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cmungall committed Oct 22, 2024
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Expand Up @@ -23,11 +23,11 @@ URI: [biolink:aggregator_knowledge_source](https://w3id.org/biolink/vocab/aggreg

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
| [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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/comments.md.txt
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Expand Up @@ -24,8 +24,8 @@ URI: [rdfs:comment](rdfs:comment)
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/evidence_type.md.txt
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Expand Up @@ -24,8 +24,8 @@ URI: [ontoassoc:evidence_type](https://w3id.org/oak/association/evidence_type)
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/negated.md.txt
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Expand Up @@ -24,8 +24,8 @@ URI: [ontoassoc:negated](https://w3id.org/oak/association/negated)
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | yes |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/object.md.txt
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Expand Up @@ -33,8 +33,8 @@ URI: [rdf:object](rdf:object)
| --- | --- | --- |
| [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | 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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/object_closure.md.txt
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Expand Up @@ -24,8 +24,8 @@ URI: [ontoassoc:object_closure](https://w3id.org/oak/association/object_closure)
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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Expand Up @@ -24,8 +24,8 @@ URI: [ontoassoc:object_closure_label](https://w3id.org/oak/association/object_cl
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/object_label.md.txt
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Expand Up @@ -28,8 +28,8 @@ URI: [sssom:object_label](https://w3id.org/sssom/object_label)
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/predicate.md.txt
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Expand Up @@ -31,8 +31,8 @@ URI: [rdf:predicate](rdf:predicate)
| --- | --- | --- |
| [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | 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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/predicate_label.md.txt
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Expand Up @@ -28,8 +28,8 @@ URI: [sssom:predicate_label](https://w3id.org/sssom/predicate_label)
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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Expand Up @@ -23,11 +23,11 @@ URI: [biolink:primary_knowledge_source](https://w3id.org/biolink/vocab/primary_k

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
| [AssociationChange](AssociationChange.md) | A change object describing a change between two associations | no |
| [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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/property_values.md.txt
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Expand Up @@ -24,8 +24,8 @@ URI: [ontoassoc:property_values](https://w3id.org/oak/association/property_value
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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4 changes: 2 additions & 2 deletions _sources/datamodels/association/publications.md.txt
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Expand Up @@ -23,10 +23,10 @@ URI: [biolink:publications](https://w3id.org/biolink/vocab/publications)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [AssociationChange](AssociationChange.md) | A change object describing a change between two 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 |
| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | 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 |



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4 changes: 2 additions & 2 deletions _sources/datamodels/association/subject.md.txt
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Expand Up @@ -23,10 +23,10 @@ URI: [rdf:subject](rdf:subject)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [AssociationChange](AssociationChange.md) | A change object describing a change between two 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 |
| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | 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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/subject_closure.md.txt
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Expand Up @@ -24,8 +24,8 @@ URI: [ontoassoc:subject_closure](https://w3id.org/oak/association/subject_closur
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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Expand Up @@ -24,8 +24,8 @@ URI: [ontoassoc:subject_closure_label](https://w3id.org/oak/association/subject_
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/subject_label.md.txt
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Expand Up @@ -28,8 +28,8 @@ URI: [sssom:subject_label](https://w3id.org/sssom/subject_label)
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/supporting_objects.md.txt
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Expand Up @@ -24,8 +24,8 @@ URI: [ontoassoc:supporting_objects](https://w3id.org/oak/association/supporting_
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/mapping-rules/description.md.txt
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Expand Up @@ -18,8 +18,8 @@ URI: [mappingrules:description](https://w3id.org/oak/mapping-rules-datamodel/des

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [MappingRule](MappingRule.md) | An individual mapping rule, if preconditions match the postconditions are app... | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/mapping-rules/prefix.md.txt
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Expand Up @@ -18,9 +18,9 @@ URI: [mappingrules:prefix](https://w3id.org/oak/mapping-rules-datamodel/prefix)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no |
| [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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/obograph/id.md.txt
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Expand Up @@ -24,9 +24,9 @@ URI: [obographs:id](https://github.com/geneontology/obographs/id)
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [SubsetDefinition](SubsetDefinition.md) | | no |
| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
| [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 |
| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |



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4 changes: 2 additions & 2 deletions _sources/datamodels/obograph/lang.md.txt
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Expand Up @@ -23,11 +23,11 @@ URI: [obographs:lang](https://github.com/geneontology/obographs/lang)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | 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 |
| [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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/obograph/lbl.md.txt
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Expand Up @@ -24,9 +24,9 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)
| Name | Description | Modifies Slot |
| --- | --- | --- |
| [SubsetDefinition](SubsetDefinition.md) | | no |
| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
| [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 |
| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |



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18 changes: 9 additions & 9 deletions _sources/datamodels/obograph/meta.md.txt
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Expand Up @@ -23,21 +23,21 @@ URI: [obographs:meta](https://github.com/geneontology/obographs/meta)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
| [EquivalentNodesSet](EquivalentNodesSet.md) | A clique of nodes that are all mutually equivalent | no |
| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |
| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
| [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | 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 |
| [DefinitionPropertyValue](DefinitionPropertyValue.md) | A property value that represents an assertion about the textual definition of... | no |
| [Node](Node.md) | A node is a class, property, or other entity in an ontology | no |
| [PropertyChainAxiom](PropertyChainAxiom.md) | An axiom that represents an OWL property chain, e | 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 |
| [DisjointClassExpressionsAxiom](DisjointClassExpressionsAxiom.md) | An axiom that defines a set of classes or class expressions as being mutually... | no |
| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
| [DomainRangeAxiom](DomainRangeAxiom.md) | This groups potentially multiple axioms that constrain the usage of a propert... | no |
| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |
| [Axiom](Axiom.md) | A generic grouping for any OWL axiom or group of axioms that is not captured ... | no |
| [Node](Node.md) | A node is a class, property, or other entity in an ontology | 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 |



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6 changes: 3 additions & 3 deletions _sources/datamodels/obograph/pred.md.txt
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Expand Up @@ -23,13 +23,13 @@ URI: [rdf:predicate](http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
| [BasicPropertyValue](BasicPropertyValue.md) | A property value that represents an assertion about an entity that is not a d... | no |
| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | 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... | no |
| [XrefPropertyValue](XrefPropertyValue.md) | A property value that represents an assertion about an external reference to ... | no |
| [Edge](Edge.md) | An edge is a simple typed relationship between two nodes | no |
| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | 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 |



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