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Page History
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OWL Element | LexGrid | Comments | |
|---|---|---|---|
OWL: RDF Schema Features |
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owl:ontology | codingScheme | Hardcoded "NCI_Thesaurus" | |
xml:lang | codingScheme.defaultLanguage | Hardcoded "en" | |
dc:title | codingScheme.formalName | Hardcoded "NCI Thesaurus" | |
rdfs:label | codingScheme.localName | Hardcoded "NCI_Thesaurus" | |
– | Hardcoded "40010" | ||
– | Hardcoded "urn:oid:2.16.840.1.113883.3.26.1.1" | – | |
URI | codingScheme.registeredName | Hardcoded "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#" | |
owl:versionInfo | codingScheme.representsVersion | – | |
dc:rights | codingScheme.copyright | Read from hardcoded "Terms.txt" file . | |
rdfs:comment | codingScheme.entityDescription | – | |
– | codingScheme.isNative | Hardcoded "true" | |
owl:Class (Thing, Nothing) | concept | – | |
code | concept.id | – | |
– | concept.isActive | Hard coded as "true" unless class "owl:DeprecatedClass", then 'false' | |
– | concept.isAnonymous | – | |
rsfs:label | concept.entityDescription | – | |
rdf:comment | concept.comment | – | |
– | conceptProperty | Indicate whether the concept is primative (has no equavalent classes) | |
– | concept.conceptProperty.propertyName | Hard coded as "primitive" | |
– | concept.conceptProperty.text | "true" | |
– | concept.conceptProperty.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | |
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– | presentation | Provide default presentation to match concept entity description if not provided as property | |
– | concept.presentation.propertyId | Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value. | |
– | concept.presentation.propertyName | Hardcoded "NCI_Preferred_Term" | |
rdfs:label | concept.presentation.text | concept.entityDescription | |
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– | conceptProperty | Property with designated concept name label (per NCI requirements and used in codeToName/nameToCode lookup). | |
– | concept.conceptProperty.propertyName | Hard coded as "CONCEPT_NAME" | |
rdfs:label | concept.conceptProperty.text | concept.entityDescription | |
– | concept.conceptProperty.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | |
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– | relation | Top-level container for associations (non-inheritable, non-defining relationships between concepts. | |
– | relations.dc | Hard coded as "associations" | |
– | relations.isNative | Hard coded as "true" | |
– | relations.entityDescription | Hard coded as "Non-inheritable non-defining relations." | |
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– | relation | Top-level container for roles (inheritable relationships) | |
– | relations.dc | Hard coded as "roles" | |
– | relations.isNative | Hard coded as "true" | |
– | relations.entityDescription | Hard coded as "Inheritable/defining relations." | |
rdfs:subClassOf | association | Association for subtype hierarchy. | |
– | association.id = "hasSubtype" | – | |
– | association.forwardName = "hasSubtype" | – | |
– | association.reverseName = "isA" | – | |
– | association.isNavigable = "true" | Hard coded as "true" | |
– | Hard coded as "true" | – | |
– | Hard coded as "false" | – | |
– | Hard coded as "true" | – | |
hasElement | association | Association used to register component classes as elements of anonymous node representations. | |
– | association.id = "hasElement" | – | |
– | association.forwardName = "hasElement" | – | |
– | association.isNavigable = "true" | Hard coded as "true" | |
– | Hard coded as "false" | – | |
– | Hard coded as "true" | – | |
rdfs:domain | association | Association for role_has_domain relations | |
– | association.id = "Role_Has_Domain" | – | |
– | association.forwardName = "roleHasDomain" | – | |
– | association.reverseName = "kindIsDomainOf" | – | |
– | association.isNavigable = "true" | Hard coded as "true" | |
– | Hard coded as "false" | – | |
– | Hard coded as "false" | – | |
– | Hard coded as "true" | – | |
rdfs:range | association | Association for range relations | |
– | association.id = "Role_Has_Range" | – | |
– | association.forwardName = "roleHasRange" | – | |
– | association.reverseName = "kindIsRangeOf" | – | |
– | association.isNavigable = "true" | Hard coded as "true" | |
– | association.isReflexive="false" | Hard coded as "false" | |
– | association.isSymmetric="false" | Hard coded as "false" | |
– | association.isTransitive="false" | Hard coded as "false" | |
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rdf:Property (ObjectProperty) | association | An association between two classes (hasDomain, hasRange) | |
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rdfs:subPropertyOf |
| Not Mapped | |
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OWL (In)Equality |
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owl:equivalentClass | association | Association for equivalent class. | |
– | association.id = "equivalentClass" | – | |
– | association.forwardName = "equivalentClass" | – | |
– | association.reverseName = "equivalentClass" | – | |
– | association.isNavigable = "true" | Hard coded as "true" | – |
– | association.isReflexive="true" | Hard coded as "true" | |
– | association.isSymmetric="true" | Hard coded as "true" | |
– | association.isTransitive="true" | Hard coded as "true" | |
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OWL: Property Characteristics |
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owl:inverseOf | association | – | |
– | association.id = "inverseOf" | – | |
– | association.forwardName = "inverseOf" | – | |
– | association.isFunctional = "false" | – | |
– | association.isNavigable = "true" | – | |
– | association.isReflexive="true" | ||
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– | |||
– | association.isSymmetric="true" | – | |
– | association.isTransitive="true" | – | |
– | association.reverseName="inverseOf" | – | |
owl:TransitiveProperty | association.isTransitive | association property 'isTransitive' | |
owl:SymmetricProperty | association.isSymmetric | association property 'isSymmetric' | |
owl:InverseFunctionalProperty | association.isReverseFunctional | association property 'isReverseFunctional' | |
owl:FunctionalProperty | association.isFunctional | association property 'isFunctional' | |
OWL: Property Restrictions |
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owl:Restriction | concept | Anonymous concept created. | |
– | concept.entityDescription = "RestrictionOn: " + association name | Concatination of "Restriction On: " and assocation name | |
– | concept.isAnonymous = true | – | |
owl: allValuesFrom | associationQualification.association.Qualifier = "AllValuesFrom" | – | |
owl: someValuesFrom | associationQualification.association.Qualifier = "someValuesFrom" | – | |
owl:intersectionOf | concept.entityDescription | Concatination of "Restriction On: " and assocation name | |
– | concept.isAnonymous = true | – | |
– | concept.presentation.propertyId | Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value. | |
– | concept.presentation.propertyName | Hardcoded "textualPresentation" | |
– | concept.presentation.isPreferred = true | Hardcoded "true" | |
– | concept.presentation.text | Set to concept.entityDescription | |
– | concept.conceptProperty.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | |
– | concept.conceptProperty.propertyName = type | Hardcoded "type" | |
– | concept.conceptProperty.text = "owl:intersectionOf" | ||
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– | |||
owl:unionOf | concept.entityDescription | Concatination of "Restriction On: " and assocation name | |
– | concept.isAnonymous = true | – | |
– | concept.presentation.propertyId | Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value. | |
– | concept.presentation.propertyName | Hardcoded "textualPresentation" | |
– | concept.presentation.isPreferred = true | Hardcoded "true" | |
– | concept.presentation.text | Set to concept.entityDescription | |
– | concept.conceptProperty.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | |
– | concept.conceptProperty.propertyName = type | Hardcoded "type" | |
– | concept.conceptProperty.text = "owl:unionOf" | ||
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– | |||
owl:oneOf | concept.conceptProperty.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | |
– | concept.conceptProperty.propertyName = "owl:oneOf" | Hardcoded "owl:oneOf" | |
– | concept.conceptProperty.text | String of oneOf values | |
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OWL: Annotation Property |
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rdfs:comment | Comment | – | |
– | concept.comment.propertyId | Generated value for property textual presentation using "P" concatenated with a steadily incremented numerical value. | |
– | concept.comment.propertyName = "comment" | Hardcoded "comment" | |
– | concept.presentation.text | Value of rdfs:comment | |
rdfs:seeAlso | conceptProperty | – | |
rdfs:isDefinedBy | conceptProperty | – | |
OWL: Versioning |
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owl:versionInfo | codingScheme.representsVersion | – | |
priorVersion | – | Not Mapped | |
backwardCompatibleWith | – | Not Mapped | |
DeprecatedClass | – | Not Mapped | |
DeprecatedProperty | – | Not Mapped |
...
Legacy Complex Properties Mapping
tag | presentation | source | represenational form | qualifier | model element | value column name | model element |
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go-term | x |
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| propertyValue |
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go-id |
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| x | propertyQualifierId | val1 | PropertyQualifier attribute content? |
go-source |
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| x | propertyQualifierId | val1 | PropertyQualifier attribute content? |
source-date |
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| x | propertyQualifierId | val1 | PropertyQualifier attribute content? |
term-name | x |
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| propertyValue |
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term-group |
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| x |
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| representationalForm | property attribute |
term-source |
| x |
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| attributeValue | source |
def-source |
| x |
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| attributeValue | source |
def-definition | x |
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| propertyValue | definition | |
Definition_Review_Date |
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| x | propertyQualifierId | val1 | PropertyQualifier attribute content? |
Definition_Reviewer_Name |
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| x | propertyQualifierId | val1 | PropertyQualifier attribute content? |
UMLS SemNet Mapping
UMLS SemNet Mapping | ||||||
RRF File Name | RRF Column Name | RRF Definition | NCI Meta only | LexGrid Model Element | comments | |
|---|---|---|---|---|---|---|
Coding Scheme | </big>
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| codingScheme.representsVersion |
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| codingScheme.codingScheme | hard coded in java file as "UMLS_SemNet" | |
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| codingScheme.formalName | hard coded in java file as "UMLS Semantic Network" | |
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| codingScheme.defaultLanguage | hard coded in java file as "en" | |
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| codingScheme.approxNumConcepts | hard coded in java file as | |
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| codingScheme.entityDescription | hard coded in java file as "The UMLS Semantic Network is one of three UMLS Knowledge Sources developed as part of the Unified Medical Language System project. The network provides a consistent categorization of all concepts represented in the UMLS Metathesaurus." | |
license.txt |
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| codingScheme.copyright | Read from license.txt file or hard coded reference in java file | |
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| codingScheme.registeredName | hard coded in java file as "urn:lsid:nlm.nih.gov:semnet" | |
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| codingScheme.concepts.dc | hard coded in java file as "concepts" | |
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| codingScheme.relations.dc | hard coded in java file as "relations" | |
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| codingScheme.mappings.dc | hard coded in java file as "mappings" | |
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| codingScheme.localNameList |
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| codingScheme.localNameList. | hard coded in java file as "UMLS_SemNet" | |
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| codingScheme.localNameList |
| codingScheme.localNameList . |
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codingScheme.source | codingScheme.source.content | codingScheme.localNameList |
| codingScheme.localNameList. |
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codingScheme.localNameList |
| codingScheme.localNameList. |
| codingScheme.localNameList source |
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codingScheme.localNameList. |
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| codingScheme.source.content |
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| codingScheme.localNameList |
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| codingScheme.localNameList. |
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| codingScheme.localNameList |
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| codingScheme.localNameList. |
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| codingScheme.localNameList |
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| codingScheme.localNameList. |
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| codingScheme.localNameList |
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| codingScheme.localNameList. |
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| mappings.supportedFormat |
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| mappings.supportedFormat.localId | hard coded in java file as "text/plain" | |
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| mappings.supportedFormat.urn | hard coded in java file as "urn:oid:2.16.840.1.113883.6.10:text_plain" | |
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| mappings.supportedAssociation |
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SRDEF | RL |
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| mappings.supportedAssociation.localId |
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| mappings.supportedContext |
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| mappings.supportedSource |
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| mappings.supportedSource.localId | hard coded in java file as "NLM" | |
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| mappings.supportedSource.urn | hard coded in java file as "urn:lsid:nlm.nih.gov" | |
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| mappings.supportedHierarchy |
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| mappings.supportedHierarchy.localId | hard coded in java file as "is_a" | |
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| mappings.supportedHierarchy.isForwardNavigable | hard coded as "true" | |
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| mappings.supportedHierarchy.rootCode | hard coded as "@" | |
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| mappings.supportedHierarchy.associationList | hard coded in java file as "hasSubtype" | |
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| mappings.supportedAssociationQualifier |
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SRFLD | COL |
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| mappings.supportedProperty |
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| mappings.supportedProperty.localId | If SRDEF appears in the FIL column then this is treated a potential supported property and is entered in supported properties as such. |
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| mappings.supportedProperty.urn | hard coded in java file as "" | |
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| mappings.supportedLanguage |
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| mappings.supportedLanguage.localId | hard coded in java file as "en" | |
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| mappings.supportedLanguage.urn | hard coded in java file as "urn:oid:2.16.840.1.113883.6.84:en" | |
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| mappings.supportedCodingScheme |
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| mappings.supportedCodingScheme.localId | hard coded in java file as "UMLS_SemNet" | |
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| mappings.supportedCodingScheme.urn | hard coded in java file as "urn:lsid:nlm.nih.gov:semnet" | |
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| mappings.supportedRepresentationalForm |
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| mappings.supportedConceptStatus |
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| mappings.supportedPropertyLink |
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| mappings.supportedPropertyQualifier |
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| mappings.supportedDataType |
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<big>Concepts</big> | ||||||
SRDEF | UI | concept.id(inherited from Entity) | ||||
SRDEF | STY/RL | concept.enitityDescription(inheritance path Entity->versionableAndDescribable) | ||||
| concept.conceptProperty | |||||
SRDEF | NH | concept.conceptProperty.text.content | ||||
| concept.conceptProperty.format | hard coded in java file as "text/plain" | ||||
| concept.conceptProperty.propertyName | hard coded in java file as "NH" | ||||
| concept.conceptProperty.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | ||||
| concept.presentation | |||||
| concept.presentation.propertyName (inherited from Property) | Hard coded in java file as "STY/RL" or "ABR" | ||||
| concept.presentation.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | ||||
SRDEF | STY/RL, ABR | concept.presentation.text.content | ||||
| concept.presentation.format | hard coded in java file as "text/plain" | ||||
| concept.presentation.isPreferred | hard coded in java file as true. | ||||
| concept.definition.propertyName (inherited from Property) | Hard coded in java file as "DEF" | ||||
| concept.definition.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | ||||
SRDEF | DEF | concept.definition.text.content | ||||
| concept.definition.format | hard coded in java file as "text/plain" | ||||
| concept.definition.isPreferred | hard coded in java file as true. | ||||
| concept.comment | |||||
SRDEF | EX | concept.comment.propertyName (inherited from Property) | Hard coded in java file as "EX" | |||
| concept.comment.text.content | |||||
| concept.comment.format | hard coded in java file as "text/plain" | ||||
| concept.comment.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | ||||
| concept.instruction | |||||
| concept.instruction.propertyName (inherited from Property) | Hard coded in java file as "UN" | ||||
SRDEF | UN | concept.instruction.text.content | ||||
| concept.instruction.format | hard coded in java file as "text/plain" | ||||
| concept.instruction.propertyId | Generated value for property using "P" concatenated with a steadily incremented numerical value. | ||||
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<big>Relations</big> | ||||||
SRSTR | RL | association.id (inherited from Entity) | In the case of RL value is "isa" the id is hard coded to hasSubtype. The direction of the association is also reversed | |||
| association.isTransitive | hard coded to true if the value of RL is "isa" | ||||
SRSTR | RL | association.forwardName | Reversed when value of RL is "isa" | |||
SRSTR | STY/RL | associationInstance.sourceId | Reversed when value of RL is "isa" | |||
SRSTR | STY/RL | associationTarget.targetId | ||||
SRDEF | RIN | association.reverseName | ||||
SRDEF | DEF | association.entityDescription.content (inheritance path for entityDescription is Entity->versionableAndDescribable) | When SRDEF value RT is "RL" | |||
SRSTRE1 | UI/STY(first argument) | associationInstance.sourceId | Reversed when value of RL is "isa" | |||
SRSTRE1 | UI/STY(2nd argument) | associationTarget.targetId | Reversed when value of RL is "isa" |
...
