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cmungall committed May 8, 2024
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Showing 354 changed files with 2,293 additions and 2,293 deletions.
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Expand Up @@ -21,11 +21,11 @@ URI: [biolink:aggregator_knowledge_source](https://w3id.org/biolink/vocab/aggreg

| 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 |
| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | 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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/comments.md.txt
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Expand Up @@ -21,9 +21,9 @@ URI: [rdfs:comment](rdfs:comment)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -21,9 +21,9 @@ URI: [ontoassoc:evidence_type](https://w3id.org/oak/association/evidence_type)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -21,9 +21,9 @@ URI: [ontoassoc:negated](https://w3id.org/oak/association/negated)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [Association](Association.md) | A generic association between a thing (subject) and another thing (object) | yes |
| [NegatedAssociation](NegatedAssociation.md) | A negated 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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4 changes: 2 additions & 2 deletions _sources/datamodels/association/object.md.txt
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Expand Up @@ -29,10 +29,10 @@ URI: [rdf:object](rdf:object)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | 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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/object_closure.md.txt
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Expand Up @@ -21,9 +21,9 @@ URI: [ontoassoc:object_closure](https://w3id.org/oak/association/object_closure)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -21,9 +21,9 @@ URI: [ontoassoc:object_closure_label](https://w3id.org/oak/association/object_cl

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -25,9 +25,9 @@ URI: [sssom:object_label](https://w3id.org/sssom/object_label)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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/predicate.md.txt
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Expand Up @@ -27,10 +27,10 @@ URI: [rdf:predicate](rdf:predicate)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [PropertyValue](PropertyValue.md) | A generic tag-value that can be associated with an association | no |
| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | 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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/predicate_label.md.txt
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Expand Up @@ -25,9 +25,9 @@ URI: [sssom:predicate_label](https://w3id.org/sssom/predicate_label)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -21,11 +21,11 @@ URI: [biolink:primary_knowledge_source](https://w3id.org/biolink/vocab/primary_k

| 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 |
| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | no |
| [PositiveOrNegativeAssociation](PositiveOrNegativeAssociation.md) | | no |
| [ParserConfiguration](ParserConfiguration.md) | Settings that determine behavior when parsing associations | 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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/association/property_values.md.txt
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Expand Up @@ -21,9 +21,9 @@ URI: [ontoassoc:property_values](https://w3id.org/oak/association/property_value

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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/publications.md.txt
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Expand Up @@ -21,10 +21,10 @@ URI: [biolink:publications](https://w3id.org/biolink/vocab/publications)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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.md.txt
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Expand Up @@ -21,10 +21,10 @@ URI: [rdf:subject](rdf:subject)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -21,9 +21,9 @@ URI: [ontoassoc:subject_closure](https://w3id.org/oak/association/subject_closur

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -21,9 +21,9 @@ URI: [ontoassoc:subject_closure_label](https://w3id.org/oak/association/subject_

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -25,9 +25,9 @@ URI: [sssom:subject_label](https://w3id.org/sssom/subject_label)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -21,9 +21,9 @@ URI: [ontoassoc:supporting_objects](https://w3id.org/oak/association/supporting_

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [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 @@ -16,8 +16,8 @@ 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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4 changes: 2 additions & 2 deletions _sources/datamodels/mapping-rules/prefix.md.txt
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Expand Up @@ -16,9 +16,9 @@ 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 |
| [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 |
| [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 |



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2 changes: 1 addition & 1 deletion _sources/datamodels/mapping-rules/rules.md.txt
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Expand Up @@ -16,8 +16,8 @@ URI: [mappingrules:rules](https://w3id.org/oak/mapping-rules-datamodel/rules)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [RuleSet](RuleSet.md) | A set of rules for generating synonyms or alternate lexical elements | no |
| [MappingRuleCollection](MappingRuleCollection.md) | A collection of mapping rules | 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/allValuesFromEdges.md.txt
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Expand Up @@ -21,8 +21,8 @@ URI: [obographs:allValuesFromEdges](https://github.com/geneontology/obographs/al

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [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 |
| [Graph](Graph.md) | A graph is a collection of nodes and edges and other axioms that represents a... | no |



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2 changes: 1 addition & 1 deletion _sources/datamodels/obograph/id.md.txt
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Expand Up @@ -21,10 +21,10 @@ URI: [obographs:id](https://github.com/geneontology/obographs/id)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
| [SubsetDefinition](SubsetDefinition.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 @@ -21,10 +21,10 @@ 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 |
| [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 |
| [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 |
| [PropertyValue](PropertyValue.md) | A generic grouping for the different kinds of key-value associations on objec... | no |


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2 changes: 1 addition & 1 deletion _sources/datamodels/obograph/lbl.md.txt
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Expand Up @@ -21,10 +21,10 @@ URI: [rdfs:label](http://www.w3.org/2000/01/rdf-schema#label)

| Name | Description | Modifies Slot |
| --- | --- | --- |
| [SynonymTypeDefinition](SynonymTypeDefinition.md) | | no |
| [SubsetDefinition](SubsetDefinition.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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20 changes: 10 additions & 10 deletions _sources/datamodels/obograph/meta.md.txt
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Expand Up @@ -21,21 +21,21 @@ URI: [obographs:meta](https://github.com/geneontology/obographs/meta)

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



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