/editor_note.html b/datamodels/ontology-metadata/editor_note.html index 6bd41a076..468dedd41 100644 --- a/datamodels/ontology-metadata/editor_note.html +++ b/datamodels/ontology-metadata/editor_note.html @@ -106,52 +106,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/editor_preferred_term.html b/datamodels/ontology-metadata/editor_preferred_term.html index dc3273a4e..24fbb8726 100644 --- a/datamodels/ontology-metadata/editor_preferred_term.html +++ b/datamodels/ontology-metadata/editor_preferred_term.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

HasSynonyms

+

a mixin for a class whose members can have synonyms

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

HasSynonyms

-

a mixin for a class whose members can have synonyms

+

Class

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/exactMatch.html b/datamodels/ontology-metadata/exactMatch.html index f06975f22..81651ae29 100644 --- a/datamodels/ontology-metadata/exactMatch.html +++ b/datamodels/ontology-metadata/exactMatch.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

yes

-

Image

+

HasMappings

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

+

no

+ +

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

yes

-

HasMappings

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

-

no

- -

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/example_of_usage.html b/datamodels/ontology-metadata/example_of_usage.html index 7036ead23..5effc1245 100644 --- a/datamodels/ontology-metadata/example_of_usage.html +++ b/datamodels/ontology-metadata/example_of_usage.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

HasUserInformation

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

HasUserInformation

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/excluded_from_QC_check.html b/datamodels/ontology-metadata/excluded_from_QC_check.html index 1b2977b09..dc55c57e0 100644 --- a/datamodels/ontology-metadata/excluded_from_QC_check.html +++ b/datamodels/ontology-metadata/excluded_from_QC_check.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

HasLifeCycle

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Image

+

HasLifeCycle

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/excluded_subClassOf.html b/datamodels/ontology-metadata/excluded_subClassOf.html index 4b11860f9..fd2761405 100644 --- a/datamodels/ontology-metadata/excluded_subClassOf.html +++ b/datamodels/ontology-metadata/excluded_subClassOf.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

HasLifeCycle

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Image

+

HasLifeCycle

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/excluded_synonym.html b/datamodels/ontology-metadata/excluded_synonym.html index e7745368c..596c768c2 100644 --- a/datamodels/ontology-metadata/excluded_synonym.html +++ b/datamodels/ontology-metadata/excluded_synonym.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

HasLifeCycle

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Image

+

HasLifeCycle

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/has_alternative_id.html b/datamodels/ontology-metadata/has_alternative_id.html index 4ccbfffea..1fafbec83 100644 --- a/datamodels/ontology-metadata/has_alternative_id.html +++ b/datamodels/ontology-metadata/has_alternative_id.html @@ -107,52 +107,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

HasLifeCycle

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Image

+

HasLifeCycle

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/has_broad_synonym.html b/datamodels/ontology-metadata/has_broad_synonym.html index d94c73666..0cb8fda85 100644 --- a/datamodels/ontology-metadata/has_broad_synonym.html +++ b/datamodels/ontology-metadata/has_broad_synonym.html @@ -110,52 +110,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

HasSynonyms

+

a mixin for a class whose members can have synonyms

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

HasSynonyms

-

a mixin for a class whose members can have synonyms

+

Class

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/has_curation_status.html b/datamodels/ontology-metadata/has_curation_status.html index f07f26003..5dad9989f 100644 --- a/datamodels/ontology-metadata/has_curation_status.html +++ b/datamodels/ontology-metadata/has_curation_status.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

HasUserInformation

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

HasUserInformation

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/has_exact_synonym.html b/datamodels/ontology-metadata/has_exact_synonym.html index 8529f5ca2..a6891e5ca 100644 --- a/datamodels/ontology-metadata/has_exact_synonym.html +++ b/datamodels/ontology-metadata/has_exact_synonym.html @@ -110,56 +110,56 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

HasSynonyms

+

a mixin for a class whose members can have synonyms

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Axiom

+

A logical or non-logical statement

no

-

Axiom

-

A logical or non-logical statement

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

HasSynonyms

-

a mixin for a class whose members can have synonyms

+

Class

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/has_narrow_synonym.html b/datamodels/ontology-metadata/has_narrow_synonym.html index d6bbe5928..6a059fbff 100644 --- a/datamodels/ontology-metadata/has_narrow_synonym.html +++ b/datamodels/ontology-metadata/has_narrow_synonym.html @@ -110,52 +110,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

HasSynonyms

+

a mixin for a class whose members can have synonyms

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

HasSynonyms

-

a mixin for a class whose members can have synonyms

+

Class

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/has_obo_namespace.html b/datamodels/ontology-metadata/has_obo_namespace.html index 42996bbb6..694dd4ebb 100644 --- a/datamodels/ontology-metadata/has_obo_namespace.html +++ b/datamodels/ontology-metadata/has_obo_namespace.html @@ -97,52 +97,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

HasCategory

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

Subset

-

A collection of terms grouped for some purpose

+

Class

+

no

-

Property

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

HasCategory

+

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/has_obsolescence_reason.html b/datamodels/ontology-metadata/has_obsolescence_reason.html index c53d7d940..21c3ff67d 100644 --- a/datamodels/ontology-metadata/has_obsolescence_reason.html +++ b/datamodels/ontology-metadata/has_obsolescence_reason.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

HasLifeCycle

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Image

+

HasLifeCycle

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/has_related_synonym.html b/datamodels/ontology-metadata/has_related_synonym.html index 93c5a25a8..640104094 100644 --- a/datamodels/ontology-metadata/has_related_synonym.html +++ b/datamodels/ontology-metadata/has_related_synonym.html @@ -97,52 +97,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

HasSynonyms

+

a mixin for a class whose members can have synonyms

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

HasSynonyms

-

a mixin for a class whose members can have synonyms

+

Class

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/id.html b/datamodels/ontology-metadata/id.html index 57e337d7c..4460a66ba 100644 --- a/datamodels/ontology-metadata/id.html +++ b/datamodels/ontology-metadata/id.html @@ -107,58 +107,58 @@

Applicable Classes

Agent

-

-

yes

- -

Class

-

+

NamedObject

+

Anything with an IRI

no

-

Image

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

HomoSapiens

-

An individual human being

-

yes

- -

ObjectProperty

-

A property that connects two objects in logical axioms

+

Property

+

no

AnnotationProperty

A property used in non-logical axioms

no

-

Subset

-

A collection of terms grouped for some purpose

+

Agent

+

+

yes

+ +

NamedIndividual

+

An instance that has a IRI

no

-

Property

-

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

NamedObject

-

Anything with an IRI

+

Subset

+

A collection of terms grouped for some purpose

no

-

NamedIndividual

-

An instance that has a IRI

+

Class

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

Image

+

no

-

Ontology

+

Ontology

An OWL ontology

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

+

HomoSapiens

+

An individual human being

+

yes

+ diff --git a/datamodels/ontology-metadata/image.html b/datamodels/ontology-metadata/image.html index 57b2ca612..767551c5f 100644 --- a/datamodels/ontology-metadata/image.html +++ b/datamodels/ontology-metadata/image.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

HasUserInformation

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

HasUserInformation

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/imported_from.html b/datamodels/ontology-metadata/imported_from.html index fac873d02..5a009e339 100644 --- a/datamodels/ontology-metadata/imported_from.html +++ b/datamodels/ontology-metadata/imported_from.html @@ -106,52 +106,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/in_subset.html b/datamodels/ontology-metadata/in_subset.html index 516cbd59a..d2e4f9ef2 100644 --- a/datamodels/ontology-metadata/in_subset.html +++ b/datamodels/ontology-metadata/in_subset.html @@ -98,52 +98,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

HasCategory

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

Subset

-

A collection of terms grouped for some purpose

+

Class

+

no

-

Property

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

HasCategory

+

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/isDefinedBy.html b/datamodels/ontology-metadata/isDefinedBy.html index bf9ad9542..84bf509e6 100644 --- a/datamodels/ontology-metadata/isDefinedBy.html +++ b/datamodels/ontology-metadata/isDefinedBy.html @@ -97,52 +97,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/is_class_level.html b/datamodels/ontology-metadata/is_class_level.html index cf09dcd94..ee3c737ed 100644 --- a/datamodels/ontology-metadata/is_class_level.html +++ b/datamodels/ontology-metadata/is_class_level.html @@ -97,24 +97,24 @@

Applicable Classes

ObjectProperty

-

A property that connects two objects in logical axioms

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Property

+

no

-

Subset

-

A collection of terms grouped for some purpose

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

diff --git a/datamodels/ontology-metadata/is_metadata_tag.html b/datamodels/ontology-metadata/is_metadata_tag.html index d0d8a93a4..5ffbf61ea 100644 --- a/datamodels/ontology-metadata/is_metadata_tag.html +++ b/datamodels/ontology-metadata/is_metadata_tag.html @@ -97,24 +97,24 @@

Applicable Classes

ObjectProperty

-

A property that connects two objects in logical axioms

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Property

+

no

-

Subset

-

A collection of terms grouped for some purpose

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

diff --git a/datamodels/ontology-metadata/label.html b/datamodels/ontology-metadata/label.html index 829c92d27..0d99cf422 100644 --- a/datamodels/ontology-metadata/label.html +++ b/datamodels/ontology-metadata/label.html @@ -106,56 +106,56 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

yes

-

Image

-

-

no

- -

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

-

A collection of terms grouped for some purpose

+

Axiom

+

A logical or non-logical statement

no

-

HasMinimalMetadata

-

Absolute minimum metadata model

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Axiom

-

A logical or non-logical statement

+

Subset

+

A collection of terms grouped for some purpose

no

-

Property

+

Class

yes

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

HasMinimalMetadata

+

Absolute minimum metadata model

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

ObjectProperty

+

A property that connects two objects in logical axioms

+

no

+ +

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/narrowMatch.html b/datamodels/ontology-metadata/narrowMatch.html index 1fc627523..e947bfc03 100644 --- a/datamodels/ontology-metadata/narrowMatch.html +++ b/datamodels/ontology-metadata/narrowMatch.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

yes

-

Image

+

HasMappings

no

-

HomoSapiens

-

An individual human being

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Agent

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Subset

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

+

no

+ +

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

yes

-

HasMappings

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

-

no

- -

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/ontology_term_requester.html b/datamodels/ontology-metadata/ontology_term_requester.html index de51748ec..ddf44de46 100644 --- a/datamodels/ontology-metadata/ontology_term_requester.html +++ b/datamodels/ontology-metadata/ontology_term_requester.html @@ -106,52 +106,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/page.html b/datamodels/ontology-metadata/page.html index bbfa83b5e..9fb285242 100644 --- a/datamodels/ontology-metadata/page.html +++ b/datamodels/ontology-metadata/page.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

HasUserInformation

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

HasUserInformation

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/range.html b/datamodels/ontology-metadata/range.html index c84e4568f..4b4185acf 100644 --- a/datamodels/ontology-metadata/range.html +++ b/datamodels/ontology-metadata/range.html @@ -106,24 +106,24 @@

Applicable Classes

ObjectProperty

-

A property that connects two objects in logical axioms

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Property

+

no

-

Subset

-

A collection of terms grouped for some purpose

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Property

-

+

Subset

+

A collection of terms grouped for some purpose

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

diff --git a/datamodels/ontology-metadata/seeAlso.html b/datamodels/ontology-metadata/seeAlso.html index e4b8e7155..a7881d943 100644 --- a/datamodels/ontology-metadata/seeAlso.html +++ b/datamodels/ontology-metadata/seeAlso.html @@ -97,56 +97,56 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

Image

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Axiom

+

A logical or non-logical statement

no

-

Subset

-

A collection of terms grouped for some purpose

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

Axiom

-

A logical or non-logical statement

+

Subset

+

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

HasUserInformation

+

Image

no

-

NamedIndividual

-

An instance that has a IRI

+

HasUserInformation

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/shorthand.html b/datamodels/ontology-metadata/shorthand.html index 989154f61..038de9518 100644 --- a/datamodels/ontology-metadata/shorthand.html +++ b/datamodels/ontology-metadata/shorthand.html @@ -97,20 +97,20 @@

Applicable Classes

Subset

-

A collection of terms grouped for some purpose

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

Subset

+

A collection of terms grouped for some purpose

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

diff --git a/datamodels/ontology-metadata/should_conform_to.html b/datamodels/ontology-metadata/should_conform_to.html index 64612b0d9..bdc79ea73 100644 --- a/datamodels/ontology-metadata/should_conform_to.html +++ b/datamodels/ontology-metadata/should_conform_to.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

HasLifeCycle

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Image

+

HasLifeCycle

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/term_editor.html b/datamodels/ontology-metadata/term_editor.html index 4b875596c..6cb472341 100644 --- a/datamodels/ontology-metadata/term_editor.html +++ b/datamodels/ontology-metadata/term_editor.html @@ -106,52 +106,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/term_replaced_by.html b/datamodels/ontology-metadata/term_replaced_by.html index 0ae79303c..b55dd4289 100644 --- a/datamodels/ontology-metadata/term_replaced_by.html +++ b/datamodels/ontology-metadata/term_replaced_by.html @@ -106,52 +106,52 @@

Applicable Classes

Agent

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Class

+

Property

no

-

HasLifeCycle

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

HomoSapiens

-

An individual human being

+

Agent

+

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

NamedIndividual

+

An instance that has a IRI

no

-

Image

+

HasLifeCycle

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/term_tracker_item.html b/datamodels/ontology-metadata/term_tracker_item.html index ca3025b2f..c4ccabac2 100644 --- a/datamodels/ontology-metadata/term_tracker_item.html +++ b/datamodels/ontology-metadata/term_tracker_item.html @@ -106,52 +106,52 @@

Applicable Classes

HasProvenance

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Agent

+

Property

no

-

Class

-

+

AnnotationProperty

+

A property used in non-logical axioms

no

-

Image

+

Agent

no

-

HomoSapiens

-

An individual human being

+

NamedIndividual

+

An instance that has a IRI

no

-

ObjectProperty

-

A property that connects two objects in logical axioms

+

HasProvenance

+

no

-

AnnotationProperty

-

A property used in non-logical axioms

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

Subset

A collection of terms grouped for some purpose

no

-

Property

+

Class

no

-

NamedIndividual

-

An instance that has a IRI

+

Image

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

ObjectProperty

+

A property that connects two objects in logical axioms

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/ontology-metadata/type.html b/datamodels/ontology-metadata/type.html index 59433b2a5..99f912b66 100644 --- a/datamodels/ontology-metadata/type.html +++ b/datamodels/ontology-metadata/type.html @@ -106,60 +106,60 @@

Applicable Classes

Agent

-

+

NamedObject

+

Anything with an IRI

no

-

Class

-

+

TransitiveProperty

+

An ObjectProperty with the property of transitivity

no

-

Image

+

Property

no

-

HomoSapiens

-

An individual human being

-

no

- -

ObjectProperty

-

A property that connects two objects in logical axioms

-

no

-

AnnotationProperty

A property used in non-logical axioms

no

-

Thing

+

Agent

no

-

Subset

-

A collection of terms grouped for some purpose

+

NamedIndividual

+

An instance that has a IRI

no

-

Property

-

+

Term

+

A NamedThing that includes classes, properties, but not ontologies

no

-

NamedObject

-

Anything with an IRI

+

Thing

+

no

-

NamedIndividual

-

An instance that has a IRI

+

Class

+

no

-

TransitiveProperty

-

An ObjectProperty with the property of transitivity

+

Image

+

no

Ontology

An OWL ontology

no

-

Term

-

A NamedThing that includes classes, properties, but not ontologies

+

Subset

+

A collection of terms grouped for some purpose

+

no

+ +

ObjectProperty

+

A property that connects two objects in logical axioms

+

no

+ +

HomoSapiens

+

An individual human being

no

diff --git a/datamodels/summary-statistics/agents.html b/datamodels/summary-statistics/agents.html index 7de1aabe0..c4a6ba408 100644 --- a/datamodels/summary-statistics/agents.html +++ b/datamodels/summary-statistics/agents.html @@ -98,16 +98,16 @@

Applicable Classes

UngroupedStatistics

-

A summary statistics report object

+

GroupedStatistics

+

summary statistics for the entire resource

no

SummaryStatisticsReport

abstract base class for all summary statistics reports

no

-

GroupedStatistics

-

summary statistics for the entire resource

+

UngroupedStatistics

+

A summary statistics report object

no

diff --git a/datamodels/summary-statistics/compared_with.html b/datamodels/summary-statistics/compared_with.html index 9a2bf15ed..2c7107c6f 100644 --- a/datamodels/summary-statistics/compared_with.html +++ b/datamodels/summary-statistics/compared_with.html @@ -98,16 +98,16 @@

Applicable Classes

UngroupedStatistics

-

A summary statistics report object

+

GroupedStatistics

+

summary statistics for the entire resource

no

SummaryStatisticsReport

abstract base class for all summary statistics reports

no

-

GroupedStatistics

-

summary statistics for the entire resource

+

UngroupedStatistics

+

A summary statistics report object

no

diff --git a/datamodels/summary-statistics/facet.html b/datamodels/summary-statistics/facet.html index 479a381ae..88106f42e 100644 --- a/datamodels/summary-statistics/facet.html +++ b/datamodels/summary-statistics/facet.html @@ -97,12 +97,12 @@

Applicable Classes

FacetedCount

-

Counts broken down by a facet

+

ChangeTypeStatistic

+

statistics for a particular kind of diff

no

-

ChangeTypeStatistic

-

statistics for a particular kind of diff

+

FacetedCount

+

Counts broken down by a facet

no

diff --git a/datamodels/summary-statistics/filtered_count.html b/datamodels/summary-statistics/filtered_count.html index 225174c03..ae45a4cd5 100644 --- a/datamodels/summary-statistics/filtered_count.html +++ b/datamodels/summary-statistics/filtered_count.html @@ -97,12 +97,12 @@

Applicable Classes

FacetedCount

-

Counts broken down by a facet

+

ChangeTypeStatistic

+

statistics for a particular kind of diff

no

-

ChangeTypeStatistic

-

statistics for a particular kind of diff

+

FacetedCount

+

Counts broken down by a facet

no

diff --git a/datamodels/summary-statistics/id.html b/datamodels/summary-statistics/id.html index f127ba76f..f615e6cf2 100644 --- a/datamodels/summary-statistics/id.html +++ b/datamodels/summary-statistics/id.html @@ -97,28 +97,28 @@

Applicable Classes

UngroupedStatistics

-

A summary statistics report object

+

SummaryStatisticsReport

+

abstract base class for all summary statistics reports

no

GroupedStatistics

summary statistics for the entire resource

no

-

ContributorRole

-

A role that a contributor can have

+

Agent

+

An agent

no

-

SummaryStatisticsReport

-

abstract base class for all summary statistics reports

+

Ontology

+

An ontology

no

-

Ontology

-

An ontology

+

UngroupedStatistics

+

A summary statistics report object

no

-

Agent

-

An agent

+

ContributorRole

+

A role that a contributor can have

no

diff --git a/datamodels/summary-statistics/ontologies.html b/datamodels/summary-statistics/ontologies.html index 9729ed67d..30464c9eb 100644 --- a/datamodels/summary-statistics/ontologies.html +++ b/datamodels/summary-statistics/ontologies.html @@ -98,16 +98,16 @@

Applicable Classes

UngroupedStatistics

-

A summary statistics report object

+

GroupedStatistics

+

summary statistics for the entire resource

no

SummaryStatisticsReport

abstract base class for all summary statistics reports

no

-

GroupedStatistics

-

summary statistics for the entire resource

+

UngroupedStatistics

+

A summary statistics report object

no

diff --git a/datamodels/summary-statistics/was_generated_by.html b/datamodels/summary-statistics/was_generated_by.html index 8449cac76..82df2a3f6 100644 --- a/datamodels/summary-statistics/was_generated_by.html +++ b/datamodels/summary-statistics/was_generated_by.html @@ -98,16 +98,16 @@

Applicable Classes

UngroupedStatistics

-

A summary statistics report object

+

GroupedStatistics

+

summary statistics for the entire resource

no

SummaryStatisticsReport

abstract base class for all summary statistics reports

no

-

GroupedStatistics

-

summary statistics for the entire resource

+

UngroupedStatistics

+

A summary statistics report object

no

diff --git a/datamodels/taxon-constraints/id.html b/datamodels/taxon-constraints/id.html index a28377021..03bca944f 100644 --- a/datamodels/taxon-constraints/id.html +++ b/datamodels/taxon-constraints/id.html @@ -98,22 +98,22 @@

Applicable Classes

PredicateTerm

-

A term that represents a relationship type

-

no

- -

Term

+

Term

An ontology term

no

-

SubjectTerm

+

SubjectTerm

A term that is the subject of a taxon constraint

no

-

Taxon

+

Taxon

A term that represents a taxonomic group, may be at species level of a higher…

no

+

PredicateTerm

+

A term that represents a relationship type

+

no

+ diff --git a/datamodels/taxon-constraints/label.html b/datamodels/taxon-constraints/label.html index aef070826..5037b6ef0 100644 --- a/datamodels/taxon-constraints/label.html +++ b/datamodels/taxon-constraints/label.html @@ -98,22 +98,22 @@

Applicable Classes

PredicateTerm

-

A term that represents a relationship type

-

no

- -

Term

+

Term

An ontology term

no

-

SubjectTerm

+

SubjectTerm

A term that is the subject of a taxon constraint

no

-

Taxon

+

Taxon

A term that represents a taxonomic group, may be at species level of a higher…

no

+

PredicateTerm

+

A term that represents a relationship type

+

no

+ diff --git a/datamodels/text-annotator/matches_whole_text.html b/datamodels/text-annotator/matches_whole_text.html index 71b2d1461..cc738eac1 100644 --- a/datamodels/text-annotator/matches_whole_text.html +++ b/datamodels/text-annotator/matches_whole_text.html @@ -97,12 +97,12 @@

Applicable Classes

TextAnnotationConfiguration

-

configuration for search

+

TextAnnotation

+

An individual text annotation

no

-

TextAnnotation

-

An individual text annotation

+

TextAnnotationConfiguration

+

configuration for search

no

diff --git a/datamodels/text-annotator/subject_end.html b/datamodels/text-annotator/subject_end.html index 005df5635..a19859bf1 100644 --- a/datamodels/text-annotator/subject_end.html +++ b/datamodels/text-annotator/subject_end.html @@ -97,12 +97,12 @@

Applicable Classes

TextAnnotation

-

An individual text annotation

+

HasSpan

+

no

-

HasSpan

-

+

TextAnnotation

+

An individual text annotation

no

diff --git a/datamodels/text-annotator/subject_label.html b/datamodels/text-annotator/subject_label.html index f3002cda2..243d5b20e 100644 --- a/datamodels/text-annotator/subject_label.html +++ b/datamodels/text-annotator/subject_label.html @@ -98,12 +98,12 @@

Applicable Classes

TextAnnotation

-

An individual text annotation

+

HasSpan

+

no

-

HasSpan

-

+

TextAnnotation

+

An individual text annotation

no

diff --git a/datamodels/text-annotator/subject_source.html b/datamodels/text-annotator/subject_source.html index 1982ef524..48ea4c71b 100644 --- a/datamodels/text-annotator/subject_source.html +++ b/datamodels/text-annotator/subject_source.html @@ -97,12 +97,12 @@

Applicable Classes

TextAnnotation

-

An individual text annotation

+

HasSpan

+

no

-

HasSpan

-

+

TextAnnotation

+

An individual text annotation

no

diff --git a/datamodels/text-annotator/subject_start.html b/datamodels/text-annotator/subject_start.html index e0645e88d..46e0a52f6 100644 --- a/datamodels/text-annotator/subject_start.html +++ b/datamodels/text-annotator/subject_start.html @@ -97,12 +97,12 @@

Applicable Classes

TextAnnotation

-

An individual text annotation

+

HasSpan

+

no

-

HasSpan

-

+

TextAnnotation

+

An individual text annotation

no

diff --git a/datamodels/text-annotator/subject_text_id.html b/datamodels/text-annotator/subject_text_id.html index 2f55fb2f9..5b1e077ae 100644 --- a/datamodels/text-annotator/subject_text_id.html +++ b/datamodels/text-annotator/subject_text_id.html @@ -97,12 +97,12 @@

Applicable Classes

TextAnnotation

-

An individual text annotation

+

HasSpan

+

no

-

HasSpan

-

+

TextAnnotation

+

An individual text annotation

no

diff --git a/datamodels/validation/info.html b/datamodels/validation/info.html index 3fb907d76..652f2c513 100644 --- a/datamodels/validation/info.html +++ b/datamodels/validation/info.html @@ -102,18 +102,18 @@

Applicable Classes

RepairOperation

-

The result of performing an individual repair

-

no

- -

MappingValidationResult

+

MappingValidationResult

A validation result where the check is to determine if a mapping is correct

no

-

ExternalReferenceValidationResult

+

ExternalReferenceValidationResult

A validation result where the check is to determine if a link to an external …

no

+

RepairOperation

+

The result of performing an individual repair

+

no

+

ValidationResult

An individual result arising from validation of a data instance using a parti…

no

diff --git a/datamodels/validation/instantiates.html b/datamodels/validation/instantiates.html index 350bd6900..472d81679 100644 --- a/datamodels/validation/instantiates.html +++ b/datamodels/validation/instantiates.html @@ -98,18 +98,18 @@

Applicable Classes

ValidationResult

-

An individual result arising from validation of a data instance using a parti…

-

no

- -

ExternalReferenceValidationResult

+

ExternalReferenceValidationResult

A validation result where the check is to determine if a link to an external …

no

-

DefinitionValidationResult

+

DefinitionValidationResult

no

+

ValidationResult

+

An individual result arising from validation of a data instance using a parti…

+

no

+ diff --git a/datamodels/validation/object.html b/datamodels/validation/object.html index 2cd8b5e08..422fb226c 100644 --- a/datamodels/validation/object.html +++ b/datamodels/validation/object.html @@ -97,18 +97,18 @@

Applicable Classes

ValidationResult

-

An individual result arising from validation of a data instance using a parti…

-

no

- -

ExternalReferenceValidationResult

+

ExternalReferenceValidationResult

A validation result where the check is to determine if a link to an external …

no

-

DefinitionValidationResult

+

DefinitionValidationResult

no

+

ValidationResult

+

An individual result arising from validation of a data instance using a parti…

+

no

+ diff --git a/datamodels/validation/object_str.html b/datamodels/validation/object_str.html index 37b647a96..7115be39e 100644 --- a/datamodels/validation/object_str.html +++ b/datamodels/validation/object_str.html @@ -97,18 +97,18 @@

Applicable Classes

ValidationResult

-

An individual result arising from validation of a data instance using a parti…

-

no

- -

ExternalReferenceValidationResult

+

ExternalReferenceValidationResult

A validation result where the check is to determine if a link to an external …

no

-

DefinitionValidationResult

+

DefinitionValidationResult

no

+

ValidationResult

+

An individual result arising from validation of a data instance using a parti…

+

no

+ diff --git a/datamodels/validation/predicate.html b/datamodels/validation/predicate.html index 9f89f04f5..819c89ce4 100644 --- a/datamodels/validation/predicate.html +++ b/datamodels/validation/predicate.html @@ -98,18 +98,18 @@

Applicable Classes

ValidationResult

-

An individual result arising from validation of a data instance using a parti…

-

no

- -

ExternalReferenceValidationResult

+

ExternalReferenceValidationResult

A validation result where the check is to determine if a link to an external …

no

-

DefinitionValidationResult

+

DefinitionValidationResult

no

+

ValidationResult

+

An individual result arising from validation of a data instance using a parti…

+

no

+ diff --git a/datamodels/validation/results.html b/datamodels/validation/results.html index bf6e9110d..020f8901b 100644 --- a/datamodels/validation/results.html +++ b/datamodels/validation/results.html @@ -98,18 +98,18 @@

Applicable Classes

RepairReport

-

A report that consists of repair operation results

-

yes

- -

ValidationReport

+

ValidationReport

A report that consists of validation results

yes

-

Report

+

Report

A report object that is a holder to multiple report results

no

+

RepairReport

+

A report that consists of repair operation results

+

yes

+ diff --git a/datamodels/validation/severity.html b/datamodels/validation/severity.html index 9f197ebcf..e45e94d4d 100644 --- a/datamodels/validation/severity.html +++ b/datamodels/validation/severity.html @@ -98,22 +98,22 @@

Applicable Classes

ValidationResult

-

An individual result arising from validation of a data instance using a parti…

-

no

- -

ExternalReferenceValidationResult

+

ExternalReferenceValidationResult

A validation result where the check is to determine if a link to an external …

no

-

DefinitionValidationResult

+

DefinitionValidationResult

no

-

TypeSeverityKeyValue

+

TypeSeverityKeyValue

key-value pair that maps a validation result type to a severity setting, for …

no

+

ValidationResult

+

An individual result arising from validation of a data instance using a parti…

+

no

+ diff --git a/datamodels/validation/source.html b/datamodels/validation/source.html index de45c1dd7..4b1358c7c 100644 --- a/datamodels/validation/source.html +++ b/datamodels/validation/source.html @@ -97,18 +97,18 @@

Applicable Classes

ValidationResult

-

An individual result arising from validation of a data instance using a parti…

-

no

- -

ExternalReferenceValidationResult

+

ExternalReferenceValidationResult

A validation result where the check is to determine if a link to an external …

no

-

DefinitionValidationResult

+

DefinitionValidationResult

no

+

ValidationResult

+

An individual result arising from validation of a data instance using a parti…

+

no

+ diff --git a/datamodels/validation/subject.html b/datamodels/validation/subject.html index 1224716f2..f12da67f3 100644 --- a/datamodels/validation/subject.html +++ b/datamodels/validation/subject.html @@ -98,18 +98,18 @@

Applicable Classes

ValidationResult

-

An individual result arising from validation of a data instance using a parti…

-

no

- -

ExternalReferenceValidationResult

+

ExternalReferenceValidationResult

A validation result where the check is to determine if a link to an external …

no

-

DefinitionValidationResult

+

DefinitionValidationResult

no

+

ValidationResult

+

An individual result arising from validation of a data instance using a parti…

+

no

+ diff --git a/datamodels/validation/type.html b/datamodels/validation/type.html index 009e263d5..e7009bc02 100644 --- a/datamodels/validation/type.html +++ b/datamodels/validation/type.html @@ -98,22 +98,22 @@

Applicable Classes

ValidationResult

-

An individual result arising from validation of a data instance using a parti…

-

no

- -

ExternalReferenceValidationResult

+

ExternalReferenceValidationResult

A validation result where the check is to determine if a link to an external …

no

-

DefinitionValidationResult

+

DefinitionValidationResult

no

-

TypeSeverityKeyValue

+

TypeSeverityKeyValue

key-value pair that maps a validation result type to a severity setting, for …

no

+

ValidationResult

+

An individual result arising from validation of a data instance using a parti…

+

no

+ diff --git a/guide/index.html b/guide/index.html index 3356f99a0..05b4b7203 100644 --- a/guide/index.html +++ b/guide/index.html @@ -192,7 +192,10 @@
  • Background
  • Concepts @@ -203,6 +206,7 @@
  • Semsimian
    • +
  • Companion Notebooks
  • Further reading
    • diff --git a/guide/similarity.html b/guide/similarity.html index a424ef64e..01b8cc984 100644 --- a/guide/similarity.html +++ b/guide/similarity.html @@ -65,7 +65,10 @@
  • Background
  • Concepts @@ -76,6 +79,7 @@
  • Semsimian
    • +
  • Companion Notebooks
  • Further reading
    • @@ -123,8 +127,7 @@

    BackgroundSimilarity between Entities, or between Terms, based on properties of the ontology. For example, when comparing two terms, we may want to score terms that are closer together in the ontology -Graph as more similar. Other measures of similarity may be on frequency of usage of terms, -or on vector Embeddings of terms.

    +Graph as more similar. Other measures of similarity may be on frequency of usage of terms,

    If Entities are annotated/associated with terms, we can also compute similarity between these based on the aggregate set of terms they are annotated with. The canonical use case for OAK here is Gene associations (e.g. to phenotypes, GO terms, anatomy or cell @@ -147,13 +150,62 @@

    Jaccard Similarity \[J(A,B) = \frac{|A \cap B|}{|A \cup B|}\]

    where \(A\) and \(B\) are sets.

    -

    When applied to pairs of ontology terms, the sets are typically the Reflexive Ancestors +

    For example given two sets {banana, apple, orange} and {apple, orange, pear}, the intersection of these +two sets is {apple, orange} (size 2) and the union is {banana, apple, orange, pear} (size 4). The Jaccard similarity +is therefore:

    +
    +\[J = \frac{2}{4} = 0.5\]
    + +
    +

    Jaccard Similarity of ontology terms

    +

    When applied to pairs of ontology Terms, the sets are typically the Reflexive Ancestors of the terms of interest. Like all OAK graph operations, the choice of Predicates used is important.

    • Phenotype ontologies typically compute this using SubClassOf links only

    • Ontologies such as GO, Uberon, and ENVO typically use SubClassOf and PartOf links

    +

    For example, given an ontology of vehicles with the following structure:

    +
    Car is-a Vehicle
+Car has-part Engine is_a Part
+Car has-part Wheel is_a Part
+Car has-part Door is_a Part
+Engine has-part Piston is_a Part
+Car has-part Seat is_a Part
+Bicycle is-a Vehicle
+Bicycle has-part Wheel is_a Part
+Bicycle has-part Handlebar is_a Part
+Bicycle has-part Seat is_a Part
+
    +
    +

    Visualized as:

    +
    +Vehicle ontology +
    +

    Vehicle ontology

    +
    +
    +

    If we follow predicates {is-a, has-part} (both of which are reflexive), then we have reflexive ancestors:

    +
      +

    • Car: {Car, Vehicle, Engine, Wheel, Door, Piston, Seat, Part}

      • +

    • Bicycle: {Bicycle, Vehicle, Wheel, Handlebar, Seat, Part}

      • +

    • Intersection: {Vehicle, Wheel, Seat, Part}

      • +

    • Union: {Car, Vehicle, Engine, Wheel, Door, Piston, Seat, Bicycle, Handlebar, Part}

      • +
    +

    The same ontology with the Most Recent Common Ancestor terms of Car and Bicycle highlighted:

    +
    +Vehicle ontology with MRCAs +
    +

    Vehicle ontology with MRCAs

    +
    +
    +

    Jaccard similarity between Car and Bicycle would be:

    +
    +\[J = \frac{4}{10} = 0.4\]
    +

    You can test this by running:

    +
    runoak -i simpleobo:tests/input/vehicles.obo similarity Car @ Bicycle
+
    +

    Information Content

    @@ -166,11 +218,18 @@

    Information ContentAssociations between entities and terms as the corpus

    -

    In both cases the ontology graph is used.

    +

    In both cases the whole ontology Graph is used. This means that a Descendant term +will always have IC that is equal to or greater than its Ancestor term (over some specified +set of predicates).

    When the ontology is used as the corpus, the probability of a term is computed as the number of descendants of a term (reflexive) divided by the total number of terms in the ontology:

    \[P(t) = \frac{|Desc*(t)|}{|T|}\]
    +

    You can see this via

    +
    runoak -i simpleobo:tests/input/vehicles.obo similarity Car @ Bicycle
+
    +
    +

    When we consider all relationships, there are multiple MRCAs (see figure above). These are tied with an IC of 1.29.

    When associations are used, the probability of a term is computed as the number of entities associated with a term (directly or indirectly) divided by the total number of entities:

    @@ -182,19 +241,74 @@

    Information Content--use-associations flag, in addition to specifying the associations themselves:

    -
    runoak  -g phenotype.hpoa -G hpoa -i sqlite:obo:hp information-content -p i --use-associations i^HP:
+
    runoak  -g phenotype.hpoa -G hpoa -i sqlite:obo:hp information-content -p i --use-associations i^HP: -o hp.ics.tsv
 
    
 
    
+
    Here we save to a file hp.ics.tsv
    
 
    IC can be used to score the Most Recent Common Ancestor (MRCAs) of two terms; also known
 as Resnik similarity.
    
+
    We can compare scores using native ontology ICs and ICs using annotations as a corpus
    
+
    runoak -i sqlite:obo:hp similarity -p i HP:0000015 @ HP:0000017
+
    
+
    
+
    Gives an IC of 9.02 for the MRCA of Bladder diverticulum and Nocturia.
    
+
    subject_id: HP:0000015
+subject_label: Bladder diverticulum
+object_id: HP:0000017
+object_label: Nocturia
+ancestor_id: HP:0000014
+ancestor_label: Abnormality of the bladder
+ancestor_information_content: 9.020517017340513
+jaccard_similarity: 0.6
+phenodigm_score: 2.3264372354319613
+
    
+
    
+
    We can plug in the association corpus based IC table using the --information-content-file option:
    
+
    runoak -i sqlite:obo:hp similarity -p i --information-content-file hp.ics.tsv HP:0000015 @ HP:0000017
+
    
+
    
+
    This will give a lower IC:
    
+
    subject_id: HP:0000015
+subject_label: Bladder diverticulum
+object_id: HP:0000017
+object_label: Nocturia
+ancestor_id: HP:0000014
+ancestor_label: Abnormality of the bladder
+ancestor_information_content: 3.042673785507031
+jaccard_similarity: 0.6
+phenodigm_score: 1.3511492409442485
+
    
+
    
+
    The higher IC for pure ontology corpus reflects a bias in depth in the ontology.
    
+

    +
    +

    Ensemble Scoring of term pairs

    +

    We can compute ensemble scores by combining existing scores. For example, the Phenodigm score combines +Jaccard similarity and Resnik similarity.

    +

    See the Phenodigm paper for details.

    +
    +
    +

    Other similarity measures

    +

    Other potential similarity measures include:

    +
      +

    • Phenologs

      • +

    • Embedding-based methods

      +
      +
        +

      • KGE embeddings, e.g. GRAPE

        • +

      • Text embeddings, e.g. using OpenAI text-ada-002

        • +
      +
      +
      • +

    Aggregate measures for comparing entities

    -

    Computing similarity between terms (classes) is relatively easy. But in general users want to compare -entities such as genes. Here we broadly have two approaches:

    +

    Computing similarity between terms (classes) is relatively easy. But in general, users want to compare +entities such as genes. Here we have two broad approaches:

      -

    • Knowledge Graph (KG): treat the entities as nodes in the graph and use the standard ontology methods above

      • -

    • Aggregate Statistics

      • +

    • Knowledge Graph (KG): treat the entities as nodes/terms in the graph and use the standard ontology methods above

      • +

    • Aggregate Statistics (e.g. Best Match Average)

    With the KG approach the entities typically become leaf nodes in the graph, and we compare using standard graph methods where both association predicates (e.g. has-phenotype) and ontology predicates (e.g. is-a and part-of) @@ -209,11 +323,18 @@

    Aggregate measures for comparing entities \[max_{t1 \in e1, t2 \in e2} IC(MRCA(t1,t2))\]

    However, this doesn’t take into account all the other associations for each entity.

    -

    A more common aggregate statistic is Best Match Average (BMA), which is the average of the maximum +

    A more common aggregate statistic is Best Match Average (BMA), which is the average of the maximum pairwise similarity between each term in the first profile and the second profile:

    \[BMA(e1,e2) = \frac{1}{|e1|} \sum_{t1 \in e1} max_{t2 \in e2} IC(MRCA(t1,t2))\]

    Currently this is the default used in OAK.

    +

    This is illustrated in this figure:

    +
    + +
    +

    Aggregate statistics, from the Phenodigm paper.

    +
    +

    To compare two profiles in OAK you can use the termset-similarity command, passing in each profile, separated by @:

    runoak -i sqlite:obo:mp termset-similarity \
@@ -279,6 +400,10 @@ 
    Data Model
+
    Companion Notebooks
    
+
    See the notebook for the `termset-similarity Command <https://github.com/INCATools/ontology-access-kit/blob/main/notebooks/Commands/TermsetSimilarity.ipynb`_
    
+

    Further reading

      diff --git a/item-list/description.md b/item-list/description.md index 58958d683..c02518245 100644 --- a/item-list/description.md +++ b/item-list/description.md @@ -16,8 +16,8 @@ URI: [itemList:description](https://w3id.org/linkml/item-list/description) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ItemList](ItemList.md) | a list of entities plus metadata | no | | [Thing](Thing.md) | | no | +| [ItemList](ItemList.md) | a list of entities plus metadata | no | diff --git a/item-list/id.md b/item-list/id.md index 3a370cc41..5d63d422f 100644 --- a/item-list/id.md +++ b/item-list/id.md @@ -16,8 +16,8 @@ URI: [itemList:id](https://w3id.org/linkml/item-list/id) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ItemList](ItemList.md) | a list of entities plus metadata | no | | [Thing](Thing.md) | | no | +| [ItemList](ItemList.md) | a list of entities plus metadata | no | diff --git a/item-list/name.md b/item-list/name.md index ce080a242..ac4ddc6e6 100644 --- a/item-list/name.md +++ b/item-list/name.md @@ -16,8 +16,8 @@ URI: [itemList:name](https://w3id.org/linkml/item-list/name) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ItemList](ItemList.md) | a list of entities plus metadata | no | | [Thing](Thing.md) | | no | +| [ItemList](ItemList.md) | a list of entities plus metadata | no | diff --git a/mapping-rules/description.md b/mapping-rules/description.md index fae46f765..2870f8a2f 100644 --- a/mapping-rules/description.md +++ b/mapping-rules/description.md @@ -16,8 +16,8 @@ URI: [mappingrules:description](https://w3id.org/oak/mapping-rules-datamodel/des | Name | Description | Modifies Slot | | --- | --- | --- | -| [Synonymizer](Synonymizer.md) | Specification of a rule for generating a synonym or alternate lexical element | no | | [MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no | +| [Synonymizer](Synonymizer.md) | Specification of a rule for generating a synonym or alternate lexical element | no | diff --git a/mapping-rules/prefix.md b/mapping-rules/prefix.md index 5be51fbc0..cf5dc00cd 100644 --- a/mapping-rules/prefix.md +++ b/mapping-rules/prefix.md @@ -17,8 +17,8 @@ URI: [mappingrules:prefix](https://w3id.org/oak/mapping-rules-datamodel/prefix) | Name | Description | Modifies Slot | | --- | --- | --- | | [Test](Test.md) | A unit test for a rule, specifies an intended output for an input | no | -| [Synonymizer](Synonymizer.md) | Specification of a rule for generating a synonym or alternate lexical element | no | | [RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no | +| [Synonymizer](Synonymizer.md) | Specification of a rule for generating a synonym or alternate lexical element | no | diff --git a/mapping-rules/rules.md b/mapping-rules/rules.md index 1b068045d..dc695747f 100644 --- a/mapping-rules/rules.md +++ b/mapping-rules/rules.md @@ -16,8 +16,8 @@ URI: [mappingrules:rules](https://w3id.org/oak/mapping-rules-datamodel/rules) | Name | Description | Modifies Slot | | --- | --- | --- | -| [MappingRuleCollection](MappingRuleCollection.md) | A collection of mapping rules | no | | [RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no | +| [MappingRuleCollection](MappingRuleCollection.md) | A collection of mapping rules | no | diff --git a/objects.inv b/objects.inv index 35c283e7b19d9f976de1164f1ef78dad1d2903e4..3f8278d12f7e52eea593387557dd9c3e5e08f891 100644 GIT binary patch delta 35246 zcmV)OK(@b;&jNtZ0Il zW`1azzUXuWqo}eql~QC+MmRBaS0UX8eJTQ;FE*Cm)+C1oFx>*GGT988#H22Ub?_ot zQbA)YQ6dG?^2BQ3+IsFxi>9U_w69tNS2nYm_tE+4PZWOP9$nzwe;atDf!#1FP9);@ zn}1iHhOqkx&qi=dDgik0RY0YB&kQok%V>wllc-XMkICJdi=&gVd+fjx_v)U%?>d7s z8}|0wdfcLKvx=Lt!&3{EXI2>SNlfj+9=(!3n*|OuOu5#_nQfTYC^5Ri{-` zaWx{blu~ozF`P37e|dl&BOhf_yVQ3t69{XXQNH~KaKcsalvx||VUG!T5 z592l?g9?GG>WbkijXOb{@?d(`qNdI(ky^y(6|9Q#&VgKiEf4+>TVWSID;xLtamBYms 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z&@^zX*HzkAQcVdoqfQl$b(H{bg|q$G9^TuAdtly4`bL?Ne4FxiWxeUKtKcN;Fr6y1 zhHinsKh^uU$nDM4@7yawyxS2)Rh&Adx9e_lj{PK0GwtYK=R^N6|69!&*j!40e|+es z^rJ)0z+Ha>ZlJ?k4b$I}wt_zVw<1~&3`G^$dxx%_VPlij`9)|k|2 zd18tzKQ`x)s=%I_n*Nm+r1J_0g zid-|uZm=F&u}0H_d`r_Fs+#lSK;(SL{Ec56ub;Z%;vtebhK`{Pg8sr&UOe_QZ0q`f8qYQxr*kd!82GY0&lua@duBPo0Vvu8}&Scg@6A39|_${ zqAM--x6lTM<ER8Pwm79rrF5a+Of!MA z-F(qa(>TFEG$bFDt%xINezR$M_;$^6)PVt4On!u6-j5_6eLt`+e<;kn&9+gz%`ife zQ`ww3>OHd?%lS^*xHLB87wmg&#ov6<$b$8F zTD~xGWgld6I>CwPvjZI&0XpiVs6FvtUfBycz6&VB>&+6Re^WHD2 z1|sWBMFqnXyf6LIQD}@QAp#;@R6rwgH$pzOk_MYI tVT6{E?y)VX7?KvX!s>qD&ASBYh5Gb!IplIx1NEE6yz}^r{|8965ab2eshj`+ diff --git a/obograph/id.md b/obograph/id.md index 7b3834f53..76ef7e43c 100644 --- a/obograph/id.md +++ b/obograph/id.md @@ -21,9 +21,9 @@ URI: [obographs:id](https://github.com/geneontology/obographs/id) | Name | Description | Modifies Slot | | --- | --- | --- | +| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | | [Node](Node.md) | A node is a class, property, or other entity in an ontology | no | | [SubsetDefinition](SubsetDefinition.md) | | no | -| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | | [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no | diff --git a/obograph/lang.md b/obograph/lang.md index 318dac109..134e96d99 100644 --- a/obograph/lang.md +++ b/obograph/lang.md @@ -21,11 +21,11 @@ URI: [obographs:lang](https://github.com/geneontology/obographs/lang) | Name | Description | Modifies Slot | | --- | --- | --- | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | -| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | | [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | | [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | diff --git a/obograph/lbl.md b/obograph/lbl.md index 065f83a47..b6c6d5c1a 100644 --- a/obograph/lbl.md +++ b/obograph/lbl.md @@ -21,9 +21,9 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label) | Name | Description | Modifies Slot | | --- | --- | --- | +| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | | [Node](Node.md) | A node is a class, property, or other entity in an ontology | no | | [SubsetDefinition](SubsetDefinition.md) | | no | -| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | | [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no | diff --git a/obograph/meta.md b/obograph/meta.md index b73cbb638..dd5dd6342 100644 --- a/obograph/meta.md +++ b/obograph/meta.md @@ -21,21 +21,21 @@ URI: [obographs:meta](https://github.com/geneontology/obographs/meta) | Name | Description | Modifies Slot | | --- | --- | --- | +| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no | +| [PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no | +| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no | +| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | +| [EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no | | [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | | [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | -| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no | -| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | +| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | | [Node](Node.md) | A node is a class, property, or other entity in an ontology | no | -| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | -| [LogicalDefinitionAxiom](LogicalDefinitionAxiom.md) | An axiom that defines a class in terms of a genus or set of genus classes and... | no | | [Axiom](Axiom.md) | A generic grouping for any OWL axiom or group of axioms that is not captured ... | no | -| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no | | [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no | -| [EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no | -| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no | -| [PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | no | -| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | +| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no | diff --git a/obograph/pred.md b/obograph/pred.md index 1b6f63d91..808182811 100644 --- a/obograph/pred.md +++ b/obograph/pred.md @@ -21,13 +21,13 @@ URI: [rdf:predicate](http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate) | Name | Description | Modifies Slot | | --- | --- | --- | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | -| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no | +| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | | [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes | +| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | +| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | | [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no | | [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | -| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | -| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | diff --git a/obograph/prefixes.md b/obograph/prefixes.md index 53707aed8..09d8fdf1d 100644 --- a/obograph/prefixes.md +++ b/obograph/prefixes.md @@ -21,8 +21,8 @@ URI: [sh:declare](https://w3id.org/shacl/declare) | Name | Description | Modifies Slot | | --- | --- | --- | -| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no | | [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no | +| [GraphDocument](GraphDocument.md) | A graph document is a collection of graphs together with a set of prefixes th... | no | diff --git a/obograph/val.md b/obograph/val.md index e810c9eea..abbd8de5f 100644 --- a/obograph/val.md +++ b/obograph/val.md @@ -21,11 +21,11 @@ URI: [rdf:object](http://www.w3.org/1999/02/22-rdf-syntax-ns#object) | Name | Description | Modifies Slot | | --- | --- | --- | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes | -| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | yes | | [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | yes | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes | | [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | yes | diff --git a/obograph/valType.md b/obograph/valType.md index 00394089a..4462f2186 100644 --- a/obograph/valType.md +++ b/obograph/valType.md @@ -21,11 +21,11 @@ URI: [obographs:valType](https://github.com/geneontology/obographs/valType) | Name | Description | Modifies Slot | | --- | --- | --- | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | -| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | | [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no | | [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | diff --git a/obograph/xrefs.md b/obograph/xrefs.md index b2a52e736..8e7772ef3 100644 --- a/obograph/xrefs.md +++ b/obograph/xrefs.md @@ -21,12 +21,12 @@ URI: [obographs:xrefs](https://github.com/geneontology/obographs/xrefs) | Name | Description | Modifies Slot | | --- | --- | --- | +| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | | [Meta](Meta.md) | A collection of annotations on an entity or ontology or edge or axiom | yes | -| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes | | [SynonymPropertyValue](SynonymPropertyValue.md) | A property value that represents an assertion about a synonym of an entity | no | -| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | -| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no | +| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | yes | | [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no | +| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no | diff --git a/ontology-metadata/IEDB_alternative_term.md b/ontology-metadata/IEDB_alternative_term.md index 99ff9c487..7e3da62d1 100644 --- a/ontology-metadata/IEDB_alternative_term.md +++ b/ontology-metadata/IEDB_alternative_term.md @@ -21,18 +21,18 @@ URI: [OBI:9991118](http://purl.obolibrary.org/obo/OBI_9991118) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/ISA_alternative_term.md b/ontology-metadata/ISA_alternative_term.md index cd84f260e..9d6742db1 100644 --- a/ontology-metadata/ISA_alternative_term.md +++ b/ontology-metadata/ISA_alternative_term.md @@ -21,18 +21,18 @@ URI: [OBI:0001847](http://purl.obolibrary.org/obo/OBI_0001847) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/OBO_foundry_unique_label.md b/ontology-metadata/OBO_foundry_unique_label.md index 643f920a4..6ca150297 100644 --- a/ontology-metadata/OBO_foundry_unique_label.md +++ b/ontology-metadata/OBO_foundry_unique_label.md @@ -21,18 +21,18 @@ URI: [IAO:0000589](http://purl.obolibrary.org/obo/IAO_0000589) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/alternative_term.md b/ontology-metadata/alternative_term.md index 9c78cbc28..5ab7cabda 100644 --- a/ontology-metadata/alternative_term.md +++ b/ontology-metadata/alternative_term.md @@ -25,18 +25,18 @@ URI: [IAO:0000118](http://purl.obolibrary.org/obo/IAO_0000118) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/broadMatch.md b/ontology-metadata/broadMatch.md index 8279ba175..ef8aa0759 100644 --- a/ontology-metadata/broadMatch.md +++ b/ontology-metadata/broadMatch.md @@ -21,18 +21,18 @@ URI: [skos:broadMatch](http://www.w3.org/2004/02/skos/core#broadMatch) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | yes | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | yes | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | yes | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/category.md b/ontology-metadata/category.md index d53a1579b..1ac32c2c5 100644 --- a/ontology-metadata/category.md +++ b/ontology-metadata/category.md @@ -21,18 +21,18 @@ URI: [biolink:category](https://w3id.org/biolink/vocab/category) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [HasCategory](HasCategory.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/closeMatch.md b/ontology-metadata/closeMatch.md index 21a6e3ad9..0c42d6ab3 100644 --- a/ontology-metadata/closeMatch.md +++ b/ontology-metadata/closeMatch.md @@ -21,18 +21,18 @@ URI: [skos:closeMatch](http://www.w3.org/2004/02/skos/core#closeMatch) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | yes | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | yes | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | yes | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/comment.md b/ontology-metadata/comment.md index 942f759df..9c04ba804 100644 --- a/ontology-metadata/comment.md +++ b/ontology-metadata/comment.md @@ -21,20 +21,20 @@ URI: [rdfs:comment](http://www.w3.org/2000/01/rdf-schema#comment) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | -| [Property](Property.md) | | no | -| [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HasUserInformation](HasUserInformation.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/conformsTo.md b/ontology-metadata/conformsTo.md index bb7b430c7..03c858cd2 100644 --- a/ontology-metadata/conformsTo.md +++ b/ontology-metadata/conformsTo.md @@ -21,18 +21,18 @@ URI: [dcterms:conformsTo](http://purl.org/dc/terms/conformsTo) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [HasCategory](HasCategory.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/consider.md b/ontology-metadata/consider.md index 2c4977080..0f9ccab7e 100644 --- a/ontology-metadata/consider.md +++ b/ontology-metadata/consider.md @@ -21,18 +21,18 @@ URI: [oio:consider](http://www.geneontology.org/formats/oboInOwl#consider) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/contributor.md b/ontology-metadata/contributor.md index 7b24a55e0..16abfae49 100644 --- a/ontology-metadata/contributor.md +++ b/ontology-metadata/contributor.md @@ -21,18 +21,18 @@ URI: [dcterms:contributor](http://purl.org/dc/terms/contributor) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/created.md b/ontology-metadata/created.md index d04bf6fed..ece805c44 100644 --- a/ontology-metadata/created.md +++ b/ontology-metadata/created.md @@ -26,19 +26,19 @@ URI: [dcterms:created](http://purl.org/dc/terms/created) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/created_by.md b/ontology-metadata/created_by.md index e745d9ab3..5e9010dbd 100644 --- a/ontology-metadata/created_by.md +++ b/ontology-metadata/created_by.md @@ -21,19 +21,19 @@ URI: [oio:created_by](http://www.geneontology.org/formats/oboInOwl#created_by) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/creation_date.md b/ontology-metadata/creation_date.md index 306768094..29c7b50fc 100644 --- a/ontology-metadata/creation_date.md +++ b/ontology-metadata/creation_date.md @@ -21,18 +21,18 @@ URI: [oio:creation_date](http://www.geneontology.org/formats/oboInOwl#creation_d | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/creator.md b/ontology-metadata/creator.md index 6cbde240c..9f921cb1a 100644 --- a/ontology-metadata/creator.md +++ b/ontology-metadata/creator.md @@ -21,19 +21,19 @@ URI: [dcterms:creator](http://purl.org/dc/terms/creator) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/curator_note.md b/ontology-metadata/curator_note.md index 02e9a7d0c..339e6ea56 100644 --- a/ontology-metadata/curator_note.md +++ b/ontology-metadata/curator_note.md @@ -21,18 +21,18 @@ URI: [IAO:0000232](http://purl.obolibrary.org/obo/IAO_0000232) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/database_cross_reference.md b/ontology-metadata/database_cross_reference.md index 6310ca3d7..e033aa969 100644 --- a/ontology-metadata/database_cross_reference.md +++ b/ontology-metadata/database_cross_reference.md @@ -21,19 +21,19 @@ URI: [oio:hasDbXref](http://www.geneontology.org/formats/oboInOwl#hasDbXref) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | yes | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | yes | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/date.md b/ontology-metadata/date.md index ffe404f92..d62a008ee 100644 --- a/ontology-metadata/date.md +++ b/ontology-metadata/date.md @@ -26,18 +26,18 @@ URI: [dcterms:date](http://purl.org/dc/terms/date) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/definition.md b/ontology-metadata/definition.md index d96988b8a..cda00c955 100644 --- a/ontology-metadata/definition.md +++ b/ontology-metadata/definition.md @@ -21,18 +21,18 @@ URI: [IAO:0000115](http://purl.obolibrary.org/obo/IAO_0000115) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | yes | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | yes | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [HasMinimalMetadata](HasMinimalMetadata.md) | Absolute minimum metadata model | no | -| [Property](Property.md) | | yes | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/definition_source.md b/ontology-metadata/definition_source.md index deca2b6fa..55d8258d7 100644 --- a/ontology-metadata/definition_source.md +++ b/ontology-metadata/definition_source.md @@ -21,18 +21,18 @@ URI: [IAO:0000119](http://purl.obolibrary.org/obo/IAO_0000119) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/depicted_by.md b/ontology-metadata/depicted_by.md index 7394ba03f..004cfec45 100644 --- a/ontology-metadata/depicted_by.md +++ b/ontology-metadata/depicted_by.md @@ -21,18 +21,18 @@ URI: [foaf:depicted_by](http://xmlns.com/foaf/0.1/depicted_by) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/deprecated.md b/ontology-metadata/deprecated.md index e9c411cf1..663eebdff 100644 --- a/ontology-metadata/deprecated.md +++ b/ontology-metadata/deprecated.md @@ -21,18 +21,18 @@ URI: [owl:deprecated](http://www.w3.org/2002/07/owl#deprecated) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/disjointWith.md b/ontology-metadata/disjointWith.md index 01ff46175..c9ea1aee2 100644 --- a/ontology-metadata/disjointWith.md +++ b/ontology-metadata/disjointWith.md @@ -21,12 +21,12 @@ URI: [owl:disjointWith](http://www.w3.org/2002/07/owl#disjointWith) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Class](Class.md) | | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [ClassExpression](ClassExpression.md) | | no | | [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Restriction](Restriction.md) | | no | | [PropertyExpression](PropertyExpression.md) | | no | +| [ClassExpression](ClassExpression.md) | | no | +| [Restriction](Restriction.md) | | no | +| [Class](Class.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/ontology-metadata/domain.md b/ontology-metadata/domain.md index b573af9bb..a937e2a5f 100644 --- a/ontology-metadata/domain.md +++ b/ontology-metadata/domain.md @@ -21,11 +21,11 @@ URI: [rdfs:domain](http://www.w3.org/2000/01/rdf-schema#domain) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/ontology-metadata/editor_note.md b/ontology-metadata/editor_note.md index 2fdd161b3..2f3a7f0d6 100644 --- a/ontology-metadata/editor_note.md +++ b/ontology-metadata/editor_note.md @@ -21,18 +21,18 @@ URI: [IAO:0000116](http://purl.obolibrary.org/obo/IAO_0000116) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/editor_preferred_term.md b/ontology-metadata/editor_preferred_term.md index 8b02292d8..2820a3dd4 100644 --- a/ontology-metadata/editor_preferred_term.md +++ b/ontology-metadata/editor_preferred_term.md @@ -21,18 +21,18 @@ URI: [IAO:0000111](http://purl.obolibrary.org/obo/IAO_0000111) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/exactMatch.md b/ontology-metadata/exactMatch.md index b643993ab..75429d24c 100644 --- a/ontology-metadata/exactMatch.md +++ b/ontology-metadata/exactMatch.md @@ -21,18 +21,18 @@ URI: [skos:exactMatch](http://www.w3.org/2004/02/skos/core#exactMatch) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | yes | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | yes | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | yes | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/example_of_usage.md b/ontology-metadata/example_of_usage.md index 3f0f79f01..5ca0003eb 100644 --- a/ontology-metadata/example_of_usage.md +++ b/ontology-metadata/example_of_usage.md @@ -21,18 +21,18 @@ URI: [IAO:0000112](http://purl.obolibrary.org/obo/IAO_0000112) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/excluded_from_QC_check.md b/ontology-metadata/excluded_from_QC_check.md index ef71d3667..ea65adff8 100644 --- a/ontology-metadata/excluded_from_QC_check.md +++ b/ontology-metadata/excluded_from_QC_check.md @@ -21,18 +21,18 @@ URI: [omoschema:excluded_from_QC_check](https://w3id.org/oak/ontology-metadata/e | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/excluded_subClassOf.md b/ontology-metadata/excluded_subClassOf.md index bebe788e8..883b6604b 100644 --- a/ontology-metadata/excluded_subClassOf.md +++ b/ontology-metadata/excluded_subClassOf.md @@ -21,18 +21,18 @@ URI: [omoschema:excluded_subClassOf](https://w3id.org/oak/ontology-metadata/excl | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/excluded_synonym.md b/ontology-metadata/excluded_synonym.md index 499fbdccc..e64e5cbcc 100644 --- a/ontology-metadata/excluded_synonym.md +++ b/ontology-metadata/excluded_synonym.md @@ -21,18 +21,18 @@ URI: [omoschema:excluded_synonym](https://w3id.org/oak/ontology-metadata/exclude | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/has_alternative_id.md b/ontology-metadata/has_alternative_id.md index f67f9ac0f..a1d3cbad8 100644 --- a/ontology-metadata/has_alternative_id.md +++ b/ontology-metadata/has_alternative_id.md @@ -26,18 +26,18 @@ URI: [oio:hasAlternativeId](http://www.geneontology.org/formats/oboInOwl#hasAlte | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/has_broad_synonym.md b/ontology-metadata/has_broad_synonym.md index d0c047028..2cc0e6c76 100644 --- a/ontology-metadata/has_broad_synonym.md +++ b/ontology-metadata/has_broad_synonym.md @@ -22,18 +22,18 @@ URI: [oio:hasBroadSynonym](http://www.geneontology.org/formats/oboInOwl#hasBroad | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/has_curation_status.md b/ontology-metadata/has_curation_status.md index d8b28ce70..c254a613f 100644 --- a/ontology-metadata/has_curation_status.md +++ b/ontology-metadata/has_curation_status.md @@ -21,18 +21,18 @@ URI: [IAO:0000114](http://purl.obolibrary.org/obo/IAO_0000114) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/has_exact_synonym.md b/ontology-metadata/has_exact_synonym.md index 18db98321..2bff7b21b 100644 --- a/ontology-metadata/has_exact_synonym.md +++ b/ontology-metadata/has_exact_synonym.md @@ -22,19 +22,19 @@ URI: [oio:hasExactSynonym](http://www.geneontology.org/formats/oboInOwl#hasExact | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/has_narrow_synonym.md b/ontology-metadata/has_narrow_synonym.md index 2b5a78794..bb5143c28 100644 --- a/ontology-metadata/has_narrow_synonym.md +++ b/ontology-metadata/has_narrow_synonym.md @@ -22,18 +22,18 @@ URI: [oio:hasNarrowSynonym](http://www.geneontology.org/formats/oboInOwl#hasNarr | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/has_obo_namespace.md b/ontology-metadata/has_obo_namespace.md index 2076712b2..1463670ef 100644 --- a/ontology-metadata/has_obo_namespace.md +++ b/ontology-metadata/has_obo_namespace.md @@ -16,18 +16,18 @@ URI: [oio:hasOBONamespace](http://www.geneontology.org/formats/oboInOwl#hasOBONa | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [HasCategory](HasCategory.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/has_obsolescence_reason.md b/ontology-metadata/has_obsolescence_reason.md index 352584f5c..365618de2 100644 --- a/ontology-metadata/has_obsolescence_reason.md +++ b/ontology-metadata/has_obsolescence_reason.md @@ -21,18 +21,18 @@ URI: [IAO:0000231](http://purl.obolibrary.org/obo/IAO_0000231) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/has_related_synonym.md b/ontology-metadata/has_related_synonym.md index 3776ccd1b..a1ca98121 100644 --- a/ontology-metadata/has_related_synonym.md +++ b/ontology-metadata/has_related_synonym.md @@ -16,18 +16,18 @@ URI: [oio:hasRelatedSynonym](http://www.geneontology.org/formats/oboInOwl#hasRel | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | | [HasSynonyms](HasSynonyms.md) | a mixin for a class whose members can have synonyms | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/id.md b/ontology-metadata/id.md index 92c0d849c..d9f6d6738 100644 --- a/ontology-metadata/id.md +++ b/ontology-metadata/id.md @@ -26,19 +26,19 @@ URI: [omoschema:id](https://w3id.org/oak/ontology-metadata/id) | Name | Description | Modifies Slot | | --- | --- | --- | +| [NamedObject](NamedObject.md) | Anything with an IRI | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | yes | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | yes | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedObject](NamedObject.md) | Anything with an IRI | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | yes | diff --git a/ontology-metadata/image.md b/ontology-metadata/image.md index 300abb335..86f468bad 100644 --- a/ontology-metadata/image.md +++ b/ontology-metadata/image.md @@ -21,18 +21,18 @@ URI: [sdo:image](http://schema.org/image) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/imported_from.md b/ontology-metadata/imported_from.md index 4faa4311d..defeab245 100644 --- a/ontology-metadata/imported_from.md +++ b/ontology-metadata/imported_from.md @@ -21,18 +21,18 @@ URI: [IAO:0000412](http://purl.obolibrary.org/obo/IAO_0000412) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/in_subset.md b/ontology-metadata/in_subset.md index a556a5f24..630a77304 100644 --- a/ontology-metadata/in_subset.md +++ b/ontology-metadata/in_subset.md @@ -21,18 +21,18 @@ URI: [oio:inSubset](http://www.geneontology.org/formats/oboInOwl#inSubset) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [HasCategory](HasCategory.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/isDefinedBy.md b/ontology-metadata/isDefinedBy.md index 7b5f12af9..d8b0d0119 100644 --- a/ontology-metadata/isDefinedBy.md +++ b/ontology-metadata/isDefinedBy.md @@ -16,18 +16,18 @@ URI: [rdfs:isDefinedBy](http://www.w3.org/2000/01/rdf-schema#isDefinedBy) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/is_class_level.md b/ontology-metadata/is_class_level.md index ba17ee809..272500536 100644 --- a/ontology-metadata/is_class_level.md +++ b/ontology-metadata/is_class_level.md @@ -16,11 +16,11 @@ URI: [oio:is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_ | Name | Description | Modifies Slot | | --- | --- | --- | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/ontology-metadata/is_metadata_tag.md b/ontology-metadata/is_metadata_tag.md index b86998bf7..7261f28ba 100644 --- a/ontology-metadata/is_metadata_tag.md +++ b/ontology-metadata/is_metadata_tag.md @@ -16,11 +16,11 @@ URI: [oio:is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metad | Name | Description | Modifies Slot | | --- | --- | --- | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/ontology-metadata/label.md b/ontology-metadata/label.md index aab579974..3b9c100d3 100644 --- a/ontology-metadata/label.md +++ b/ontology-metadata/label.md @@ -21,19 +21,19 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | yes | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | yes | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [HasMinimalMetadata](HasMinimalMetadata.md) | Absolute minimum metadata model | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | -| [Property](Property.md) | | yes | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/narrowMatch.md b/ontology-metadata/narrowMatch.md index 484b4d313..e2d818aee 100644 --- a/ontology-metadata/narrowMatch.md +++ b/ontology-metadata/narrowMatch.md @@ -21,18 +21,18 @@ URI: [skos:narrowMatch](http://www.w3.org/2004/02/skos/core#narrowMatch) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | yes | -| [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | yes | | [HasMappings](HasMappings.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | yes | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/ontology_term_requester.md b/ontology-metadata/ontology_term_requester.md index 69b0bc5cf..412a513e4 100644 --- a/ontology-metadata/ontology_term_requester.md +++ b/ontology-metadata/ontology_term_requester.md @@ -21,18 +21,18 @@ URI: [IAO:0000234](http://purl.obolibrary.org/obo/IAO_0000234) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/page.md b/ontology-metadata/page.md index 65fe63dbd..a0f04f245 100644 --- a/ontology-metadata/page.md +++ b/ontology-metadata/page.md @@ -21,18 +21,18 @@ URI: [foaf:page](http://xmlns.com/foaf/0.1/page) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/range.md b/ontology-metadata/range.md index 9c3574f89..92abc8765 100644 --- a/ontology-metadata/range.md +++ b/ontology-metadata/range.md @@ -21,11 +21,11 @@ URI: [rdfs:range](http://www.w3.org/2000/01/rdf-schema#range) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/ontology-metadata/seeAlso.md b/ontology-metadata/seeAlso.md index 86f601489..d7e8b3959 100644 --- a/ontology-metadata/seeAlso.md +++ b/ontology-metadata/seeAlso.md @@ -16,19 +16,19 @@ URI: [rdfs:seeAlso](http://www.w3.org/2000/01/rdf-schema#seeAlso) | Name | Description | Modifies Slot | | --- | --- | --- | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Axiom](Axiom.md) | A logical or non-logical statement | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Axiom](Axiom.md) | A logical or non-logical statement | no | -| [Property](Property.md) | | no | | [HasUserInformation](HasUserInformation.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/shorthand.md b/ontology-metadata/shorthand.md index 7d5adf07e..5016fd3b4 100644 --- a/ontology-metadata/shorthand.md +++ b/ontology-metadata/shorthand.md @@ -16,10 +16,10 @@ URI: [oio:shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | | [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | diff --git a/ontology-metadata/should_conform_to.md b/ontology-metadata/should_conform_to.md index 646f83627..d1bae1035 100644 --- a/ontology-metadata/should_conform_to.md +++ b/ontology-metadata/should_conform_to.md @@ -21,18 +21,18 @@ URI: [omoschema:should_conform_to](https://w3id.org/oak/ontology-metadata/should | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/term_editor.md b/ontology-metadata/term_editor.md index b61f241cc..ca1a7f2e8 100644 --- a/ontology-metadata/term_editor.md +++ b/ontology-metadata/term_editor.md @@ -21,18 +21,18 @@ URI: [IAO:0000117](http://purl.obolibrary.org/obo/IAO_0000117) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/term_replaced_by.md b/ontology-metadata/term_replaced_by.md index 8648f9228..4e054b2c5 100644 --- a/ontology-metadata/term_replaced_by.md +++ b/ontology-metadata/term_replaced_by.md @@ -21,18 +21,18 @@ URI: [IAO:0100001](http://purl.obolibrary.org/obo/IAO_0100001) | Name | Description | Modifies Slot | | --- | --- | --- | -| [Agent](Agent.md) | | no | -| [Class](Class.md) | | no | -| [HasLifeCycle](HasLifeCycle.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [Image](Image.md) | | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | +| [Agent](Agent.md) | | no | | [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [HasLifeCycle](HasLifeCycle.md) | | no | | [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [Class](Class.md) | | no | +| [Image](Image.md) | | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/term_tracker_item.md b/ontology-metadata/term_tracker_item.md index d29df3596..ae7bce31e 100644 --- a/ontology-metadata/term_tracker_item.md +++ b/ontology-metadata/term_tracker_item.md @@ -21,18 +21,18 @@ URI: [IAO:0000233](http://purl.obolibrary.org/obo/IAO_0000233) | Name | Description | Modifies Slot | | --- | --- | --- | -| [HasProvenance](HasProvenance.md) | | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [HasProvenance](HasProvenance.md) | | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | | [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/ontology-metadata/type.md b/ontology-metadata/type.md index 9a3807adc..f131efe34 100644 --- a/ontology-metadata/type.md +++ b/ontology-metadata/type.md @@ -21,20 +21,20 @@ URI: [rdf:type](http://www.w3.org/1999/02/22-rdf-syntax-ns#type) | Name | Description | Modifies Slot | | --- | --- | --- | +| [NamedObject](NamedObject.md) | Anything with an IRI | no | +| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | +| [Property](Property.md) | | no | +| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | | [Agent](Agent.md) | | no | +| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | +| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Thing](Thing.md) | | no | | [Class](Class.md) | | no | | [Image](Image.md) | | no | -| [HomoSapiens](HomoSapiens.md) | An individual human being | no | -| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | -| [AnnotationProperty](AnnotationProperty.md) | A property used in non-logical axioms | no | -| [Thing](Thing.md) | | no | -| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | -| [Property](Property.md) | | no | -| [NamedObject](NamedObject.md) | Anything with an IRI | no | -| [NamedIndividual](NamedIndividual.md) | An instance that has a IRI | no | -| [TransitiveProperty](TransitiveProperty.md) | An ObjectProperty with the property of transitivity | no | | [Ontology](Ontology.md) | An OWL ontology | no | -| [Term](Term.md) | A NamedThing that includes classes, properties, but not ontologies | no | +| [Subset](Subset.md) | A collection of terms grouped for some purpose | no | +| [ObjectProperty](ObjectProperty.md) | A property that connects two objects in logical axioms | no | +| [HomoSapiens](HomoSapiens.md) | An individual human being | no | diff --git a/searchindex.js b/searchindex.js index 096caa5cb..10bece154 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["cli", "concepts", "contributing", "datamodels/association/Association", "datamodels/association/AssociationChange", "datamodels/association/Boolean", "datamodels/association/Curie", "datamodels/association/Date", "datamodels/association/DateOrDatetime", "datamodels/association/Datetime", "datamodels/association/Decimal", "datamodels/association/Double", "datamodels/association/Float", "datamodels/association/Integer", "datamodels/association/Jsonpath", "datamodels/association/Jsonpointer", "datamodels/association/Ncname", "datamodels/association/NegatedAssociation", "datamodels/association/Nodeidentifier", "datamodels/association/Objectidentifier", "datamodels/association/PairwiseCoAssociation", "datamodels/association/ParserConfiguration", "datamodels/association/PositiveOrNegativeAssociation", "datamodels/association/PropertyValue", "datamodels/association/RollupGroup", "datamodels/association/Sparqlpath", "datamodels/association/String", "datamodels/association/Time", "datamodels/association/Uri", "datamodels/association/Uriorcurie", "datamodels/association/aggregator_knowledge_source", "datamodels/association/association", "datamodels/association/associations", "datamodels/association/associations_for_subjects_in_common", "datamodels/association/closure_delta", "datamodels/association/closure_information_content_delta", "datamodels/association/closure_predicates", "datamodels/association/comments", "datamodels/association/core_triple", "datamodels/association/creation_date", "datamodels/association/date", "datamodels/association/denormalized_slot", "datamodels/association/diff_slot", "datamodels/association/evidence_type", "datamodels/association/group_object", "datamodels/association/include_association_attributes", "datamodels/association/index", "datamodels/association/is_creation", "datamodels/association/is_deletion", "datamodels/association/is_generalization", "datamodels/association/is_migration", "datamodels/association/is_specialization", "datamodels/association/modification_date", "datamodels/association/negated", "datamodels/association/new_date", "datamodels/association/new_object", "datamodels/association/new_predicate", "datamodels/association/number_subject_unique_to_entity1", "datamodels/association/number_subject_unique_to_entity2", "datamodels/association/number_subjects_in_common", "datamodels/association/number_subjects_in_union", "datamodels/association/object", "datamodels/association/object1", "datamodels/association/object1_label", "datamodels/association/object2", "datamodels/association/object2_label", "datamodels/association/object_closure", "datamodels/association/object_closure_label", "datamodels/association/object_label", "datamodels/association/old_date", "datamodels/association/old_object", "datamodels/association/old_object_obsolete", "datamodels/association/old_predicate", "datamodels/association/original_object", "datamodels/association/original_predicate", "datamodels/association/original_subject", "datamodels/association/predicate", "datamodels/association/predicate_label", "datamodels/association/preserve_negated_associations", "datamodels/association/primary_knowledge_source", "datamodels/association/property_values", "datamodels/association/proportion_subjects_in_common", "datamodels/association/publication_is_added", "datamodels/association/publication_is_deleted", "datamodels/association/publications", "datamodels/association/sub_groups", "datamodels/association/subject", "datamodels/association/subject_closure", "datamodels/association/subject_closure_label", "datamodels/association/subject_label", "datamodels/association/subjects_in_common", "datamodels/association/summary_group", "datamodels/association/supporting_objects", "datamodels/class-enrichment/Boolean", "datamodels/class-enrichment/ClassEnrichmentConfiguration", "datamodels/class-enrichment/ClassEnrichmentResult", "datamodels/class-enrichment/ClassEnrichmentResultSet", "datamodels/class-enrichment/Curie", "datamodels/class-enrichment/Date", "datamodels/class-enrichment/DateOrDatetime", "datamodels/class-enrichment/Datetime", "datamodels/class-enrichment/Decimal", "datamodels/class-enrichment/Double", "datamodels/class-enrichment/Float", "datamodels/class-enrichment/Integer", "datamodels/class-enrichment/Jsonpath", "datamodels/class-enrichment/Jsonpointer", "datamodels/class-enrichment/Ncname", "datamodels/class-enrichment/Nodeidentifier", "datamodels/class-enrichment/Objectidentifier", "datamodels/class-enrichment/Position", "datamodels/class-enrichment/SortFieldEnum", "datamodels/class-enrichment/Sparqlpath", "datamodels/class-enrichment/String", "datamodels/class-enrichment/Time", "datamodels/class-enrichment/Uri", "datamodels/class-enrichment/Uriorcurie", "datamodels/class-enrichment/ancestor_of_more_informative_result", "datamodels/class-enrichment/background_count", "datamodels/class-enrichment/background_total", "datamodels/class-enrichment/class-enrichment", "datamodels/class-enrichment/class_id", "datamodels/class-enrichment/class_label", "datamodels/class-enrichment/descendant_of_more_informative_result", "datamodels/class-enrichment/direction", "datamodels/class-enrichment/false_discovery_rate", "datamodels/class-enrichment/fold_enrichment", "datamodels/class-enrichment/index", "datamodels/class-enrichment/p_value", "datamodels/class-enrichment/p_value_adjusted", "datamodels/class-enrichment/p_value_cutoff", "datamodels/class-enrichment/probability", "datamodels/class-enrichment/rank", "datamodels/class-enrichment/results", "datamodels/class-enrichment/sample_count", "datamodels/class-enrichment/sample_total", "datamodels/cross-ontology-diff/Boolean", "datamodels/cross-ontology-diff/Curie", "datamodels/cross-ontology-diff/Date", "datamodels/cross-ontology-diff/DateOrDatetime", "datamodels/cross-ontology-diff/Datetime", "datamodels/cross-ontology-diff/Decimal", "datamodels/cross-ontology-diff/DiffCategory", "datamodels/cross-ontology-diff/Double", "datamodels/cross-ontology-diff/EntityReference", "datamodels/cross-ontology-diff/Float", "datamodels/cross-ontology-diff/Integer", "datamodels/cross-ontology-diff/Jsonpath", "datamodels/cross-ontology-diff/Jsonpointer", "datamodels/cross-ontology-diff/Label", "datamodels/cross-ontology-diff/MappingCardinalityEnum", "datamodels/cross-ontology-diff/Ncname", "datamodels/cross-ontology-diff/Nodeidentifier", "datamodels/cross-ontology-diff/Objectidentifier", "datamodels/cross-ontology-diff/Position", "datamodels/cross-ontology-diff/RelationalDiff", "datamodels/cross-ontology-diff/Source", "datamodels/cross-ontology-diff/Sparqlpath", "datamodels/cross-ontology-diff/String", "datamodels/cross-ontology-diff/StructureDiffResultSet", "datamodels/cross-ontology-diff/Time", "datamodels/cross-ontology-diff/Uri", "datamodels/cross-ontology-diff/Uriorcurie", "datamodels/cross-ontology-diff/category", "datamodels/cross-ontology-diff/cross-ontology-diff", "datamodels/cross-ontology-diff/index", "datamodels/cross-ontology-diff/is_functional", "datamodels/cross-ontology-diff/label", "datamodels/cross-ontology-diff/left_object_id", "datamodels/cross-ontology-diff/left_object_is_functional", "datamodels/cross-ontology-diff/left_object_label", "datamodels/cross-ontology-diff/left_object_name", "datamodels/cross-ontology-diff/left_predicate_id", "datamodels/cross-ontology-diff/left_predicate_label", "datamodels/cross-ontology-diff/left_predicate_name", "datamodels/cross-ontology-diff/left_side", "datamodels/cross-ontology-diff/left_source", "datamodels/cross-ontology-diff/left_subject_id", "datamodels/cross-ontology-diff/left_subject_is_functional", "datamodels/cross-ontology-diff/left_subject_label", "datamodels/cross-ontology-diff/left_subject_name", "datamodels/cross-ontology-diff/object", "datamodels/cross-ontology-diff/object_mapping_cardinality", "datamodels/cross-ontology-diff/object_mapping_predicate", "datamodels/cross-ontology-diff/predicate", "datamodels/cross-ontology-diff/results", "datamodels/cross-ontology-diff/right_intermediate_ids", "datamodels/cross-ontology-diff/right_object_id", "datamodels/cross-ontology-diff/right_object_label", "datamodels/cross-ontology-diff/right_object_name", "datamodels/cross-ontology-diff/right_predicate_ids", "datamodels/cross-ontology-diff/right_predicate_labels", "datamodels/cross-ontology-diff/right_predicate_names", "datamodels/cross-ontology-diff/right_side", "datamodels/cross-ontology-diff/right_source", "datamodels/cross-ontology-diff/right_subject_id", "datamodels/cross-ontology-diff/right_subject_label", "datamodels/cross-ontology-diff/right_subject_name", "datamodels/cross-ontology-diff/side", "datamodels/cross-ontology-diff/subject", "datamodels/cross-ontology-diff/subject_mapping_cardinality", "datamodels/cross-ontology-diff/subject_mapping_predicate", "datamodels/cross-ontology-diff/types", "datamodels/funowl/index", "datamodels/index", "datamodels/item-list/Boolean", "datamodels/item-list/Curie", "datamodels/item-list/Date", "datamodels/item-list/DateOrDatetime", "datamodels/item-list/Datetime", "datamodels/item-list/Decimal", "datamodels/item-list/Double", "datamodels/item-list/Float", "datamodels/item-list/Integer", "datamodels/item-list/ItemList", "datamodels/item-list/ItemListCollection", "datamodels/item-list/ItemListOrderType", "datamodels/item-list/Jsonpath", "datamodels/item-list/Jsonpointer", "datamodels/item-list/ListItem", "datamodels/item-list/Ncname", "datamodels/item-list/Nodeidentifier", "datamodels/item-list/Objectidentifier", "datamodels/item-list/Sparqlpath", "datamodels/item-list/String", "datamodels/item-list/Thing", "datamodels/item-list/Time", "datamodels/item-list/Uri", "datamodels/item-list/Uriorcurie", "datamodels/item-list/additionalType", "datamodels/item-list/categories", "datamodels/item-list/description", "datamodels/item-list/elementId", "datamodels/item-list/id", "datamodels/item-list/idType", "datamodels/item-list/identifiers", "datamodels/item-list/index", "datamodels/item-list/item", "datamodels/item-list/itemList", "datamodels/item-list/itemListElements", "datamodels/item-list/itemLists", "datamodels/item-list/itemMetadataMap", "datamodels/item-list/keywords", "datamodels/item-list/name", "datamodels/item-list/numberOfItems", "datamodels/item-list/position", "datamodels/item-list/previousItem", "datamodels/item-list/type", "datamodels/item-list/url", "datamodels/item-list/wasGeneratedBy", "datamodels/kgcl/index", "datamodels/lexical-index/Activity", "datamodels/lexical-index/Any", "datamodels/lexical-index/Boolean", "datamodels/lexical-index/Curie", "datamodels/lexical-index/Date", "datamodels/lexical-index/DateOrDatetime", "datamodels/lexical-index/Datetime", "datamodels/lexical-index/Decimal", "datamodels/lexical-index/Double", "datamodels/lexical-index/Float", "datamodels/lexical-index/Integer", "datamodels/lexical-index/Jsonpath", "datamodels/lexical-index/Jsonpointer", "datamodels/lexical-index/LexicalGrouping", "datamodels/lexical-index/LexicalIndex", "datamodels/lexical-index/LexicalTransformation", "datamodels/lexical-index/LexicalTransformationPipeline", "datamodels/lexical-index/Ncname", "datamodels/lexical-index/Nodeidentifier", "datamodels/lexical-index/Objectidentifier", "datamodels/lexical-index/RelationshipToTerm", "datamodels/lexical-index/Sparqlpath", "datamodels/lexical-index/String", "datamodels/lexical-index/Time", "datamodels/lexical-index/TransformationType", "datamodels/lexical-index/Uri", "datamodels/lexical-index/Uriorcurie", "datamodels/lexical-index/element", "datamodels/lexical-index/element_term", "datamodels/lexical-index/groupings", "datamodels/lexical-index/index", "datamodels/lexical-index/lexical-index", "datamodels/lexical-index/lexican-index", "datamodels/lexical-index/name", "datamodels/lexical-index/params", "datamodels/lexical-index/pipeline", "datamodels/lexical-index/pipelines", "datamodels/lexical-index/predicate", "datamodels/lexical-index/relationships", "datamodels/lexical-index/source", "datamodels/lexical-index/synonymized", "datamodels/lexical-index/term", "datamodels/lexical-index/transformations", "datamodels/lexical-index/type", "datamodels/lexical-index/types", "datamodels/mapping-rules/Activity", "datamodels/mapping-rules/Any", "datamodels/mapping-rules/Boolean", "datamodels/mapping-rules/Curie", "datamodels/mapping-rules/Date", "datamodels/mapping-rules/DateOrDatetime", "datamodels/mapping-rules/Datetime", "datamodels/mapping-rules/Decimal", "datamodels/mapping-rules/Double", "datamodels/mapping-rules/Float", "datamodels/mapping-rules/Integer", "datamodels/mapping-rules/Jsonpath", "datamodels/mapping-rules/Jsonpointer", "datamodels/mapping-rules/LexicalGrouping", "datamodels/mapping-rules/LexicalIndex", "datamodels/mapping-rules/LexicalTransformation", "datamodels/mapping-rules/LexicalTransformationPipeline", "datamodels/mapping-rules/MappingRule", "datamodels/mapping-rules/MappingRuleCollection", "datamodels/mapping-rules/Ncname", "datamodels/mapping-rules/Nodeidentifier", "datamodels/mapping-rules/Objectidentifier", "datamodels/mapping-rules/Postcondition", "datamodels/mapping-rules/Precondition", "datamodels/mapping-rules/RegularExpressionString", "datamodels/mapping-rules/RelationshipToTerm", "datamodels/mapping-rules/RuleSet", "datamodels/mapping-rules/Sparqlpath", "datamodels/mapping-rules/String", "datamodels/mapping-rules/Synonymizer", "datamodels/mapping-rules/Test", "datamodels/mapping-rules/Time", "datamodels/mapping-rules/TransformationType", "datamodels/mapping-rules/Uri", "datamodels/mapping-rules/Uriorcurie", "datamodels/mapping-rules/description", "datamodels/mapping-rules/element", "datamodels/mapping-rules/element_term", "datamodels/mapping-rules/groupings", "datamodels/mapping-rules/in_place", "datamodels/mapping-rules/index", "datamodels/mapping-rules/input", "datamodels/mapping-rules/lexical-index", "datamodels/mapping-rules/lexican-index", "datamodels/mapping-rules/mapping-rules", "datamodels/mapping-rules/mapping-rules-datamodel", "datamodels/mapping-rules/mapping_source_one_of", "datamodels/mapping-rules/match", "datamodels/mapping-rules/match_scope", "datamodels/mapping-rules/minimum_confidence", "datamodels/mapping-rules/name", "datamodels/mapping-rules/object_match_field_one_of", "datamodels/mapping-rules/object_source_one_of", "datamodels/mapping-rules/oneway", "datamodels/mapping-rules/output", "datamodels/mapping-rules/params", "datamodels/mapping-rules/pipeline", "datamodels/mapping-rules/pipelines", "datamodels/mapping-rules/postconditions", "datamodels/mapping-rules/preconditions", "datamodels/mapping-rules/predicate", "datamodels/mapping-rules/predicate_id", "datamodels/mapping-rules/predicate_id_one_of", "datamodels/mapping-rules/prefix", "datamodels/mapping-rules/qualifier", "datamodels/mapping-rules/relationships", "datamodels/mapping-rules/replacement", "datamodels/mapping-rules/rules", "datamodels/mapping-rules/source", "datamodels/mapping-rules/subject_match_field_one_of", "datamodels/mapping-rules/subject_source_one_of", "datamodels/mapping-rules/synonymized", "datamodels/mapping-rules/synonymizer", "datamodels/mapping-rules/term", "datamodels/mapping-rules/tests", "datamodels/mapping-rules/transformations", "datamodels/mapping-rules/transformations_included_in", "datamodels/mapping-rules/type", "datamodels/mapping-rules/types", "datamodels/mapping-rules/weight", "datamodels/obograph/Axiom", "datamodels/obograph/BasicPropertyValue", "datamodels/obograph/Boolean", "datamodels/obograph/Curie", "datamodels/obograph/Date", "datamodels/obograph/DateOrDatetime", "datamodels/obograph/Datetime", "datamodels/obograph/Decimal", "datamodels/obograph/DefinitionPropertyValue", "datamodels/obograph/DisjointClassExpressionsAxiom", "datamodels/obograph/DomainRangeAxiom", "datamodels/obograph/Double", "datamodels/obograph/Edge", "datamodels/obograph/EquivalentNodesSet", "datamodels/obograph/ExistentialRestrictionExpression", "datamodels/obograph/Float", "datamodels/obograph/Graph", "datamodels/obograph/GraphDocument", "datamodels/obograph/Integer", "datamodels/obograph/Jsonpath", "datamodels/obograph/Jsonpointer", "datamodels/obograph/LogicalDefinitionAxiom", "datamodels/obograph/Meta", "datamodels/obograph/Ncname", "datamodels/obograph/Node", "datamodels/obograph/NodeTypeEnum", "datamodels/obograph/Nodeidentifier", "datamodels/obograph/Objectidentifier", "datamodels/obograph/OboIdentifierString", "datamodels/obograph/PredsEnum", "datamodels/obograph/PrefixDeclaration", "datamodels/obograph/PropertyChainAxiom", "datamodels/obograph/PropertyTypeEnum", "datamodels/obograph/PropertyValue", "datamodels/obograph/ScopeEnum", "datamodels/obograph/ScopesEnum", "datamodels/obograph/Sparqlpath", "datamodels/obograph/String", "datamodels/obograph/SubsetDefinition", "datamodels/obograph/SynonymPropertyValue", "datamodels/obograph/SynonymTypeDefinition", "datamodels/obograph/SynonymTypeIdentifierString", "datamodels/obograph/Time", "datamodels/obograph/Uri", "datamodels/obograph/Uriorcurie", "datamodels/obograph/XrefPropertyValue", "datamodels/obograph/XrefString", "datamodels/obograph/allValuesFromEdges", "datamodels/obograph/basicPropertyValues", "datamodels/obograph/chainPredicateIds", "datamodels/obograph/classExpressions", "datamodels/obograph/classIds", "datamodels/obograph/comments", "datamodels/obograph/definedClassId", "datamodels/obograph/definition", "datamodels/obograph/deprecated", "datamodels/obograph/disjointClassExpressionsAxioms", "datamodels/obograph/domainClassIds", "datamodels/obograph/domainRangeAxioms", "datamodels/obograph/edges", "datamodels/obograph/equivalentNodesSets", "datamodels/obograph/fillerId", "datamodels/obograph/genusIds", "datamodels/obograph/graphs", "datamodels/obograph/id", "datamodels/obograph/index", "datamodels/obograph/isExact", "datamodels/obograph/label", "datamodels/obograph/lang", "datamodels/obograph/lbl", "datamodels/obograph/logicalDefinitionAxioms", "datamodels/obograph/meta", "datamodels/obograph/namespace", "datamodels/obograph/nodeIds", "datamodels/obograph/nodes", "datamodels/obograph/obj", "datamodels/obograph/obographs_datamodel", "datamodels/obograph/obographs_linkml_model", "datamodels/obograph/pred", "datamodels/obograph/predicateId", "datamodels/obograph/prefix", "datamodels/obograph/prefixes", "datamodels/obograph/propertyChainAxioms", "datamodels/obograph/propertyId", "datamodels/obograph/propertyType", "datamodels/obograph/rangeClassIds", "datamodels/obograph/representativeNodeId", "datamodels/obograph/representitiveNodeId", "datamodels/obograph/restrictions", "datamodels/obograph/scope", "datamodels/obograph/sub", "datamodels/obograph/subsetDefinitions", "datamodels/obograph/subsets", "datamodels/obograph/synonymType", "datamodels/obograph/synonymTypeDefinitions", "datamodels/obograph/synonyms", "datamodels/obograph/type", "datamodels/obograph/types", "datamodels/obograph/unionEquivalentTo", "datamodels/obograph/unionEquivalentToExpression", "datamodels/obograph/val", "datamodels/obograph/valType", "datamodels/obograph/version", "datamodels/obograph/xrefs", "datamodels/ontology-metadata/Agent", "datamodels/ontology-metadata/AllotropePermittedProfile", "datamodels/ontology-metadata/AllotropeRequiredProfile", "datamodels/ontology-metadata/Annotation", "datamodels/ontology-metadata/AnnotationProperty", "datamodels/ontology-metadata/AnnotationPropertyMixin", "datamodels/ontology-metadata/Anonymous", "datamodels/ontology-metadata/AnonymousClassExpression", "datamodels/ontology-metadata/Any", "datamodels/ontology-metadata/Axiom", "datamodels/ontology-metadata/Boolean", "datamodels/ontology-metadata/CURIELiteral", "datamodels/ontology-metadata/Class", "datamodels/ontology-metadata/ClassExpression", "datamodels/ontology-metadata/Curie", "datamodels/ontology-metadata/Date", "datamodels/ontology-metadata/DateOrDatetime", "datamodels/ontology-metadata/Datetime", "datamodels/ontology-metadata/Decimal", "datamodels/ontology-metadata/DefinitionConstraintComponent", "datamodels/ontology-metadata/Double", "datamodels/ontology-metadata/Expression", "datamodels/ontology-metadata/Float", "datamodels/ontology-metadata/GoPermittedProfile", "datamodels/ontology-metadata/GoRecommendedProfile", "datamodels/ontology-metadata/GoRequiredProfile", "datamodels/ontology-metadata/HasCategory", "datamodels/ontology-metadata/HasLifeCycle", "datamodels/ontology-metadata/HasMappings", "datamodels/ontology-metadata/HasMinimalMetadata", "datamodels/ontology-metadata/HasProvenance", "datamodels/ontology-metadata/HasSynonyms", "datamodels/ontology-metadata/HasUserInformation", "datamodels/ontology-metadata/HomoSapiens", "datamodels/ontology-metadata/IEDB_alternative_term", "datamodels/ontology-metadata/ISA_alternative_term", "datamodels/ontology-metadata/Image", "datamodels/ontology-metadata/Integer", "datamodels/ontology-metadata/IriType", "datamodels/ontology-metadata/Jsonpath", "datamodels/ontology-metadata/Jsonpointer", "datamodels/ontology-metadata/LabelType", "datamodels/ontology-metadata/NCIT_definition_source", "datamodels/ontology-metadata/NCIT_term_source", "datamodels/ontology-metadata/NCIT_term_type", "datamodels/ontology-metadata/NamedIndividual", "datamodels/ontology-metadata/NamedObject", "datamodels/ontology-metadata/NarrativeText", "datamodels/ontology-metadata/Ncname", "datamodels/ontology-metadata/Nodeidentifier", "datamodels/ontology-metadata/NotObsoleteAspect", "datamodels/ontology-metadata/OBO_foundry_unique_label", "datamodels/ontology-metadata/ObiPermittedProfile", "datamodels/ontology-metadata/ObiRequiredProfile", "datamodels/ontology-metadata/ObjectProperty", "datamodels/ontology-metadata/Objectidentifier", "datamodels/ontology-metadata/ObsoleteAspect", "datamodels/ontology-metadata/Ontology", "datamodels/ontology-metadata/Ontology-Metadata", "datamodels/ontology-metadata/Property", "datamodels/ontology-metadata/PropertyExpression", "datamodels/ontology-metadata/Restriction", "datamodels/ontology-metadata/Sparqlpath", "datamodels/ontology-metadata/String", "datamodels/ontology-metadata/Subset", "datamodels/ontology-metadata/Term", "datamodels/ontology-metadata/Thing", "datamodels/ontology-metadata/TidyString", "datamodels/ontology-metadata/Time", "datamodels/ontology-metadata/TransitiveProperty", "datamodels/ontology-metadata/URLLiteral", "datamodels/ontology-metadata/Uri", "datamodels/ontology-metadata/Uriorcurie", "datamodels/ontology-metadata/allValuesFrom", "datamodels/ontology-metadata/alternative_term", "datamodels/ontology-metadata/annotatedProperty", "datamodels/ontology-metadata/annotatedSource", "datamodels/ontology-metadata/annotatedTarget", "datamodels/ontology-metadata/annotations", "datamodels/ontology-metadata/broadMatch", "datamodels/ontology-metadata/cardinality", "datamodels/ontology-metadata/category", "datamodels/ontology-metadata/changeNote", "datamodels/ontology-metadata/closeMatch", "datamodels/ontology-metadata/comment", "datamodels/ontology-metadata/complementOf", "datamodels/ontology-metadata/conformsTo", "datamodels/ontology-metadata/consider", "datamodels/ontology-metadata/contributor", "datamodels/ontology-metadata/core_property", "datamodels/ontology-metadata/created", "datamodels/ontology-metadata/created_by", "datamodels/ontology-metadata/creation_date", "datamodels/ontology-metadata/creator", "datamodels/ontology-metadata/curator_note", "datamodels/ontology-metadata/database_cross_reference", "datamodels/ontology-metadata/date", "datamodels/ontology-metadata/date_retrieved", "datamodels/ontology-metadata/defaultLanguage", "datamodels/ontology-metadata/definition", "datamodels/ontology-metadata/definition_source", "datamodels/ontology-metadata/depicted_by", "datamodels/ontology-metadata/deprecated", "datamodels/ontology-metadata/disconnected_from", "datamodels/ontology-metadata/disjointWith", "datamodels/ontology-metadata/distinctMembers", "datamodels/ontology-metadata/domain", "datamodels/ontology-metadata/editor_note", "datamodels/ontology-metadata/editor_preferred_term", "datamodels/ontology-metadata/equivalentClass", "datamodels/ontology-metadata/equivalentProperty", "datamodels/ontology-metadata/evidence", "datamodels/ontology-metadata/exactMatch", "datamodels/ontology-metadata/example_of_usage", "datamodels/ontology-metadata/excluded_axiom", "datamodels/ontology-metadata/excluded_from_QC_check", "datamodels/ontology-metadata/excluded_subClassOf", "datamodels/ontology-metadata/excluded_synonym", "datamodels/ontology-metadata/external_ontology", "datamodels/ontology-metadata/hasValue", "datamodels/ontology-metadata/has_alternative_id", "datamodels/ontology-metadata/has_axiom_label", "datamodels/ontology-metadata/has_broad_synonym", "datamodels/ontology-metadata/has_curation_status", "datamodels/ontology-metadata/has_exact_synonym", "datamodels/ontology-metadata/has_narrow_synonym", "datamodels/ontology-metadata/has_obo_namespace", "datamodels/ontology-metadata/has_obsolescence_reason", "datamodels/ontology-metadata/has_ontology_root_term", "datamodels/ontology-metadata/has_rank", "datamodels/ontology-metadata/has_related_synonym", "datamodels/ontology-metadata/has_synonym_type", "datamodels/ontology-metadata/id", "datamodels/ontology-metadata/image", "datamodels/ontology-metadata/imported_from", "datamodels/ontology-metadata/imports", "datamodels/ontology-metadata/in_subset", "datamodels/ontology-metadata/index", "datamodels/ontology-metadata/informative_property", "datamodels/ontology-metadata/intersectionOf", "datamodels/ontology-metadata/inverseOf", "datamodels/ontology-metadata/isDefinedBy", "datamodels/ontology-metadata/is_a_defining_property_chain_axiom", "datamodels/ontology-metadata/is_a_defining_property_chain_axiom_where_second_argument_is_reflexive", "datamodels/ontology-metadata/is_class_level", "datamodels/ontology-metadata/is_cyclic", "datamodels/ontology-metadata/is_inferred", "datamodels/ontology-metadata/is_metadata_tag", "datamodels/ontology-metadata/is_transitive", "datamodels/ontology-metadata/label", "datamodels/ontology-metadata/language", "datamodels/ontology-metadata/license", "datamodels/ontology-metadata/logical_predicate", "datamodels/ontology-metadata/match", "datamodels/ontology-metadata/match_aspect", "datamodels/ontology-metadata/maxQualifiedCardinality", "datamodels/ontology-metadata/members", "datamodels/ontology-metadata/minCardinality", "datamodels/ontology-metadata/minQualifiedCardinality", "datamodels/ontology-metadata/narrowMatch", "datamodels/ontology-metadata/never_in_taxon", "datamodels/ontology-metadata/notes", "datamodels/ontology-metadata/object", "datamodels/ontology-metadata/oboInOwl_id", "datamodels/ontology-metadata/oboInOwl_ontology", "datamodels/ontology-metadata/obsoletion_related_property", "datamodels/ontology-metadata/omo-schema", "datamodels/ontology-metadata/onClass", "datamodels/ontology-metadata/onProperty", "datamodels/ontology-metadata/oneOf", "datamodels/ontology-metadata/ontology_term_requester", "datamodels/ontology-metadata/page", "datamodels/ontology-metadata/predicate", "datamodels/ontology-metadata/propertyChainAxiom", "datamodels/ontology-metadata/provenance_property", "datamodels/ontology-metadata/qualifiedCardinality", "datamodels/ontology-metadata/range", "datamodels/ontology-metadata/reification_predicate", "datamodels/ontology-metadata/sameAs", "datamodels/ontology-metadata/seeAlso", "datamodels/ontology-metadata/shortcut_annotation_property", "datamodels/ontology-metadata/shorthand", "datamodels/ontology-metadata/should_conform_to", "datamodels/ontology-metadata/someValuesFrom", "datamodels/ontology-metadata/source", "datamodels/ontology-metadata/subClassOf", "datamodels/ontology-metadata/synonym", "datamodels/ontology-metadata/temporal_interpretation", "datamodels/ontology-metadata/term_editor", "datamodels/ontology-metadata/term_replaced_by", "datamodels/ontology-metadata/term_tracker_item", "datamodels/ontology-metadata/title", "datamodels/ontology-metadata/type", "datamodels/ontology-metadata/types", "datamodels/ontology-metadata/unionOf", "datamodels/ontology-metadata/url", "datamodels/ontology-metadata/versionIRI", "datamodels/ontology-metadata/versionInfo", "datamodels/ontology-metadata/version_property", "datamodels/search/Boolean", "datamodels/search/BooleanOperator", "datamodels/search/ComplexQuery", "datamodels/search/Curie", "datamodels/search/Date", "datamodels/search/DateOrDatetime", "datamodels/search/Datetime", "datamodels/search/Decimal", "datamodels/search/Double", "datamodels/search/Float", "datamodels/search/GraphFunction", "datamodels/search/Integer", "datamodels/search/Jsonpath", "datamodels/search/Jsonpointer", "datamodels/search/Ncname", "datamodels/search/Nodeidentifier", "datamodels/search/Objectidentifier", "datamodels/search/PathExpression", "datamodels/search/SearchBaseConfiguration", "datamodels/search/SearchProperty", "datamodels/search/SearchResult", "datamodels/search/SearchResultSet", "datamodels/search/SearchTerm", "datamodels/search/SearchTermSyntax", "datamodels/search/Sparqlpath", "datamodels/search/String", "datamodels/search/Time", "datamodels/search/Uri", "datamodels/search/Uriorcurie", "datamodels/search/all_of", "datamodels/search/any_of", "datamodels/search/atom", "datamodels/search/categories", "datamodels/search/configuration", "datamodels/search/cursor", "datamodels/search/force_case_insensitive", "datamodels/search/graph_predicates", "datamodels/search/include_aliases", "datamodels/search/include_definition", "datamodels/search/include_id", "datamodels/search/include_label", "datamodels/search/include_obsoletes_in_results", "datamodels/search/index", "datamodels/search/is_complete", "datamodels/search/is_fuzzy", "datamodels/search/is_partial", "datamodels/search/is_regular_expression", "datamodels/search/limit", "datamodels/search/matches_full_search_term", "datamodels/search/none_of", "datamodels/search/object_id", "datamodels/search/object_label", "datamodels/search/object_match_field", "datamodels/search/object_source", "datamodels/search/object_source_version", "datamodels/search/path_to", "datamodels/search/properties", "datamodels/search/rank", "datamodels/search/result_count", "datamodels/search/results", "datamodels/search/search-datamodel", "datamodels/search/search_term", "datamodels/search/search_terms", "datamodels/search/snippet", "datamodels/search/syntax", "datamodels/search/traversal", "datamodels/search/types", "datamodels/semsql/index", "datamodels/similarity/BestMatch", "datamodels/similarity/Boolean", "datamodels/similarity/Curie", "datamodels/similarity/Date", "datamodels/similarity/DateOrDatetime", "datamodels/similarity/Datetime", "datamodels/similarity/Decimal", "datamodels/similarity/Double", "datamodels/similarity/Float", "datamodels/similarity/Integer", "datamodels/similarity/ItemCount", "datamodels/similarity/Jsonpath", "datamodels/similarity/Jsonpointer", "datamodels/similarity/Ncname", "datamodels/similarity/NegativeLogValue", "datamodels/similarity/Nodeidentifier", "datamodels/similarity/NonNegativeFloat", "datamodels/similarity/Objectidentifier", "datamodels/similarity/PairwiseSimilarity", "datamodels/similarity/Sparqlpath", "datamodels/similarity/String", "datamodels/similarity/TermInfo", "datamodels/similarity/TermPairwiseSimilarity", "datamodels/similarity/TermSetPairwiseSimilarity", "datamodels/similarity/Time", "datamodels/similarity/Uri", "datamodels/similarity/Uriorcurie", "datamodels/similarity/ZeroToOne", "datamodels/similarity/ancestor_id", "datamodels/similarity/ancestor_information_content", "datamodels/similarity/ancestor_label", "datamodels/similarity/ancestor_source", "datamodels/similarity/average_score", "datamodels/similarity/best_score", "datamodels/similarity/cosine_similarity", "datamodels/similarity/dice_similarity", "datamodels/similarity/id", "datamodels/similarity/index", "datamodels/similarity/information_content", "datamodels/similarity/intersection_count", "datamodels/similarity/jaccard_similarity", "datamodels/similarity/label", "datamodels/similarity/match_source", "datamodels/similarity/match_source_label", "datamodels/similarity/match_subsumer", "datamodels/similarity/match_subsumer_label", "datamodels/similarity/match_target", "datamodels/similarity/match_target_label", "datamodels/similarity/metric", "datamodels/similarity/object_best_matches", "datamodels/similarity/object_id", "datamodels/similarity/object_information_content", "datamodels/similarity/object_label", "datamodels/similarity/object_source", "datamodels/similarity/object_termset", "datamodels/similarity/overlap_coefficient", "datamodels/similarity/phenodigm_score", "datamodels/similarity/score", "datamodels/similarity/similarity", "datamodels/similarity/subject_best_matches", "datamodels/similarity/subject_id", "datamodels/similarity/subject_information_content", "datamodels/similarity/subject_label", "datamodels/similarity/subject_source", "datamodels/similarity/subject_termset", "datamodels/similarity/subsumed_by_score", "datamodels/similarity/subsumes_score", "datamodels/similarity/types", "datamodels/similarity/union_count", "datamodels/sssom/index", "datamodels/summary-statistics/Agent", "datamodels/summary-statistics/Boolean", "datamodels/summary-statistics/ChangeTypeStatistic", "datamodels/summary-statistics/ContributorRole", "datamodels/summary-statistics/ContributorStatistics", "datamodels/summary-statistics/Curie", "datamodels/summary-statistics/Date", "datamodels/summary-statistics/DateOrDatetime", "datamodels/summary-statistics/Datetime", "datamodels/summary-statistics/Decimal", "datamodels/summary-statistics/Double", "datamodels/summary-statistics/FacetStatistics", "datamodels/summary-statistics/FacetedCount", "datamodels/summary-statistics/Float", "datamodels/summary-statistics/GlobalStatistics", "datamodels/summary-statistics/GroupedStatistics", "datamodels/summary-statistics/Integer", "datamodels/summary-statistics/Jsonpath", "datamodels/summary-statistics/Jsonpointer", "datamodels/summary-statistics/Ncname", "datamodels/summary-statistics/Nodeidentifier", "datamodels/summary-statistics/Objectidentifier", "datamodels/summary-statistics/Ontology", "datamodels/summary-statistics/Sparqlpath", "datamodels/summary-statistics/String", "datamodels/summary-statistics/SummaryStatisticCollection", "datamodels/summary-statistics/SummaryStatisticsCalculationActivity", "datamodels/summary-statistics/SummaryStatisticsReport", "datamodels/summary-statistics/Time", "datamodels/summary-statistics/UngroupedStatistics", "datamodels/summary-statistics/Uri", "datamodels/summary-statistics/Uriorcurie", "datamodels/summary-statistics/acted_on_behalf_of", "datamodels/summary-statistics/agents", "datamodels/summary-statistics/annotation_property_count", "datamodels/summary-statistics/anonymous_class_expression_count", "datamodels/summary-statistics/anonymous_individual_count", "datamodels/summary-statistics/by_category", "datamodels/summary-statistics/by_ontology", "datamodels/summary-statistics/by_subset", "datamodels/summary-statistics/by_taxon", "datamodels/summary-statistics/change_summary", "datamodels/summary-statistics/class_count", "datamodels/summary-statistics/class_count_by_category", "datamodels/summary-statistics/class_count_by_subset", "datamodels/summary-statistics/class_count_excluding_deprecated", "datamodels/summary-statistics/class_count_with_definitions", "datamodels/summary-statistics/class_count_with_text_definitions", "datamodels/summary-statistics/class_count_without_text_definitions", "datamodels/summary-statistics/class_statistic_group", "datamodels/summary-statistics/compared_with", "datamodels/summary-statistics/contributor_id", "datamodels/summary-statistics/contributor_name", "datamodels/summary-statistics/contributor_summary", "datamodels/summary-statistics/count_statistic", "datamodels/summary-statistics/datatype_property_count", "datamodels/summary-statistics/deprecated_class_count", "datamodels/summary-statistics/deprecated_object_property_count", "datamodels/summary-statistics/description", "datamodels/summary-statistics/description_logic_profile", "datamodels/summary-statistics/distinct_synonym_count", "datamodels/summary-statistics/edge_count_by_predicate", "datamodels/summary-statistics/ended_at_time", "datamodels/summary-statistics/entailed_edge_count_by_predicate", "datamodels/summary-statistics/equivalent_classes_axiom_count", "datamodels/summary-statistics/equivalentclasses_axiom_count", "datamodels/summary-statistics/facet", "datamodels/summary-statistics/filtered_count", "datamodels/summary-statistics/id", "datamodels/summary-statistics/index", "datamodels/summary-statistics/individual_count", "datamodels/summary-statistics/individual_statistic_group", "datamodels/summary-statistics/label", "datamodels/summary-statistics/mapping_count", "datamodels/summary-statistics/mapping_statement_count_by_object_source", "datamodels/summary-statistics/mapping_statement_count_by_predicate", "datamodels/summary-statistics/mapping_statement_count_subject_by_object_source", "datamodels/summary-statistics/merged_class_count", "datamodels/summary-statistics/metadata_statistic_group", "datamodels/summary-statistics/named_individual_count", "datamodels/summary-statistics/non_deprecated_class_count", "datamodels/summary-statistics/non_deprecated_object_property_count", "datamodels/summary-statistics/normalization_comments", "datamodels/summary-statistics/object_property_count", "datamodels/summary-statistics/ontologies", "datamodels/summary-statistics/ontology_count", "datamodels/summary-statistics/owl_axiom_count", "datamodels/summary-statistics/owl_statistic_group", "datamodels/summary-statistics/partitions", "datamodels/summary-statistics/prefix", "datamodels/summary-statistics/property_count", "datamodels/summary-statistics/property_statistic_group", "datamodels/summary-statistics/rdf_triple_count", "datamodels/summary-statistics/role_counts", "datamodels/summary-statistics/started_at_time", "datamodels/summary-statistics/subclass_of_axiom_count", "datamodels/summary-statistics/subset_count", "datamodels/summary-statistics/summary-statistics", "datamodels/summary-statistics/synonym_statement_count", "datamodels/summary-statistics/synonym_statement_count_by_predicate", "datamodels/summary-statistics/title", "datamodels/summary-statistics/types", "datamodels/summary-statistics/unsatisfiable_class_count", "datamodels/summary-statistics/untyped_entity_count", "datamodels/summary-statistics/version", "datamodels/summary-statistics/version_info", "datamodels/summary-statistics/was_associated_with", "datamodels/summary-statistics/was_generated_by", "datamodels/taxon-constraints/Boolean", "datamodels/taxon-constraints/ConfigurationOption", "datamodels/taxon-constraints/Curie", "datamodels/taxon-constraints/Date", "datamodels/taxon-constraints/DateOrDatetime", "datamodels/taxon-constraints/Datetime", "datamodels/taxon-constraints/Decimal", "datamodels/taxon-constraints/Double", "datamodels/taxon-constraints/Float", "datamodels/taxon-constraints/Integer", "datamodels/taxon-constraints/Jsonpath", "datamodels/taxon-constraints/Jsonpointer", "datamodels/taxon-constraints/Ncname", "datamodels/taxon-constraints/Nodeidentifier", "datamodels/taxon-constraints/Objectidentifier", "datamodels/taxon-constraints/PredicateTerm", "datamodels/taxon-constraints/Sparqlpath", "datamodels/taxon-constraints/String", "datamodels/taxon-constraints/SubjectTerm", "datamodels/taxon-constraints/Taxon", "datamodels/taxon-constraints/TaxonConstraint", "datamodels/taxon-constraints/Term", "datamodels/taxon-constraints/Time", "datamodels/taxon-constraints/Uri", "datamodels/taxon-constraints/Uriorcurie", "datamodels/taxon-constraints/asserted", "datamodels/taxon-constraints/candidate", "datamodels/taxon-constraints/comments", "datamodels/taxon-constraints/contradicted_by", "datamodels/taxon-constraints/description", "datamodels/taxon-constraints/evolutionary", "datamodels/taxon-constraints/id", "datamodels/taxon-constraints/index", "datamodels/taxon-constraints/label", "datamodels/taxon-constraints/never_in", "datamodels/taxon-constraints/only_in", "datamodels/taxon-constraints/predicate", "datamodels/taxon-constraints/predicates", "datamodels/taxon-constraints/present_in", "datamodels/taxon-constraints/present_in_ancestor_of", "datamodels/taxon-constraints/redundant", "datamodels/taxon-constraints/redundant_with", "datamodels/taxon-constraints/redundant_with_only_in", "datamodels/taxon-constraints/sources", "datamodels/taxon-constraints/subject", "datamodels/taxon-constraints/taxon", "datamodels/taxon-constraints/taxon-constraints", "datamodels/taxon-constraints/unsatisfiable", "datamodels/taxon-constraints/via_terms", "datamodels/text-annotator/Boolean", "datamodels/text-annotator/Curie", "datamodels/text-annotator/Date", "datamodels/text-annotator/DateOrDatetime", "datamodels/text-annotator/Datetime", "datamodels/text-annotator/Decimal", "datamodels/text-annotator/Double", "datamodels/text-annotator/Float", "datamodels/text-annotator/HasSpan", "datamodels/text-annotator/Integer", "datamodels/text-annotator/Jsonpath", "datamodels/text-annotator/Jsonpointer", "datamodels/text-annotator/Ncname", "datamodels/text-annotator/Nodeidentifier", "datamodels/text-annotator/Objectidentifier", "datamodels/text-annotator/Position", "datamodels/text-annotator/Sparqlpath", "datamodels/text-annotator/String", "datamodels/text-annotator/TextAnnotation", "datamodels/text-annotator/TextAnnotationConfiguration", "datamodels/text-annotator/TextAnnotationResultSet", "datamodels/text-annotator/TextualElement", "datamodels/text-annotator/Time", "datamodels/text-annotator/TransformationType", "datamodels/text-annotator/Uri", "datamodels/text-annotator/Uriorcurie", "datamodels/text-annotator/annotations", "datamodels/text-annotator/categories", "datamodels/text-annotator/confidence", "datamodels/text-annotator/id", "datamodels/text-annotator/include_aliases", "datamodels/text-annotator/index", "datamodels/text-annotator/info", "datamodels/text-annotator/is_longest_match", "datamodels/text-annotator/limit", "datamodels/text-annotator/match_string", "datamodels/text-annotator/match_type", "datamodels/text-annotator/matches_whole_text", "datamodels/text-annotator/model", "datamodels/text-annotator/object_aliases", "datamodels/text-annotator/object_categories", "datamodels/text-annotator/object_id", "datamodels/text-annotator/object_label", "datamodels/text-annotator/object_source", "datamodels/text-annotator/parent_document", "datamodels/text-annotator/predicate_id", "datamodels/text-annotator/source_text", "datamodels/text-annotator/sources", "datamodels/text-annotator/subject_end", "datamodels/text-annotator/subject_label", "datamodels/text-annotator/subject_source", "datamodels/text-annotator/subject_start", "datamodels/text-annotator/subject_text_id", "datamodels/text-annotator/text", "datamodels/text-annotator/text-annotator", "datamodels/text-annotator/token_exclusion_list", "datamodels/text-annotator/types", "datamodels/validation/Boolean", "datamodels/validation/ConstraintComponent", "datamodels/validation/Curie", "datamodels/validation/Date", "datamodels/validation/DateOrDatetime", "datamodels/validation/Datetime", "datamodels/validation/Decimal", "datamodels/validation/DefinitionValidationResult", "datamodels/validation/Double", "datamodels/validation/ExternalReferenceValidationResult", "datamodels/validation/Float", "datamodels/validation/Integer", "datamodels/validation/Jsonpath", "datamodels/validation/Jsonpointer", "datamodels/validation/MappingValidationResult", "datamodels/validation/NamedResource", "datamodels/validation/Ncname", "datamodels/validation/Node", "datamodels/validation/Nodeidentifier", "datamodels/validation/Objectidentifier", "datamodels/validation/RepairConfiguration", "datamodels/validation/RepairOperation", "datamodels/validation/RepairReport", "datamodels/validation/Report", "datamodels/validation/Result", "datamodels/validation/SeverityOptions", "datamodels/validation/Sparqlpath", "datamodels/validation/String", "datamodels/validation/Time", "datamodels/validation/TypeSeverityKeyValue", "datamodels/validation/Uri", "datamodels/validation/Uriorcurie", "datamodels/validation/ValidationConfiguration", "datamodels/validation/ValidationReport", "datamodels/validation/ValidationResult", "datamodels/validation/ValidationResultType", "datamodels/validation/category", "datamodels/validation/confidence", "datamodels/validation/definition", "datamodels/validation/definition_source", "datamodels/validation/documentation_objects", "datamodels/validation/dry_run", 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1140], "bioinformat": [1, 1116, 1127, 1143], "bridg": [1, 1142], "essenti": [1, 1127], "well": [1, 2, 31, 46, 392, 409, 441, 450, 1110, 1116, 1118, 1119, 1120, 1134, 1140, 1143, 1151, 1178, 1185, 1188], "defin": [1, 214, 229, 385, 392, 397, 426, 427, 429, 434, 438, 441, 446, 447, 458, 464, 474, 475, 945, 961, 1118, 1119, 1123, 1127, 1128, 1148, 1177, 1178, 1184, 1192, 1193], "expans": [1, 1178], "method": [1, 1109, 1112, 1113, 1116, 1117, 1123, 1125, 1127, 1128, 1129, 1141, 1142, 1143, 1147, 1152, 1177, 1178, 1180, 1182, 1183, 1184, 1190, 1192, 1193, 1194, 1203], "accept": [1, 1110, 1134, 1146, 1151, 1204], "alwai": [1, 397, 464, 1115, 1116, 1134, 1137, 1140, 1177], "contract": [1, 1178], "A": [1, 2, 3, 4, 5, 10, 11, 12, 14, 15, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 42, 43, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 76, 77, 79, 80, 81, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 95, 96, 101, 102, 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"standard": [1, 2, 275, 328, 376, 398, 415, 422, 424, 441, 469, 997, 1110, 1112, 1114, 1116, 1117, 1118, 1120, 1121, 1124, 1126, 1127, 1128, 1129, 1134, 1140, 1142, 1143, 1203], "construct": [1, 376, 441, 1112, 1116, 1119, 1127, 1129, 1178, 1203], "directli": [1, 22, 28, 115, 161, 227, 251, 276, 296, 329, 376, 409, 419, 486, 539, 545, 546, 551, 706, 765, 772, 844, 847, 946, 948, 998, 1054, 1055, 1061, 1116, 1120, 1123, 1124, 1128, 1133, 1140, 1144, 1147, 1151, 1152, 1177, 1184], "correspond": [1, 2, 155, 165, 167, 184, 191, 192, 193, 318, 375, 398, 424, 441, 1038, 1040, 1065, 1103, 1116, 1124, 1127, 1137, 1178], "call": [1, 1113, 1116, 1118, 1128, 1140, 1147, 1151, 1159, 1178, 1202], "owlinterfac": [1, 204, 1139, 1182, 1185], "rdfinterfac": 1, "common": [1, 31, 46, 318, 375, 769, 775, 784, 1114, 1116, 1117, 1119, 1123, 1125, 1126, 1127, 1128, 1134, 1138, 1140, 1148, 1151, 1152, 1182, 1189], "opaqu": 1, "each": [1, 142, 155, 163, 165, 204, 275, 325, 328, 336, 341, 370, 441, 452, 831, 997, 1110, 1112, 1116, 1117, 1119, 1124, 1127, 1128, 1129, 1133, 1137, 1140, 1143, 1151, 1152, 1175, 1178, 1180, 1183, 1187, 1188, 1190, 1192, 1193, 1203], "exactli": [1, 142, 155, 163, 165, 166, 1134, 1152], "uniqu": [1, 2, 155, 165, 166, 169, 175, 178, 219, 225, 232, 392, 400, 414, 416, 440, 441, 480, 489, 509, 513, 516, 525, 545, 629, 817, 820, 832, 839, 844, 846, 886, 1116, 1119, 1120, 1137, 1140, 1178], "human": [1, 31, 46, 149, 165, 167, 392, 398, 400, 414, 416, 441, 445, 513, 514, 515, 521, 527, 531, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 587, 588, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 613, 614, 616, 617, 621, 629, 639, 650, 651, 659, 662, 668, 669, 670, 672, 698, 940, 943, 944, 946, 957, 958, 1116, 1117, 1118, 1119, 1120, 1121, 1127, 1128, 1203], "represent": [1, 6, 97, 137, 206, 254, 299, 379, 421, 441, 452, 491, 494, 550, 617, 682, 749, 822, 927, 975, 1033, 1116, 1119, 1121, 1125, 1127, 1128], "repres": [1, 18, 19, 27, 31, 46, 108, 109, 114, 120, 127, 144, 152, 153, 160, 164, 165, 204, 214, 219, 221, 222, 226, 236, 237, 238, 239, 241, 250, 269, 270, 274, 281, 282, 283, 316, 317, 327, 336, 338, 339, 377, 384, 386, 388, 389, 392, 393, 398, 402, 403, 404, 407, 409, 410, 415, 417, 418, 421, 422, 423, 425, 434, 435, 436, 440, 441, 442, 444, 445, 446, 447, 450, 452, 454, 455, 457, 458, 462, 467, 469, 470, 476, 477, 479, 529, 535, 548, 617, 694, 695, 705, 721, 739, 746, 762, 764, 765, 771, 784, 816, 837, 838, 845, 886, 938, 939, 940, 944, 947, 956, 957, 958, 971, 987, 988, 996, 1005, 1028, 1049, 1050, 1059, 1075, 1116, 1118, 1119, 1121, 1123, 1124, 1144, 1154, 1174, 1177, 1178, 1203], "mean": [1, 111, 142, 150, 216, 275, 328, 392, 401, 405, 408, 409, 410, 411, 441, 446, 499, 680, 689, 698, 702, 769, 784, 803, 926, 997, 1056, 1066, 1115, 1116, 1117, 1119, 1127, 1140, 1142, 1148, 1178], "univers": [1, 386, 392, 423, 441, 1117, 1126], "non": [1, 6, 21, 45, 46, 97, 137, 142, 206, 254, 275, 299, 328, 379, 484, 486, 489, 494, 514, 515, 531, 554, 555, 556, 557, 558, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 577, 579, 580, 581, 582, 586, 587, 588, 591, 592, 593, 595, 596, 597, 598, 600, 601, 602, 603, 604, 605, 606, 607, 610, 611, 612, 613, 614, 616, 617, 621, 622, 623, 624, 626, 627, 629, 639, 641, 650, 651, 656, 659, 661, 662, 664, 668, 669, 670, 672, 675, 682, 749, 822, 846, 886, 897, 898, 927, 975, 997, 1033, 1112, 1116, 1121, 1133, 1134, 1140, 1190, 1203], "omit": [1, 1126, 1144, 1174, 1178], "separ": [1, 2, 1110, 1117, 1118, 1125, 1128, 1129, 1134, 1147, 1148, 1152, 1177], "field": [1, 4, 46, 91, 111, 127, 219, 225, 232, 319, 336, 347, 365, 699, 702, 721, 727, 731, 742, 1109, 1118, 1140, 1177, 1183], "sko": [1, 219, 234, 318, 357, 480, 484, 489, 492, 507, 508, 509, 511, 512, 513, 516, 525, 534, 539, 544, 545, 549, 554, 559, 562, 563, 579, 592, 593, 597, 629, 639, 698, 846, 892, 1116, 1117, 1119, 1120, 1124, 1126, 1140, 1193, 1203], "preflabel": [1, 219, 234, 480, 489, 509, 513, 516, 525, 545, 629, 992, 1016, 1116, 1126, 1203], "dangl": [1, 1134, 1178, 1182, 1184], "do": [1, 204, 390, 769, 775, 1113, 1116, 1118, 1123, 1127, 1129, 1133, 1135, 1137, 1140, 1146, 1147, 1151, 1171, 1174, 1178, 1180, 1183, 1184, 1187, 1188, 1190, 1193, 1194], "popul": [1, 1123, 1129, 1178, 1183], "share": [1, 202, 264, 281, 289, 292, 295, 309, 336, 361, 369, 374, 473, 673, 745, 814, 918, 1030, 1105, 1115, 1116, 1118, 1124, 1128, 1178], "intent": [1, 1178, 1203], "languag": [1, 377, 384, 409, 415, 421, 441, 444, 617, 618, 1114, 1116, 1121, 1126, 1130, 1138, 1147, 1178, 1182, 1194, 1203], "unintent": 1, "version": [1, 2, 155, 165, 398, 441, 677, 699, 721, 733, 839, 846, 858, 886, 922, 1117, 1120, 1127, 1130, 1133, 1134, 1140, 1178, 1183], "allow": [1, 415, 441, 469, 697, 721, 724, 1063, 1066, 1075, 1089, 1093, 1104, 1110, 1116, 1117, 1124, 1126, 1133, 1134, 1137, 1140, 1143, 1144, 1147, 1159, 1188], "complet": [1, 28, 46, 115, 127, 161, 165, 227, 236, 276, 281, 329, 336, 419, 441, 551, 617, 706, 721, 772, 784, 847, 886, 948, 957, 998, 1005, 1061, 1075, 1112, 1124, 1127, 1176, 1178], "give": [1, 155, 165, 1117, 1127, 1133, 1140, 1151, 1185], "freedom": 1, "model": [1, 18, 19, 31, 41, 95, 108, 109, 127, 131, 152, 153, 165, 203, 204, 221, 222, 238, 269, 270, 281, 316, 317, 336, 402, 403, 409, 441, 452, 509, 511, 529, 535, 579, 617, 629, 694, 695, 721, 746, 762, 764, 784, 816, 837, 838, 886, 938, 939, 946, 957, 987, 988, 993, 1005, 1028, 1049, 1050, 1052, 1113, 1114, 1116, 1119, 1121, 1124, 1125, 1127, 1130, 1138, 1151, 1154, 1163, 1177, 1178, 1192], "thei": [1, 204, 1114, 1116, 1123, 1124, 1125, 1127, 1128, 1129, 1140, 1142, 1143, 1146, 1151, 1173, 1178, 1182, 1193], "obojson": 1, "littl": [1, 1140, 1151], "restrict": [1, 385, 386, 390, 392, 397, 423, 426, 437, 441, 459, 480, 484, 487, 489, 492, 493, 507, 510, 512, 513, 516, 525, 534, 539, 540, 544, 545, 549, 553, 556, 557, 560, 565, 572, 580, 584, 586, 589, 599, 607, 617, 619, 620, 648, 649, 653, 656, 658, 659, 663, 665, 670, 674, 1116, 1123, 1127, 1143, 1175, 1178, 1184], "disallow": 1, "suit": [1, 1116, 1129], "qc": [1, 1143], "check": [1, 19, 109, 153, 222, 270, 317, 403, 535, 695, 764, 838, 939, 988, 1038, 1040, 1045, 1050, 1063, 1065, 1067, 1068, 1073, 1075, 1076, 1077, 1078, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1094, 1095, 1096, 1097, 1098, 1100, 1101, 1102, 1103, 1106, 1123, 1135, 1178, 1185, 1193], "dashboard": 1, "align": [1, 377, 398, 409, 415, 421, 479, 1116, 1148, 1193], "aim": [1, 1110, 1117, 1133, 1203], "conveni": [1, 1112, 1116, 1118, 1178], "certain": [1, 1112, 1120, 1134, 1178], "obograph": [1, 204, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 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1045, 1046, 1048, 1051, 1052, 1053, 1054, 1055, 1060, 1063, 1064, 1065, 1066, 1193], "1": [1, 3, 4, 17, 20, 21, 22, 23, 24, 94, 95, 131, 142, 150, 155, 159, 214, 219, 225, 264, 266, 267, 271, 309, 311, 312, 313, 314, 318, 321, 322, 325, 326, 375, 376, 377, 384, 385, 386, 388, 389, 390, 392, 393, 397, 398, 400, 406, 407, 409, 414, 415, 416, 421, 480, 483, 484, 489, 492, 493, 499, 506, 507, 509, 510, 512, 513, 516, 525, 526, 534, 537, 539, 541, 544, 545, 549, 681, 696, 697, 699, 700, 747, 768, 769, 770, 817, 819, 820, 821, 828, 829, 831, 832, 839, 842, 843, 844, 846, 940, 943, 944, 945, 946, 982, 992, 993, 995, 1032, 1038, 1040, 1045, 1046, 1048, 1051, 1052, 1060, 1063, 1065, 1112, 1116, 1123, 1125, 1126, 1128, 1130, 1138, 1139, 1188, 1193], "g": [1, 4, 50, 55, 70, 71, 318, 325, 344, 357, 392, 393, 406, 407, 421, 441, 457, 721, 739, 846, 876, 892, 945, 961, 1038, 1040, 1065, 1103, 1112, 1116, 1117, 1118, 1123, 1124, 1125, 1127, 1128, 1137, 1151, 1159, 1175, 1177, 1178, 1180, 1183, 1187, 1188, 1190, 1193, 1194], "pronto": [1, 1112, 1115, 1116, 1144, 1151, 1152, 1163, 1165, 1172, 1176, 1178], "ol": [1, 1112, 1116, 1123, 1139, 1147, 1148, 1163, 1176, 1178], "bioport": [1, 1113, 1116, 1139, 1147, 1148, 1163, 1176, 1178, 1183, 1192], "roughli": [1, 1127], "adher": [1, 1116, 1143], "welcom": [2, 1110, 1111, 1113, 1139], "tracker": [2, 1110, 1130], "question": [2, 1110, 1118, 1127, 1133], "bug": [2, 1111, 1129], "enhanc": [2, 1133], "featur": [2, 397, 441, 464, 1111, 1112, 1118, 1119, 1127, 1137, 1140, 1146, 1147, 1148, 1204], "tutori": [2, 1113, 1121, 1124, 1127, 1136, 1138, 1140, 1141, 1144, 1146, 1204], "sourc": [2, 46, 165, 171, 174, 180, 281, 336, 617, 721, 784, 957, 1005, 1075, 1109, 1110, 1112, 1121, 1135, 1140, 1144, 1159, 1164, 1174, 1177, 1178, 1180, 1183, 1184, 1185, 1186, 1187, 1188, 1189, 1190, 1191, 1192, 1193, 1204], "resid": 2, "folder": [2, 1110, 1112, 1135, 1140, 1146, 1160, 1171], "github": [2, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 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[415, 441], "scopeenum": [415, 441], "instead": [415, 442, 1116, 1125, 1127, 1129, 1134, 1140, 1147, 1151, 1175, 1178], "commonli": [417, 1116, 1203], "plain": [417, 702, 1117], "abbrevi": [417, 1139], "pmid": [421, 1063, 1078, 1118, 1140], "12345": 421, "relax": [422, 1178], "registri": [422, 1194], "bioregistri": 422, "usag": [423, 433, 441, 447, 455, 461, 1116, 1117, 1119, 1128, 1139, 1140, 1176, 1180, 1186], "propert": [423, 433, 447, 455, 461], "principl": [441, 452, 1038, 1040, 1065, 1103, 1127], "attach": [441, 452, 698, 1178, 1186], "metedata": [441, 452], "Not": [441, 452, 1127, 1151], "complex": [441, 452, 1127, 1134, 1148, 1174, 1186], "obographs_datamodel": 441, "expr": 441, "nodetypeenum": 441, "objec": [444, 447, 454, 476, 477, 479], "benchmark": 453, "scopesenum": 465, "namedobject": [480, 484, 489, 492, 513, 516, 525, 534, 537, 539, 544, 545, 546, 549, 556, 612, 617, 672], "hassynonym": [480, 484, 485, 489, 492, 513, 514, 515, 516, 525, 526, 531, 534, 539, 544, 545, 549, 554, 588, 602, 604, 605, 610, 617, 666], "haslifecycl": [480, 484, 485, 488, 492, 513, 516, 525, 526, 530, 534, 536, 539, 544, 545, 546, 549, 567, 582, 595, 596, 597, 600, 607, 617, 662, 669], "hasproven": [480, 484, 485, 489, 492, 513, 516, 525, 526, 534, 537, 539, 544, 545, 549, 568, 570, 571, 572, 573, 576, 580, 587, 614, 617, 621, 650, 668, 670], "hasmap": [480, 484, 485, 489, 492, 513, 516, 525, 526, 534, 539, 544, 545, 546, 549, 559, 563, 575, 592, 617, 639], "hascategori": [480, 484, 485, 492, 513, 516, 525, 526, 534, 539, 544, 545, 546, 549, 561, 566, 606, 616, 617], "hasuserinform": [480, 484, 485, 489, 492, 513, 516, 525, 526, 534, 537, 539, 544, 545, 546, 549, 564, 574, 581, 593, 603, 613, 617, 651, 659], "hasminimalmetadata": [480, 484, 485, 489, 492, 513, 516, 525, 526, 534, 539, 544, 545, 549, 579, 617, 629], "has_exact_synonym": [480, 484, 489, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 617, 666], "labeltyp": [480, 484, 489, 492, 509, 511, 513, 516, 525, 534, 539, 544, 545, 549, 602, 604, 605, 610, 617, 629, 666], "has_narrow_synonym": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 617, 666], "has_broad_synonym": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 617, 666], "has_related_synonym": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 617], "alternative_term": [480, 481, 484, 492, 511, 513, 514, 515, 516, 525, 531, 534, 539, 544, 545, 549, 588, 602, 604, 605, 617, 666], "isa_alternative_term": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 554, 617], "iedb_alternative_term": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 554, 617], "editor_preferred_term": [480, 484, 492, 511, 513, 516, 525, 532, 534, 539, 544, 545, 549, 554, 617], "obo_foundry_unique_label": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 554, 617], "has_obsolescence_reason": [480, 484, 492, 507, 513, 516, 525, 534, 536, 539, 544, 545, 549, 617, 645], "term_replaced_bi": [480, 481, 484, 488, 492, 503, 507, 513, 516, 525, 532, 534, 536, 539, 544, 545, 549, 617, 645], "has_alternative_id": [480, 484, 492, 503, 507, 513, 516, 525, 530, 534, 539, 544, 545, 549, 617, 645], "excluded_from_qc_check": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 546, 549, 594, 617], "excluded_subclassof": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 594, 617], "excluded_synonym": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 594, 617], "should_conform_to": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 546, 549, 594, 617], "created_bi": [480, 484, 489, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 617, 654], "contributor": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 617, 654, 820, 821, 868, 869, 885, 886, 899, 910, 1186], "creator": [480, 484, 489, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 571, 617, 654, 1186], "came": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 570, 617], "isdefinedbi": [480, 484, 492, 510, 513, 516, 523, 525, 534, 537, 539, 544, 545, 549, 617, 1178], "editor_not": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 617, 654], "narrativetext": [480, 484, 492, 509, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 579, 587, 617, 671], "term_editor": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 617, 654], "definition_sourc": [480, 484, 492, 510, 513, 516, 522, 525, 532, 534, 539, 544, 545, 549, 617, 654, 1038, 1075], "ontology_term_request": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 617, 654], "imported_from": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 617, 654], "term_tracker_item": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 617, 654], "broadmatch": [480, 484, 492, 508, 513, 516, 525, 534, 539, 544, 545, 546, 549, 617, 633, 1124], "closematch": [480, 484, 492, 508, 513, 516, 525, 534, 539, 544, 545, 546, 549, 617, 633, 698, 1140], "exactmatch": [480, 484, 492, 508, 513, 516, 525, 534, 539, 544, 545, 546, 549, 617, 633, 1193], "narrowmatch": [480, 484, 492, 508, 513, 516, 525, 534, 539, 544, 545, 546, 549, 617, 633, 1124], "database_cross_refer": [480, 484, 489, 492, 508, 513, 516, 525, 534, 539, 544, 545, 549, 617, 633], "curieliter": [480, 484, 489, 492, 508, 513, 516, 525, 534, 539, 544, 545, 549, 575, 617], "has_obo_namespac": [480, 484, 492, 506, 513, 516, 525, 534, 539, 544, 545, 549, 617], "in_subset": [480, 484, 489, 492, 506, 507, 509, 510, 511, 512, 513, 516, 525, 534, 539, 544, 545, 549, 554, 562, 567, 579, 580, 582, 588, 593, 600, 617, 629, 669], "conformsto": [480, 484, 492, 506, 513, 516, 525, 534, 539, 544, 545, 546, 549, 617, 618], "imag": [480, 484, 488, 492, 512, 513, 514, 515, 525, 530, 531, 534, 536, 537, 539, 544, 545, 546, 549, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 587, 588, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 614, 616, 617, 618, 621, 629, 639, 650, 651, 659, 662, 668, 669, 670, 672, 1140, 1171], "example_of_usag": [480, 481, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 618], "curator_not": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 654], "has_curation_statu": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 618], "depicted_bi": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 618], "page": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 618, 1116, 1119], "transitiveproperti": [480, 488, 492, 514, 515, 516, 525, 530, 531, 534, 536, 537, 539, 544, 546, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 584, 586, 587, 588, 590, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 613, 614, 616, 617, 620, 621, 624, 625, 627, 628, 629, 639, 650, 651, 653, 656, 659, 661, 662, 667, 668, 669, 670, 672, 1178], "homosapien": [480, 488, 492, 514, 515, 516, 525, 530, 531, 536, 537, 544, 546, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 587, 588, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 613, 614, 616, 617, 621, 629, 639, 650, 651, 659, 662, 668, 669, 670, 672], "orcid": [480, 513, 1117], "omoschema": [480, 483, 484, 485, 486, 487, 488, 489, 492, 493, 499, 501, 506, 507, 508, 509, 510, 511, 512, 513, 516, 525, 526, 530, 534, 536, 537, 539, 540, 541, 544, 545, 546, 549, 558, 569, 583, 594, 595, 596, 597, 609, 612, 618, 632, 633, 634, 642, 645, 652, 654, 657, 660, 662, 678], "id_prefix": [480, 513, 940, 944, 1178], "disjoint_with": [480, 484, 489, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 604], "allotrop": [480, 481, 482, 484, 489, 492, 507, 509, 511, 512, 513, 516, 525, 534, 539, 544, 545, 549, 554, 562, 579, 582, 593, 629, 669], "permit": [480, 484, 489, 492, 507, 510, 511, 512, 513, 516, 525, 534, 539, 544, 545, 549, 554, 562, 567, 580, 582, 588, 593, 600, 669], "profil": [480, 484, 489, 492, 507, 509, 510, 511, 512, 513, 516, 525, 534, 539, 544, 545, 549, 554, 562, 567, 579, 580, 582, 588, 593, 600, 629, 669, 846, 876, 886, 1120, 1126, 1128, 1190], "altlabel": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 554, 698, 1117], "0000118": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 554, 1117, 1178], "0001847": [480, 484, 492, 511, 513, 515, 516, 525, 534, 539, 544, 545, 549], "9991118": [480, 484, 492, 511, 513, 514, 516, 525, 534, 539, 544, 545, 549], "0000111": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 588], "add": [480, 484, 492, 511, 513, 516, 525, 531, 534, 539, 544, 545, 549, 1064, 1126, 1127, 1133, 1135, 1137, 1141, 1159, 1177, 1178, 1183], "uniquekei": [480, 484, 492, 511, 513, 516, 525, 531, 534, 539, 544, 545, 549], "0000589": [480, 484, 492, 511, 513, 516, 525, 531, 534, 539, 544, 545, 549], "obsoletion_related_properti": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 567, 582, 600, 607, 617, 669], "obsoleteaspect": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 567, 582, 607, 617, 669], "0000231": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 607, 1125], "isreplacedbi": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 669], "0100001": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 669, 1125, 1178], "redund": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 945, 953, 957, 966, 1134, 1190], "invers": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 1128], "replaced_bi": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600], "NOT": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 680, 943, 959, 1130, 1135, 1146, 1171, 1178, 1194], "owlc": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600], "owlapi": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 1185], "317": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600], "notobsoleteaspect": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 617], "hasalternativeid": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 1125], "excluded_axiom": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 595, 596, 597, 617, 662], "hiddensynonym": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 597], "propos": [480, 484, 489, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 571, 572, 945, 951, 957, 1116, 1137, 1147], "omo": [480, 484, 489, 492, 510, 513, 516, 522, 523, 524, 525, 534, 539, 544, 545, 549, 571, 572, 1063, 1075, 1093, 1117, 1125, 1126], "2022": [480, 484, 489, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 571, 572], "04": [480, 484, 489, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 571, 572], "12": [480, 484, 489, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 571, 572], "deprecated_element_has_exact_replac": [480, 484, 489, 492, 510, 513, 516, 522, 523, 524, 525, 534, 539, 544, 545, 549, 571, 572, 628, 644], "provenance_properti": [480, 484, 489, 492, 510, 512, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 570, 571, 572, 573, 574, 576, 577, 580, 587, 601, 614, 617, 650, 664, 668, 670], "wasattributedto": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "structured_pattern": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "orcid_regex": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "interpol": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "partial_match": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "pav": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 570, 576, 621, 677], "createdon": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 570], "authoredon": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 576], "importedfrom": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 621], "0000116": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 587], "narr": [480, 484, 492, 509, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 579, 587, 671], "0000117": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 668], "0000119": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 580], "0000234": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 650], "0000412": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 614], "0000233": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 670], "hasobonamespac": [480, 484, 492, 506, 513, 516, 525, 534, 539, 544, 545, 549, 606, 1125], "informative_properti": [480, 484, 489, 492, 506, 512, 513, 516, 525, 534, 537, 539, 544, 545, 549, 561, 562, 564, 566, 578, 581, 593, 603, 608, 613, 617, 630, 631, 651], "sdo": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 613], "0000112": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 593], "0000232": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 574], "0000114": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 603], "foaf": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 581, 651, 1126, 1203], "guidelin": [480, 489, 509, 513, 516, 525, 545, 629, 1110, 1133, 1138, 1152], "core_properti": [480, 484, 489, 492, 509, 513, 516, 525, 526, 534, 537, 539, 544, 545, 549, 579, 612, 617, 629], "aristotelian": [480, 509, 513, 516, 525, 545, 579, 1123], "logical_pred": [480, 484, 492, 493, 513, 516, 525, 526, 534, 537, 539, 540, 541, 544, 545, 546, 549, 553, 560, 565, 584, 585, 586, 589, 590, 599, 617, 619, 620, 635, 636, 637, 638, 647, 648, 649, 653, 655, 656, 658, 663, 665, 672, 674], "designates_typ": [480, 484, 492, 513, 516, 525, 526, 534, 537, 539, 544, 545, 546, 549, 672], "gitlab": [481, 482], "devop": [481, 482], "allotrope_framework_term_curation_style_guid": [481, 482], "pdf": [481, 482, 499], "changenot": [481, 617, 618], "reifi": [483, 617, 642, 652], "relational_rol": [483, 489, 555, 556, 557, 642, 652], "represents_relationship": [483, 489], "shorthand": [484, 534, 544, 549, 617, 1116, 1118, 1194], "is_class_level": [484, 534, 539, 544, 549, 617], "is_metadata_tag": [484, 534, 539, 544, 549, 617], "annotatedproperti": [484, 489, 617, 657], "has_synonym_typ": [484, 489, 617], "bundl": [485, 617, 1124, 1145, 1151], "root": [486, 617, 1116, 1140, 1178, 1182, 1184, 1191], "anonymousclassexpress": [486, 541, 617], "anonym": [487, 541, 617, 846, 852, 853, 886, 887, 1123, 1178], "annotatedtarget": [488, 489, 617, 657], "statement": [489, 555, 556, 557, 558, 564, 571, 575, 577, 591, 598, 601, 604, 611, 617, 622, 623, 626, 629, 641, 659, 664, 675, 846, 886, 915, 916, 945, 955, 957, 1116, 1163, 1174, 1178], "annotatedsourc": [489, 526, 617, 657], "is_inf": [489, 617], "has_axiom_label": [489, 546, 617, 654], "is_a_defining_property_chain_axiom": [489, 617], "is_a_defining_property_chain_axiom_where_second_argument_is_reflex": [489, 617], "date_retriev": [489, 617, 654], "external_ontologi": [489, 617], "reification_pred": [489, 555, 556, 557, 617], "dc": [489, 537, 664], "0010000": [489, 601], "ro": [489, 492, 534, 549, 622, 623, 640, 667, 940, 943, 959, 960, 963, 1110, 1116, 1123, 1127, 1141, 1142, 1146, 1148, 1178], "0002581": [489, 622], "0002582": [489, 623], "hassynonymtyp": [489, 611], "never_in_taxon": [492, 617], "disconnected_from": [492, 617, 660], "has_rank": [492, 546, 617], "disjointwith": [492, 493, 534, 540, 541, 549, 617, 632], "intersectionof": [492, 493, 541, 617, 632], "complementof": [492, 493, 541, 617, 632], "oneof": [492, 493, 541, 617, 632], "unionof": [492, 493, 541, 617, 632], "has_ontology_root_term": [492, 537, 617, 618], "0002161": [492, 640, 943, 959], "shortcut_annotation_properti": [492, 583, 617], "ncbitaxon": [492, 513, 609, 944, 1142, 1151, 1177, 1178], "taxslim": [492, 609], "propertyexpress": [492, 493, 501, 534, 539, 541, 549, 584, 617, 648], "match_aspect": [492, 493, 534, 541, 549, 559, 563, 575, 589, 590, 592, 617, 632, 633, 639, 658], "extens": [499, 617, 1118, 1119, 1123, 1127, 1133, 1147, 1171], "shacl": [499, 617, 1038, 1040, 1065, 1103, 1135, 1193], "definitionconstraint": 499, "dcc": 499, "problem": [499, 1045, 1075, 1193, 1203], "definitionpres": 499, "s0": 499, "s1": 499, "harmon": 499, "genusdifferentiaform": 499, "s3": [499, 1135, 1146, 1194], "singlegenu": 499, "circular": [499, 1123], "s7": 499, "matchtextandlog": 499, "s11": 499, "matchtextandlogicalgenusnotintext": 499, "matchtextandlogicaldifferentianotintext": 499, "matchtextandrefer": 499, "s20": 499, "cite": [499, 1133], "referencenotfound": 499, "citat": 499, "referenceisretract": 499, "retract": [499, 1063, 1078], "incatool": [499, 1110, 1116, 1135, 1184, 1203], "kit": [499, 1110, 1112, 1119, 1133, 1184, 1203], "305": 499, "philpap": 499, "archiv": 499, "sepgfw": 499, "annotationpropertymixin": [506, 507, 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"class-definitionpropertyvalue"]], "Class: DisjointClassExpressionsAxiom": [[385, "class-disjointclassexpressionsaxiom"]], "Class: DomainRangeAxiom": [[386, "class-domainrangeaxiom"]], "Class: Edge": [[388, "class-edge"]], "Class: EquivalentNodesSet": [[389, "class-equivalentnodesset"]], "Class: ExistentialRestrictionExpression": [[390, "class-existentialrestrictionexpression"]], "Annotations": [[390, "annotations"], [397, "annotations"], [851, "annotations"], [853, "annotations"], [859, "annotations"], [860, "annotations"], [861, "annotations"], [864, "annotations"], [865, "annotations"], [866, "annotations"], [872, "annotations"], [873, "annotations"], [874, "annotations"], [877, "annotations"], [878, "annotations"], [880, "annotations"], [887, "annotations"], [890, "annotations"], [891, "annotations"], [892, "annotations"], [893, "annotations"], [894, "annotations"], [896, "annotations"], [897, "annotations"], [898, "annotations"], [900, "annotations"], [902, "annotations"], [903, "annotations"], [908, "annotations"], [915, "annotations"], [916, "annotations"], [919, "annotations"]], "Class: Graph": [[392, "class-graph"]], "Class: GraphDocument": [[393, "class-graphdocument"]], "Class: LogicalDefinitionAxiom": [[397, "class-logicaldefinitionaxiom"]], "Class: Meta": [[398, "class-meta"]], "Class: Node": [[400, "class-node"], [1048, "class-node"]], "Enum: NodeTypeEnum": [[401, "enum-nodetypeenum"]], "Type: OboIdentifierString": [[404, "type-oboidentifierstring"]], "PredsEnum": [[405, "predsenum"]], "Class: PrefixDeclaration": [[406, "class-prefixdeclaration"]], "Class: PropertyChainAxiom": [[407, "class-propertychainaxiom"]], "Enum: PropertyTypeEnum": [[408, "enum-propertytypeenum"]], "Enum: ScopeEnum": [[410, "enum-scopeenum"]], "ScopesEnum": [[411, "scopesenum"]], "Class: SubsetDefinition": [[414, "class-subsetdefinition"]], "Class: SynonymPropertyValue": [[415, "class-synonympropertyvalue"]], "Class: SynonymTypeDefinition": [[416, "class-synonymtypedefinition"]], "Type: SynonymTypeIdentifierString": [[417, "type-synonymtypeidentifierstring"]], "Class: XrefPropertyValue": [[421, "class-xrefpropertyvalue"]], "Type: XrefString": [[422, "type-xrefstring"]], "Slot: allValuesFromEdges": [[423, "slot-allvaluesfromedges"]], "Slot: basicPropertyValues": [[424, "slot-basicpropertyvalues"]], "Slot: chainPredicateIds": [[425, "slot-chainpredicateids"]], "Slot: classExpressions": [[426, "slot-classexpressions"]], "Slot: classIds": [[427, "slot-classids"]], "Slot: definedClassId": [[429, "slot-definedclassid"]], "Slot: definition": [[430, "slot-definition"], [579, "slot-definition"], [1069, "slot-definition"]], "Slot: deprecated": [[431, "slot-deprecated"], [582, "slot-deprecated"]], "Slot: disjointClassExpressionsAxioms": [[432, "slot-disjointclassexpressionsaxioms"]], "Slot: domainClassIds": [[433, "slot-domainclassids"]], "Slot: domainRangeAxioms": [[434, "slot-domainrangeaxioms"]], "Slot: edges": [[435, "slot-edges"]], "Slot: equivalentNodesSets": [[436, "slot-equivalentnodessets"]], "Slot: fillerId": [[437, "slot-fillerid"]], "Slot: genusIds": [[438, "slot-genusids"]], "Slot: graphs": [[439, "slot-graphs"]], "Obographs Datamodel": [[441, "obographs-datamodel"]], "Slot: isExact": [[442, "slot-isexact"]], "Slot: lang": [[444, "slot-lang"]], "Slot: lbl": [[445, "slot-lbl"]], "Slot: logicalDefinitionAxioms": [[446, "slot-logicaldefinitionaxioms"]], "Slot: meta": [[447, "slot-meta"]], "Slot: namespace": [[448, "slot-namespace"]], "Slot: nodeIds": [[449, "slot-nodeids"]], "Slot: nodes": [[450, "slot-nodes"]], "Slot: obj": [[451, "slot-obj"]], "obographs_datamodel": [[452, "obographs-datamodel"]], "obographs_linkml_model": [[453, "obographs-linkml-model"]], "Slot: pred": [[454, "slot-pred"]], "Slot: predicateId": [[455, "slot-predicateid"]], "Slot: prefixes": [[457, "slot-prefixes"]], "Slot: propertyChainAxioms": [[458, "slot-propertychainaxioms"]], "Slot: propertyId": [[459, "slot-propertyid"]], "Slot: propertyType": [[460, "slot-propertytype"]], "Slot: rangeClassIds": [[461, "slot-rangeclassids"]], "Slot: representativeNodeId": [[462, "slot-representativenodeid"]], "Slot: representitiveNodeId": [[463, "slot-representitivenodeid"]], "Slot: restrictions": [[464, "slot-restrictions"]], "Slot: scope": [[465, "slot-scope"]], "Slot: sub": [[466, "slot-sub"]], "Slot: subsetDefinitions": [[467, "slot-subsetdefinitions"]], "Slot: subsets": [[468, "slot-subsets"]], "Slot: synonymType": [[469, "slot-synonymtype"]], "Slot: synonymTypeDefinitions": [[470, "slot-synonymtypedefinitions"]], "Slot: synonyms": [[471, "slot-synonyms"]], "Slot: unionEquivalentTo": [[474, "slot-unionequivalentto"]], "Slot: unionEquivalentToExpression": [[475, "slot-unionequivalenttoexpression"]], "Slot: val": [[476, "slot-val"]], "Slot: valType": [[477, "slot-valtype"]], "Slot: version": [[478, "slot-version"], [921, "slot-version"]], "Slot: xrefs": [[479, "slot-xrefs"]], "Class: Agent": [[480, "class-agent"], [817, 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"slot-annotatedtarget"]], "Slot: annotations": [[558, "slot-annotations"], [1000, "slot-annotations"]], "Slot: broadMatch": [[559, "slot-broadmatch"]], "Slot: cardinality": [[560, "slot-cardinality"]], "Slot: changeNote": [[562, "slot-changenote"]], "Slot: closeMatch": [[563, "slot-closematch"]], "Slot: comment": [[564, "slot-comment"]], "Slot: complementOf": [[565, "slot-complementof"]], "Slot: conformsTo": [[566, "slot-conformsto"]], "Slot: consider": [[567, "slot-consider"]], "Slot: contributor": [[568, "slot-contributor"]], "Slot: core_property": [[569, "slot-core-property"]], "Slot: created": [[570, "slot-created"]], "Slot: created_by": [[571, "slot-created-by"]], "Slot: creator": [[573, "slot-creator"]], "Slot: curator_note": [[574, "slot-curator-note"]], "Slot: database_cross_reference": [[575, "slot-database-cross-reference"]], "Slot: date_retrieved": [[577, "slot-date-retrieved"]], "Slot: defaultLanguage": [[578, "slot-defaultlanguage"]], "Slot: definition_source": [[580, "slot-definition-source"], [1070, "slot-definition-source"]], "Slot: depicted_by": [[581, "slot-depicted-by"]], "Slot: disconnected_from": [[583, "slot-disconnected-from"]], "Slot: disjointWith": [[584, "slot-disjointwith"]], "Slot: distinctMembers": [[585, "slot-distinctmembers"]], "Slot: domain": [[586, "slot-domain"]], "Slot: editor_note": [[587, "slot-editor-note"]], "Slot: editor_preferred_term": [[588, "slot-editor-preferred-term"]], "Slot: equivalentClass": [[589, "slot-equivalentclass"]], "Slot: equivalentProperty": [[590, "slot-equivalentproperty"]], "Slot: evidence": [[591, "slot-evidence"]], "Slot: exactMatch": [[592, "slot-exactmatch"]], "Slot: example_of_usage": [[593, "slot-example-of-usage"]], "Slot: excluded_axiom": [[594, "slot-excluded-axiom"]], "Slot: excluded_from_QC_check": [[595, "slot-excluded-from-qc-check"]], "Slot: excluded_subClassOf": [[596, "slot-excluded-subclassof"]], "Slot: excluded_synonym": [[597, "slot-excluded-synonym"]], "Slot: external_ontology": [[598, "slot-external-ontology"]], "Slot: hasValue": [[599, "slot-hasvalue"]], "Slot: has_alternative_id": [[600, "slot-has-alternative-id"]], "Slot: has_axiom_label": [[601, "slot-has-axiom-label"]], "Slot: has_broad_synonym": [[602, "slot-has-broad-synonym"]], "Slot: has_curation_status": [[603, "slot-has-curation-status"]], "Slot: has_exact_synonym": [[604, "slot-has-exact-synonym"]], "Slot: has_narrow_synonym": [[605, "slot-has-narrow-synonym"]], "Slot: has_obo_namespace": [[606, "slot-has-obo-namespace"]], "Slot: has_obsolescence_reason": [[607, "slot-has-obsolescence-reason"]], "Slot: has_ontology_root_term": [[608, "slot-has-ontology-root-term"]], "Slot: has_rank": [[609, "slot-has-rank"]], "Slot: has_related_synonym": [[610, "slot-has-related-synonym"]], "Slot: has_synonym_type": [[611, "slot-has-synonym-type"]], "Slot: image": [[613, "slot-image"]], "Slot: imported_from": [[614, "slot-imported-from"]], "Slot: imports": [[615, "slot-imports"]], "Slot: in_subset": [[616, "slot-in-subset"]], "Ontology Metadata Ontology Schema": [[617, "ontology-metadata-ontology-schema"]], "Slot: informative_property": [[618, "slot-informative-property"]], "Slot: intersectionOf": [[619, "slot-intersectionof"]], "Slot: inverseOf": [[620, "slot-inverseof"]], "Slot: isDefinedBy": [[621, "slot-isdefinedby"]], "Slot: is_a_defining_property_chain_axiom": [[622, "slot-is-a-defining-property-chain-axiom"]], "Slot: is_a_defining_property_chain_axiom_where_second_argument_is_reflexive": [[623, "slot-is-a-defining-property-chain-axiom-where-second-argument-is-reflexive"]], "Slot: is_class_level": [[624, "slot-is-class-level"]], "Slot: is_cyclic": [[625, "slot-is-cyclic"]], "Slot: is_inferred": [[626, "slot-is-inferred"]], "Slot: is_metadata_tag": [[627, "slot-is-metadata-tag"]], "Slot: is_transitive": [[628, "slot-is-transitive"]], "Slot: language": [[630, "slot-language"]], "Slot: license": [[631, "slot-license"]], "Slot: logical_predicate": [[632, "slot-logical-predicate"]], "Slot: match_aspect": [[634, "slot-match-aspect"]], "Slot: maxQualifiedCardinality": [[635, "slot-maxqualifiedcardinality"]], "Slot: members": [[636, "slot-members"]], "Slot: minCardinality": [[637, "slot-mincardinality"]], "Slot: minQualifiedCardinality": [[638, "slot-minqualifiedcardinality"]], "Slot: narrowMatch": [[639, "slot-narrowmatch"]], "Slot: never_in_taxon": [[640, "slot-never-in-taxon"]], "Slot: notes": [[641, "slot-notes"]], "Slot: oboInOwl_id": [[643, "slot-oboinowl-id"]], "Slot: oboInOwl_ontology": [[644, "slot-oboinowl-ontology"]], "Slot: obsoletion_related_property": [[645, "slot-obsoletion-related-property"]], "omo-schema": [[646, "omo-schema"]], "Slot: onClass": [[647, "slot-onclass"]], "Slot: onProperty": [[648, "slot-onproperty"]], "Slot: oneOf": [[649, "slot-oneof"]], "Slot: ontology_term_requester": [[650, "slot-ontology-term-requester"]], "Slot: page": [[651, "slot-page"]], "Slot: propertyChainAxiom": [[653, "slot-propertychainaxiom"]], "Slot: provenance_property": [[654, "slot-provenance-property"]], "Slot: qualifiedCardinality": [[655, "slot-qualifiedcardinality"]], "Slot: range": [[656, "slot-range"]], "Slot: reification_predicate": [[657, "slot-reification-predicate"]], "Slot: sameAs": [[658, "slot-sameas"]], "Slot: seeAlso": [[659, "slot-seealso"]], "Slot: shortcut_annotation_property": [[660, "slot-shortcut-annotation-property"]], "Slot: shorthand": [[661, "slot-shorthand"]], "Slot: should_conform_to": [[662, "slot-should-conform-to"]], "Slot: someValuesFrom": [[663, "slot-somevaluesfrom"]], "Slot: subClassOf": [[665, "slot-subclassof"]], "Slot: synonym": [[666, "slot-synonym"]], "Slot: temporal_interpretation": [[667, "slot-temporal-interpretation"]], "Slot: term_editor": [[668, "slot-term-editor"]], "Slot: term_replaced_by": [[669, "slot-term-replaced-by"]], "Slot: term_tracker_item": [[670, "slot-term-tracker-item"]], "Slot: title": [[671, "slot-title"], [917, "slot-title"]], "Slot: unionOf": [[674, "slot-unionof"]], "Slot: versionIRI": [[676, "slot-versioniri"]], "Slot: versionInfo": [[677, "slot-versioninfo"]], "Slot: version_property": [[678, "slot-version-property"]], "Enum: BooleanOperator": [[680, "enum-booleanoperator"]], "Class: ComplexQuery": [[681, "class-complexquery"]], "Enum: GraphFunction": [[689, "enum-graphfunction"]], "Class: PathExpression": [[696, "class-pathexpression"]], "Class: SearchBaseConfiguration": [[697, "class-searchbaseconfiguration"]], "Enum: SearchProperty": [[698, "enum-searchproperty"]], "Class: SearchResult": [[699, "class-searchresult"]], "Class: SearchResultSet": [[700, "class-searchresultset"]], "Type: SearchTerm": [[701, "type-searchterm"]], "Enum: SearchTermSyntax": [[702, "enum-searchtermsyntax"]], "Slot: all_of": [[708, "slot-all-of"]], "Slot: any_of": [[709, "slot-any-of"]], "Slot: atom": [[710, "slot-atom"]], "Slot: configuration": [[712, "slot-configuration"]], "Slot: cursor": [[713, "slot-cursor"]], "Slot: force_case_insensitive": [[714, "slot-force-case-insensitive"]], "Slot: graph_predicates": [[715, "slot-graph-predicates"]], "Slot: include_aliases": [[716, "slot-include-aliases"], [1004, "slot-include-aliases"]], "Slot: include_definition": [[717, "slot-include-definition"]], "Slot: include_id": [[718, "slot-include-id"]], "Slot: include_label": [[719, "slot-include-label"]], "Slot: include_obsoletes_in_results": [[720, "slot-include-obsoletes-in-results"]], "search datamodel": [[721, "search-datamodel"]], "Slot: is_complete": [[722, "slot-is-complete"]], "Slot: is_fuzzy": [[723, "slot-is-fuzzy"]], "Slot: is_partial": [[724, "slot-is-partial"]], "Slot: is_regular_expression": [[725, "slot-is-regular-expression"]], "Slot: limit": [[726, "slot-limit"], [1008, "slot-limit"]], "Slot: matches_full_search_term": [[727, "slot-matches-full-search-term"]], "Slot: none_of": [[728, "slot-none-of"]], "Slot: object_id": [[729, "slot-object-id"], [797, "slot-object-id"], [1015, "slot-object-id"], [1083, "slot-object-id"]], "Slot: object_match_field": [[731, "slot-object-match-field"]], "Slot: object_source": [[732, "slot-object-source"], [800, "slot-object-source"], [1017, "slot-object-source"]], "Slot: object_source_version": [[733, "slot-object-source-version"]], "Slot: path_to": [[734, "slot-path-to"]], "Slot: properties": [[735, "slot-properties"]], "Slot: result_count": [[737, "slot-result-count"]], "search-datamodel": [[739, "search-datamodel"]], "Slot: search_term": [[740, "slot-search-term"]], "Slot: search_terms": [[741, "slot-search-terms"]], "Slot: snippet": [[742, "slot-snippet"]], "Slot: syntax": [[743, "slot-syntax"]], "Slot: traversal": [[744, "slot-traversal"]], "SemSQL": [[746, "semsql"]], "Class: BestMatch": [[747, "class-bestmatch"]], "Type: ItemCount": [[757, "type-itemcount"]], "Type: NegativeLogValue": [[761, "type-negativelogvalue"]], "Type: NonNegativeFloat": [[763, "type-nonnegativefloat"]], "Class: PairwiseSimilarity": [[765, "class-pairwisesimilarity"]], "Class: TermInfo": [[768, "class-terminfo"]], "Class: TermPairwiseSimilarity": [[769, "class-termpairwisesimilarity"]], "Class: TermSetPairwiseSimilarity": [[770, "class-termsetpairwisesimilarity"]], "Type: ZeroToOne": [[774, "type-zerotoone"]], "Slot: ancestor_id": [[775, "slot-ancestor-id"]], "Slot: ancestor_information_content": [[776, "slot-ancestor-information-content"]], "Slot: ancestor_label": [[777, "slot-ancestor-label"]], "Slot: ancestor_source": [[778, "slot-ancestor-source"]], "Slot: average_score": [[779, "slot-average-score"]], "Slot: best_score": [[780, "slot-best-score"]], "Slot: cosine_similarity": [[781, "slot-cosine-similarity"]], "Slot: dice_similarity": [[782, "slot-dice-similarity"]], "Semantic Similarity": [[784, "semantic-similarity"]], "Slot: information_content": [[785, "slot-information-content"]], "Slot: intersection_count": [[786, "slot-intersection-count"]], "Slot: jaccard_similarity": [[787, "slot-jaccard-similarity"]], "Slot: match_source": [[789, 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"slot-match-string"]], "Slot: match_type": [[1010, "slot-match-type"]], "Slot: matches_whole_text": [[1011, "slot-matches-whole-text"]], "Slot: model": [[1012, "slot-model"]], "Slot: object_aliases": [[1013, "slot-object-aliases"]], "Slot: object_categories": [[1014, "slot-object-categories"]], "Slot: parent_document": [[1018, "slot-parent-document"]], "Slot: source_text": [[1020, "slot-source-text"]], "Slot: subject_end": [[1022, "slot-subject-end"]], "Slot: subject_start": [[1025, "slot-subject-start"]], "Slot: subject_text_id": [[1026, "slot-subject-text-id"]], "Slot: text": [[1027, "slot-text"]], "text-annotator": [[1028, "text-annotator"]], "Slot: token_exclusion_list": [[1029, "slot-token-exclusion-list"]], "Class: ConstraintComponent": [[1032, "class-constraintcomponent"]], "Class: DefinitionValidationResult": [[1038, "class-definitionvalidationresult"]], "Class: ExternalReferenceValidationResult": [[1040, "class-externalreferencevalidationresult"]], "Class: 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Data Model": [[1075, "validation-results-data-model"]], "Slot: instantiates": [[1077, "slot-instantiates"]], "Slot: lookup_references": [[1078, "slot-lookup-references"]], "Slot: max_number_results_per_type": [[1079, "slot-max-number-results-per-type"]], "Slot: modified": [[1080, "slot-modified"]], "Slot: number_of_attempts": [[1081, "slot-number-of-attempts"]], "Slot: object_info": [[1084, "slot-object-info"]], "Slot: object_str": [[1085, "slot-object-str"]], "Slot: problem": [[1088, "slot-problem"]], "Slot: prompt_info": [[1089, "slot-prompt-info"]], "Slot: proposed_new_definition": [[1090, "slot-proposed-new-definition"]], "Slot: repairs": [[1091, "slot-repairs"]], "Slot: schema_path": [[1093, "slot-schema-path"]], "Slot: severity": [[1094, "slot-severity"]], "Slot: subject_info": [[1098, "slot-subject-info"]], "Slot: successful": [[1099, "slot-successful"]], "Slot: suggested_modifications": [[1100, "slot-suggested-modifications"]], "Slot: suggested_predicate": [[1101, "slot-suggested-predicate"]], "Slot: time_checked": [[1102, "slot-time-checked"]], "Slot: type_severity_map": [[1104, "slot-type-severity-map"]], "Slot: validation_configuration": [[1107, "slot-validation-configuration"]], "validaton-results": [[1108, "validaton-results"]], "FAQ: Architecture and Design": [[1109, "faq-architecture-and-design"]], "What is an interface?": [[1109, "what-is-an-interface"]], "What is a Data Model?": [[1109, "what-is-a-data-model"]], "What is an iterator and why does OAK use them so much?": [[1109, "what-is-an-iterator-and-why-does-oak-use-them-so-much"]], "FAQ: Command Line": [[1110, "faq-command-line"]], "How do I see a list of commands?": [[1110, "how-do-i-see-a-list-of-commands"]], "How do I get help on a command?": [[1110, "how-do-i-get-help-on-a-command"]], "How do I get more examples of command line usage?": [[1110, "how-do-i-get-more-examples-of-command-line-usage"]], "I want to query an ontology, what do I pass for the --input option?": [[1110, "i-want-to-query-an-ontology-what-do-i-pass-for-the-input-option"]], "Why do I get a \u201cno such option\u201d error when I pass the \u201c\u2013input\u201d option?": [[1110, "why-do-i-get-a-no-such-option-error-when-i-pass-the-input-option"]], "What do the codes \u201ci\u201d and \u201cp\u201d mean?": [[1110, "what-do-the-codes-i-and-p-mean"]], "Can I pass a list of IDs (CURIEs) as input to a command?": [[1110, "can-i-pass-a-list-of-ids-curies-as-input-to-a-command"]], "Can I pass entity labels as command inputs?": [[1110, "can-i-pass-entity-labels-as-command-inputs"]], "Can I pass lexical queries as command inputs?": [[1110, "can-i-pass-lexical-queries-as-command-inputs"]], "Can I pass the results of graph queries as command inputs?": [[1110, "can-i-pass-the-results-of-graph-queries-as-command-inputs"]], "Can I make boolean combinations of query terms?": [[1110, "can-i-make-boolean-combinations-of-query-terms"]], "Can I chain commands together, unix-style?": [[1110, "can-i-chain-commands-together-unix-style"]], "What does the symbol @ mean in a query term list": [[1110, "what-does-the-symbol-mean-in-a-query-term-list"]], "Can I use the command line to visualize a subgraph?": [[1110, "can-i-use-the-command-line-to-visualize-a-subgraph"]], "Is there an over-arching philosophy or set of design principles to the OAK command line?": [[1110, "is-there-an-over-arching-philosophy-or-set-of-design-principles-to-the-oak-command-line"]], "The command isn\u2019t working the way I expected - how do I get help?": [[1110, "the-command-isn-t-working-the-way-i-expected-how-do-i-get-help"]], "FAQ: Contributing": [[1111, "faq-contributing"]], "How can I contribute?": [[1111, "how-can-i-contribute"]], "How do I stay involved?": [[1111, "how-do-i-stay-involved"]], "FAQ: General": [[1112, "faq-general"]], "What is OAK?": [[1112, "what-is-oak"]], "Are there any tutorials for OAK?": [[1112, "are-there-any-tutorials-for-oak"]], "Are there runnable examples of how to use OAK?": [[1112, "are-there-runnable-examples-of-how-to-use-oak"]], "I am familiar with both Python and Ontologies. Where should I start?": [[1112, "i-am-familiar-with-both-python-and-ontologies-where-should-i-start"]], "I find ontologies confusing. Is there a general guide to help me?": [[1112, "i-find-ontologies-confusing-is-there-a-general-guide-to-help-me"]], "Why is it called OAK?": [[1112, "why-is-it-called-oak"]], "How do I install OAK?": [[1112, "how-do-i-install-oak"]], "Can I use OAK if I don\u2019t know Python?": [[1112, "can-i-use-oak-if-i-don-t-know-python"]], "Can I contribute to OAK?": [[1112, "can-i-contribute-to-oak"]], "Is OAK just for bio-ontologies?": [[1112, "is-oak-just-for-bio-ontologies"]], "Can OAK access ontologies in ontology portals such as MatPortal or BioPortal?": [[1112, "can-oak-access-ontologies-in-ontology-portals-such-as-matportal-or-bioportal"]], "Can OAK access ontologies in triplestores such as OntoBee or Ubergraph?": [[1112, "can-oak-access-ontologies-in-triplestores-such-as-ontobee-or-ubergraph"]], "Can OAK access local files?": [[1112, "can-oak-access-local-files"]], "Can OAK access OBO Format files?": [[1112, "can-oak-access-obo-format-files"]], "Does OAK support all of OWL?": [[1112, "does-oak-support-all-of-owl"]], "Does OAK support reasoning?": [[1112, "does-oak-support-reasoning"]], "Can I use OAK to do graph queries over ontologies?": [[1112, "can-i-use-oak-to-do-graph-queries-over-ontologies"]], "Can I use OAK to do lexical search?": [[1112, "can-i-use-oak-to-do-lexical-search"]], "Can I use OAK as a text annotator?": [[1112, "can-i-use-oak-as-a-text-annotator"]], "FAQ": [[1113, "faq"]], "FAQ: Ontologies": [[1114, "faq-ontologies"]], "What is an ontology?": [[1114, "what-is-an-ontology"]], "Do we need ontologies now we have ChatGPT?": [[1114, "do-we-need-ontologies-now-we-have-chatgpt"]], "What is OWL?": [[1114, "what-is-owl"]], "What is OBO Format?": [[1114, "what-is-obo-format"]], "What is OBO": [[1114, "what-is-obo"]], "What\u2019s a synonym and how do I access them?": [[1114, "what-s-a-synonym-and-how-do-i-access-them"]], "Ancestor statistics": [[1114, "id2"], [1140, "id2"], [1146, "id1"]], "FAQ: Troubleshooting": [[1115, "faq-troubleshooting"]], "Why do I get a \u201cError: No such option: -i\u201d message": [[1115, "why-do-i-get-a-error-no-such-option-i-message"]], "How do I get a BioPortal API key?": [[1115, "how-do-i-get-a-bioportal-api-key"]], "My OBO Format file won\u2019t parse": [[1115, "my-obo-format-file-won-t-parse"]], "My OWL file takes too long to load": [[1115, "my-owl-file-takes-too-long-to-load"]], "My cached SQLite ontology is out of date": [[1115, "my-cached-sqlite-ontology-is-out-of-date"]], "I don\u2019t understand the interface/method I want to use": [[1115, "i-don-t-understand-the-interface-method-i-want-to-use"]], "Glossary": [[1116, "glossary"]], "Aliases and Synonyms": [[1117, "aliases-and-synonyms"]], "Use Cases": [[1117, "use-cases"]], "Search": [[1117, "search"], [1140, "search"], [1160, "search"], [1175, "search"]], "Text mining and NLP": [[1117, "text-mining-and-nlp"]], "Different aliases for different communities": [[1117, "different-aliases-for-different-communities"]], "Different Languages": [[1117, "different-languages"]], "Different approaches to representing synonym metadata": [[1117, "different-approaches-to-representing-synonym-metadata"]], "Representation of synonyms in OAK": [[1117, "representation-of-synonyms-in-oak"]], "Simple Core Model": [[1117, "simple-core-model"]], "HPO basic aliases": [[1117, "id1"]], "Obo Graph Data Model": [[1117, "obo-graph-data-model"]], "HPO full aliases": [[1117, "id2"]], "Associations and Curated Annotations": [[1118, "associations-and-curated-annotations"]], "Background": [[1118, "background"], [1128, "background"]], "Association support in OAK": [[1118, "association-support-in-oak"]], "Data Model": [[1118, "data-model"], [1128, "data-model"], [1183, "data-model"]], "Selecting association sources": [[1118, "selecting-association-sources"]], "Further reading": [[1118, "further-reading"], [1120, "further-reading"], [1123, "further-reading"], [1124, "further-reading"], [1126, "further-reading"], [1128, "further-reading"]], "OAK Basics": [[1119, "oak-basics"]], "What is an ontology and why would I want to access one?": [[1119, "what-is-an-ontology-and-why-would-i-want-to-access-one"]], "Ontology languages, standards, and formats": [[1119, "ontology-languages-standards-and-formats"]], "Core OAK concepts": [[1119, "core-oak-concepts"]], "Identifying entities: CURIEs and URIs": [[1120, "curies-and-uris"]], "Prefix maps": [[1120, "prefix-maps"]], "Querying prefixmaps": [[1120, "querying-prefixmaps"]], "Example prefixes": [[1120, "id1"]], "Non-default prefixmaps": [[1120, "non-default-prefixmaps"]], "Structure of identifiers": [[1120, "structure-of-identifiers"]], "The OAK Guide": [[1121, "the-oak-guide"]], "Learning More": [[1122, "learning-more"]], "Logical Definitions": [[1123, "logical-definitions"]], "Logical Definitions in OWL": [[1123, "logical-definitions-in-owl"]], "Genus-differentia form logical definitions": [[1123, "genus-differentia-form-logical-definitions"]], "The Obo Graphs Model": [[1123, "the-obo-graphs-model"]], "Querying for logical definitions in OAK": [[1123, "querying-for-logical-definitions-in-oak"]], "uberon nail logical definitions": [[1123, "id2"]], "Reasoning using logical definitions": [[1123, "reasoning-using-logical-definitions"]], "Logical definitions and design patterns": [[1123, "logical-definitions-and-design-patterns"]], "Generating logical definitions": [[1123, "generating-logical-definitions"]], "Analyzing logical definitions": [[1123, "analyzing-logical-definitions"]], "Validating logical definitions": [[1123, "validating-logical-definitions"]], "Mappings and Cross-References": [[1124, "mappings-and-cross-references"]], "Mappings in OAK": [[1124, "mappings-in-oak"]], "uberon sssom mappings": [[1124, "id2"]], "In Python": [[1124, "in-python"]], "Directionality of mappings": [[1124, "directionality-of-mappings"]], "Support for SSSOM": [[1124, "support-for-sssom"]], "Generating Mappings": [[1124, "generating-mappings"]], "Obsoletion": [[1125, "obsoletion"]], "Looking up obsoleted entities": [[1125, "looking-up-obsoleted-entities"]], "Conventions and standards": [[1125, "conventions-and-standards"]], "obsolete entities should not be in the signature of any logical axiom": [[1125, "obsolete-entities-should-not-be-in-the-signature-of-any-logical-axiom"]], "obsolete entities should be accompanied by metadata that provides additional context for humans and machines": [[1125, "obsolete-entities-should-be-accompanied-by-metadata-that-provides-additional-context-for-humans-and-machines"]], "Merged entities": [[1125, "merged-entities"]], "Further Reading": [[1125, "further-reading"]], "Primary Labels": [[1126, "primary-labels"]], "Looking up labels": [[1126, "looking-up-labels"]], "Custom label annotation properties": [[1126, "custom-label-annotation-properties"]], "Multilingual ontologies": [[1126, "multilingual-ontologies"]], "Other edge cases": [[1126, "other-edge-cases"]], "Relationships and Graphs": [[1127, "relationships-and-graphs"]], "Exploring relationships": [[1127, "exploring-relationships"]], "Graph Traversal and Relation Graph Reasoning": [[1127, "graph-traversal-and-relation-graph-reasoning"]], "Graph Traversal Strategies": [[1127, "graph-traversal-strategies"]], "Examples of where entailment yields more": [[1127, "examples-of-where-entailment-yields-more"]], "Examples of where graph traversal yields more ancestors than entailment": [[1127, "examples-of-where-graph-traversal-yields-more-ancestors-than-entailment"]], "Which strategy should I use?": [[1127, "which-strategy-should-i-use"]], "A note on entailed direct edges": [[1127, "a-note-on-entailed-direct-edges"]], "Computing Similarity between Entities": [[1128, "computing-similarity-between-entities"]], "Concepts": [[1128, "concepts"]], "Jaccard Similarity": [[1128, "jaccard-similarity"]], "Information Content": [[1128, "information-content"]], "Aggregate measures for comparing entities": [[1128, "aggregate-measures-for-comparing-entities"]], "Vector-based approaches": [[1128, "vector-based-approaches"]], "Implementations": [[1128, "implementations"], [1151, "implementations"], [1163, "implementations"]], "Default Implementation": [[1128, "default-implementation"]], "Ubergraph": [[1128, "ubergraph"], [1142, "ubergraph"]], "Semsimian": [[1128, "semsimian"]], "FHIR Conversions": [[1129, "fhir-conversions"]], "CLI": [[1129, "cli"]], "Config file": [[1129, "config-file"]], "How-To Guides": [[1130, "how-to-guides"]], "How to use Large Language Models (LLMs) with OAK": [[1133, "how-to-use-large-language-models-llms-with-oak"]], "LLM frameworks that use OAK": [[1133, "llm-frameworks-that-use-oak"]], "OntoGPT": [[1133, "ontogpt"]], "CurateGPT": [[1133, "curategpt"]], "Talisman": [[1133, "talisman"]], "Using OAK in conjunction with existing LLM tools": [[1133, "using-oak-in-conjunction-with-existing-llm-tools"]], "OAK LLM Adapter": [[1133, "oak-llm-adapter"]], "Annotation": [[1133, "annotation"], [1162, "annotation"], [1164, "annotation"], [1169, "annotation"]], "Suggesting Definitions": [[1133, "suggesting-definitions"]], "Validating Definitions": [[1133, "validating-definitions"]], "Validating Mappings": [[1133, "validating-mappings"]], "Selecting alternative models": [[1133, "selecting-alternative-models"]], "Installing LLM plugins": [[1133, "installing-llm-plugins"]], "Mixtral via Ollama and LiteLLM": [[1133, "mixtral-via-ollama-and-litellm"]], "Mixtral via groq and LiteLLM": [[1133, "mixtral-via-groq-and-litellm"]], "Using the OAK Expression Language": [[1134, "using-the-oak-expression-language"]], "Basics": [[1134, "basics"], [1140, "basics"]], "IDs (CURIEs)": [[1134, "ids-curies"]], "Lists of IDs": [[1134, "lists-of-ids"]], "Label Queries": [[1134, "label-queries"]], "Search Queries": [[1134, "search-queries"]], "Exact Match": [[1134, "exact-match"]], "Starts With": [[1134, "starts-with"]], "Contains": [[1134, "contains"]], "Regular Expressions": [[1134, "regular-expressions"]], "Graph Queries": [[1134, "graph-queries"]], "Ancestors": [[1134, "ancestors"]], "Descendants": [[1134, "descendants"]], "MRCAs": [[1134, "mrcas"]], "Boolean Combinations": [[1134, "boolean-combinations"], [1204, "boolean-combinations"]], "AND": [[1134, "and"]], "OR": [[1134, "or"]], "NOT": [[1134, "not"]], "Nesting": [[1134, "nesting"]], "Using files and redirects": [[1134, "using-files-and-redirects"]], "IDFILE": [[1134, "idfile"]], "STDIN": [[1134, "stdin"]], "Other Operators": [[1134, "other-operators"]], "IN": [[1134, "in"]], "FILTER": [[1134, "filter"]], "NR": [[1134, "nr"]], "Others": [[1134, "others"]], "How to Validate an OBO ontology using Obo Metadata Ontology schema": [[1135, "how-to-validate-an-obo-ontology-using-obo-metadata-ontology-schema"]], "Steps": [[1135, "steps"]], "Step 1: Obtain the sqlite version of the ontology": [[1135, "step-1-obtain-the-sqlite-version-of-the-ontology"]], "Step 2: Install oaklib": [[1135, "step-2-install-oaklib"]], "Step 3: Validate an individual ontology": [[1135, "step-3-validate-an-individual-ontology"]], "Step 3 (alternative): Validate multiple ontologies": [[1135, "step-3-alternative-validate-multiple-ontologies"]], "Caveats": [[1135, "caveats"]], "Using your own schema": [[1135, "using-your-own-schema"]], "How this works": [[1135, "how-this-works"], [1144, "how-this-works"]], "Analysis": [[1135, "analysis"]], "How to write a plugin": [[1137, "how-to-write-a-plugin"]], "What is a plugin?": [[1137, "what-is-a-plugin"]], "An example plugin": [[1137, "an-example-plugin"]], "Creating a plugin": [[1137, "creating-a-plugin"]], "Discuss on the issue tracker": [[1137, "discuss-on-the-issue-tracker"]], "Create a new project": [[1137, "create-a-new-project"], [1141, "create-a-new-project"]], "Implement one or more interfaces": [[1137, "implement-one-or-more-interfaces"]], "Implement a selector": [[1137, "implement-a-selector"]], "Write tests": [[1137, "write-tests"]], "Ontology Access Kit (OAK) Documentation": [[1138, "ontology-access-kit-oak-documentation"]], "Indices and tables": [[1138, "indices-and-tables"]], "Tutorial": [[1139, "tutorial"]], "Part 1: Getting Started": [[1140, "part-1-getting-started"]], "Installation": [[1140, "installation"]], "Install from PyPI": [[1140, "install-from-pypi"]], "Run the OAK command": [[1140, "run-the-oak-command"]], "Query the OBO Library": [[1140, "query-the-obo-library"]], "Working with local files": [[1140, "working-with-local-files"]], "Introduction to graphs and trees": [[1140, "introduction-to-graphs-and-trees"]], "Fetching ancestors": [[1140, "fetching-ancestors"]], "Predicate Abbreviations": [[1140, "predicate-abbreviations"]], "Ancestor Statistics": [[1140, "ancestor-statistics"]], "Oak Trees": [[1140, "oak-trees"]], "Advanced Search": [[1140, "advanced-search"]], "Using search terms as parameters": [[1140, "using-search-terms-as-parameters"]], "Chaining Commands": [[1140, "chaining-commands"]], "Visualization": [[1140, "visualization"]], "Using other backends": [[1140, "using-other-backends"]], "Using Ubergraph": [[1140, "using-ubergraph"]], "Using Ontobee": [[1140, "using-ontobee"]], "Using BioPortal and OntoPortal": [[1140, "using-bioportal-and-ontoportal"]], "Annotate results": [[1140, "id3"]], "Using OLS": [[1140, "using-ols"]], "OLS SSSOM": [[1140, "id4"]], "Next steps": [[1140, "next-steps"]], "Part 2: Basic Python": [[1141, "part-2-basic-python"]], "Install Poetry": [[1141, "install-poetry"]], "Basic Concepts": [[1141, "basic-concepts"]], "Code the first example": [[1141, "code-the-first-example"]], "Extending the example": [[1141, "extending-the-example"]], "Part 3: Triplestore Backends": [[1142, "part-3-triplestore-backends"]], "Triplestore Concepts": [[1142, "triplestore-concepts"]], "Connecting": [[1142, "connecting"], [1175, "connecting"]], "Basic Operations": [[1142, "basic-operations"]], "Relationships": [[1142, "relationships"]], "Part 4: OboGraphs": [[1143, "part-4-obographs"]], "OboGraphs": [[1143, "obographs"]], "OboGraph Interface": [[1143, "obograph-interface"], [1184, "obograph-interface"]], "Code examples": [[1143, "code-examples"]], "Part 5: Graph Visualization": [[1144, "part-5-graph-visualization"]], "Install Graphviz": [[1144, "install-graphviz"]], "Install OBOGraphViz": [[1144, "install-obographviz"]], "Command Line Usage": [[1144, "command-line-usage"], [1154, "command-line-usage"], [1159, "command-line-usage"]], "Programmatic usage": [[1144, "programmatic-usage"]], "Part 6: Working With OWL": [[1145, "part-6-working-with-owl"]], "OWL Datamodel": [[1145, "owl-datamodel"]], "OwlInterface": [[1145, "owlinterface"]], "ROBOT Plugin": [[1145, "robot-plugin"]], "Part 7: SQLite files": [[1146, "part-7-sqlite-files"]], "Download a SQLite file": [[1146, "download-a-sqlite-file"]], "Example": [[1146, "example"]], "Fetching ready-made SQLite files": [[1146, "fetching-ready-made-sqlite-files"]], "Building your own SQLite files": [[1146, "building-your-own-sqlite-files"]], "With docker": [[1146, "with-docker"]], "Without docker": [[1146, "without-docker"]], "Validating an ontology": [[1146, "validating-an-ontology"]], "Other RDBMSs": [[1146, "other-rdbmss"]], "Python ORM": [[1146, "python-orm"]], "Part 8: Applying Changes to Ontologies": [[1147, "part-8-applying-changes-to-ontologies"]], "About KGCL": [[1147, "about-kgcl"]], "Example: Sqlite3": [[1147, "example-sqlite3"]], "Example: OBO Files": [[1147, "example-obo-files"]], "Introduction": [[1148, "introduction"]], "Basic Python Example": [[1148, "basic-python-example"]], "Basic Command Line Example": [[1148, "basic-command-line-example"]], "Jupyter Notebooks": [[1150, "jupyter-notebooks"]], "Architecture": [[1151, "architecture"]], "Ontology Interfaces": [[1151, "ontology-interfaces"]], "Other Interfaces": [[1151, "other-interfaces"]], "Example: OWL Ontology Interface": [[1151, "example-owl-ontology-interface"]], "Partial and Complete Implementation": [[1151, "partial-and-complete-implementation"]], "Best Practice": [[1152, "best-practice"]], "External Services": [[1152, "external-services"]], "Iterators": [[1152, "iterators"]], "Weaving calls together": [[1152, "weaving-calls-together"]], "Chunking": [[1152, "chunking"]], "Abstract Class": [[1153, "abstract-class"]], "Converters": [[1154, "converters"]], "Converting from Obo Graphs": [[1154, "converting-from-obo-graphs"]], "OBO Graph to CX Converter": [[1155, "obo-graph-to-cx-converter"]], "OBO Graph to FHIR Converter": [[1156, "obo-graph-to-fhir-converter"]], "OBO Graph to OBO Format Converter": [[1157, "obo-graph-to-obo-format-converter"]], "OBO Graph to OWL Converter": [[1158, "obo-graph-to-owl-converter"]], "Aggregator Adapter": [[1159, "aggregator-adapter"]], "Documentation": [[1159, "documentation"], [1167, "documentation"]], "Bioportal Adapter": [[1160, "bioportal-adapter"]], "API Keys": [[1160, "api-keys"]], "Command Line Examples": [[1160, "command-line-examples"], [1162, "command-line-examples"], [1164, "command-line-examples"], [1169, "command-line-examples"], [1171, "command-line-examples"]], "Code": [[1160, "code"], [1162, "code"], [1164, "code"], [1165, "code"], [1166, "code"], [1168, "code"], [1169, "code"], [1170, "code"], [1172, "code"], [1173, "code"], [1174, "code"], [1175, "code"]], "FunOwl Adapter": [[1161, "funowl-adapter"]], "Gilda Adapter": [[1162, "gilda-adapter"]], "LLM Adapter": [[1164, "llm-adapter"]], "Validation of Mappings": [[1164, "validation-of-mappings"]], "OBO Graph Adapter": [[1165, "obo-graph-adapter"]], "About": [[1165, "about"], [1168, "about"], [1170, "about"], [1172, "about"], [1175, "about"]], "Initialization": [[1165, "initialization"], [1170, "initialization"], [1172, "initialization"], [1174, "initialization"]], "Ontology Lookup Service (OLS) Adapter": [[1166, "ontology-lookup-service-ols-adapter"]], "Ontobee Adapter": [[1167, "ontobee-adapter"]], "Owlery Adapter": [[1168, "owlery-adapter"]], "PantherDB Adapter": [[1169, "pantherdb-adapter"]], "Enrichment": [[1169, "enrichment"]], "Mapping": [[1169, "mapping"]], "Pronto / OBO Files Adapter": [[1170, "pronto-obo-files-adapter"]], "ROBOT Template Adapter": [[1171, "robot-template-adapter"]], "Basic operations": [[1171, "basic-operations"]], "Applying KGCL commands": [[1171, "applying-kgcl-commands"]], "Simple OBO Adapter": [[1172, "simple-obo-adapter"]], "Sparql Adapter": [[1173, "sparql-adapter"]], "SQL Database Adapter": [[1174, "sql-database-adapter"]], "SQL Alchemy ORM Model": [[1174, "sql-alchemy-orm-model"]], "Ubergraph Adapter": [[1175, "ubergraph-adapter"]], "Interfaces Implemented": [[1175, "interfaces-implemented"]], "OAK Library Documentation": [[1176, "oak-library-documentation"]], "Association Provider Interface": [[1177, "association-provider-interface"]], "Command Line Use": [[1177, "command-line-use"], [1183, "command-line-use"]], "Basic Ontology Interface": [[1178, "basic-ontology-interface"]], "Example:": [[1178, "example"], [1178, "id2"], [1178, "id3"], [1178, "id4"]], "Class Enrichment Calculation Interface": [[1179, "class-enrichment-calculation-interface"]], "Differ Interface": [[1180, "differ-interface"]], "Dumper Interface": [[1181, "dumper-interface"]], "Interfaces": [[1182, "interfaces"]], "Mapping Provider Interface": [[1183, "mapping-provider-interface"]], "OWL Interface": [[1185, "owl-interface"]], "Patcher Interface": [[1186, "patcher-interface"]], "Relation Graph": [[1187, "relation-graph"]], "Search Interface": [[1188, "search-interface"]], "Semantic Similarity Interface": [[1189, "semantic-similarity-interface"]], "Subsetting": [[1190, "subsetting"]], "Summary Statistics": [[1191, "summary-statistics"]], "Text Annotator Interface": [[1192, "text-annotator-interface"]], "Validator Interface": [[1193, "validator-interface"]], "Schema Validation": [[1193, "schema-validation"]], "LLM-based validation": [[1193, "llm-based-validation"]], "Ontology Adapter Selectors": [[1194, "ontology-adapter-selectors"]], "Syntax": [[1194, "syntax"]], "Schemes": [[1194, "schemes"]], "pronto": [[1194, "pronto"]], "prontolib": [[1194, "prontolib"]], "sqlite": [[1194, "sqlite"]], "obosqlite": [[1194, "obosqlite"]], "ontobee": [[1194, "ontobee"]], "ols": [[1194, "ols"]], "bioportal": [[1194, "bioportal"]], "funowl": [[1194, "funowl"]], "Functions": [[1194, "functions"]], "oaklib.utilities.apikey_manager": [[1195, "module-oaklib.utilities.apikey_manager"]], "oaklib.utilities.graph.networkx_bridge": [[1196, "module-oaklib.utilities.graph.networkx_bridge"]], "Utilities for working with networkx": [[1196, "utilities-for-working-with-networkx"]], "oaklib.utilities.graph.relationship_walker": [[1197, "module-oaklib.utilities.graph.relationship_walker"]], "Utilities for traversing Ontology Graphs": [[1197, "utilities-for-traversing-ontology-graphs"]], "oaklib.utilities.lexical.lexical_indexer": [[1198, "module-oaklib.utilities.lexical.lexical_indexer"]], "Lexical Utilities": [[1198, "lexical-utilities"]], "oaklib.utilities.obograph_utils": [[1199, "module-oaklib.utilities.obograph_utils"]], "Utilities for the OBOGraph Datamodel": [[1199, "utilities-for-the-obograph-datamodel"]], "oaklib.utilities.subsets.slimmer_utils": [[1200, "module-oaklib.utilities.subsets.slimmer_utils"]], "Utilities for working with ontology subsets (slims)": [[1200, "utilities-for-working-with-ontology-subsets-slims"]], "oaklib.utilities.taxon.taxon_constraint_utils": [[1201, "module-oaklib.utilities.taxon.taxon_constraint_utils"]], "Utilities": [[1202, "utilities"]], "Layering on RDF/OWL": [[1203, "layering-on-rdf-owl"]], "CURIEs, URIs, and prefixmaps": [[1203, "curies-uris-and-prefixmaps"]], "Relationships between entities": [[1203, "relationships-between-entities"]], "Metadata about entities": [[1203, "metadata-about-entities"]], "Challenges": [[1203, "challenges"]], "OMO": [[1203, "omo"]], "Ontology portals": [[1203, "ontology-portals"]], "OAK Approach": [[1203, "oak-approach"]], "Labels": [[1203, "labels"]], "Obsoletion and obsoletion metadata": [[1203, "obsoletion-and-obsoletion-metadata"]], "Search Syntax": [[1204, "search-syntax"]], "Search Datamodel": [[1204, "search-datamodel"]]}, "indexentries": {"ancestor": [[1116, "term-Ancestor"]], "annotation": [[1116, "term-Annotation"]], "annotationproperty": [[1116, "term-AnnotationProperty"]], "asserted": [[1116, "term-Asserted"]], "association": [[1116, "term-Association"]], "bioportal": [[1116, "term-Bioportal"]], "curie": [[1116, "term-CURIE"]], "category": [[1116, "term-Category"]], "class": [[1116, "term-Class"]], "closure": [[1116, "term-Closure"]], "concept": [[1116, "term-Concept"]], "datamodel": [[1116, "term-Datamodel"]], "datatypeproperty": [[1116, "term-DatatypeProperty"]], "descendant": [[1116, "term-Descendant"]], "diff": [[1116, "term-Diff"]], "edge": [[1116, "term-Edge"]], "entailed": [[1116, "term-Entailed"]], "funowl": [[1116, "term-FunOWL"]], "functional syntax": [[1116, "term-Functional-Syntax"]], "graph": [[1116, "term-Graph"]], "graph traversal": [[1116, "term-Graph-Traversal"]], "is_a:": [[1116, "term-IS_A"]], "identifier": [[1116, "term-Identifier"]], "implementation": [[1116, "term-Implementation"]], "information content": [[1116, "term-Information-Content"]], "input selector": [[1116, "term-Input-Selector"]], "interface": [[1116, "term-Interface"]], "iterator": [[1116, "term-Iterator"]], "kgcl": [[1116, "term-KGCL"]], "label": [[1116, "term-Label"]], "logical definition": [[1116, "term-Logical-Definition"]], "mrca": [[1116, "term-MRCA"]], "mapping": [[1116, "term-Mapping"]], "name": [[1116, "term-Name"]], "named individual": [[1116, "term-Named-Individual"]], "node": [[1116, "term-Node"]], "obo format": [[1116, "term-OBO-Format"]], "obo graphs": [[1116, "term-OBO-Graphs"]], "ols": [[1116, "term-OLS"]], "owl": [[1116, "term-OWL"]], "owl annotation": [[1116, "term-OWL-Annotation"]], "object": [[1116, "term-Object"]], "object closure": [[1116, "term-Object-Closure"]], "objectproperty": [[1116, "term-ObjectProperty"]], "ontogpt": [[1116, "term-OntoGPT"]], "ontoportal": [[1116, "term-OntoPortal"]], "ontobee": [[1116, "term-Ontobee"]], "ontology": [[1116, "term-Ontology"]], "ontology element": [[1116, "term-Ontology-Element"]], "ontology format": [[1116, "term-Ontology-Format"]], "ontology graph projection": [[1116, "term-Ontology-Graph-Projection"]], "part of": [[1116, "term-Part-Of"]], "patch": [[1116, "term-Patch"]], "predicate": [[1116, "term-Predicate"]], "pronto": [[1116, "term-Pronto"]], "property": [[1116, "term-Property"]], "rdf": [[1116, "term-RDF"]], "reasoner": [[1116, "term-Reasoner"]], "reasoning": [[1116, "term-Reasoning"]], "reflexive": [[1116, "term-Reflexive"]], "relation graph": [[1116, "term-Relation-Graph"]], "relationship": [[1116, "term-Relationship"]], "relationship type": [[1116, "term-Relationship-Type"]], "sparql": [[1116, "term-SPARQL"]], "sql": [[1116, "term-SQL"]], "sssom": [[1116, "term-SSSOM"]], "semantic sql": [[1116, "term-Semantic-SQL"]], "semantic similarity": [[1116, "term-Semantic-Similarity"]], "subject": [[1116, "term-Subject"]], "subject closure": [[1116, "term-Subject-Closure"]], "subset": [[1116, "term-Subset"]], "tautology": [[1116, "term-Tautology"]], "term": [[1116, "term-Term"]], "text annotation": [[1116, "term-Text-Annotation"]], "triple": [[1116, "term-Triple"]], "triplestore": [[1116, "term-Triplestore"]], "uri": [[1116, "term-URI"]], "ubergraph": [[1116, "term-Ubergraph"]], "aggregatorimplementation (class in oaklib.implementations.aggregator.aggregator_implementation)": [[1159, "oaklib.implementations.aggregator.aggregator_implementation.AggregatorImplementation"]], "edge (class in semsql.sqla.semsql)": [[1174, "semsql.sqla.semsql.Edge"]], "entailededge (class in semsql.sqla.semsql)": [[1174, "semsql.sqla.semsql.EntailedEdge"]], "statements (class in semsql.sqla.semsql)": [[1174, "semsql.sqla.semsql.Statements"]], "associationproviderinterface (class in oaklib.interfaces.association_provider_interface)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface"]], "add_associations() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface.add_associations"]], "association_counts() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface.association_counts"]], "association_pairwise_coassociations() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface.association_pairwise_coassociations"]], "association_subject_counts() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface.association_subject_counts"]], "associations() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface.associations"]], "associations_subject_search() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface.associations_subject_search"]], "associations_subjects() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface.associations_subjects"]], "map_associations() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, 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"datamodels/association/include_association_attributes", "datamodels/association/index", "datamodels/association/is_creation", "datamodels/association/is_deletion", "datamodels/association/is_generalization", "datamodels/association/is_migration", "datamodels/association/is_specialization", "datamodels/association/modification_date", "datamodels/association/negated", "datamodels/association/new_date", "datamodels/association/new_object", "datamodels/association/new_predicate", "datamodels/association/number_subject_unique_to_entity1", "datamodels/association/number_subject_unique_to_entity2", "datamodels/association/number_subjects_in_common", "datamodels/association/number_subjects_in_union", "datamodels/association/object", "datamodels/association/object1", "datamodels/association/object1_label", "datamodels/association/object2", "datamodels/association/object2_label", "datamodels/association/object_closure", "datamodels/association/object_closure_label", "datamodels/association/object_label", "datamodels/association/old_date", "datamodels/association/old_object", "datamodels/association/old_object_obsolete", "datamodels/association/old_predicate", "datamodels/association/original_object", "datamodels/association/original_predicate", "datamodels/association/original_subject", "datamodels/association/predicate", "datamodels/association/predicate_label", "datamodels/association/preserve_negated_associations", "datamodels/association/primary_knowledge_source", "datamodels/association/property_values", "datamodels/association/proportion_subjects_in_common", "datamodels/association/publication_is_added", "datamodels/association/publication_is_deleted", "datamodels/association/publications", "datamodels/association/sub_groups", "datamodels/association/subject", "datamodels/association/subject_closure", "datamodels/association/subject_closure_label", "datamodels/association/subject_label", "datamodels/association/subjects_in_common", "datamodels/association/summary_group", "datamodels/association/supporting_objects", "datamodels/class-enrichment/Boolean", "datamodels/class-enrichment/ClassEnrichmentConfiguration", "datamodels/class-enrichment/ClassEnrichmentResult", "datamodels/class-enrichment/ClassEnrichmentResultSet", "datamodels/class-enrichment/Curie", "datamodels/class-enrichment/Date", "datamodels/class-enrichment/DateOrDatetime", "datamodels/class-enrichment/Datetime", "datamodels/class-enrichment/Decimal", "datamodels/class-enrichment/Double", "datamodels/class-enrichment/Float", "datamodels/class-enrichment/Integer", "datamodels/class-enrichment/Jsonpath", "datamodels/class-enrichment/Jsonpointer", "datamodels/class-enrichment/Ncname", "datamodels/class-enrichment/Nodeidentifier", "datamodels/class-enrichment/Objectidentifier", "datamodels/class-enrichment/Position", "datamodels/class-enrichment/SortFieldEnum", "datamodels/class-enrichment/Sparqlpath", "datamodels/class-enrichment/String", "datamodels/class-enrichment/Time", "datamodels/class-enrichment/Uri", "datamodels/class-enrichment/Uriorcurie", "datamodels/class-enrichment/ancestor_of_more_informative_result", "datamodels/class-enrichment/background_count", "datamodels/class-enrichment/background_total", "datamodels/class-enrichment/class-enrichment", "datamodels/class-enrichment/class_id", "datamodels/class-enrichment/class_label", "datamodels/class-enrichment/descendant_of_more_informative_result", "datamodels/class-enrichment/direction", "datamodels/class-enrichment/false_discovery_rate", "datamodels/class-enrichment/fold_enrichment", "datamodels/class-enrichment/index", "datamodels/class-enrichment/p_value", "datamodels/class-enrichment/p_value_adjusted", "datamodels/class-enrichment/p_value_cutoff", "datamodels/class-enrichment/probability", "datamodels/class-enrichment/rank", "datamodels/class-enrichment/results", "datamodels/class-enrichment/sample_count", "datamodels/class-enrichment/sample_total", "datamodels/cross-ontology-diff/Boolean", "datamodels/cross-ontology-diff/Curie", "datamodels/cross-ontology-diff/Date", "datamodels/cross-ontology-diff/DateOrDatetime", "datamodels/cross-ontology-diff/Datetime", "datamodels/cross-ontology-diff/Decimal", "datamodels/cross-ontology-diff/DiffCategory", "datamodels/cross-ontology-diff/Double", "datamodels/cross-ontology-diff/EntityReference", "datamodels/cross-ontology-diff/Float", "datamodels/cross-ontology-diff/Integer", "datamodels/cross-ontology-diff/Jsonpath", "datamodels/cross-ontology-diff/Jsonpointer", "datamodels/cross-ontology-diff/Label", "datamodels/cross-ontology-diff/MappingCardinalityEnum", "datamodels/cross-ontology-diff/Ncname", "datamodels/cross-ontology-diff/Nodeidentifier", "datamodels/cross-ontology-diff/Objectidentifier", "datamodels/cross-ontology-diff/Position", "datamodels/cross-ontology-diff/RelationalDiff", "datamodels/cross-ontology-diff/Source", "datamodels/cross-ontology-diff/Sparqlpath", "datamodels/cross-ontology-diff/String", "datamodels/cross-ontology-diff/StructureDiffResultSet", "datamodels/cross-ontology-diff/Time", "datamodels/cross-ontology-diff/Uri", "datamodels/cross-ontology-diff/Uriorcurie", "datamodels/cross-ontology-diff/category", "datamodels/cross-ontology-diff/cross-ontology-diff", "datamodels/cross-ontology-diff/index", "datamodels/cross-ontology-diff/is_functional", "datamodels/cross-ontology-diff/label", "datamodels/cross-ontology-diff/left_object_id", "datamodels/cross-ontology-diff/left_object_is_functional", "datamodels/cross-ontology-diff/left_object_label", "datamodels/cross-ontology-diff/left_object_name", "datamodels/cross-ontology-diff/left_predicate_id", "datamodels/cross-ontology-diff/left_predicate_label", "datamodels/cross-ontology-diff/left_predicate_name", "datamodels/cross-ontology-diff/left_side", "datamodels/cross-ontology-diff/left_source", "datamodels/cross-ontology-diff/left_subject_id", "datamodels/cross-ontology-diff/left_subject_is_functional", "datamodels/cross-ontology-diff/left_subject_label", "datamodels/cross-ontology-diff/left_subject_name", "datamodels/cross-ontology-diff/object", "datamodels/cross-ontology-diff/object_mapping_cardinality", "datamodels/cross-ontology-diff/object_mapping_predicate", "datamodels/cross-ontology-diff/predicate", "datamodels/cross-ontology-diff/results", "datamodels/cross-ontology-diff/right_intermediate_ids", "datamodels/cross-ontology-diff/right_object_id", "datamodels/cross-ontology-diff/right_object_label", "datamodels/cross-ontology-diff/right_object_name", "datamodels/cross-ontology-diff/right_predicate_ids", "datamodels/cross-ontology-diff/right_predicate_labels", "datamodels/cross-ontology-diff/right_predicate_names", "datamodels/cross-ontology-diff/right_side", "datamodels/cross-ontology-diff/right_source", "datamodels/cross-ontology-diff/right_subject_id", "datamodels/cross-ontology-diff/right_subject_label", "datamodels/cross-ontology-diff/right_subject_name", "datamodels/cross-ontology-diff/side", "datamodels/cross-ontology-diff/subject", "datamodels/cross-ontology-diff/subject_mapping_cardinality", "datamodels/cross-ontology-diff/subject_mapping_predicate", "datamodels/cross-ontology-diff/types", "datamodels/funowl/index", "datamodels/index", "datamodels/item-list/Boolean", "datamodels/item-list/Curie", "datamodels/item-list/Date", "datamodels/item-list/DateOrDatetime", "datamodels/item-list/Datetime", "datamodels/item-list/Decimal", "datamodels/item-list/Double", "datamodels/item-list/Float", "datamodels/item-list/Integer", "datamodels/item-list/ItemList", "datamodels/item-list/ItemListCollection", "datamodels/item-list/ItemListOrderType", "datamodels/item-list/Jsonpath", "datamodels/item-list/Jsonpointer", "datamodels/item-list/ListItem", "datamodels/item-list/Ncname", "datamodels/item-list/Nodeidentifier", "datamodels/item-list/Objectidentifier", "datamodels/item-list/Sparqlpath", "datamodels/item-list/String", "datamodels/item-list/Thing", "datamodels/item-list/Time", "datamodels/item-list/Uri", "datamodels/item-list/Uriorcurie", "datamodels/item-list/additionalType", "datamodels/item-list/categories", "datamodels/item-list/description", "datamodels/item-list/elementId", "datamodels/item-list/id", "datamodels/item-list/idType", "datamodels/item-list/identifiers", "datamodels/item-list/index", "datamodels/item-list/item", "datamodels/item-list/itemList", "datamodels/item-list/itemListElements", "datamodels/item-list/itemLists", "datamodels/item-list/itemMetadataMap", "datamodels/item-list/keywords", "datamodels/item-list/name", "datamodels/item-list/numberOfItems", "datamodels/item-list/position", "datamodels/item-list/previousItem", "datamodels/item-list/type", "datamodels/item-list/url", "datamodels/item-list/wasGeneratedBy", "datamodels/kgcl/index", "datamodels/lexical-index/Activity", "datamodels/lexical-index/Any", "datamodels/lexical-index/Boolean", "datamodels/lexical-index/Curie", "datamodels/lexical-index/Date", "datamodels/lexical-index/DateOrDatetime", "datamodels/lexical-index/Datetime", "datamodels/lexical-index/Decimal", "datamodels/lexical-index/Double", "datamodels/lexical-index/Float", "datamodels/lexical-index/Integer", "datamodels/lexical-index/Jsonpath", "datamodels/lexical-index/Jsonpointer", "datamodels/lexical-index/LexicalGrouping", "datamodels/lexical-index/LexicalIndex", "datamodels/lexical-index/LexicalTransformation", "datamodels/lexical-index/LexicalTransformationPipeline", "datamodels/lexical-index/Ncname", "datamodels/lexical-index/Nodeidentifier", "datamodels/lexical-index/Objectidentifier", "datamodels/lexical-index/RelationshipToTerm", "datamodels/lexical-index/Sparqlpath", "datamodels/lexical-index/String", "datamodels/lexical-index/Time", "datamodels/lexical-index/TransformationType", "datamodels/lexical-index/Uri", "datamodels/lexical-index/Uriorcurie", "datamodels/lexical-index/element", "datamodels/lexical-index/element_term", "datamodels/lexical-index/groupings", "datamodels/lexical-index/index", "datamodels/lexical-index/lexical-index", "datamodels/lexical-index/lexican-index", "datamodels/lexical-index/name", "datamodels/lexical-index/params", "datamodels/lexical-index/pipeline", "datamodels/lexical-index/pipelines", "datamodels/lexical-index/predicate", "datamodels/lexical-index/relationships", "datamodels/lexical-index/source", "datamodels/lexical-index/synonymized", "datamodels/lexical-index/term", "datamodels/lexical-index/transformations", "datamodels/lexical-index/type", "datamodels/lexical-index/types", "datamodels/mapping-rules/Activity", "datamodels/mapping-rules/Any", "datamodels/mapping-rules/Boolean", "datamodels/mapping-rules/Curie", "datamodels/mapping-rules/Date", "datamodels/mapping-rules/DateOrDatetime", "datamodels/mapping-rules/Datetime", "datamodels/mapping-rules/Decimal", "datamodels/mapping-rules/Double", "datamodels/mapping-rules/Float", "datamodels/mapping-rules/Integer", "datamodels/mapping-rules/Jsonpath", "datamodels/mapping-rules/Jsonpointer", "datamodels/mapping-rules/LexicalGrouping", "datamodels/mapping-rules/LexicalIndex", "datamodels/mapping-rules/LexicalTransformation", "datamodels/mapping-rules/LexicalTransformationPipeline", "datamodels/mapping-rules/MappingRule", "datamodels/mapping-rules/MappingRuleCollection", "datamodels/mapping-rules/Ncname", "datamodels/mapping-rules/Nodeidentifier", "datamodels/mapping-rules/Objectidentifier", "datamodels/mapping-rules/Postcondition", "datamodels/mapping-rules/Precondition", "datamodels/mapping-rules/RegularExpressionString", "datamodels/mapping-rules/RelationshipToTerm", "datamodels/mapping-rules/RuleSet", "datamodels/mapping-rules/Sparqlpath", "datamodels/mapping-rules/String", "datamodels/mapping-rules/Synonymizer", "datamodels/mapping-rules/Test", "datamodels/mapping-rules/Time", "datamodels/mapping-rules/TransformationType", "datamodels/mapping-rules/Uri", "datamodels/mapping-rules/Uriorcurie", "datamodels/mapping-rules/description", "datamodels/mapping-rules/element", "datamodels/mapping-rules/element_term", "datamodels/mapping-rules/groupings", "datamodels/mapping-rules/in_place", "datamodels/mapping-rules/index", "datamodels/mapping-rules/input", "datamodels/mapping-rules/lexical-index", "datamodels/mapping-rules/lexican-index", "datamodels/mapping-rules/mapping-rules", "datamodels/mapping-rules/mapping-rules-datamodel", "datamodels/mapping-rules/mapping_source_one_of", "datamodels/mapping-rules/match", "datamodels/mapping-rules/match_scope", "datamodels/mapping-rules/minimum_confidence", "datamodels/mapping-rules/name", "datamodels/mapping-rules/object_match_field_one_of", "datamodels/mapping-rules/object_source_one_of", "datamodels/mapping-rules/oneway", "datamodels/mapping-rules/output", "datamodels/mapping-rules/params", "datamodels/mapping-rules/pipeline", "datamodels/mapping-rules/pipelines", "datamodels/mapping-rules/postconditions", "datamodels/mapping-rules/preconditions", "datamodels/mapping-rules/predicate", "datamodels/mapping-rules/predicate_id", "datamodels/mapping-rules/predicate_id_one_of", "datamodels/mapping-rules/prefix", "datamodels/mapping-rules/qualifier", "datamodels/mapping-rules/relationships", "datamodels/mapping-rules/replacement", "datamodels/mapping-rules/rules", "datamodels/mapping-rules/source", "datamodels/mapping-rules/subject_match_field_one_of", "datamodels/mapping-rules/subject_source_one_of", "datamodels/mapping-rules/synonymized", "datamodels/mapping-rules/synonymizer", "datamodels/mapping-rules/term", "datamodels/mapping-rules/tests", "datamodels/mapping-rules/transformations", "datamodels/mapping-rules/transformations_included_in", "datamodels/mapping-rules/type", "datamodels/mapping-rules/types", "datamodels/mapping-rules/weight", "datamodels/obograph/Axiom", "datamodels/obograph/BasicPropertyValue", "datamodels/obograph/Boolean", "datamodels/obograph/Curie", "datamodels/obograph/Date", "datamodels/obograph/DateOrDatetime", "datamodels/obograph/Datetime", "datamodels/obograph/Decimal", "datamodels/obograph/DefinitionPropertyValue", "datamodels/obograph/DisjointClassExpressionsAxiom", "datamodels/obograph/DomainRangeAxiom", "datamodels/obograph/Double", "datamodels/obograph/Edge", "datamodels/obograph/EquivalentNodesSet", "datamodels/obograph/ExistentialRestrictionExpression", "datamodels/obograph/Float", "datamodels/obograph/Graph", "datamodels/obograph/GraphDocument", "datamodels/obograph/Integer", "datamodels/obograph/Jsonpath", "datamodels/obograph/Jsonpointer", "datamodels/obograph/LogicalDefinitionAxiom", "datamodels/obograph/Meta", "datamodels/obograph/Ncname", "datamodels/obograph/Node", "datamodels/obograph/NodeTypeEnum", "datamodels/obograph/Nodeidentifier", "datamodels/obograph/Objectidentifier", "datamodels/obograph/OboIdentifierString", "datamodels/obograph/PredsEnum", "datamodels/obograph/PrefixDeclaration", "datamodels/obograph/PropertyChainAxiom", "datamodels/obograph/PropertyTypeEnum", "datamodels/obograph/PropertyValue", "datamodels/obograph/ScopeEnum", "datamodels/obograph/ScopesEnum", "datamodels/obograph/Sparqlpath", "datamodels/obograph/String", "datamodels/obograph/SubsetDefinition", "datamodels/obograph/SynonymPropertyValue", "datamodels/obograph/SynonymTypeDefinition", "datamodels/obograph/SynonymTypeIdentifierString", "datamodels/obograph/Time", "datamodels/obograph/Uri", "datamodels/obograph/Uriorcurie", "datamodels/obograph/XrefPropertyValue", "datamodels/obograph/XrefString", "datamodels/obograph/allValuesFromEdges", "datamodels/obograph/basicPropertyValues", "datamodels/obograph/chainPredicateIds", "datamodels/obograph/classExpressions", "datamodels/obograph/classIds", "datamodels/obograph/comments", "datamodels/obograph/definedClassId", "datamodels/obograph/definition", "datamodels/obograph/deprecated", "datamodels/obograph/disjointClassExpressionsAxioms", "datamodels/obograph/domainClassIds", "datamodels/obograph/domainRangeAxioms", "datamodels/obograph/edges", "datamodels/obograph/equivalentNodesSets", "datamodels/obograph/fillerId", "datamodels/obograph/genusIds", "datamodels/obograph/graphs", "datamodels/obograph/id", "datamodels/obograph/index", "datamodels/obograph/isExact", "datamodels/obograph/label", "datamodels/obograph/lang", "datamodels/obograph/lbl", "datamodels/obograph/logicalDefinitionAxioms", "datamodels/obograph/meta", "datamodels/obograph/namespace", "datamodels/obograph/nodeIds", "datamodels/obograph/nodes", "datamodels/obograph/obj", "datamodels/obograph/obographs_datamodel", "datamodels/obograph/obographs_linkml_model", "datamodels/obograph/pred", "datamodels/obograph/predicateId", "datamodels/obograph/prefix", "datamodels/obograph/prefixes", "datamodels/obograph/propertyChainAxioms", "datamodels/obograph/propertyId", "datamodels/obograph/propertyType", "datamodels/obograph/rangeClassIds", "datamodels/obograph/representativeNodeId", "datamodels/obograph/representitiveNodeId", "datamodels/obograph/restrictions", "datamodels/obograph/scope", "datamodels/obograph/sub", "datamodels/obograph/subsetDefinitions", "datamodels/obograph/subsets", "datamodels/obograph/synonymType", "datamodels/obograph/synonymTypeDefinitions", "datamodels/obograph/synonyms", "datamodels/obograph/type", "datamodels/obograph/types", "datamodels/obograph/unionEquivalentTo", "datamodels/obograph/unionEquivalentToExpression", "datamodels/obograph/val", "datamodels/obograph/valType", "datamodels/obograph/version", "datamodels/obograph/xrefs", "datamodels/ontology-metadata/Agent", "datamodels/ontology-metadata/AllotropePermittedProfile", "datamodels/ontology-metadata/AllotropeRequiredProfile", "datamodels/ontology-metadata/Annotation", "datamodels/ontology-metadata/AnnotationProperty", "datamodels/ontology-metadata/AnnotationPropertyMixin", "datamodels/ontology-metadata/Anonymous", "datamodels/ontology-metadata/AnonymousClassExpression", "datamodels/ontology-metadata/Any", "datamodels/ontology-metadata/Axiom", "datamodels/ontology-metadata/Boolean", "datamodels/ontology-metadata/CURIELiteral", "datamodels/ontology-metadata/Class", "datamodels/ontology-metadata/ClassExpression", "datamodels/ontology-metadata/Curie", "datamodels/ontology-metadata/Date", "datamodels/ontology-metadata/DateOrDatetime", "datamodels/ontology-metadata/Datetime", "datamodels/ontology-metadata/Decimal", "datamodels/ontology-metadata/DefinitionConstraintComponent", "datamodels/ontology-metadata/Double", "datamodels/ontology-metadata/Expression", "datamodels/ontology-metadata/Float", "datamodels/ontology-metadata/GoPermittedProfile", "datamodels/ontology-metadata/GoRecommendedProfile", "datamodels/ontology-metadata/GoRequiredProfile", "datamodels/ontology-metadata/HasCategory", "datamodels/ontology-metadata/HasLifeCycle", "datamodels/ontology-metadata/HasMappings", "datamodels/ontology-metadata/HasMinimalMetadata", "datamodels/ontology-metadata/HasProvenance", "datamodels/ontology-metadata/HasSynonyms", "datamodels/ontology-metadata/HasUserInformation", "datamodels/ontology-metadata/HomoSapiens", "datamodels/ontology-metadata/IEDB_alternative_term", "datamodels/ontology-metadata/ISA_alternative_term", "datamodels/ontology-metadata/Image", "datamodels/ontology-metadata/Integer", "datamodels/ontology-metadata/IriType", "datamodels/ontology-metadata/Jsonpath", "datamodels/ontology-metadata/Jsonpointer", "datamodels/ontology-metadata/LabelType", "datamodels/ontology-metadata/NCIT_definition_source", "datamodels/ontology-metadata/NCIT_term_source", "datamodels/ontology-metadata/NCIT_term_type", "datamodels/ontology-metadata/NamedIndividual", "datamodels/ontology-metadata/NamedObject", "datamodels/ontology-metadata/NarrativeText", "datamodels/ontology-metadata/Ncname", "datamodels/ontology-metadata/Nodeidentifier", "datamodels/ontology-metadata/NotObsoleteAspect", "datamodels/ontology-metadata/OBO_foundry_unique_label", "datamodels/ontology-metadata/ObiPermittedProfile", "datamodels/ontology-metadata/ObiRequiredProfile", "datamodels/ontology-metadata/ObjectProperty", "datamodels/ontology-metadata/Objectidentifier", "datamodels/ontology-metadata/ObsoleteAspect", "datamodels/ontology-metadata/Ontology", "datamodels/ontology-metadata/Ontology-Metadata", "datamodels/ontology-metadata/Property", "datamodels/ontology-metadata/PropertyExpression", "datamodels/ontology-metadata/Restriction", "datamodels/ontology-metadata/Sparqlpath", "datamodels/ontology-metadata/String", "datamodels/ontology-metadata/Subset", "datamodels/ontology-metadata/Term", "datamodels/ontology-metadata/Thing", "datamodels/ontology-metadata/TidyString", "datamodels/ontology-metadata/Time", "datamodels/ontology-metadata/TransitiveProperty", "datamodels/ontology-metadata/URLLiteral", "datamodels/ontology-metadata/Uri", "datamodels/ontology-metadata/Uriorcurie", "datamodels/ontology-metadata/allValuesFrom", "datamodels/ontology-metadata/alternative_term", "datamodels/ontology-metadata/annotatedProperty", "datamodels/ontology-metadata/annotatedSource", "datamodels/ontology-metadata/annotatedTarget", "datamodels/ontology-metadata/annotations", "datamodels/ontology-metadata/broadMatch", "datamodels/ontology-metadata/cardinality", "datamodels/ontology-metadata/category", "datamodels/ontology-metadata/changeNote", "datamodels/ontology-metadata/closeMatch", "datamodels/ontology-metadata/comment", "datamodels/ontology-metadata/complementOf", "datamodels/ontology-metadata/conformsTo", "datamodels/ontology-metadata/consider", "datamodels/ontology-metadata/contributor", "datamodels/ontology-metadata/core_property", "datamodels/ontology-metadata/created", "datamodels/ontology-metadata/created_by", "datamodels/ontology-metadata/creation_date", "datamodels/ontology-metadata/creator", "datamodels/ontology-metadata/curator_note", "datamodels/ontology-metadata/database_cross_reference", "datamodels/ontology-metadata/date", "datamodels/ontology-metadata/date_retrieved", "datamodels/ontology-metadata/defaultLanguage", "datamodels/ontology-metadata/definition", "datamodels/ontology-metadata/definition_source", "datamodels/ontology-metadata/depicted_by", "datamodels/ontology-metadata/deprecated", "datamodels/ontology-metadata/disconnected_from", "datamodels/ontology-metadata/disjointWith", "datamodels/ontology-metadata/distinctMembers", "datamodels/ontology-metadata/domain", "datamodels/ontology-metadata/editor_note", "datamodels/ontology-metadata/editor_preferred_term", "datamodels/ontology-metadata/equivalentClass", "datamodels/ontology-metadata/equivalentProperty", "datamodels/ontology-metadata/evidence", "datamodels/ontology-metadata/exactMatch", "datamodels/ontology-metadata/example_of_usage", "datamodels/ontology-metadata/excluded_axiom", "datamodels/ontology-metadata/excluded_from_QC_check", "datamodels/ontology-metadata/excluded_subClassOf", "datamodels/ontology-metadata/excluded_synonym", "datamodels/ontology-metadata/external_ontology", "datamodels/ontology-metadata/hasValue", "datamodels/ontology-metadata/has_alternative_id", "datamodels/ontology-metadata/has_axiom_label", "datamodels/ontology-metadata/has_broad_synonym", "datamodels/ontology-metadata/has_curation_status", "datamodels/ontology-metadata/has_exact_synonym", "datamodels/ontology-metadata/has_narrow_synonym", "datamodels/ontology-metadata/has_obo_namespace", "datamodels/ontology-metadata/has_obsolescence_reason", "datamodels/ontology-metadata/has_ontology_root_term", "datamodels/ontology-metadata/has_rank", "datamodels/ontology-metadata/has_related_synonym", "datamodels/ontology-metadata/has_synonym_type", "datamodels/ontology-metadata/id", "datamodels/ontology-metadata/image", "datamodels/ontology-metadata/imported_from", "datamodels/ontology-metadata/imports", "datamodels/ontology-metadata/in_subset", "datamodels/ontology-metadata/index", "datamodels/ontology-metadata/informative_property", "datamodels/ontology-metadata/intersectionOf", "datamodels/ontology-metadata/inverseOf", "datamodels/ontology-metadata/isDefinedBy", "datamodels/ontology-metadata/is_a_defining_property_chain_axiom", "datamodels/ontology-metadata/is_a_defining_property_chain_axiom_where_second_argument_is_reflexive", "datamodels/ontology-metadata/is_class_level", "datamodels/ontology-metadata/is_cyclic", "datamodels/ontology-metadata/is_inferred", "datamodels/ontology-metadata/is_metadata_tag", "datamodels/ontology-metadata/is_transitive", "datamodels/ontology-metadata/label", "datamodels/ontology-metadata/language", "datamodels/ontology-metadata/license", "datamodels/ontology-metadata/logical_predicate", "datamodels/ontology-metadata/match", "datamodels/ontology-metadata/match_aspect", "datamodels/ontology-metadata/maxQualifiedCardinality", "datamodels/ontology-metadata/members", "datamodels/ontology-metadata/minCardinality", "datamodels/ontology-metadata/minQualifiedCardinality", "datamodels/ontology-metadata/narrowMatch", "datamodels/ontology-metadata/never_in_taxon", "datamodels/ontology-metadata/notes", "datamodels/ontology-metadata/object", "datamodels/ontology-metadata/oboInOwl_id", "datamodels/ontology-metadata/oboInOwl_ontology", "datamodels/ontology-metadata/obsoletion_related_property", "datamodels/ontology-metadata/omo-schema", "datamodels/ontology-metadata/onClass", "datamodels/ontology-metadata/onProperty", "datamodels/ontology-metadata/oneOf", "datamodels/ontology-metadata/ontology_term_requester", "datamodels/ontology-metadata/page", "datamodels/ontology-metadata/predicate", "datamodels/ontology-metadata/propertyChainAxiom", "datamodels/ontology-metadata/provenance_property", "datamodels/ontology-metadata/qualifiedCardinality", "datamodels/ontology-metadata/range", "datamodels/ontology-metadata/reification_predicate", "datamodels/ontology-metadata/sameAs", "datamodels/ontology-metadata/seeAlso", "datamodels/ontology-metadata/shortcut_annotation_property", "datamodels/ontology-metadata/shorthand", "datamodels/ontology-metadata/should_conform_to", "datamodels/ontology-metadata/someValuesFrom", "datamodels/ontology-metadata/source", "datamodels/ontology-metadata/subClassOf", "datamodels/ontology-metadata/synonym", "datamodels/ontology-metadata/temporal_interpretation", "datamodels/ontology-metadata/term_editor", "datamodels/ontology-metadata/term_replaced_by", "datamodels/ontology-metadata/term_tracker_item", "datamodels/ontology-metadata/title", "datamodels/ontology-metadata/type", "datamodels/ontology-metadata/types", "datamodels/ontology-metadata/unionOf", "datamodels/ontology-metadata/url", "datamodels/ontology-metadata/versionIRI", "datamodels/ontology-metadata/versionInfo", "datamodels/ontology-metadata/version_property", "datamodels/search/Boolean", "datamodels/search/BooleanOperator", "datamodels/search/ComplexQuery", "datamodels/search/Curie", "datamodels/search/Date", "datamodels/search/DateOrDatetime", "datamodels/search/Datetime", "datamodels/search/Decimal", "datamodels/search/Double", "datamodels/search/Float", "datamodels/search/GraphFunction", "datamodels/search/Integer", "datamodels/search/Jsonpath", "datamodels/search/Jsonpointer", "datamodels/search/Ncname", "datamodels/search/Nodeidentifier", "datamodels/search/Objectidentifier", "datamodels/search/PathExpression", "datamodels/search/SearchBaseConfiguration", "datamodels/search/SearchProperty", "datamodels/search/SearchResult", "datamodels/search/SearchResultSet", "datamodels/search/SearchTerm", "datamodels/search/SearchTermSyntax", "datamodels/search/Sparqlpath", "datamodels/search/String", "datamodels/search/Time", "datamodels/search/Uri", "datamodels/search/Uriorcurie", "datamodels/search/all_of", "datamodels/search/any_of", "datamodels/search/atom", "datamodels/search/categories", "datamodels/search/configuration", "datamodels/search/cursor", "datamodels/search/force_case_insensitive", "datamodels/search/graph_predicates", "datamodels/search/include_aliases", "datamodels/search/include_definition", "datamodels/search/include_id", "datamodels/search/include_label", "datamodels/search/include_obsoletes_in_results", "datamodels/search/index", "datamodels/search/is_complete", "datamodels/search/is_fuzzy", "datamodels/search/is_partial", "datamodels/search/is_regular_expression", "datamodels/search/limit", "datamodels/search/matches_full_search_term", "datamodels/search/none_of", "datamodels/search/object_id", "datamodels/search/object_label", "datamodels/search/object_match_field", "datamodels/search/object_source", "datamodels/search/object_source_version", "datamodels/search/path_to", "datamodels/search/properties", "datamodels/search/rank", "datamodels/search/result_count", "datamodels/search/results", "datamodels/search/search-datamodel", "datamodels/search/search_term", "datamodels/search/search_terms", "datamodels/search/snippet", "datamodels/search/syntax", "datamodels/search/traversal", "datamodels/search/types", "datamodels/semsql/index", "datamodels/similarity/BestMatch", "datamodels/similarity/Boolean", "datamodels/similarity/Curie", "datamodels/similarity/Date", "datamodels/similarity/DateOrDatetime", "datamodels/similarity/Datetime", "datamodels/similarity/Decimal", "datamodels/similarity/Double", "datamodels/similarity/Float", "datamodels/similarity/Integer", "datamodels/similarity/ItemCount", "datamodels/similarity/Jsonpath", "datamodels/similarity/Jsonpointer", "datamodels/similarity/Ncname", "datamodels/similarity/NegativeLogValue", "datamodels/similarity/Nodeidentifier", "datamodels/similarity/NonNegativeFloat", "datamodels/similarity/Objectidentifier", "datamodels/similarity/PairwiseSimilarity", "datamodels/similarity/Sparqlpath", "datamodels/similarity/String", "datamodels/similarity/TermInfo", "datamodels/similarity/TermPairwiseSimilarity", "datamodels/similarity/TermSetPairwiseSimilarity", "datamodels/similarity/Time", "datamodels/similarity/Uri", "datamodels/similarity/Uriorcurie", "datamodels/similarity/ZeroToOne", "datamodels/similarity/ancestor_id", "datamodels/similarity/ancestor_information_content", "datamodels/similarity/ancestor_label", "datamodels/similarity/ancestor_source", "datamodels/similarity/average_score", "datamodels/similarity/best_score", "datamodels/similarity/cosine_similarity", "datamodels/similarity/dice_similarity", "datamodels/similarity/id", "datamodels/similarity/index", "datamodels/similarity/information_content", "datamodels/similarity/intersection_count", "datamodels/similarity/jaccard_similarity", "datamodels/similarity/label", "datamodels/similarity/match_source", "datamodels/similarity/match_source_label", "datamodels/similarity/match_subsumer", "datamodels/similarity/match_subsumer_label", "datamodels/similarity/match_target", "datamodels/similarity/match_target_label", "datamodels/similarity/metric", "datamodels/similarity/object_best_matches", "datamodels/similarity/object_id", "datamodels/similarity/object_information_content", "datamodels/similarity/object_label", "datamodels/similarity/object_source", "datamodels/similarity/object_termset", "datamodels/similarity/overlap_coefficient", "datamodels/similarity/phenodigm_score", "datamodels/similarity/score", "datamodels/similarity/similarity", "datamodels/similarity/subject_best_matches", "datamodels/similarity/subject_id", "datamodels/similarity/subject_information_content", "datamodels/similarity/subject_label", "datamodels/similarity/subject_source", "datamodels/similarity/subject_termset", "datamodels/similarity/subsumed_by_score", "datamodels/similarity/subsumes_score", "datamodels/similarity/types", "datamodels/similarity/union_count", "datamodels/sssom/index", "datamodels/summary-statistics/Agent", "datamodels/summary-statistics/Boolean", "datamodels/summary-statistics/ChangeTypeStatistic", "datamodels/summary-statistics/ContributorRole", "datamodels/summary-statistics/ContributorStatistics", "datamodels/summary-statistics/Curie", "datamodels/summary-statistics/Date", "datamodels/summary-statistics/DateOrDatetime", "datamodels/summary-statistics/Datetime", "datamodels/summary-statistics/Decimal", "datamodels/summary-statistics/Double", "datamodels/summary-statistics/FacetStatistics", "datamodels/summary-statistics/FacetedCount", "datamodels/summary-statistics/Float", "datamodels/summary-statistics/GlobalStatistics", "datamodels/summary-statistics/GroupedStatistics", "datamodels/summary-statistics/Integer", "datamodels/summary-statistics/Jsonpath", "datamodels/summary-statistics/Jsonpointer", "datamodels/summary-statistics/Ncname", "datamodels/summary-statistics/Nodeidentifier", "datamodels/summary-statistics/Objectidentifier", "datamodels/summary-statistics/Ontology", "datamodels/summary-statistics/Sparqlpath", "datamodels/summary-statistics/String", "datamodels/summary-statistics/SummaryStatisticCollection", "datamodels/summary-statistics/SummaryStatisticsCalculationActivity", "datamodels/summary-statistics/SummaryStatisticsReport", "datamodels/summary-statistics/Time", "datamodels/summary-statistics/UngroupedStatistics", "datamodels/summary-statistics/Uri", "datamodels/summary-statistics/Uriorcurie", "datamodels/summary-statistics/acted_on_behalf_of", "datamodels/summary-statistics/agents", "datamodels/summary-statistics/annotation_property_count", "datamodels/summary-statistics/anonymous_class_expression_count", "datamodels/summary-statistics/anonymous_individual_count", "datamodels/summary-statistics/by_category", "datamodels/summary-statistics/by_ontology", "datamodels/summary-statistics/by_subset", "datamodels/summary-statistics/by_taxon", 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"datamodels/taxon-constraints/Integer", "datamodels/taxon-constraints/Jsonpath", "datamodels/taxon-constraints/Jsonpointer", "datamodels/taxon-constraints/Ncname", "datamodels/taxon-constraints/Nodeidentifier", "datamodels/taxon-constraints/Objectidentifier", "datamodels/taxon-constraints/PredicateTerm", "datamodels/taxon-constraints/Sparqlpath", "datamodels/taxon-constraints/String", "datamodels/taxon-constraints/SubjectTerm", "datamodels/taxon-constraints/Taxon", "datamodels/taxon-constraints/TaxonConstraint", "datamodels/taxon-constraints/Term", "datamodels/taxon-constraints/Time", "datamodels/taxon-constraints/Uri", "datamodels/taxon-constraints/Uriorcurie", "datamodels/taxon-constraints/asserted", "datamodels/taxon-constraints/candidate", "datamodels/taxon-constraints/comments", "datamodels/taxon-constraints/contradicted_by", "datamodels/taxon-constraints/description", "datamodels/taxon-constraints/evolutionary", "datamodels/taxon-constraints/id", 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"datamodels/text-annotator/index", "datamodels/text-annotator/info", "datamodels/text-annotator/is_longest_match", "datamodels/text-annotator/limit", "datamodels/text-annotator/match_string", "datamodels/text-annotator/match_type", "datamodels/text-annotator/matches_whole_text", "datamodels/text-annotator/model", "datamodels/text-annotator/object_aliases", "datamodels/text-annotator/object_categories", "datamodels/text-annotator/object_id", "datamodels/text-annotator/object_label", "datamodels/text-annotator/object_source", "datamodels/text-annotator/parent_document", "datamodels/text-annotator/predicate_id", "datamodels/text-annotator/source_text", "datamodels/text-annotator/sources", "datamodels/text-annotator/subject_end", "datamodels/text-annotator/subject_label", "datamodels/text-annotator/subject_source", "datamodels/text-annotator/subject_start", "datamodels/text-annotator/subject_text_id", "datamodels/text-annotator/text", "datamodels/text-annotator/text-annotator", "datamodels/text-annotator/token_exclusion_list", "datamodels/text-annotator/types", "datamodels/validation/Boolean", "datamodels/validation/ConstraintComponent", "datamodels/validation/Curie", "datamodels/validation/Date", "datamodels/validation/DateOrDatetime", "datamodels/validation/Datetime", "datamodels/validation/Decimal", "datamodels/validation/DefinitionValidationResult", "datamodels/validation/Double", "datamodels/validation/ExternalReferenceValidationResult", "datamodels/validation/Float", "datamodels/validation/Integer", "datamodels/validation/Jsonpath", "datamodels/validation/Jsonpointer", "datamodels/validation/MappingValidationResult", "datamodels/validation/NamedResource", "datamodels/validation/Ncname", "datamodels/validation/Node", "datamodels/validation/Nodeidentifier", "datamodels/validation/Objectidentifier", "datamodels/validation/RepairConfiguration", "datamodels/validation/RepairOperation", "datamodels/validation/RepairReport", "datamodels/validation/Report", 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422, 424, 428, 430, 431, 440, 441, 442, 444, 445, 447, 454, 460, 468, 469, 471, 472, 476, 477, 478, 479, 499, 521, 526, 617, 698, 721, 739, 747, 769, 775, 784, 793, 797, 799, 800, 807, 809, 810, 846, 886, 893, 920, 993, 1001, 1004, 1005, 1028, 1116, 1117, 1118, 1119, 1121, 1126, 1127, 1133, 1138, 1140, 1143, 1152, 1159, 1174, 1177, 1178, 1182, 1183, 1184, 1185, 1186, 1189, 1190, 1191, 1193], "lot": [1, 1109, 1117, 1119, 1124, 1127, 1140], "tool": [1, 4, 49, 51, 214, 229, 1112, 1116, 1118, 1123, 1128, 1130, 1137, 1144, 1171], "make": [1, 831, 1109, 1111, 1115, 1116, 1117, 1118, 1126, 1127, 1128, 1129, 1133, 1135, 1137, 1140, 1141, 1146, 1147, 1152, 1203], "assumpt": [1, 155, 165, 1126, 1129], "In": [1, 2, 214, 229, 946, 957, 1109, 1116, 1117, 1118, 1119, 1120, 1121, 1123, 1125, 1126, 1127, 1128, 1129, 1137, 1140, 1142, 1143, 1146, 1151, 1178, 1185, 1194, 1203], "fact": [1, 1119, 1123, 1127, 1140, 1151], "organ": [1, 831, 857, 1116, 1119, 1127, 1202], "modular": 1, "compon": [1, 499, 617, 1125, 1137, 1184, 1192], "much": [1, 1113, 1151, 1203], "softwar": [1, 1137, 1144], "evolv": 1, "program": [1, 1116, 1119, 1137, 1140, 1141], "system": [1, 1116, 1117, 1118, 1119, 1123, 1127, 1129, 1133, 1137, 1146, 1178], "releas": [1, 1112, 1127, 1130, 1178], "merg": [1, 386, 480, 484, 492, 503, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 617, 846, 886, 894, 1121, 1126, 1133, 1140, 1145, 1146, 1178], "appear": [1, 1129], "piec": [1, 1116, 1118, 1119, 1192], "incorpor": [1, 1127, 1140], "design": [1, 165, 175, 193, 204, 1113, 1116, 1127, 1133, 1134, 1138, 1151], "scenario": [1, 1178], "don": [1, 2, 204, 1110, 1113, 1118, 1124, 1127, 1129, 1137, 1140, 1146, 1151, 1160, 1174, 1203], "worri": [1, 1109, 1140, 1151, 1182], "about": [1, 3, 4, 17, 22, 37, 41, 46, 80, 86, 89, 376, 377, 384, 385, 386, 388, 389, 392, 393, 397, 398, 400, 407, 409, 415, 421, 428, 441, 442, 444, 447, 454, 469, 476, 477, 479, 945, 957, 970, 1038, 1040, 1065, 1075, 1076, 1086, 1096, 1109, 1116, 1117, 1118, 1124, 1125, 1127, 1134, 1139, 1141, 1142, 1144, 1151, 1163, 1178, 1182, 1183, 1185], "where": [1, 142, 388, 441, 697, 721, 724, 1040, 1045, 1066, 1067, 1068, 1073, 1075, 1076, 1077, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1094, 1095, 1096, 1097, 1098, 1100, 1101, 1102, 1103, 1106, 1109, 1113, 1116, 1117, 1119, 1120, 1121, 1123, 1124, 1125, 1126, 1128, 1129, 1133, 1151, 1178, 1183, 1185, 1187, 1189, 1191, 1202, 1203], "everyth": [1, 441, 452, 1110, 1116, 1119, 1120, 1127], "were": [1, 1125, 1133, 1142, 1164, 1178], "singl": [1, 95, 117, 118, 119, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 134, 135, 392, 393, 397, 398, 428, 438, 441, 499, 1118, 1126, 1134, 1147, 1174, 1178, 1183, 1191, 1193, 1203], "even": [1, 2, 1117, 1119, 1126, 1127, 1140, 1151, 1152, 1178, 1203], "actual": [1, 946, 957, 1109, 1116, 1127, 1133], "combin": [1, 9, 46, 100, 127, 140, 165, 209, 236, 257, 281, 302, 336, 382, 386, 441, 497, 617, 685, 721, 752, 784, 825, 886, 930, 943, 957, 972, 978, 1005, 1036, 1075, 1112, 1116, 1118, 1128, 1130, 1177, 1178, 1184, 1189, 1203], "let": [1, 1127, 1141], "explor": [1, 1121, 1122, 1128, 1188], "composit": 1, "detail": [1, 3, 4, 17, 20, 21, 22, 23, 24, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 95, 96, 111, 117, 118, 119, 121, 122, 123, 124, 125, 126, 128, 129, 130, 131, 132, 133, 134, 135, 142, 150, 155, 159, 163, 166, 167, 168, 169, 170, 172, 173, 175, 176, 177, 178, 179, 181, 182, 183, 184, 185, 186, 187, 188, 190, 191, 193, 194, 195, 196, 198, 199, 200, 201, 214, 215, 216, 219, 225, 229, 230, 231, 232, 233, 234, 235, 237, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 251, 252, 264, 265, 266, 267, 271, 275, 278, 279, 280, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 296, 297, 309, 310, 311, 312, 313, 314, 318, 319, 321, 322, 325, 326, 328, 331, 332, 333, 334, 335, 337, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 375, 376, 377, 384, 385, 386, 388, 389, 390, 392, 393, 397, 398, 400, 401, 406, 407, 408, 409, 410, 414, 415, 416, 421, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 442, 444, 445, 446, 447, 448, 449, 450, 451, 454, 455, 456, 457, 458, 459, 460, 461, 462, 464, 466, 467, 468, 469, 470, 471, 472, 474, 475, 476, 477, 478, 479, 480, 483, 484, 485, 486, 487, 488, 489, 492, 493, 499, 501, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 522, 523, 524, 525, 526, 530, 531, 534, 536, 537, 539, 540, 541, 544, 545, 546, 549, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611, 612, 613, 614, 615, 616, 618, 619, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 642, 643, 644, 645, 647, 648, 649, 650, 651, 652, 653, 654, 655, 656, 657, 658, 659, 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671, 672, 674, 675, 676, 677, 678, 680, 681, 689, 696, 697, 698, 699, 700, 702, 708, 709, 710, 711, 712, 713, 714, 715, 720, 722, 723, 724, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 740, 741, 742, 743, 744, 747, 765, 768, 769, 770, 775, 776, 777, 778, 779, 780, 781, 782, 783, 785, 786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 815, 817, 819, 820, 821, 828, 829, 831, 832, 839, 842, 843, 844, 846, 849, 850, 851, 852, 853, 858, 859, 860, 861, 864, 865, 866, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 883, 884, 885, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 896, 897, 898, 899, 900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911, 912, 913, 915, 916, 917, 919, 920, 921, 922, 923, 924, 926, 940, 943, 944, 945, 946, 950, 951, 952, 953, 954, 955, 956, 958, 959, 960, 961, 962, 963, 964, 965, 966, 967, 968, 969, 970, 972, 973, 982, 992, 993, 994, 995, 997, 1000, 1001, 1002, 1003, 1004, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1029, 1032, 1038, 1040, 1045, 1046, 1048, 1051, 1052, 1053, 1054, 1055, 1056, 1060, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1072, 1073, 1074, 1076, 1077, 1078, 1079, 1080, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1091, 1092, 1093, 1094, 1095, 1096, 1097, 1098, 1099, 1100, 1101, 1102, 1103, 1104, 1106, 1107, 1109, 1116, 1118, 1119, 1120, 1122, 1128, 1133, 1140, 1146, 1174, 1177, 1182, 1184, 1193], "prefer": [1, 2, 698, 1140, 1183], "0008152": 1, "driven": [1, 1135], "infrastructur": 1, "semant": [1, 2, 204, 377, 384, 386, 398, 409, 415, 421, 479, 746, 1110, 1116, 1118, 1120, 1126, 1128, 1135, 1138, 1142, 1146, 1174, 1176, 1182, 1194, 1203], "web": [1, 1114, 1116, 1119, 1120, 1126, 1142, 1144, 1203], "stack": 1, "data": [1, 31, 41, 203, 204, 238, 408, 441, 452, 746, 816, 828, 886, 914, 1052, 1065, 1076, 1077, 1082, 1085, 1086, 1094, 1095, 1096, 1103, 1108, 1112, 1113, 1114, 1115, 1116, 1119, 1120, 1121, 1123, 1124, 1129, 1133, 1138, 1140, 1143, 1146, 1151, 1154, 1171, 1177, 1191, 1192], "scienc": [1, 1116, 1140], "bioinformat": [1, 1116, 1127, 1143], "bridg": [1, 1142], "essenti": [1, 1127], "well": [1, 2, 31, 46, 392, 409, 441, 450, 1110, 1116, 1118, 1119, 1120, 1134, 1140, 1143, 1151, 1178, 1185, 1188], "defin": [1, 214, 229, 385, 392, 397, 426, 427, 429, 434, 438, 441, 446, 447, 458, 464, 474, 475, 945, 961, 1118, 1119, 1123, 1127, 1128, 1148, 1177, 1178, 1184, 1192, 1193], "expans": [1, 1178], "method": [1, 1109, 1112, 1113, 1116, 1117, 1123, 1125, 1127, 1128, 1129, 1141, 1142, 1143, 1147, 1152, 1177, 1178, 1180, 1182, 1183, 1184, 1190, 1192, 1193, 1194, 1203], "accept": [1, 1110, 1134, 1146, 1151, 1204], "alwai": [1, 397, 464, 1115, 1116, 1128, 1134, 1137, 1140, 1177], "contract": [1, 1178], "A": [1, 2, 3, 4, 5, 10, 11, 12, 14, 15, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 42, 43, 46, 47, 48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 76, 77, 79, 80, 81, 82, 83, 84, 86, 87, 88, 89, 90, 91, 92, 93, 95, 96, 101, 102, 103, 105, 106, 108, 109, 112, 113, 114, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 141, 143, 144, 145, 147, 148, 149, 152, 153, 155, 157, 158, 159, 160, 163, 164, 165, 168, 169, 170, 172, 173, 176, 177, 178, 179, 182, 183, 185, 186, 187, 188, 190, 191, 194, 195, 196, 200, 201, 205, 210, 211, 212, 214, 217, 218, 221, 222, 223, 224, 225, 226, 235, 236, 238, 248, 253, 258, 259, 260, 262, 263, 264, 267, 269, 270, 271, 272, 273, 274, 275, 278, 279, 281, 282, 283, 284, 286, 288, 289, 290, 291, 292, 293, 298, 303, 304, 305, 307, 308, 309, 312, 314, 316, 317, 318, 319, 321, 322, 323, 324, 326, 327, 328, 332, 333, 336, 337, 338, 339, 340, 341, 342, 345, 346, 347, 348, 350, 352, 356, 358, 359, 361, 363, 364, 365, 366, 367, 369, 371, 372, 375, 376, 377, 378, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 395, 396, 397, 398, 400, 402, 403, 404, 406, 407, 409, 410, 412, 413, 415, 417, 418, 421, 422, 423, 424, 425, 428, 430, 431, 432, 434, 435, 436, 439, 440, 441, 442, 444, 445, 446, 447, 448, 449, 450, 452, 454, 456, 457, 458, 460, 462, 467, 468, 469, 470, 471, 472, 476, 477, 478, 479, 483, 484, 489, 490, 491, 498, 499, 500, 502, 506, 507, 508, 509, 510, 511, 512, 514, 515, 519, 520, 521, 527, 529, 531, 534, 535, 540, 542, 543, 544, 545, 548, 550, 554, 555, 556, 557, 558, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 577, 579, 580, 581, 582, 584, 586, 587, 588, 590, 591, 592, 593, 595, 596, 597, 598, 600, 601, 602, 603, 604, 605, 606, 607, 610, 611, 612, 613, 614, 616, 617, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 639, 641, 642, 650, 651, 652, 653, 656, 659, 661, 662, 664, 667, 668, 669, 670, 672, 675, 679, 686, 687, 688, 691, 692, 694, 695, 696, 697, 698, 703, 704, 705, 711, 713, 714, 715, 720, 721, 722, 723, 724, 726, 735, 739, 740, 741, 743, 744, 748, 753, 754, 755, 758, 759, 762, 764, 766, 767, 769, 770, 771, 775, 776, 777, 778, 779, 780, 781, 782, 784, 787, 795, 796, 797, 798, 799, 800, 801, 803, 806, 807, 808, 809, 810, 811, 818, 820, 826, 827, 830, 834, 835, 837, 838, 840, 841, 842, 845, 846, 850, 851, 852, 853, 858, 859, 860, 861, 864, 865, 867, 870, 872, 873, 874, 876, 877, 878, 880, 881, 885, 886, 887, 890, 891, 892, 893, 894, 896, 897, 898, 900, 901, 902, 903, 907, 909, 912, 913, 914, 915, 916, 919, 920, 924, 925, 931, 932, 933, 935, 936, 938, 939, 940, 941, 942, 943, 944, 947, 954, 956, 957, 958, 959, 960, 963, 964, 971, 972, 974, 979, 980, 981, 984, 985, 987, 988, 990, 991, 993, 994, 996, 997, 1000, 1001, 1005, 1028, 1029, 1031, 1037, 1039, 1040, 1041, 1043, 1044, 1045, 1049, 1050, 1053, 1054, 1057, 1058, 1059, 1064, 1067, 1068, 1073, 1075, 1076, 1077, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1092, 1094, 1095, 1096, 1097, 1098, 1100, 1101, 1102, 1103, 1106, 1108, 1109, 1116, 1118, 1119, 1121, 1123, 1125, 1128, 1137, 1140, 1141, 1142, 1147, 1148, 1152, 1174, 1177, 1178, 1180, 1186, 1188, 1192, 1194], "seem": [1, 1123, 1151], "surpris": [1, 1140], "standard": [1, 2, 275, 328, 376, 398, 415, 422, 424, 441, 469, 997, 1110, 1112, 1114, 1116, 1117, 1118, 1120, 1121, 1124, 1126, 1127, 1128, 1129, 1134, 1140, 1142, 1143, 1203], "construct": [1, 376, 441, 1112, 1116, 1119, 1127, 1129, 1178, 1203], "directli": [1, 22, 28, 115, 161, 227, 251, 276, 296, 329, 376, 409, 419, 486, 539, 545, 546, 551, 706, 765, 772, 844, 847, 946, 948, 998, 1054, 1055, 1061, 1116, 1120, 1123, 1124, 1128, 1133, 1140, 1144, 1147, 1151, 1152, 1177, 1184], "correspond": [1, 2, 155, 165, 167, 184, 191, 192, 193, 318, 375, 398, 424, 441, 1038, 1040, 1065, 1103, 1116, 1124, 1127, 1137, 1178], "call": [1, 1113, 1116, 1118, 1128, 1140, 1147, 1151, 1159, 1178, 1202], "owlinterfac": [1, 204, 1139, 1182, 1185], "rdfinterfac": 1, "common": [1, 31, 46, 318, 375, 769, 775, 784, 1114, 1116, 1117, 1119, 1123, 1125, 1126, 1127, 1128, 1134, 1138, 1140, 1148, 1151, 1152, 1182, 1189], "opaqu": 1, "each": [1, 142, 155, 163, 165, 204, 275, 325, 328, 336, 341, 370, 441, 452, 831, 997, 1110, 1112, 1116, 1117, 1119, 1124, 1127, 1128, 1129, 1133, 1137, 1140, 1143, 1151, 1152, 1175, 1178, 1180, 1183, 1187, 1188, 1190, 1192, 1193, 1203], "exactli": [1, 142, 155, 163, 165, 166, 1134, 1152], "uniqu": [1, 2, 155, 165, 166, 169, 175, 178, 219, 225, 232, 392, 400, 414, 416, 440, 441, 480, 489, 509, 513, 516, 525, 545, 629, 817, 820, 832, 839, 844, 846, 886, 1116, 1119, 1120, 1137, 1140, 1178], "human": [1, 31, 46, 149, 165, 167, 392, 398, 400, 414, 416, 441, 445, 513, 514, 515, 521, 527, 531, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 587, 588, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 613, 614, 616, 617, 621, 629, 639, 650, 651, 659, 662, 668, 669, 670, 672, 698, 940, 943, 944, 946, 957, 958, 1116, 1117, 1118, 1119, 1120, 1121, 1127, 1128, 1203], "represent": [1, 6, 97, 137, 206, 254, 299, 379, 421, 441, 452, 491, 494, 550, 617, 682, 749, 822, 927, 975, 1033, 1116, 1119, 1121, 1125, 1127, 1128], "repres": [1, 18, 19, 27, 31, 46, 108, 109, 114, 120, 127, 144, 152, 153, 160, 164, 165, 204, 214, 219, 221, 222, 226, 236, 237, 238, 239, 241, 250, 269, 270, 274, 281, 282, 283, 316, 317, 327, 336, 338, 339, 377, 384, 386, 388, 389, 392, 393, 398, 402, 403, 404, 407, 409, 410, 415, 417, 418, 421, 422, 423, 425, 434, 435, 436, 440, 441, 442, 444, 445, 446, 447, 450, 452, 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264, 281, 289, 292, 295, 309, 336, 361, 369, 374, 473, 673, 745, 814, 918, 1030, 1105, 1115, 1116, 1118, 1124, 1128, 1178], "intent": [1, 1178, 1203], "languag": [1, 377, 384, 409, 415, 421, 441, 444, 617, 618, 1114, 1116, 1121, 1126, 1130, 1138, 1147, 1178, 1182, 1194, 1203], "unintent": 1, "version": [1, 2, 155, 165, 398, 441, 677, 699, 721, 733, 839, 846, 858, 886, 922, 1117, 1120, 1127, 1130, 1133, 1134, 1140, 1178, 1183], "allow": [1, 415, 441, 469, 697, 721, 724, 1063, 1066, 1075, 1089, 1093, 1104, 1110, 1116, 1117, 1124, 1126, 1133, 1134, 1137, 1140, 1143, 1144, 1147, 1159, 1188], "complet": [1, 28, 46, 115, 127, 161, 165, 227, 236, 276, 281, 329, 336, 419, 441, 551, 617, 706, 721, 772, 784, 847, 886, 948, 957, 998, 1005, 1061, 1075, 1112, 1124, 1127, 1176, 1178], "give": [1, 155, 165, 1117, 1127, 1128, 1133, 1140, 1151, 1185], "freedom": 1, "model": [1, 18, 19, 31, 41, 95, 108, 109, 127, 131, 152, 153, 165, 203, 204, 221, 222, 238, 269, 270, 281, 316, 317, 336, 402, 403, 409, 441, 452, 509, 511, 529, 535, 579, 617, 629, 694, 695, 721, 746, 762, 764, 784, 816, 837, 838, 886, 938, 939, 946, 957, 987, 988, 993, 1005, 1028, 1049, 1050, 1052, 1113, 1114, 1116, 1119, 1121, 1124, 1125, 1127, 1130, 1138, 1151, 1154, 1163, 1177, 1178, 1192], "thei": [1, 204, 1114, 1116, 1123, 1124, 1125, 1127, 1128, 1129, 1140, 1142, 1143, 1146, 1151, 1173, 1178, 1182, 1193], "obojson": 1, "littl": [1, 1140, 1151], "restrict": [1, 385, 386, 390, 392, 397, 423, 426, 437, 441, 459, 480, 484, 487, 489, 492, 493, 507, 510, 512, 513, 516, 525, 534, 539, 540, 544, 545, 549, 553, 556, 557, 560, 565, 572, 580, 584, 586, 589, 599, 607, 617, 619, 620, 648, 649, 653, 656, 658, 659, 663, 665, 670, 674, 1116, 1123, 1127, 1143, 1175, 1178, 1184], "disallow": 1, "suit": [1, 1116, 1129], "qc": [1, 1143], "check": [1, 19, 109, 153, 222, 270, 317, 403, 535, 695, 764, 838, 939, 988, 1038, 1040, 1045, 1050, 1063, 1065, 1067, 1068, 1073, 1075, 1076, 1077, 1078, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 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"question": [2, 1110, 1118, 1127, 1133], "bug": [2, 1111, 1129], "enhanc": [2, 1133], "featur": [2, 397, 441, 464, 1111, 1112, 1118, 1119, 1127, 1137, 1140, 1146, 1147, 1148, 1204], "tutori": [2, 1113, 1121, 1124, 1127, 1136, 1138, 1140, 1141, 1144, 1146, 1204], "sourc": [2, 46, 165, 171, 174, 180, 281, 336, 617, 721, 784, 957, 1005, 1075, 1109, 1110, 1112, 1121, 1135, 1140, 1144, 1159, 1164, 1174, 1177, 1178, 1180, 1183, 1184, 1185, 1186, 1187, 1188, 1189, 1190, 1191, 1192, 1193, 1204], "resid": 2, "folder": [2, 1110, 1112, 1135, 1140, 1146, 1160, 1171], "github": [2, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 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484, 489, 492, 512, 513, 516, 525, 534, 537, 539, 544, 545, 549, 564, 945, 950, 957, 1063, 1066, 1075, 1079, 1116, 1117, 1118, 1119, 1121, 1125, 1128, 1134, 1140, 1147, 1152, 1178], "later": [2, 1127, 1128, 1140, 1177], "mark": [2, 1125, 1127], "your": [2, 1110, 1115, 1120, 1130, 1133, 1137, 1139, 1140, 1141, 1152, 1160, 1171], "draft": 2, "readi": [2, 1135, 1139], "review": [2, 1123, 1133], "If": [2, 4, 21, 42, 45, 46, 56, 72, 78, 155, 165, 184, 190, 193, 385, 404, 422, 441, 474, 697, 741, 769, 775, 943, 945, 953, 957, 966, 972, 993, 1004, 1005, 1110, 1115, 1119, 1123, 1124, 1125, 1127, 1128, 1129, 1133, 1134, 1137, 1140, 1141, 1144, 1146, 1151, 1152, 1174, 1177, 1178, 1183, 1184, 1186, 1192], "sure": [2, 1134, 1137, 1140], "unit": [2, 265, 280, 281, 287, 310, 325, 326, 334, 336, 337, 350, 353, 359, 370, 1112], "exist": [2, 376, 385, 390, 392, 400, 414, 416, 441, 445, 1117, 1123, 1125, 1127, 1128, 1130, 1137, 1143, 1147, 1164, 1178], "avoid": [2, 1109, 1140, 1146, 1151, 1175], "print": [2, 1109, 1117, 1120, 1124, 1125, 1126, 1127, 1137, 1141, 1142, 1148, 1151, 1152, 1159, 1177, 1178, 1180, 1182, 1183, 1184, 1188, 1192, 1203], "ing": 2, "log": [2, 784, 785, 1128], "diagnost": [2, 1128], "captur": [2, 376, 441, 447, 1118, 1178], "output": [2, 21, 46, 78, 326, 336, 337, 359, 1110, 1120, 1124, 1129, 1133, 1135, 1140, 1144, 1147, 1154], "explicitli": [2, 697, 720, 1134, 1140, 1174, 1177, 1178], "oakx": [2, 1137, 1145], "robot": [2, 1112, 1123, 1137, 1139, 1146, 1163, 1176, 1178, 1185], "exemplar": 2, "regist": [2, 422], "scheme": [2, 1137, 1165, 1172, 1174, 1176], "__init__": 2, "py": [2, 816, 1141, 1185], "least": [2, 319, 342, 347, 348, 358, 365, 366, 1127, 1137], "__post_init__": [2, 1137], "cli": [2, 1112, 1130, 1133, 1134, 1140, 1152, 1194, 1203], "refactor": 2, "substanti": 2, "prior": [2, 46, 73, 74, 75], "0": [2, 3, 4, 17, 20, 21, 22, 23, 24, 95, 96, 131, 150, 155, 159, 214, 215, 219, 225, 264, 265, 266, 267, 271, 309, 310, 311, 312, 313, 314, 318, 319, 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1183, 1184, 1185, 1186, 1187, 1188, 1189, 1190, 1191, 1193], "plu": [214, 229, 230, 231, 233, 236, 239, 241, 242, 243, 244, 249, 943, 957, 972, 1116, 1140, 1144, 1178, 1194, 1198], "recommend": [214, 397, 406, 438, 456, 464, 484, 492, 534, 539, 544, 549, 699, 730, 1038, 1040, 1065, 1103, 1112, 1115, 1123, 1133, 1134, 1135, 1137, 1140, 1177, 1186, 1193, 1203], "itemlistel": [214, 219, 236], "listitem": [214, 225, 232, 234, 236, 237, 239, 241, 245, 246], "numberofitem": [214, 216, 236], "itemlistordertyp": [214, 236, 244], "order": [214, 216, 236, 244, 275, 328, 997, 1109, 1110, 1134, 1177], "itemmetadatamap": [214, 219, 236], "control": [214, 230, 236, 275, 281, 328, 336, 997, 1005, 1119, 1134, 1140, 1178, 1180, 1183, 1187, 1188, 1190, 1193], "keyword": [214, 230, 236], "additionaltyp": [214, 236], "wasgeneratedbi": [214, 236], "proven": [214, 236, 249, 409, 441, 499, 1063, 1075, 1078, 1118, 1133], "script": [214, 236, 249], "itemlistcollect": [214, 236, 240], "close": [214, 377, 398, 409, 410, 415, 421, 479, 492, 1116, 1141, 1149, 1193], "close_map": [214, 377, 409, 415, 421, 479, 480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 570, 573, 576, 621, 677], "henc": 214, "declar": [214, 392, 393, 406, 441, 448, 456, 457, 1185], "mtor": 214, "pathwai": [214, 1177], "my": [214, 1113, 1133, 1137, 1141, 1160, 1169, 1171], "shop": 214, "bui": 214, "supermarket": 214, "singular_nam": [214, 230, 239, 242], "wish": [214, 215, 230, 1123, 1125, 1133, 1146, 1193], "uncontrol": [214, 230], "dcterm": [214, 230, 480, 484, 489, 492, 506, 507, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 566, 568, 570, 573, 576, 621, 630, 631, 664, 669, 671, 839, 875, 917], "extern": [214, 229, 384, 421, 441, 444, 447, 454, 476, 477, 479, 846, 886, 891, 893, 1040, 1073, 1075, 1076, 1077, 1081, 1082, 1085, 1086, 1094, 1095, 1096, 1102, 1103, 1106, 1109, 1140, 1147, 1193], "vocabulari": [214, 229, 377, 384, 398, 409, 410, 415, 421, 422, 441, 479, 846, 886, 891, 893, 1038, 1040, 1065, 1103, 1109, 1117, 1119, 1124, 1126, 1127, 1129, 1135, 1142, 1177, 1178, 1184, 1203], "microdata": [214, 229], "rdfa": [214, 229], "better": [214, 229, 1111, 1128, 1140, 1152], "weaker": [214, 229], "extra": [214, 229, 1133, 1140], "itemlist": [215, 219, 225, 229, 230, 231, 232, 233, 234, 235, 236, 239, 241, 242, 243, 244, 247, 248, 249], "catalog": 215, "pass": [215, 1063, 1075, 1089, 1116, 1117, 1118, 1125, 1128, 1133, 1134, 1135, 1140, 1144, 1147, 1177, 1183, 1193, 1194], "around": [215, 1114, 1115, 1116, 1117, 1134, 1140, 1146, 1184], "ascend": 216, "itemlistorderascend": 216, "descend": [216, 943, 957, 959, 960, 963, 1109, 1110, 1112, 1116, 1118, 1128, 1130, 1133, 1143, 1146, 1177, 1182, 1184], "itemlistorderdescend": 216, "unord": 216, "itemlistunord": 216, "enum_uri": 216, "elementid": [219, 236], "idtyp": [219, 236], "previousitem": [219, 236], "previou": [219, 236, 246, 1127, 1140], "proper": [219, 225, 232, 1189], "symbol": [219, 225, 232, 234, 235, 702, 1140], "url": 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287, 288, 289, 290, 291, 292, 293, 294], "param": [252, 266, 281, 297, 311, 336, 1178, 1184, 1186], "relationshiptoterm": [264, 267, 278, 279, 281, 286, 288, 289, 290, 291, 309, 312, 332, 333, 336, 352, 356, 361, 364, 367], "lexicalindex": [264, 267, 280, 281, 287, 309, 312, 334, 336, 353, 1192], "lexicalgroup": [265, 271, 280, 281, 289, 292, 310, 321, 334, 336, 361, 369], "pipelin": [265, 267, 271, 281, 310, 312, 321, 336, 1192], "atom": [266, 267, 281, 284, 285, 293, 294, 311, 312, 336, 346, 351, 371, 373, 681, 697, 721, 769, 775, 776, 777, 778, 781, 782, 784, 787, 797, 798, 799, 800, 803, 807, 808, 809, 810, 1186], "transform": [266, 267, 275, 281, 284, 285, 294, 311, 312, 328, 336, 346, 351, 373, 997, 1005, 1123], "appli": [266, 267, 275, 281, 284, 285, 293, 294, 311, 312, 313, 325, 328, 335, 336, 341, 346, 351, 354, 371, 373, 393, 441, 821, 886, 899, 945, 957, 969, 997, 1005, 1116, 1125, 1128, 1138, 1139, 1148, 1163, 1186, 1192, 1203], "yield": [266, 275, 281, 285, 294, 311, 328, 336, 351, 373, 997, 1109, 1116, 1121, 1134, 1152, 1177, 1178, 1180, 1183, 1184, 1185, 1187, 1189, 1190, 1192, 1193], "activ": [266, 267, 281, 311, 312, 336, 843, 849, 879, 886, 911, 923, 1125, 1128, 1140, 1180, 1186], "transformationtyp": [266, 281, 294, 311, 336, 373, 1005], "paramet": [266, 281, 285, 311, 336, 351, 1051, 1063, 1071, 1072, 1075, 1078, 1079, 1089, 1093, 1104, 1107, 1129, 1134, 1139, 1177, 1178, 1180, 1183, 1184, 1185, 1186, 1187, 1188, 1189, 1190, 1191, 1192, 1193, 1204], "algorithm": [266, 281, 285, 311, 336, 351], "fashion": [267, 281, 312, 336, 1116], "element_term": [271, 281, 321, 336], "synonym": [271, 275, 281, 313, 321, 322, 326, 328, 331, 335, 336, 343, 344, 359, 360, 362, 363, 370, 377, 398, 410, 415, 417, 424, 441, 442, 444, 447, 454, 469, 476, 477, 479, 480, 484, 489, 492, 511, 513, 514, 515, 516, 525, 531, 534, 539, 544, 545, 549, 554, 588, 602, 604, 605, 610, 617, 698, 846, 877, 886, 915, 916, 993, 1004, 1005, 1113, 1116, 1119, 1121, 1138, 1148, 1178, 1188, 1192, 1193, 1203], "stem": [275, 328, 997, 1129], "few": [275, 328, 997, 1112, 1115, 1151, 1171], "word": [275, 328, 997], "wo": [275, 328, 997], "lemmat": [275, 328, 997], "contextu": [275, 328, 997, 1117, 1118], "reduct": [275, 328, 997, 1190], "its": [275, 328, 507, 943, 959, 960, 997, 1117, 1119, 1124, 1125, 1128, 1129, 1133, 1134, 1148, 1194], "wordordernorm": [275, 328, 997], "reorder": [275, 328, 997], "comparison": [275, 328, 997], "deplur": [275, 328, 997], "plural": [275, 328, 997], "singular": [275, 328, 997], "casenorm": [275, 328, 997], "lowercas": [275, 328, 997], "whitespacenorm": [275, 328, 997], "trim": [275, 328, 997], "whitespac": [275, 328, 997], "condens": [275, 328, 997], "white": [275, 328, 997], "termexpanson": [275, 328, 997], "dictionari": [275, 328, 997, 1143, 1178, 1180, 1191], "matcher_rul": [275, 328], "lexical_index": [283, 338, 339, 1176, 1182, 1192], "fa": [284, 293, 346, 371], "transf": [285, 294, 351, 373], "mappingrul": [296, 297, 309, 310, 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1143, 1147, 1152, 1154, 1177], "against": [319, 336, 342, 347, 348, 358, 365, 366, 372, 832, 844, 846, 867, 886, 1038, 1040, 1065, 1103, 1112, 1116, 1133, 1177, 1180, 1189, 1193], "subject_source_one_of": [319, 336], "object_source_one_of": [319, 336], "mapping_source_one_of": [319, 336], "subject_match_field_one_of": [319, 336], "object_match_field_one_of": [319, 336], "transformations_included_in": [319, 336], "predicate_id_one_of": [319, 336], "altern": [322, 325, 331, 335, 336, 343, 344, 359, 360, 362, 363, 370, 1117, 1119, 1130, 1165, 1172], "qualifi": [322, 325, 326, 336], "test": [322, 325, 336, 337, 350, 359, 1109, 1111, 1112, 1120, 1126, 1127, 1128, 1129, 1130, 1143, 1146, 1152, 1154, 1178, 1180, 1183, 1184, 1192, 1193, 1194], "regularexpressionstr": [325, 336, 343, 362], "reg": [325, 336, 343, 344, 362], "ex": [325, 336, 343, 344, 362], "substr": [325, 336, 343, 362], "match_scop": [325, 336], "scope": [325, 336, 344, 410, 417, 441, 511, 721, 739, 846, 886, 916, 1112, 1125, 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516, 525, 534, 539, 544, 545, 549, 602, 1117], "hasrelatedsynonym": [405, 410, 480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 610, 1114, 1117], "go_": [406, 441, 1178], "strongli": [406, 456], "r1": [407, 441], "rn": [407, 441], "chainpredicateid": [407, 441], "claus": [407, 425, 441], "prope": [407, 441], "subtyp": [408, 441], "minim": [409, 441, 1112, 1178, 1183], "nest": [409, 1123, 1130], "broader": [410, 1116, 1140], "bu": 410, "subsetproperti": [414, 1178], "synonymtyp": [415, 416, 441, 442, 1117], "synonymtypeidentifierstr": [415, 441, 469], "oboinowl": [415, 441, 469, 484, 489, 534, 539, 544, 549, 591, 598, 624, 625, 626, 627, 628, 641, 661, 675, 1117, 1120, 1124, 1125, 1178, 1203], "isexact": [415, 441], "scopeenum": [415, 441], "instead": [415, 442, 1116, 1125, 1127, 1129, 1134, 1140, 1147, 1151, 1175, 1178], "commonli": [417, 1116, 1203], "plain": [417, 702, 1117], "abbrevi": [417, 1139], "pmid": [421, 1063, 1078, 1118, 1140], "12345": 421, "relax": [422, 1178], 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484, 489, 492, 508, 513, 516, 525, 534, 539, 544, 545, 549, 575, 617], "has_obo_namespac": [480, 484, 492, 506, 513, 516, 525, 534, 539, 544, 545, 549, 617], "in_subset": [480, 484, 489, 492, 506, 507, 509, 510, 511, 512, 513, 516, 525, 534, 539, 544, 545, 549, 554, 562, 567, 579, 580, 582, 588, 593, 600, 617, 629, 669], "conformsto": [480, 484, 492, 506, 513, 516, 525, 534, 539, 544, 545, 546, 549, 617, 618], "imag": [480, 484, 488, 492, 512, 513, 514, 515, 525, 530, 531, 534, 536, 537, 539, 544, 545, 546, 549, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 587, 588, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 614, 616, 617, 618, 621, 629, 639, 650, 651, 659, 662, 668, 669, 670, 672, 1140, 1171], "example_of_usag": [480, 481, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 618], "curator_not": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 654], "has_curation_statu": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 618], "depicted_bi": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 618], "page": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 617, 618, 1116, 1119], "transitiveproperti": [480, 488, 492, 514, 515, 516, 525, 530, 531, 534, 536, 537, 539, 544, 546, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 584, 586, 587, 588, 590, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 613, 614, 616, 617, 620, 621, 624, 625, 627, 628, 629, 639, 650, 651, 653, 656, 659, 661, 662, 667, 668, 669, 670, 672, 1178], "homosapien": [480, 488, 492, 514, 515, 516, 525, 530, 531, 536, 537, 544, 546, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 587, 588, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 613, 614, 616, 617, 621, 629, 639, 650, 651, 659, 662, 668, 669, 670, 672], "orcid": [480, 513, 1117], "omoschema": [480, 483, 484, 485, 486, 487, 488, 489, 492, 493, 499, 501, 506, 507, 508, 509, 510, 511, 512, 513, 516, 525, 526, 530, 534, 536, 537, 539, 540, 541, 544, 545, 546, 549, 558, 569, 583, 594, 595, 596, 597, 609, 612, 618, 632, 633, 634, 642, 645, 652, 654, 657, 660, 662, 678], "id_prefix": [480, 513, 940, 944, 1178], "disjoint_with": [480, 484, 489, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 604], "allotrop": [480, 481, 482, 484, 489, 492, 507, 509, 511, 512, 513, 516, 525, 534, 539, 544, 545, 549, 554, 562, 579, 582, 593, 629, 669], "permit": [480, 484, 489, 492, 507, 510, 511, 512, 513, 516, 525, 534, 539, 544, 545, 549, 554, 562, 567, 580, 582, 588, 593, 600, 669], "profil": [480, 484, 489, 492, 507, 509, 510, 511, 512, 513, 516, 525, 534, 539, 544, 545, 549, 554, 562, 567, 579, 580, 582, 588, 593, 600, 629, 669, 846, 876, 886, 1120, 1126, 1128, 1190], "altlabel": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 554, 698, 1117], "0000118": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 554, 1117, 1178], "0001847": [480, 484, 492, 511, 513, 515, 516, 525, 534, 539, 544, 545, 549], "9991118": [480, 484, 492, 511, 513, 514, 516, 525, 534, 539, 544, 545, 549], "0000111": [480, 484, 492, 511, 513, 516, 525, 534, 539, 544, 545, 549, 588], "add": [480, 484, 492, 511, 513, 516, 525, 531, 534, 539, 544, 545, 549, 1064, 1126, 1127, 1133, 1135, 1137, 1141, 1159, 1177, 1178, 1183], "uniquekei": [480, 484, 492, 511, 513, 516, 525, 531, 534, 539, 544, 545, 549], "0000589": [480, 484, 492, 511, 513, 516, 525, 531, 534, 539, 544, 545, 549], "obsoletion_related_properti": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 567, 582, 600, 607, 617, 669], "obsoleteaspect": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 567, 582, 607, 617, 669], "0000231": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 607, 1125], "isreplacedbi": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 669], "0100001": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 669, 1125, 1178], "redund": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 945, 953, 957, 966, 1134, 1190], "invers": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 1128], "replaced_bi": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600], "NOT": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 680, 943, 959, 1130, 1135, 1146, 1171, 1178, 1194], "owlc": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600], "owlapi": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 1185], "317": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600], "notobsoleteaspect": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 617], "hasalternativeid": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 600, 1125], "excluded_axiom": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 595, 596, 597, 617, 662], "hiddensynonym": [480, 484, 492, 507, 513, 516, 525, 534, 539, 544, 545, 549, 597], "propos": [480, 484, 489, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 571, 572, 945, 951, 957, 1116, 1137, 1147], "omo": [480, 484, 489, 492, 510, 513, 516, 522, 523, 524, 525, 534, 539, 544, 545, 549, 571, 572, 1063, 1075, 1093, 1117, 1125, 1126], "2022": [480, 484, 489, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 571, 572], "04": [480, 484, 489, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 571, 572], "12": [480, 484, 489, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 571, 572], "deprecated_element_has_exact_replac": [480, 484, 489, 492, 510, 513, 516, 522, 523, 524, 525, 534, 539, 544, 545, 549, 571, 572, 628, 644], "provenance_properti": [480, 484, 489, 492, 510, 512, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 570, 571, 572, 573, 574, 576, 577, 580, 587, 601, 614, 617, 650, 664, 668, 670], "wasattributedto": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "structured_pattern": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "orcid_regex": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "interpol": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "partial_match": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 568, 573], "pav": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 570, 576, 621, 677], "createdon": [480, 484, 492, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 570], "authoredon": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 576], "importedfrom": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 621], "0000116": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 587], "narr": [480, 484, 492, 509, 510, 513, 516, 525, 534, 537, 539, 544, 545, 549, 579, 587, 671], "0000117": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 668], "0000119": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 580], "0000234": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 650], "0000412": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 614], "0000233": [480, 484, 492, 510, 513, 516, 525, 534, 539, 544, 545, 549, 670], "hasobonamespac": [480, 484, 492, 506, 513, 516, 525, 534, 539, 544, 545, 549, 606, 1125], "informative_properti": [480, 484, 489, 492, 506, 512, 513, 516, 525, 534, 537, 539, 544, 545, 549, 561, 562, 564, 566, 578, 581, 593, 603, 608, 613, 617, 630, 631, 651], "sdo": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 613], "0000112": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 593], "0000232": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 574], "0000114": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 603], "foaf": [480, 484, 492, 512, 513, 516, 525, 534, 539, 544, 545, 549, 581, 651, 1126, 1203], "guidelin": [480, 489, 509, 513, 516, 525, 545, 629, 1110, 1133, 1138, 1152], "core_properti": [480, 484, 489, 492, 509, 513, 516, 525, 526, 534, 537, 539, 544, 545, 549, 579, 612, 617, 629], "aristotelian": [480, 509, 513, 516, 525, 545, 579, 1123], "logical_pred": [480, 484, 492, 493, 513, 516, 525, 526, 534, 537, 539, 540, 541, 544, 545, 546, 549, 553, 560, 565, 584, 585, 586, 589, 590, 599, 617, 619, 620, 635, 636, 637, 638, 647, 648, 649, 653, 655, 656, 658, 663, 665, 672, 674], "designates_typ": [480, 484, 492, 513, 516, 525, 526, 534, 537, 539, 544, 545, 546, 549, 672], "gitlab": [481, 482], "devop": [481, 482], "allotrope_framework_term_curation_style_guid": [481, 482], "pdf": [481, 482, 499], "changenot": [481, 617, 618], "reifi": [483, 617, 642, 652], "relational_rol": [483, 489, 555, 556, 557, 642, 652], "represents_relationship": [483, 489], "shorthand": [484, 534, 544, 549, 617, 1116, 1118, 1194], "is_class_level": [484, 534, 539, 544, 549, 617], "is_metadata_tag": [484, 534, 539, 544, 549, 617], "annotatedproperti": [484, 489, 617, 657], "has_synonym_typ": [484, 489, 617], "bundl": [485, 617, 1124, 1145, 1151], "root": [486, 617, 1116, 1140, 1178, 1182, 1184, 1191], "anonymousclassexpress": [486, 541, 617], "anonym": [487, 541, 617, 846, 852, 853, 886, 887, 1123, 1178], "annotatedtarget": [488, 489, 617, 657], "statement": [489, 555, 556, 557, 558, 564, 571, 575, 577, 591, 598, 601, 604, 611, 617, 622, 623, 626, 629, 641, 659, 664, 675, 846, 886, 915, 916, 945, 955, 957, 1116, 1163, 1174, 1178], "annotatedsourc": [489, 526, 617, 657], "is_inf": [489, 617], "has_axiom_label": [489, 546, 617, 654], "is_a_defining_property_chain_axiom": [489, 617], "is_a_defining_property_chain_axiom_where_second_argument_is_reflex": [489, 617], "date_retriev": [489, 617, 654], "external_ontologi": [489, 617], "reification_pred": [489, 555, 556, 557, 617], "dc": [489, 537, 664], "0010000": [489, 601], "ro": [489, 492, 534, 549, 622, 623, 640, 667, 940, 943, 959, 960, 963, 1110, 1116, 1123, 1127, 1141, 1142, 1146, 1148, 1178], "0002581": [489, 622], "0002582": [489, 623], "hassynonymtyp": [489, 611], "never_in_taxon": [492, 617], "disconnected_from": [492, 617, 660], "has_rank": [492, 546, 617], "disjointwith": [492, 493, 534, 540, 541, 549, 617, 632], "intersectionof": [492, 493, 541, 617, 632], "complementof": [492, 493, 541, 617, 632], "oneof": [492, 493, 541, 617, 632], "unionof": [492, 493, 541, 617, 632], "has_ontology_root_term": [492, 537, 617, 618], "0002161": [492, 640, 943, 959], "shortcut_annotation_properti": [492, 583, 617], "ncbitaxon": [492, 513, 609, 944, 1142, 1151, 1177, 1178], "taxslim": [492, 609], "propertyexpress": [492, 493, 501, 534, 539, 541, 549, 584, 617, 648], "match_aspect": [492, 493, 534, 541, 549, 559, 563, 575, 589, 590, 592, 617, 632, 633, 639, 658], "extens": [499, 617, 1118, 1119, 1123, 1127, 1133, 1147, 1171], "shacl": [499, 617, 1038, 1040, 1065, 1103, 1135, 1193], "definitionconstraint": 499, "dcc": 499, "problem": [499, 1045, 1075, 1193, 1203], "definitionpres": 499, "s0": 499, "s1": 499, "harmon": 499, "genusdifferentiaform": 499, "s3": [499, 1135, 1146, 1194], "singlegenu": 499, "circular": [499, 1123], "s7": 499, "matchtextandlog": 499, "s11": 499, "matchtextandlogicalgenusnotintext": 499, "matchtextandlogicaldifferentianotintext": 499, "matchtextandrefer": 499, "s20": 499, "cite": [499, 1133], "referencenotfound": 499, "citat": 499, "referenceisretract": 499, "retract": [499, 1063, 1078], "incatool": [499, 1110, 1116, 1128, 1135, 1184, 1203], "kit": [499, 1110, 1112, 1119, 1128, 1133, 1184, 1203], "305": 499, "philpap": 499, "archiv": 499, "sepgfw": 499, "annotationpropertymixin": [506, 507, 508, 509, 510, 511, 512, 617], "namedth": [506, 507, 508, 509, 510, 511, 512, 514, 515, 531, 545, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 587, 588, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 613, 614, 616, 617, 621, 629, 639, 650, 651, 659, 662, 668, 669, 670, 672], "slot_condit": [507, 530, 536], "any_of": [507, 681, 721], "none_of": [507, 530, 681, 721], "absolut": [509, 579, 617, 629], "whose": [511, 514, 515, 531, 554, 588, 602, 604, 605, 610, 617, 846, 886, 920, 1116, 1117, 1127, 1148], "member": [511, 514, 515, 531, 554, 588, 602, 604, 605, 610, 617, 632], "style": [511, 702, 1123, 1133, 1193], "four": 511, "subproperti": 511, "9606": [513, 1169], "transit": [514, 515, 531, 549, 554, 559, 561, 563, 564, 566, 567, 568, 570, 571, 572, 573, 574, 575, 576, 579, 580, 581, 582, 584, 586, 587, 588, 590, 592, 593, 595, 596, 597, 600, 602, 603, 604, 605, 606, 607, 610, 612, 613, 614, 616, 617, 620, 621, 624, 625, 627, 628, 629, 639, 650, 651, 653, 656, 659, 661, 662, 667, 668, 669, 670, 672, 1112, 1134, 1180, 1184, 1185, 1190], "0000101": 516, "tidi": 521, "ncit": [522, 523, 524, 1117, 1178], "p378": 522, "p384": 523, "p383": 524, "temporal_interpret": [525, 534, 549, 617], "auto": [530, 536, 617, 1178, 1180, 1183, 1187, 1188, 1190, 1193], "classifi": [530, 536, 617, 1127], "classification_rul": [530, 536], "jsonobj": [530, 1188, 1192, 1204], "is_cycl": [534, 549, 617], "is_transit": [534, 549, 617, 1127], "equivalentproperti": [534, 539, 549, 617, 632, 634], "inverseof": [534, 539, 549, 617, 632], "0001900": [534, 549, 667], "licens": [537, 546, 617, 618], "versioniri": [537, 617, 678, 839, 921], "0000700": [537, 608], "version_properti": [537, 617, 676, 677], "onproperti": [540, 541, 617, 632], "allvaluesfrom": [541, 617, 632], "proteg": 578, "defaultlanguag": [617, 618], "distinctmemb": [617, 632], "hasvalu": [617, 632], "maxqualifiedcardin": [617, 632], "mincardin": [617, 632], "minqualifiedcardin": [617, 632], "ncit_definition_sourc": 617, "ncit_term_sourc": 617, "ncit_term_typ": 617, "oboinowl_id": 617, "oboinowl_ontologi": 617, "lifecycl": [617, 645, 1125], "onclass": [617, 632], "qualifiedcardin": [617, 632], "samea": [617, 632, 634, 1124], "definitionconstraintcompon": 617, "irityp": 617, "tidystr": 617, "urlliter": 617, "allotropepermittedprofil": 617, "allotroperequiredprofil": 617, "gopermittedprofil": 617, "gorecommendedprofil": 617, "gorequiredprofil": 617, "obipermittedprofil": 617, "obirequiredprofil": 617, "dce": 630, "OR": [680, 1112, 1130, 1183, 1194, 1204], "xor": 680, "ontosearch": [681, 696, 697, 699, 700, 708, 709, 710, 711, 712, 713, 714, 715, 720, 722, 723, 724, 726, 727, 728, 734, 735, 736, 737, 738, 740, 741, 742, 743, 744], "all_of": [681, 721], "path_to": [681, 721], "searchbaseconfigur": [681, 696, 700, 710, 711, 712, 713, 714, 720, 721, 722, 723, 724, 726, 735, 740, 741, 743], "descendant_of": 689, "ancestor_of": 689, "proper_descendant_of": 689, "proper_ancestor_of": 689, "parent_of": 689, "child_of": 689, "travers": [689, 696, 721, 1112, 1116, 1121, 1134, 1140, 1148, 1184], "graphfunct": [696, 721, 744], "graph_pred": [696, 721], "search_term": [696, 697, 721, 1188], "searchterm": [697, 721, 741], "searchtermsyntax": [697, 721, 743, 1159, 1188, 1204], "searchproperti": [697, 721, 735, 1188], "return": [697, 721, 726, 993, 1005, 1008, 1117, 1120, 1123, 1124, 1125, 1126, 1127, 1134, 1140, 1143, 1151, 1152, 1160, 1171, 1177, 1178, 1180, 1183, 1184, 1185, 1186, 1187, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1204], "batch": [697, 721, 726, 1152, 1175], "cursor": [697, 700, 721], "exce": [697, 721], "iterat": [697, 721], "is_parti": [697, 721, 722, 1188], "full": [697, 699, 721, 724, 727, 1110, 1112, 1120, 1124, 1129, 1134, 1140, 1142, 1151, 1184, 1191], "span": [697, 721, 724, 1116, 1177], "is_complet": [697, 721], "include_obsoletes_in_result": [697, 721], "is_fuzzi": [697, 721], "force_case_insensit": [697, 721], "forc": [697, 714, 721, 1146], "insensit": [697, 714, 721], "complexqueri": [697, 708, 709, 710, 721, 728, 734], "pathexpress": [697, 715, 721, 740, 744], "searchresultset": [697, 699, 712, 713, 721, 737, 738], "renam": [697, 1171], "searchconfigur": [697, 1159, 1182, 1188, 1204], "parameter": [697, 721, 739, 741, 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"class-textannotation"]], "Class: TextAnnotationConfiguration": [[993, "class-textannotationconfiguration"]], "Class: TextAnnotationResultSet": [[994, "class-textannotationresultset"]], "Class: TextualElement": [[995, "class-textualelement"]], "Slot: confidence": [[1002, "slot-confidence"], [1068, "slot-confidence"]], "Text Annotator Datamodel": [[1005, "text-annotator-datamodel"]], "Slot: info": [[1006, "slot-info"], [1076, "slot-info"]], "Slot: is_longest_match": [[1007, "slot-is-longest-match"]], "Slot: match_string": [[1009, "slot-match-string"]], "Slot: match_type": [[1010, "slot-match-type"]], "Slot: matches_whole_text": [[1011, "slot-matches-whole-text"]], "Slot: model": [[1012, "slot-model"]], "Slot: object_aliases": [[1013, "slot-object-aliases"]], "Slot: object_categories": [[1014, "slot-object-categories"]], "Slot: parent_document": [[1018, "slot-parent-document"]], "Slot: source_text": [[1020, "slot-source-text"]], "Slot: subject_end": [[1022, "slot-subject-end"]], "Slot: subject_start": [[1025, "slot-subject-start"]], "Slot: subject_text_id": [[1026, "slot-subject-text-id"]], "Slot: text": [[1027, "slot-text"]], "text-annotator": [[1028, "text-annotator"]], "Slot: token_exclusion_list": [[1029, "slot-token-exclusion-list"]], "Class: ConstraintComponent": [[1032, "class-constraintcomponent"]], "Class: DefinitionValidationResult": [[1038, "class-definitionvalidationresult"]], "Class: ExternalReferenceValidationResult": [[1040, "class-externalreferencevalidationresult"]], "Class: MappingValidationResult": [[1045, "class-mappingvalidationresult"]], "Class: NamedResource": [[1046, "class-namedresource"]], "Class: RepairConfiguration": [[1051, "class-repairconfiguration"]], "Class: RepairOperation": [[1052, "class-repairoperation"]], "Class: RepairReport": [[1053, "class-repairreport"]], "Class: Report": [[1054, "class-report"]], "Class: Result": [[1055, "class-result"]], "Enum: SeverityOptions": [[1056, "enum-severityoptions"]], "Class: TypeSeverityKeyValue": [[1060, "class-typeseveritykeyvalue"]], "Class: ValidationConfiguration": [[1063, "class-validationconfiguration"]], "Class: ValidationReport": [[1064, "class-validationreport"]], "Class: ValidationResult": [[1065, "class-validationresult"]], "Enum: ValidationResultType": [[1066, "enum-validationresulttype"]], "Slot: documentation_objects": [[1071, "slot-documentation-objects"]], "Slot: dry_run": [[1072, "slot-dry-run"]], "Slot: http_response_code": [[1073, "slot-http-response-code"]], "Validation Results Data Model": [[1075, "validation-results-data-model"]], "Slot: instantiates": [[1077, "slot-instantiates"]], "Slot: lookup_references": [[1078, "slot-lookup-references"]], "Slot: max_number_results_per_type": [[1079, "slot-max-number-results-per-type"]], "Slot: modified": [[1080, "slot-modified"]], "Slot: number_of_attempts": [[1081, "slot-number-of-attempts"]], "Slot: object_info": [[1084, "slot-object-info"]], "Slot: object_str": [[1085, "slot-object-str"]], "Slot: problem": [[1088, "slot-problem"]], "Slot: prompt_info": [[1089, "slot-prompt-info"]], "Slot: proposed_new_definition": [[1090, "slot-proposed-new-definition"]], "Slot: repairs": [[1091, "slot-repairs"]], "Slot: schema_path": [[1093, "slot-schema-path"]], "Slot: severity": [[1094, "slot-severity"]], "Slot: subject_info": [[1098, "slot-subject-info"]], "Slot: successful": [[1099, "slot-successful"]], "Slot: suggested_modifications": [[1100, "slot-suggested-modifications"]], "Slot: suggested_predicate": [[1101, "slot-suggested-predicate"]], "Slot: time_checked": [[1102, "slot-time-checked"]], "Slot: type_severity_map": [[1104, "slot-type-severity-map"]], "Slot: validation_configuration": [[1107, "slot-validation-configuration"]], "validaton-results": [[1108, "validaton-results"]], "FAQ: Architecture and Design": [[1109, "faq-architecture-and-design"]], "What is an interface?": [[1109, "what-is-an-interface"]], "What is a Data Model?": [[1109, "what-is-a-data-model"]], "What is an iterator and why does OAK use them so much?": [[1109, "what-is-an-iterator-and-why-does-oak-use-them-so-much"]], "FAQ: Command Line": [[1110, "faq-command-line"]], "How do I see a list of commands?": [[1110, "how-do-i-see-a-list-of-commands"]], "How do I get help on a command?": [[1110, "how-do-i-get-help-on-a-command"]], "How do I get more examples of command line usage?": [[1110, "how-do-i-get-more-examples-of-command-line-usage"]], "I want to query an ontology, what do I pass for the --input option?": [[1110, "i-want-to-query-an-ontology-what-do-i-pass-for-the-input-option"]], "Why do I get a \u201cno such option\u201d error when I pass the \u201c\u2013input\u201d option?": [[1110, "why-do-i-get-a-no-such-option-error-when-i-pass-the-input-option"]], "What do the codes \u201ci\u201d and \u201cp\u201d mean?": [[1110, "what-do-the-codes-i-and-p-mean"]], "Can I pass a list of IDs (CURIEs) as input to a command?": [[1110, "can-i-pass-a-list-of-ids-curies-as-input-to-a-command"]], "Can I pass entity labels as command inputs?": [[1110, "can-i-pass-entity-labels-as-command-inputs"]], "Can I pass lexical queries as command inputs?": [[1110, "can-i-pass-lexical-queries-as-command-inputs"]], "Can I pass the results of graph queries as command inputs?": [[1110, "can-i-pass-the-results-of-graph-queries-as-command-inputs"]], "Can I make boolean combinations of query terms?": [[1110, "can-i-make-boolean-combinations-of-query-terms"]], "Can I chain commands together, unix-style?": [[1110, "can-i-chain-commands-together-unix-style"]], "What does the symbol @ mean in a query term list": [[1110, "what-does-the-symbol-mean-in-a-query-term-list"]], "Can I use the command line to visualize a subgraph?": [[1110, "can-i-use-the-command-line-to-visualize-a-subgraph"]], "Is there an over-arching philosophy or set of design principles to the OAK command line?": [[1110, "is-there-an-over-arching-philosophy-or-set-of-design-principles-to-the-oak-command-line"]], "The command isn\u2019t working the way I expected - how do I get help?": [[1110, "the-command-isn-t-working-the-way-i-expected-how-do-i-get-help"]], "FAQ: Contributing": [[1111, "faq-contributing"]], "How can I contribute?": [[1111, "how-can-i-contribute"]], "How do I stay involved?": [[1111, "how-do-i-stay-involved"]], "FAQ: General": [[1112, "faq-general"]], "What is OAK?": [[1112, "what-is-oak"]], "Are there any tutorials for OAK?": [[1112, "are-there-any-tutorials-for-oak"]], "Are there runnable examples of how to use OAK?": [[1112, "are-there-runnable-examples-of-how-to-use-oak"]], "I am familiar with both Python and Ontologies. Where should I start?": [[1112, "i-am-familiar-with-both-python-and-ontologies-where-should-i-start"]], "I find ontologies confusing. Is there a general guide to help me?": [[1112, "i-find-ontologies-confusing-is-there-a-general-guide-to-help-me"]], "Why is it called OAK?": [[1112, "why-is-it-called-oak"]], "How do I install OAK?": [[1112, "how-do-i-install-oak"]], "Can I use OAK if I don\u2019t know Python?": [[1112, "can-i-use-oak-if-i-don-t-know-python"]], "Can I contribute to OAK?": [[1112, "can-i-contribute-to-oak"]], "Is OAK just for bio-ontologies?": [[1112, "is-oak-just-for-bio-ontologies"]], "Can OAK access ontologies in ontology portals such as MatPortal or BioPortal?": [[1112, "can-oak-access-ontologies-in-ontology-portals-such-as-matportal-or-bioportal"]], "Can OAK access ontologies in triplestores such as OntoBee or Ubergraph?": [[1112, "can-oak-access-ontologies-in-triplestores-such-as-ontobee-or-ubergraph"]], "Can OAK access local files?": [[1112, "can-oak-access-local-files"]], "Can OAK access OBO Format files?": [[1112, "can-oak-access-obo-format-files"]], "Does OAK support all of OWL?": [[1112, "does-oak-support-all-of-owl"]], "Does OAK support reasoning?": [[1112, "does-oak-support-reasoning"]], "Can I use OAK to do graph queries over ontologies?": [[1112, "can-i-use-oak-to-do-graph-queries-over-ontologies"]], "Can I use OAK to do lexical search?": [[1112, "can-i-use-oak-to-do-lexical-search"]], "Can I use OAK as a text annotator?": [[1112, "can-i-use-oak-as-a-text-annotator"]], "FAQ": [[1113, "faq"]], "FAQ: Ontologies": [[1114, "faq-ontologies"]], "What is an ontology?": [[1114, "what-is-an-ontology"]], "Do we need ontologies now we have ChatGPT?": [[1114, "do-we-need-ontologies-now-we-have-chatgpt"]], "What is OWL?": [[1114, "what-is-owl"]], "What is OBO Format?": [[1114, "what-is-obo-format"]], "What is OBO": [[1114, "what-is-obo"]], "What\u2019s a synonym and how do I access them?": [[1114, "what-s-a-synonym-and-how-do-i-access-them"]], "Ancestor statistics": [[1114, "id2"], [1140, "id2"], [1146, "id1"]], "FAQ: Troubleshooting": [[1115, "faq-troubleshooting"]], "Why do I get a \u201cError: No such option: -i\u201d message": [[1115, "why-do-i-get-a-error-no-such-option-i-message"]], "How do I get a BioPortal API key?": [[1115, "how-do-i-get-a-bioportal-api-key"]], "My OBO Format file won\u2019t parse": [[1115, "my-obo-format-file-won-t-parse"]], "My OWL file takes too long to load": [[1115, "my-owl-file-takes-too-long-to-load"]], "My cached SQLite ontology is out of date": [[1115, "my-cached-sqlite-ontology-is-out-of-date"]], "I don\u2019t understand the interface/method I want to use": [[1115, "i-don-t-understand-the-interface-method-i-want-to-use"]], "Glossary": [[1116, "glossary"]], "Aliases and Synonyms": [[1117, "aliases-and-synonyms"]], "Use Cases": [[1117, "use-cases"]], "Search": [[1117, "search"], [1140, "search"], [1160, "search"], [1175, "search"]], "Text mining and NLP": [[1117, "text-mining-and-nlp"]], "Different aliases for different communities": [[1117, "different-aliases-for-different-communities"]], "Different Languages": [[1117, "different-languages"]], "Different approaches to representing synonym metadata": [[1117, "different-approaches-to-representing-synonym-metadata"]], "Representation of synonyms in OAK": [[1117, "representation-of-synonyms-in-oak"]], "Simple Core Model": [[1117, "simple-core-model"]], "HPO basic aliases": [[1117, "id1"]], "Obo Graph Data Model": [[1117, "obo-graph-data-model"]], "HPO full aliases": [[1117, "id2"]], "Associations and Curated Annotations": [[1118, "associations-and-curated-annotations"]], "Background": [[1118, "background"], [1128, "background"]], "Association support in OAK": [[1118, "association-support-in-oak"]], "Data Model": [[1118, "data-model"], [1128, "data-model"], [1183, "data-model"]], "Selecting association sources": [[1118, "selecting-association-sources"]], "Further reading": [[1118, "further-reading"], [1120, "further-reading"], [1123, "further-reading"], [1124, "further-reading"], [1126, "further-reading"], [1128, "further-reading"]], "OAK Basics": [[1119, "oak-basics"]], "What is an ontology and why would I want to access one?": [[1119, "what-is-an-ontology-and-why-would-i-want-to-access-one"]], "Ontology languages, standards, and formats": [[1119, "ontology-languages-standards-and-formats"]], "Core OAK concepts": [[1119, "core-oak-concepts"]], "Identifying entities: CURIEs and URIs": [[1120, "curies-and-uris"]], "Prefix maps": [[1120, "prefix-maps"]], "Querying prefixmaps": [[1120, "querying-prefixmaps"]], "Example prefixes": [[1120, "id1"]], "Non-default prefixmaps": [[1120, "non-default-prefixmaps"]], "Structure of identifiers": [[1120, "structure-of-identifiers"]], "The OAK Guide": [[1121, "the-oak-guide"]], "Learning More": [[1122, "learning-more"]], "Logical Definitions": [[1123, "logical-definitions"]], "Logical Definitions in OWL": [[1123, "logical-definitions-in-owl"]], "Genus-differentia form logical definitions": [[1123, "genus-differentia-form-logical-definitions"]], "The Obo Graphs Model": [[1123, "the-obo-graphs-model"]], "Querying for logical definitions in OAK": [[1123, "querying-for-logical-definitions-in-oak"]], "uberon nail logical definitions": [[1123, "id2"]], "Reasoning using logical definitions": [[1123, "reasoning-using-logical-definitions"]], "Logical definitions and design patterns": [[1123, "logical-definitions-and-design-patterns"]], "Generating logical definitions": [[1123, "generating-logical-definitions"]], "Analyzing logical definitions": [[1123, "analyzing-logical-definitions"]], "Validating logical definitions": [[1123, "validating-logical-definitions"]], "Mappings and Cross-References": [[1124, "mappings-and-cross-references"]], "Mappings in OAK": [[1124, "mappings-in-oak"]], "uberon sssom mappings": [[1124, "id2"]], "In Python": [[1124, "in-python"]], "Directionality of mappings": [[1124, "directionality-of-mappings"]], "Support for SSSOM": [[1124, "support-for-sssom"]], "Generating Mappings": [[1124, "generating-mappings"]], "Obsoletion": [[1125, "obsoletion"]], "Looking up obsoleted entities": [[1125, "looking-up-obsoleted-entities"]], "Conventions and standards": [[1125, "conventions-and-standards"]], "obsolete entities should not be in the signature of any logical axiom": [[1125, "obsolete-entities-should-not-be-in-the-signature-of-any-logical-axiom"]], "obsolete entities should be accompanied by metadata that provides additional context for humans and machines": [[1125, "obsolete-entities-should-be-accompanied-by-metadata-that-provides-additional-context-for-humans-and-machines"]], "Merged entities": [[1125, "merged-entities"]], "Further Reading": [[1125, "further-reading"]], "Primary Labels": [[1126, "primary-labels"]], "Looking up labels": [[1126, "looking-up-labels"]], "Custom label annotation properties": [[1126, "custom-label-annotation-properties"]], "Multilingual ontologies": [[1126, "multilingual-ontologies"]], "Other edge cases": [[1126, "other-edge-cases"]], "Relationships and Graphs": [[1127, "relationships-and-graphs"]], "Exploring relationships": [[1127, "exploring-relationships"]], "Graph Traversal and Relation Graph Reasoning": [[1127, "graph-traversal-and-relation-graph-reasoning"]], "Graph Traversal Strategies": [[1127, "graph-traversal-strategies"]], "Examples of where entailment yields more": [[1127, "examples-of-where-entailment-yields-more"]], "Examples of where graph traversal yields more ancestors than entailment": [[1127, "examples-of-where-graph-traversal-yields-more-ancestors-than-entailment"]], "Which strategy should I use?": [[1127, "which-strategy-should-i-use"]], "A note on entailed direct edges": [[1127, "a-note-on-entailed-direct-edges"]], "Computing Similarity between Entities": [[1128, "computing-similarity-between-entities"]], "Concepts": [[1128, "concepts"]], "Jaccard Similarity": [[1128, "jaccard-similarity"]], "Jaccard Similarity of ontology terms": [[1128, "jaccard-similarity-of-ontology-terms"]], "Information Content": [[1128, "information-content"]], "Ensemble Scoring of term pairs": [[1128, "ensemble-scoring-of-term-pairs"]], "Other similarity measures": [[1128, "other-similarity-measures"]], "Aggregate measures for comparing entities": [[1128, "aggregate-measures-for-comparing-entities"]], "Vector-based approaches": [[1128, "vector-based-approaches"]], "Implementations": [[1128, "implementations"], [1151, "implementations"], [1163, "implementations"]], "Default Implementation": [[1128, "default-implementation"]], "Ubergraph": [[1128, "ubergraph"], [1142, "ubergraph"]], "Semsimian": [[1128, "semsimian"]], "Companion Notebooks": [[1128, "companion-notebooks"]], "FHIR Conversions": [[1129, "fhir-conversions"]], "CLI": [[1129, "cli"]], "Config file": [[1129, "config-file"]], "How-To Guides": [[1130, "how-to-guides"]], "How to use Large Language Models (LLMs) with OAK": [[1133, "how-to-use-large-language-models-llms-with-oak"]], "LLM frameworks that use OAK": [[1133, "llm-frameworks-that-use-oak"]], "OntoGPT": [[1133, "ontogpt"]], "CurateGPT": [[1133, "curategpt"]], "Talisman": [[1133, "talisman"]], "Using OAK in conjunction with existing LLM tools": [[1133, "using-oak-in-conjunction-with-existing-llm-tools"]], "OAK LLM Adapter": [[1133, "oak-llm-adapter"]], "Annotation": [[1133, "annotation"], [1162, "annotation"], [1164, "annotation"], [1169, "annotation"]], "Suggesting Definitions": [[1133, "suggesting-definitions"]], "Validating Definitions": [[1133, "validating-definitions"]], "Validating Mappings": [[1133, "validating-mappings"]], "Selecting alternative models": [[1133, "selecting-alternative-models"]], "Installing LLM plugins": [[1133, "installing-llm-plugins"]], "Mixtral via Ollama and LiteLLM": [[1133, "mixtral-via-ollama-and-litellm"]], "Mixtral via groq and LiteLLM": [[1133, "mixtral-via-groq-and-litellm"]], "Using the OAK Expression Language": [[1134, "using-the-oak-expression-language"]], "Basics": [[1134, "basics"], [1140, "basics"]], "IDs (CURIEs)": [[1134, "ids-curies"]], "Lists of IDs": [[1134, "lists-of-ids"]], "Label Queries": [[1134, "label-queries"]], "Search Queries": [[1134, "search-queries"]], "Exact Match": [[1134, "exact-match"]], "Starts With": [[1134, "starts-with"]], "Contains": [[1134, "contains"]], "Regular Expressions": [[1134, "regular-expressions"]], "Graph Queries": [[1134, "graph-queries"]], "Ancestors": [[1134, "ancestors"]], "Descendants": [[1134, "descendants"]], "MRCAs": [[1134, "mrcas"]], "Boolean Combinations": [[1134, "boolean-combinations"], [1204, "boolean-combinations"]], "AND": [[1134, "and"]], "OR": [[1134, "or"]], "NOT": [[1134, "not"]], "Nesting": [[1134, "nesting"]], "Using files and redirects": [[1134, "using-files-and-redirects"]], "IDFILE": [[1134, "idfile"]], "STDIN": [[1134, "stdin"]], "Other Operators": [[1134, "other-operators"]], "IN": [[1134, "in"]], "FILTER": [[1134, "filter"]], "NR": [[1134, "nr"]], "Others": [[1134, "others"]], "How to Validate an OBO ontology using Obo Metadata Ontology schema": [[1135, "how-to-validate-an-obo-ontology-using-obo-metadata-ontology-schema"]], "Steps": [[1135, "steps"]], "Step 1: Obtain the sqlite version of the ontology": [[1135, "step-1-obtain-the-sqlite-version-of-the-ontology"]], "Step 2: Install oaklib": [[1135, "step-2-install-oaklib"]], "Step 3: Validate an individual ontology": [[1135, "step-3-validate-an-individual-ontology"]], "Step 3 (alternative): Validate multiple ontologies": [[1135, "step-3-alternative-validate-multiple-ontologies"]], "Caveats": [[1135, "caveats"]], "Using your own schema": [[1135, "using-your-own-schema"]], "How this works": [[1135, "how-this-works"], [1144, "how-this-works"]], "Analysis": [[1135, "analysis"]], "How to write a plugin": [[1137, "how-to-write-a-plugin"]], "What is a plugin?": [[1137, "what-is-a-plugin"]], "An example plugin": [[1137, "an-example-plugin"]], "Creating a plugin": [[1137, "creating-a-plugin"]], "Discuss on the issue tracker": [[1137, "discuss-on-the-issue-tracker"]], "Create a new project": [[1137, "create-a-new-project"], [1141, "create-a-new-project"]], "Implement one or more interfaces": [[1137, "implement-one-or-more-interfaces"]], "Implement a selector": [[1137, "implement-a-selector"]], "Write tests": [[1137, "write-tests"]], "Ontology Access Kit (OAK) Documentation": [[1138, "ontology-access-kit-oak-documentation"]], "Indices and tables": [[1138, "indices-and-tables"]], "Tutorial": [[1139, "tutorial"]], "Part 1: Getting Started": [[1140, "part-1-getting-started"]], "Installation": [[1140, "installation"]], "Install from PyPI": [[1140, "install-from-pypi"]], "Run the OAK command": [[1140, "run-the-oak-command"]], "Query the OBO Library": [[1140, "query-the-obo-library"]], "Working with local files": [[1140, "working-with-local-files"]], "Introduction to graphs and trees": [[1140, "introduction-to-graphs-and-trees"]], "Fetching ancestors": [[1140, "fetching-ancestors"]], "Predicate Abbreviations": [[1140, "predicate-abbreviations"]], "Ancestor Statistics": [[1140, "ancestor-statistics"]], "Oak Trees": [[1140, "oak-trees"]], "Advanced Search": [[1140, "advanced-search"]], "Using search terms as parameters": [[1140, "using-search-terms-as-parameters"]], "Chaining Commands": [[1140, "chaining-commands"]], "Visualization": [[1140, "visualization"]], "Using other backends": [[1140, "using-other-backends"]], "Using Ubergraph": [[1140, "using-ubergraph"]], "Using Ontobee": [[1140, "using-ontobee"]], "Using BioPortal and OntoPortal": [[1140, "using-bioportal-and-ontoportal"]], "Annotate results": [[1140, "id3"]], "Using OLS": [[1140, "using-ols"]], "OLS SSSOM": [[1140, "id4"]], "Next steps": [[1140, "next-steps"]], "Part 2: Basic Python": [[1141, "part-2-basic-python"]], "Install Poetry": [[1141, "install-poetry"]], "Basic Concepts": [[1141, "basic-concepts"]], "Code the first example": [[1141, "code-the-first-example"]], "Extending the example": [[1141, "extending-the-example"]], "Part 3: Triplestore Backends": [[1142, "part-3-triplestore-backends"]], "Triplestore Concepts": [[1142, "triplestore-concepts"]], "Connecting": [[1142, "connecting"], [1175, "connecting"]], "Basic Operations": [[1142, "basic-operations"]], "Relationships": [[1142, "relationships"]], "Part 4: OboGraphs": [[1143, "part-4-obographs"]], "OboGraphs": [[1143, "obographs"]], "OboGraph Interface": [[1143, "obograph-interface"], [1184, "obograph-interface"]], "Code examples": [[1143, "code-examples"]], "Part 5: Graph Visualization": [[1144, "part-5-graph-visualization"]], "Install Graphviz": [[1144, "install-graphviz"]], "Install OBOGraphViz": [[1144, "install-obographviz"]], "Command Line Usage": [[1144, "command-line-usage"], [1154, "command-line-usage"], [1159, "command-line-usage"]], "Programmatic usage": [[1144, "programmatic-usage"]], "Part 6: Working With OWL": [[1145, "part-6-working-with-owl"]], "OWL Datamodel": [[1145, "owl-datamodel"]], "OwlInterface": [[1145, "owlinterface"]], "ROBOT Plugin": [[1145, "robot-plugin"]], "Part 7: SQLite files": [[1146, "part-7-sqlite-files"]], "Download a SQLite file": [[1146, "download-a-sqlite-file"]], "Example": [[1146, "example"]], "Fetching ready-made SQLite files": [[1146, "fetching-ready-made-sqlite-files"]], "Building your own SQLite files": [[1146, "building-your-own-sqlite-files"]], "With docker": [[1146, "with-docker"]], "Without docker": [[1146, "without-docker"]], "Validating an ontology": [[1146, "validating-an-ontology"]], "Other RDBMSs": [[1146, "other-rdbmss"]], "Python ORM": [[1146, "python-orm"]], "Part 8: Applying Changes to Ontologies": [[1147, "part-8-applying-changes-to-ontologies"]], "About KGCL": [[1147, "about-kgcl"]], "Example: Sqlite3": [[1147, "example-sqlite3"]], "Example: OBO Files": [[1147, "example-obo-files"]], "Introduction": [[1148, "introduction"]], "Basic Python Example": [[1148, "basic-python-example"]], "Basic Command Line Example": [[1148, "basic-command-line-example"]], "Jupyter Notebooks": [[1150, "jupyter-notebooks"]], "Architecture": [[1151, "architecture"]], "Ontology Interfaces": [[1151, "ontology-interfaces"]], "Other Interfaces": [[1151, "other-interfaces"]], "Example: OWL Ontology Interface": [[1151, "example-owl-ontology-interface"]], "Partial and Complete Implementation": [[1151, "partial-and-complete-implementation"]], "Best Practice": [[1152, "best-practice"]], "External Services": [[1152, "external-services"]], "Iterators": [[1152, "iterators"]], "Weaving calls together": [[1152, "weaving-calls-together"]], "Chunking": [[1152, "chunking"]], "Abstract Class": [[1153, "abstract-class"]], "Converters": [[1154, "converters"]], "Converting from Obo Graphs": [[1154, "converting-from-obo-graphs"]], "OBO Graph to CX Converter": [[1155, "obo-graph-to-cx-converter"]], "OBO Graph to FHIR Converter": [[1156, "obo-graph-to-fhir-converter"]], "OBO Graph to OBO Format Converter": [[1157, "obo-graph-to-obo-format-converter"]], "OBO Graph to OWL Converter": [[1158, "obo-graph-to-owl-converter"]], "Aggregator Adapter": [[1159, "aggregator-adapter"]], "Documentation": [[1159, "documentation"], [1167, "documentation"]], "Bioportal Adapter": [[1160, "bioportal-adapter"]], "API Keys": [[1160, "api-keys"]], "Command Line Examples": [[1160, "command-line-examples"], [1162, "command-line-examples"], [1164, "command-line-examples"], [1169, "command-line-examples"], [1171, "command-line-examples"]], "Code": [[1160, "code"], [1162, "code"], [1164, "code"], [1165, "code"], [1166, "code"], [1168, "code"], [1169, "code"], [1170, "code"], [1172, "code"], [1173, "code"], [1174, "code"], [1175, "code"]], "FunOwl Adapter": [[1161, "funowl-adapter"]], "Gilda Adapter": [[1162, "gilda-adapter"]], "LLM Adapter": [[1164, "llm-adapter"]], "Validation of Mappings": [[1164, "validation-of-mappings"]], "OBO Graph Adapter": [[1165, "obo-graph-adapter"]], "About": [[1165, "about"], [1168, "about"], [1170, "about"], [1172, "about"], [1175, "about"]], "Initialization": [[1165, "initialization"], [1170, "initialization"], [1172, "initialization"], [1174, "initialization"]], "Ontology Lookup Service (OLS) Adapter": [[1166, "ontology-lookup-service-ols-adapter"]], "Ontobee Adapter": [[1167, "ontobee-adapter"]], "Owlery Adapter": [[1168, "owlery-adapter"]], "PantherDB Adapter": [[1169, "pantherdb-adapter"]], "Enrichment": [[1169, "enrichment"]], "Mapping": [[1169, "mapping"]], "Pronto / OBO Files Adapter": [[1170, "pronto-obo-files-adapter"]], "ROBOT Template Adapter": [[1171, "robot-template-adapter"]], "Basic operations": [[1171, "basic-operations"]], "Applying KGCL commands": [[1171, "applying-kgcl-commands"]], "Simple OBO Adapter": [[1172, "simple-obo-adapter"]], "Sparql Adapter": [[1173, "sparql-adapter"]], "SQL Database Adapter": [[1174, "sql-database-adapter"]], "SQL Alchemy ORM Model": [[1174, "sql-alchemy-orm-model"]], "Ubergraph Adapter": [[1175, "ubergraph-adapter"]], "Interfaces Implemented": [[1175, "interfaces-implemented"]], "OAK Library Documentation": [[1176, "oak-library-documentation"]], "Association Provider Interface": [[1177, "association-provider-interface"]], "Command Line Use": [[1177, "command-line-use"], [1183, "command-line-use"]], "Basic Ontology Interface": [[1178, "basic-ontology-interface"]], "Example:": [[1178, "example"], [1178, "id2"], [1178, "id3"], [1178, "id4"]], "Class Enrichment Calculation Interface": [[1179, "class-enrichment-calculation-interface"]], "Differ Interface": [[1180, "differ-interface"]], "Dumper Interface": [[1181, "dumper-interface"]], "Interfaces": [[1182, "interfaces"]], "Mapping Provider Interface": [[1183, "mapping-provider-interface"]], "OWL Interface": [[1185, "owl-interface"]], "Patcher Interface": [[1186, "patcher-interface"]], "Relation Graph": [[1187, "relation-graph"]], "Search Interface": [[1188, "search-interface"]], "Semantic Similarity Interface": [[1189, "semantic-similarity-interface"]], "Subsetting": [[1190, "subsetting"]], "Summary Statistics": [[1191, "summary-statistics"]], "Text Annotator Interface": [[1192, "text-annotator-interface"]], "Validator Interface": [[1193, "validator-interface"]], "Schema Validation": [[1193, "schema-validation"]], "LLM-based validation": [[1193, "llm-based-validation"]], "Ontology Adapter Selectors": [[1194, "ontology-adapter-selectors"]], "Syntax": [[1194, "syntax"]], "Schemes": [[1194, "schemes"]], "pronto": [[1194, "pronto"]], "prontolib": [[1194, "prontolib"]], "sqlite": [[1194, "sqlite"]], "obosqlite": [[1194, "obosqlite"]], "ontobee": [[1194, "ontobee"]], "ols": [[1194, "ols"]], "bioportal": [[1194, "bioportal"]], "funowl": [[1194, "funowl"]], "Functions": [[1194, "functions"]], "oaklib.utilities.apikey_manager": [[1195, "module-oaklib.utilities.apikey_manager"]], "oaklib.utilities.graph.networkx_bridge": [[1196, "module-oaklib.utilities.graph.networkx_bridge"]], "Utilities for working with networkx": [[1196, "utilities-for-working-with-networkx"]], "oaklib.utilities.graph.relationship_walker": [[1197, "module-oaklib.utilities.graph.relationship_walker"]], "Utilities for traversing Ontology Graphs": [[1197, "utilities-for-traversing-ontology-graphs"]], "oaklib.utilities.lexical.lexical_indexer": [[1198, "module-oaklib.utilities.lexical.lexical_indexer"]], "Lexical Utilities": [[1198, "lexical-utilities"]], "oaklib.utilities.obograph_utils": [[1199, "module-oaklib.utilities.obograph_utils"]], "Utilities for the OBOGraph Datamodel": [[1199, "utilities-for-the-obograph-datamodel"]], "oaklib.utilities.subsets.slimmer_utils": [[1200, "module-oaklib.utilities.subsets.slimmer_utils"]], "Utilities for working with ontology subsets (slims)": [[1200, "utilities-for-working-with-ontology-subsets-slims"]], "oaklib.utilities.taxon.taxon_constraint_utils": [[1201, "module-oaklib.utilities.taxon.taxon_constraint_utils"]], "Utilities": [[1202, "utilities"]], "Layering on RDF/OWL": [[1203, "layering-on-rdf-owl"]], "CURIEs, URIs, and prefixmaps": [[1203, "curies-uris-and-prefixmaps"]], "Relationships 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"datatypeproperty": [[1116, "term-DatatypeProperty"]], "descendant": [[1116, "term-Descendant"]], "diff": [[1116, "term-Diff"]], "edge": [[1116, "term-Edge"]], "entailed": [[1116, "term-Entailed"]], "funowl": [[1116, "term-FunOWL"]], "functional syntax": [[1116, "term-Functional-Syntax"]], "graph": [[1116, "term-Graph"]], "graph traversal": [[1116, "term-Graph-Traversal"]], "is_a:": [[1116, "term-IS_A"]], "identifier": [[1116, "term-Identifier"]], "implementation": [[1116, "term-Implementation"]], "information content": [[1116, "term-Information-Content"]], "input selector": [[1116, "term-Input-Selector"]], "interface": [[1116, "term-Interface"]], "iterator": [[1116, "term-Iterator"]], "kgcl": [[1116, "term-KGCL"]], "label": [[1116, "term-Label"]], "logical definition": [[1116, "term-Logical-Definition"]], "mrca": [[1116, "term-MRCA"]], "mapping": [[1116, "term-Mapping"]], "name": [[1116, "term-Name"]], "named individual": [[1116, "term-Named-Individual"]], "node": [[1116, "term-Node"]], "obo format": [[1116, "term-OBO-Format"]], "obo graphs": [[1116, "term-OBO-Graphs"]], "ols": [[1116, "term-OLS"]], "owl": [[1116, "term-OWL"]], "owl annotation": [[1116, "term-OWL-Annotation"]], "object": [[1116, "term-Object"]], "object closure": [[1116, "term-Object-Closure"]], "objectproperty": [[1116, "term-ObjectProperty"]], "ontogpt": [[1116, "term-OntoGPT"]], "ontoportal": [[1116, "term-OntoPortal"]], "ontobee": [[1116, "term-Ontobee"]], "ontology": [[1116, "term-Ontology"]], "ontology element": [[1116, "term-Ontology-Element"]], "ontology format": [[1116, "term-Ontology-Format"]], "ontology graph projection": [[1116, "term-Ontology-Graph-Projection"]], "part of": [[1116, "term-Part-Of"]], "patch": [[1116, "term-Patch"]], "predicate": [[1116, "term-Predicate"]], "pronto": [[1116, "term-Pronto"]], "property": [[1116, "term-Property"]], "rdf": [[1116, "term-RDF"]], "reasoner": [[1116, "term-Reasoner"]], "reasoning": [[1116, "term-Reasoning"]], "reflexive": [[1116, "term-Reflexive"]], "relation graph": [[1116, "term-Relation-Graph"]], "relationship": [[1116, "term-Relationship"]], "relationship type": [[1116, "term-Relationship-Type"]], "sparql": [[1116, "term-SPARQL"]], "sql": [[1116, "term-SQL"]], "sssom": [[1116, "term-SSSOM"]], "semantic sql": [[1116, "term-Semantic-SQL"]], "semantic similarity": [[1116, "term-Semantic-Similarity"]], "subject": [[1116, "term-Subject"]], "subject closure": [[1116, "term-Subject-Closure"]], "subset": [[1116, "term-Subset"]], "tautology": [[1116, "term-Tautology"]], "term": [[1116, "term-Term"]], "text annotation": [[1116, "term-Text-Annotation"]], "triple": [[1116, "term-Triple"]], "triplestore": [[1116, "term-Triplestore"]], "uri": [[1116, "term-URI"]], "ubergraph": [[1116, "term-Ubergraph"]], "aggregatorimplementation (class in oaklib.implementations.aggregator.aggregator_implementation)": [[1159, "oaklib.implementations.aggregator.aggregator_implementation.AggregatorImplementation"]], "edge (class in semsql.sqla.semsql)": [[1174, "semsql.sqla.semsql.Edge"]], "entailededge (class in semsql.sqla.semsql)": [[1174, "semsql.sqla.semsql.EntailedEdge"]], "statements (class in semsql.sqla.semsql)": [[1174, "semsql.sqla.semsql.Statements"]], "associationproviderinterface (class in oaklib.interfaces.association_provider_interface)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface"]], "add_associations() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface.add_associations"]], "association_counts() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, "oaklib.interfaces.association_provider_interface.AssociationProviderInterface.association_counts"]], "association_pairwise_coassociations() (oaklib.interfaces.association_provider_interface.associationproviderinterface method)": [[1177, 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"oaklib.interfaces.summary_statistics_interface.SummaryStatisticsInterface.summary_statistic_description"]], "textannotation (class in oaklib.datamodels.text_annotator)": [[1192, "oaklib.datamodels.text_annotator.TextAnnotation"]], "textannotatorinterface (class in oaklib.interfaces.text_annotator_interface)": [[1192, "oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface"]], "annotate_file() (oaklib.interfaces.text_annotator_interface.textannotatorinterface method)": [[1192, "oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface.annotate_file"]], "annotate_tabular_file() (oaklib.interfaces.text_annotator_interface.textannotatorinterface method)": [[1192, "oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface.annotate_tabular_file"]], "annotate_text() (oaklib.interfaces.text_annotator_interface.textannotatorinterface method)": [[1192, "oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface.annotate_text"]], "cache_directory (oaklib.interfaces.text_annotator_interface.textannotatorinterface attribute)": [[1192, "oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface.cache_directory"]], "lexical_index (oaklib.interfaces.text_annotator_interface.textannotatorinterface attribute)": [[1192, "oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface.lexical_index"]], "rule_collection (oaklib.interfaces.text_annotator_interface.textannotatorinterface attribute)": [[1192, "oaklib.interfaces.text_annotator_interface.TextAnnotatorInterface.rule_collection"]], "validatorinterface (class in oaklib.interfaces.validator_interface)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface"]], "autosave (oaklib.interfaces.validator_interface.validatorinterface attribute)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.autosave"]], "exclude_owl_top_and_bottom (oaklib.interfaces.validator_interface.validatorinterface attribute)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.exclude_owl_top_and_bottom"]], "is_coherent() (oaklib.interfaces.validator_interface.validatorinterface method)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.is_coherent"]], "lookup_references() (oaklib.interfaces.validator_interface.validatorinterface method)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.lookup_references"]], "repair() (oaklib.interfaces.validator_interface.validatorinterface method)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.repair"]], "term_curies_without_definitions() (oaklib.interfaces.validator_interface.validatorinterface method)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.term_curies_without_definitions"]], "unsatisfiable_classes() (oaklib.interfaces.validator_interface.validatorinterface method)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.unsatisfiable_classes"]], "validate() (oaklib.interfaces.validator_interface.validatorinterface method)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.validate"]], "validate_definitions() (oaklib.interfaces.validator_interface.validatorinterface method)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.validate_definitions"]], "validate_mappings() (oaklib.interfaces.validator_interface.validatorinterface method)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.validate_mappings"]], "validate_synonyms() (oaklib.interfaces.validator_interface.validatorinterface method)": [[1193, "oaklib.interfaces.validator_interface.ValidatorInterface.validate_synonyms"]], "module": [[1195, "module-oaklib.utilities.apikey_manager"], [1196, "module-oaklib.utilities.graph.networkx_bridge"], [1197, "module-oaklib.utilities.graph.relationship_walker"], [1198, "module-oaklib.utilities.lexical.lexical_indexer"], [1199, "module-oaklib.utilities.obograph_utils"], [1200, "module-oaklib.utilities.subsets.slimmer_utils"], [1201, "module-oaklib.utilities.taxon.taxon_constraint_utils"], [1204, "module-oaklib.datamodels.search"]], "oaklib.utilities.apikey_manager": [[1195, "module-oaklib.utilities.apikey_manager"]], "oaklib.utilities.graph.networkx_bridge": [[1196, "module-oaklib.utilities.graph.networkx_bridge"]], "oaklib.utilities.graph.relationship_walker": [[1197, "module-oaklib.utilities.graph.relationship_walker"]], "oaklib.utilities.lexical.lexical_indexer": [[1198, "module-oaklib.utilities.lexical.lexical_indexer"]], "oaklib.utilities.obograph_utils": [[1199, "module-oaklib.utilities.obograph_utils"]], "oaklib.utilities.subsets.slimmer_utils": [[1200, "module-oaklib.utilities.subsets.slimmer_utils"]], "oaklib.utilities.taxon.taxon_constraint_utils": [[1201, "module-oaklib.utilities.taxon.taxon_constraint_utils"]], "searchconfiguration (class in oaklib.datamodels.search)": [[1204, "oaklib.datamodels.search.SearchConfiguration"]], "create_search_configuration() (in module oaklib.datamodels.search)": [[1204, "oaklib.datamodels.search.create_search_configuration"]], "oaklib.datamodels.search": [[1204, "module-oaklib.datamodels.search"]]}}) \ No newline at end of file diff --git a/summary-statistics/agents.md b/summary-statistics/agents.md index aa492661a..d51dbc70f 100644 --- a/summary-statistics/agents.md +++ b/summary-statistics/agents.md @@ -21,9 +21,9 @@ URI: [summary_statistics:agents](https://w3id.org/oaklib/summary_statistics.agen | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | | [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | +| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | diff --git a/summary-statistics/compared_with.md b/summary-statistics/compared_with.md index 038302f2c..662a82f23 100644 --- a/summary-statistics/compared_with.md +++ b/summary-statistics/compared_with.md @@ -21,9 +21,9 @@ URI: [summary_statistics:compared_with](https://w3id.org/oaklib/summary_statisti | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | | [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | +| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | diff --git a/summary-statistics/facet.md b/summary-statistics/facet.md index bc3f4e4fc..f8e97e1c3 100644 --- a/summary-statistics/facet.md +++ b/summary-statistics/facet.md @@ -16,8 +16,8 @@ URI: [summary_statistics:facet](https://w3id.org/oaklib/summary_statistics.facet | Name | Description | Modifies Slot | | --- | --- | --- | -| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no | | [ChangeTypeStatistic](ChangeTypeStatistic.md) | statistics for a particular kind of diff | no | +| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no | diff --git a/summary-statistics/filtered_count.md b/summary-statistics/filtered_count.md index a6467f518..db4e278e2 100644 --- a/summary-statistics/filtered_count.md +++ b/summary-statistics/filtered_count.md @@ -16,8 +16,8 @@ URI: [summary_statistics:filtered_count](https://w3id.org/oaklib/summary_statist | Name | Description | Modifies Slot | | --- | --- | --- | -| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no | | [ChangeTypeStatistic](ChangeTypeStatistic.md) | statistics for a particular kind of diff | no | +| [FacetedCount](FacetedCount.md) | Counts broken down by a facet | no | diff --git a/summary-statistics/id.md b/summary-statistics/id.md index 630cf5fd5..406a141b0 100644 --- a/summary-statistics/id.md +++ b/summary-statistics/id.md @@ -16,12 +16,12 @@ URI: [summary_statistics:id](https://w3id.org/oaklib/summary_statistics.id) | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | -| [ContributorRole](ContributorRole.md) | A role that a contributor can have | no | | [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | -| [Ontology](Ontology.md) | An ontology | no | +| [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | | [Agent](Agent.md) | An agent | no | +| [Ontology](Ontology.md) | An ontology | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | +| [ContributorRole](ContributorRole.md) | A role that a contributor can have | no | diff --git a/summary-statistics/ontologies.md b/summary-statistics/ontologies.md index 1a6515a33..0b45b44e7 100644 --- a/summary-statistics/ontologies.md +++ b/summary-statistics/ontologies.md @@ -21,9 +21,9 @@ URI: [summary_statistics:ontologies](https://w3id.org/oaklib/summary_statistics. | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | | [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | +| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | diff --git a/summary-statistics/was_generated_by.md b/summary-statistics/was_generated_by.md index 144936119..6ce702663 100644 --- a/summary-statistics/was_generated_by.md +++ b/summary-statistics/was_generated_by.md @@ -21,9 +21,9 @@ URI: [summary_statistics:was_generated_by](https://w3id.org/oaklib/summary_stati | Name | Description | Modifies Slot | | --- | --- | --- | -| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | -| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | | [GroupedStatistics](GroupedStatistics.md) | summary statistics for the entire resource | no | +| [SummaryStatisticsReport](SummaryStatisticsReport.md) | abstract base class for all summary statistics reports | no | +| [UngroupedStatistics](UngroupedStatistics.md) | A summary statistics report object | no | diff --git a/taxon-constraints/id.md b/taxon-constraints/id.md index b31598f1d..b7738b1ad 100644 --- a/taxon-constraints/id.md +++ b/taxon-constraints/id.md @@ -21,10 +21,10 @@ URI: [tc:id](https://w3id.org/linkml/taxon_constraints/id) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no | | [Term](Term.md) | An ontology term | no | | [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no | | [Taxon](Taxon.md) | A term that represents a taxonomic group, may be at species level of a higher... | no | +| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no | diff --git a/taxon-constraints/label.md b/taxon-constraints/label.md index 440b35870..7546fd9dc 100644 --- a/taxon-constraints/label.md +++ b/taxon-constraints/label.md @@ -21,10 +21,10 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label) | Name | Description | Modifies Slot | | --- | --- | --- | -| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no | | [Term](Term.md) | An ontology term | no | | [SubjectTerm](SubjectTerm.md) | A term that is the subject of a taxon constraint | no | | [Taxon](Taxon.md) | A term that represents a taxonomic group, may be at species level of a higher... | no | +| [PredicateTerm](PredicateTerm.md) | A term that represents a relationship type | no | diff --git a/text-annotator/matches_whole_text.md b/text-annotator/matches_whole_text.md index efb807866..5e009d3f7 100644 --- a/text-annotator/matches_whole_text.md +++ b/text-annotator/matches_whole_text.md @@ -16,8 +16,8 @@ URI: [ann:matches_whole_text](https://w3id.org/linkml/text_annotator/matches_who | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no | | [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | +| [TextAnnotationConfiguration](TextAnnotationConfiguration.md) | configuration for search | no | diff --git a/text-annotator/subject_end.md b/text-annotator/subject_end.md index d161bde14..20c0707b2 100644 --- a/text-annotator/subject_end.md +++ b/text-annotator/subject_end.md @@ -16,8 +16,8 @@ URI: [ann:subject_end](https://w3id.org/linkml/text_annotator/subject_end) | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/text-annotator/subject_label.md b/text-annotator/subject_label.md index 58117545c..ab71b81bd 100644 --- a/text-annotator/subject_label.md +++ b/text-annotator/subject_label.md @@ -21,8 +21,8 @@ URI: [ann:subject_label](https://w3id.org/linkml/text_annotator/subject_label) | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/text-annotator/subject_source.md b/text-annotator/subject_source.md index be42b1ff3..a483bfe2d 100644 --- a/text-annotator/subject_source.md +++ b/text-annotator/subject_source.md @@ -16,8 +16,8 @@ URI: [sssom:subject_source](http://w3id.org/sssom/subject_source) | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/text-annotator/subject_start.md b/text-annotator/subject_start.md index 46c36d570..b65647c1f 100644 --- a/text-annotator/subject_start.md +++ b/text-annotator/subject_start.md @@ -16,8 +16,8 @@ URI: [ann:subject_start](https://w3id.org/linkml/text_annotator/subject_start) | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/text-annotator/subject_text_id.md b/text-annotator/subject_text_id.md index 37a81887b..6ac072152 100644 --- a/text-annotator/subject_text_id.md +++ b/text-annotator/subject_text_id.md @@ -16,8 +16,8 @@ URI: [ann:subject_text_id](https://w3id.org/linkml/text_annotator/subject_text_i | Name | Description | Modifies Slot | | --- | --- | --- | -| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | | [HasSpan](HasSpan.md) | | no | +| [TextAnnotation](TextAnnotation.md) | An individual text annotation | no | diff --git a/validation/info.md b/validation/info.md index 1910dc182..48a4a2da3 100644 --- a/validation/info.md +++ b/validation/info.md @@ -22,9 +22,9 @@ URI: [sh:resultMessage](http://www.w3.org/ns/shacl#resultMessage) | Name | Description | Modifies Slot | | --- | --- | --- | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | -| [RepairOperation](RepairOperation.md) | The result of performing an individual repair | no | | [MappingValidationResult](MappingValidationResult.md) | A validation result where the check is to determine if a mapping is correct | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | +| [RepairOperation](RepairOperation.md) | The result of performing an individual repair | no | | [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/validation/instantiates.md b/validation/instantiates.md index ca2ffcee6..3a5e8c295 100644 --- a/validation/instantiates.md +++ b/validation/instantiates.md @@ -21,9 +21,9 @@ URI: [vm:instantiates](https://w3id.org/linkml/validation-model/instantiates) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/validation/object.md b/validation/object.md index 16fac1880..2e3592269 100644 --- a/validation/object.md +++ b/validation/object.md @@ -16,9 +16,9 @@ URI: [sh:value](http://www.w3.org/ns/shacl#value) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/validation/object_str.md b/validation/object_str.md index 4420d0363..840d518ef 100644 --- a/validation/object_str.md +++ b/validation/object_str.md @@ -16,9 +16,9 @@ URI: [vm:object_str](https://w3id.org/linkml/validation-model/object_str) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/validation/predicate.md b/validation/predicate.md index d89de45b9..3f80dcdd1 100644 --- a/validation/predicate.md +++ b/validation/predicate.md @@ -21,9 +21,9 @@ URI: [vm:predicate](https://w3id.org/linkml/validation-model/predicate) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/validation/results.md b/validation/results.md index 8693bd211..af5b91fe3 100644 --- a/validation/results.md +++ b/validation/results.md @@ -21,9 +21,9 @@ URI: [sh:result](http://www.w3.org/ns/shacl#result) | Name | Description | Modifies Slot | | --- | --- | --- | -| [RepairReport](RepairReport.md) | A report that consists of repair operation results | yes | | [ValidationReport](ValidationReport.md) | A report that consists of validation results | yes | | [Report](Report.md) | A report object that is a holder to multiple report results | no | +| [RepairReport](RepairReport.md) | A report that consists of repair operation results | yes | diff --git a/validation/severity.md b/validation/severity.md index 2afbdc29e..6e6889306 100644 --- a/validation/severity.md +++ b/validation/severity.md @@ -21,10 +21,10 @@ URI: [sh:resultSeverity](http://www.w3.org/ns/shacl#resultSeverity) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | | [TypeSeverityKeyValue](TypeSeverityKeyValue.md) | key-value pair that maps a validation result type to a severity setting, for ... | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/validation/source.md b/validation/source.md index 64609f55d..0902c4d63 100644 --- a/validation/source.md +++ b/validation/source.md @@ -16,9 +16,9 @@ URI: [vm:source](https://w3id.org/linkml/validation-model/source) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/validation/subject.md b/validation/subject.md index e4af7da44..cdbab69a6 100644 --- a/validation/subject.md +++ b/validation/subject.md @@ -21,9 +21,9 @@ URI: [sh:focusNode](http://www.w3.org/ns/shacl#focusNode) | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | diff --git a/validation/type.md b/validation/type.md index 4f005ecf2..d1d7d06df 100644 --- a/validation/type.md +++ b/validation/type.md @@ -21,10 +21,10 @@ URI: [sh:sourceConstraintComponent](http://www.w3.org/ns/shacl#sourceConstraintC | Name | Description | Modifies Slot | | --- | --- | --- | -| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no | | [ExternalReferenceValidationResult](ExternalReferenceValidationResult.md) | A validation result where the check is to determine if a link to an external ... | no | | [DefinitionValidationResult](DefinitionValidationResult.md) | | no | | [TypeSeverityKeyValue](TypeSeverityKeyValue.md) | key-value pair that maps a validation result type to a severity setting, for ... | no | +| [ValidationResult](ValidationResult.md) | An individual result arising from validation of a data instance using a parti... | no |