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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="b43cb29ad2f611b5-cc78e06e-41c24d16-86d99ad2-047a4fb72faccd5d2affd775"><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="675260a63c54e9b9-36e8d85a-42fa43bd-aa9b9593-ac7ab5cc5289757933adf84e"><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="98ca2e200a325f95-be7648f2-415d4ff6-8104a53c-4d6d0ecb475dd19dc6c0a081"><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="3f13b87ff2271c67-0057ca07-4ac64471-8ef3b0de-19fc334eabd307a1df127541"><ac:plain-text-body><![CDATA[ |
|
| 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="4baf73c9e40666c9-d5acf7d4-41284eba-abbdb2f2-c93f31c5482dfbc5294e79eb"><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="e738bd838e636075-357f7ae3-4cc44ddd-ac18a3a9-45dd25251e54e7661317534f"><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="bc18fb5b56ab8aa2-380ab6f8-494949c0-b534b7e2-679f8eba4b2e92cd1255d7a5"><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="194d77d4d95d5ba9-021def75-422547dc-88568a4a-0d9181c76f6410600331997a"><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="cf1f78307c8594cd-c8612e3e-44a44486-83d29f81-e3cfb129af78404f27657102"><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="dcc99f3fe1944db9-00fb5b92-48454797-8b84a6bb-16f9e0c6c1f57ff89ca53912"><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="2fcbd237e9ff3890-5c64db6a-4c5f4214-af1a944c-38c749005c9759038b7d5c6a"><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="81fe78a0148e2410-70eec7dc-44074998-ac33be62-d4f7478b78fa4ca74a4c0322"><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="75851547f65d0175-395521c7-4c1a4c13-b8e884ae-bce202fd031c961989bd77b2"><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="77d87d8104384591-83fe2578-4d0d44c3-b8c2a242-6f7f8bd3954e3b224ac41ab4"><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="f9154423d626c2bd-6bfa7ac5-43cc48a9-b6d9884a-45481efeaa1342547b4c58fb"><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="5ea21676ea94730c-c0193452-4b844c9a-b1468c40-820090e8ee7daa82f12a071d"><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="966cc1eb8357d3e5-a287de4a-4ec54262-b10b82b9-3f3a06e4c706e5732b7ceb55"><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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