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OBO Class | OBO Entity | LexGrid Model Element | Notes | ||
---|---|---|---|---|---|
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. | ||
|
| codingScheme.defaultLanguage | Hardcoded "en" | ||
|
| 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="dc89f2994649bc98-a8660418-430c4f5a-bcf1a4e5-a022791d5a165fb81d3f3e14"><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="219216d2677e3916-732ae14d-46cf4279-ad60af26-1d6bb9eea17c1e49b9fbbc79"><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="d254806c7c4c3876-3eeeb7b8-49294808-9bd4ba4e-426883f005ec28383e31058b"><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="f230a673c1161076-35d8c901-40de4b8b-82e59baa-ffcfb207869b8e6ca001ac7a"><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 | ||
|
| 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="946358477cafb2c9-118a0afd-445f4a49-a20fa8c7-035f36d2a3d21eceb1e15a58"><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="7994620dd20f7e8f-3068c259-48cf468d-b140852c-f551a8fad7411ce788d3aa03"><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="2bd5451470025f39-39d1f53d-45544a18-aaee8b55-d156617015edb388f4903976"><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="e81c9e85e343950e-0e9080c8-43cf412c-a3edaa4d-37bdfb7b72937e4e25454104"><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="ea1e79a7c11329cf-e4dfa6ff-41f54024-95d99014-1fe061bc30da529f09df9eb4"><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="4ee6670153646b01-244eb052-45d740d2-aca0bb9e-39c652bbf9e7d40ffcde196f"><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 | ||
|
| 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="80195de419a6d861-40b40190-432f4818-b137aa3b-b4ce166508ec003b5af481e3"><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="d8a85aad74f97618-add86ce1-4edc4120-a3f3bfef-402795d3f660689784107d7e"><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="826953c6feb9a273-bcb2ef53-4112481e-9c8ea8fa-971ebce3ea2fdd2bdea291e5"><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="6f98a0b05f83fa1f-52c36ed0-4a8c49a2-8f11adb2-cbdece5d46a11aaf4cb15170"><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="f3177c3a22b0120a-bb165ce6-437546e7-adce8b72-13ec4a59bebdb0b6eb1ad8c2"><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="ccacf90a84c3f847-fd2b186c-43d34520-8c66974a-aea8a380b55914313c739707"><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="cb7bc78a102ef5f6-abf839e1-42c44ec3-bb9c83d5-89d0c7b8796c7b922e38d335"><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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