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OBO Class | OBO Entity | LexGrid Model Element | Notes | ||||
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Document Header | format-version | None | Not mapped. | ||||
Document Header | data-version | CodingScheme.representsVersion | Creates a codingSchemeVersion and SystemRelease record. If not specified, then hard coded "UNASSIGNED" | ||||
Document Header | version | CodingScheme.representsVersion | Deprecated - use data-version if present. | ||||
Document Header | date | None | Not mapped. | ||||
Document Header | saved-by | None | Ignored but included if contained in the remark entity. | ||||
Document Header | auto-generated-by | None | Ignored but included if contained in the remark entity. | ||||
Document Header | subsetdef | None | Not mapped. | ||||
Document Header | import | None | Deprecated - Imports are used to assemble a larger document from smaller. | ||||
Document Header | typeref | None | Deprecated. | ||||
Document Header | synonymtypedef | None | Not mapped. | ||||
Document Header | idspace | None | Not mapped.The idspace is a triple - localName, URN and description. | ||||
Document Header | default-relationship-id-prefix | None | Not mapped. | ||||
Document Header | id-mapping | CodingScheme.supportedAssociation | This is more generalized than the LexGrid model, as it supports mapping between *any* id's. Note that its primary purpose, however, is to handle supportedAssociation. | ||||
Document Header | remark | CodingScheme.entityDescription | Will combine multiple remark entities into the entityDescription. | ||||
Document Header | default-namespace | codingScheme.codingSchemeName | Will use default-namespace if provided; otherwise will use filename without the extension. | ||||
Document Header | default-namespace | codingScheme.formalName | Will use default-namespace if provided; otherwise will use filename without the extension. | ||||
Document Header | default-namespace | codingScheme.codingSchemeURI | Combination of "urn:lsid:bioontology.org:" and if provided, the value in "default-namespace"; but if not will use filename without the extension. | ||||
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| codingScheme.defaultLanguage | Hardcoded "en" | ||||
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| codingScheme.isNative | Hardcoded "true" | ||||
Stanza | id | Entity.entityCode | No notes | ||||
Stanza | name | Entity.entityDescription | No notes | ||||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="4b37d772-23dc-4381-92fa-2020d47c804e"><ac:plain-text-body><![CDATA[ |
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| Entity.presentation['textualPresentation'].text | No notes]]></ac:plain-text-body></ac:structured-macro> | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="d05bd241-ad1c-4e1f-b8ee-2d99980b359e"><ac:plain-text-body><![CDATA[ | ||
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| Entity.presentation['textualPresentation'].isPreferred = true | No notes]]></ac:plain-text-body></ac:structured-macro> | ||||
Stanza | alt_id | Entity.property.property="alt_id" | No notes<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ab0d4954-430a-450d-88ec-abd083ae2a84"><ac:plain-text-body><![CDATA[ | ||||
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| Entity.property['alt_id'].propertyId | No notes]]></ac:plain-text-body></ac:structured-macro> | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="e8d47994-c6b8-4d78-b42f-e9dc59675914"><ac:plain-text-body><![CDATA[ | |||
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| Entity.property['alt_id'].text | No notes]]></ac:plain-text-body></ac:structured-macro> | ||||
Stanza | is_anonymous | Entity.isAnonymous = true | No notes | ||||
Stanza | is_obsolete | Entity.isActive = false | No notes | ||||
Stanza | def | Entity.definition | No notes | ||||
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| Entity.definition.isPreferred = true | No notes | ||||
Stanza | def.dbxref | None | See dbxref | ||||
Stanza | comment | Entity.comment.text | No notes | ||||
Stanza | subset | property[subset tag] | See subsetdef | ||||
]]></ac:plain-text-body></ac:structured-macro> | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ecb72ad8-19ea-455f-80c2-038485019d95"><ac:plain-text-body><![CDATA[ | Stanza | syonym | presentation['textualPresentation'].text | No notes | ]]></ac:plain-text-body></ac:structured-macro> | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2a26f325-fc4c-4a18-ae00-c3d0839d6266"><ac:plain-text-body><![CDATA[ |
Stanza | synonym.scope | presentation['textualPresentation'].degreeOfFidelity | No notes | ||||
]]></ac:plain-text-body></ac:structured-macro> | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="80ad8865-3981-4d15-9fc7-dc0ea75dc813"><ac:plain-text-body><![CDATA[ | Stanza | synonym.type | presentation['textualPresentation'].representationalForm | No notes]]></ac:plain-text-body></ac:structured-macro> | ||
Stanza | synonym.dbxref | (see dbxref) | No notes | ||||
Stanza | exact_synonym | None | See synonym | ||||
Stanza | narrow_synonym | None | See synonym | ||||
Stanza | broad_synonym | None | See synonym<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="4ac03928-973d-4c3f-a2b0-0763622689f1"><ac:plain-text-body><![CDATA[ | ||||
Stanza | xref | Property.['xref'] | No notes | ]]></ac:plain-text-body></ac:structured-macro> | |||
Stanza | xref_analog | None | See synonym | ||||
Stanza | xref_unk | None | No notes | ||||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="526e8406-de84-4a8b-81cb-d9c3576a5d01"><ac:plain-text-body><![CDATA[ | Stanza | is_a | AssociationPredicate.['is_a'] | Reverse of the source and target.]]></ac:plain-text-body></ac:structured-macro> | |||
Stanza | is_a.namespace | None | If present, the supplied namespace becomes the owning "codingScheme". | ||||
Stanza | is_a.derived | AssociationPredicate.is_a.AssociationSource.AssociationTarget.associationQualifier | If present, need to include derived in the supportedAssociationQualifiers section | ||||
Stanza | intersection_of | None | Processed the same way that OWL intersection operator is processed. This includes creation of anonymous sets. | ||||
Stanza | union_of | None | Same as OWL | ||||
Stanza | disjoint_from | None | Same as OWL | ||||
Stanza | relationship | associations. | No notes | ||||
Stanza | relationship.not_necessary | AssociationTarget..associationQualifier | No notes | ||||
Stanza | relationship.inverse_necessary | AssociationTarget..associationQualifier | No notes | ||||
Stanza | relationship.namespace | None | If present, the supplied namespace becomes the owning "codingScheme". | ||||
Stanza | relationship.derived | AssociationTarget..associationQualifier | No notes | ||||
Stanza | relationship.cardinality | AssociationTarget..associationQualifier | No notes | ||||
Stanza | relationship.maxCardinality | AssociationTarget..associationQualifier | No notes | ||||
Stanza | relationship.minCardinality | AssociationTarget..associationQualifier | No notes | ||||
Stanza | is_obsolete | Entity.isActive = false | No notes | ||||
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| Entity.conceptStatus="is_obsolete" | No notes | ||||
Stanza | replaced_by | None | No notes | ||||
Stanza | consider | None | Not Mapped | ||||
Stanza | use_term | None | (deprecated) | ||||
dbxref | dbxref name | Entity.source | No notes | ||||
dbxref | dbxref name | supportedSource | dbxref name format is inconsistent. In most cases, it can be the localName of supportedSource, but special processing may be necessary in the case of URL's, etc | ||||
dbxref | dbxref description | None | Not mapped. | ||||
dbxref | trailing modifiers | None | Not mapped.<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="aa872200-b04d-4b69-8990-a6a868870bae"><ac:plain-text-body><![CDATA[ | ||||
typeDef Stanza | domain | AssociationPredicate.['has_domain'] | No notes | ||||
]]></ac:plain-text-body></ac:structured-macro> | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="cb47eb48-4ab6-4ba5-88cb-5073acb3f0d4"><ac:plain-text-body><![CDATA[ | typeDef Stanza | range | AssociationPredicate.['has_range'] | No notes | ]]></ac:plain-text-body></ac:structured-macro> | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="e099bb3e-c128-4a4c-bcbf-0945fbaa6769"><ac:plain-text-body><![CDATA[ |
typeDef Stanza | is_cyclic | property['is_cyclic'] | No notes]]></ac:plain-text-body></ac:structured-macro> | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="214e218d-5616-4788-96d5-639222b1ba91"><ac:plain-text-body><![CDATA[ | |||
typeDef Stanza | is_reflexive | property['is_reflexive'] | No notes | ]]></ac:plain-text-body></ac:structured-macro> | |||
typeDef Stanza | is_reflexive | AssociationEntity.isReflexive | No notes<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="91087b5b-fc6e-4865-9be7-8ddc254b4f00"><ac:plain-text-body><![CDATA[ | ||||
typeDef Stanza | is_symmetric | property['is_symmetric'] | No notes]]></ac:plain-text-body></ac:structured-macro> | ||||
typeDef Stanza | is_symmetric | association.isSymmetric | No notes | ||||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="5293ab1a-6684-46b2-99dc-08638b516459"><ac:plain-text-body><![CDATA[ | typeDef Stanza | is_transitive | property['is_transitive'] | No notes | ]]></ac:plain-text-body></ac:structured-macro> | ||
typeDef Stanza | is_transitive | association.isTransitive | No notes | ||||
typeDef Stanza | inverse_of | association.inverse | No notes | ||||
instance stanza | id | same rules as general stanza | same rules as general stanza | ||||
instance stanza | name | same rules as general stanza | same rules as general stanza<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="c467922f-f77c-4425-b3ab-6e8b9c2616a4"><ac:plain-text-body><![CDATA[ | ||||
instance stanza | instance_of | AssociationPredicate['has_instance'] | No notes | ||||
instance stanza | instance_of | Entity.property.property="" | data type properties go in Coded Entry property section |
...