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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="0d01db3b-5e75-4b62-852e-337849fd3c9c"><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="909b3f3c-8cdb-4518-b5c1-e22a992cf799"><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="05202b0c-f407-4758-ad51-950692882b65"><ac:plain-text-body><![CDATA[ |
|
| 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="75acb8b4-7540-48e7-9b56-82371a939a7b"><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 | ||||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="749ba5dc-0b37-417f-aefa-3751e9861604"><ac:plain-text-body><![CDATA[ | 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="bf3ff000-2b6b-4c7d-8286-0ab73f0d0219"><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="b16360fc-d71d-4bda-b3a5-fcc13bc0ad41"><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="02b6e903-cabb-4639-9308-ee71e797f4c7"><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="d70d5531-af09-44e3-9460-0016391100f8"><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="4296600a-4dcc-4af8-adac-a49630f2cea1"><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="de9d47c5-5d31-4b55-8a40-92af584eba03"><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="3c3fc9f4-8a0c-4215-9c7d-9f756c9fe00d"><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="39b56a91-760b-41fb-95a1-4addcadfc92d"><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="c27870d3-bdeb-4fae-a746-08edd2958f8c"><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="295d446f-679e-4440-b671-fdbae4715f97"><ac:plain-text-body><![CDATA[ |
| AssociationEntity.isReflexive | 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="53bc538b-b335-41aa-8503-b9775b605731"><ac:plain-text-body><![CDATA[ |
| association.isSymmetric | 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="28059330-97cb-4fb5-96a9-2462e110e696"><ac:plain-text-body><![CDATA[ | instance stanza | instance_of | AssociationPredicate['has_instance'] | No notes | ]]></ac:plain-text-body></ac:structured-macro> | ||
instance stanza |
| instance_of |
| Entity.property.property="" | data type properties go in Coded Entry property section |
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