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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="94ef6971-e08a-42c2-951f-5758987ced27"><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="19b762b0-d76c-4062-b07d-bcba6c2bbdaf"><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="23877818-39c8-4265-b53a-99708c852c2b"><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="edd8ac9a-9403-4576-807a-d7613a9ccf50"><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="3649dda1-4095-4977-8c7d-ff975a7bf8e1"><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="dc25fcc2-4c59-4fa2-a2d4-c3cb32c660aa"><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="5fa218cd-c8ce-40b9-8555-b84f71f20d10"><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="46cd81c0-530c-4452-b461-b1c7af1cd670"><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="905f51c5-1934-43f6-be24-41615f70e676"><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="c01589b8-5aa3-4215-aef0-85c7f29153ab"><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="b77acf8c-e0d8-4868-80b8-6eca8a1e8fa6"><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="fd4f386b-0ad8-4f3f-8ff7-8562cabf78ae"><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="0bd6b040-3897-4b3b-88f5-5e0566cc90eb"><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="74150b12-cdef-4dc4-8e01-5106188ea8fa"><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="6667c2aa-88f1-4741-a53d-794fb9c65f9b"><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="6ab49507-f22a-4c8d-9e95-b022cb36dd4c"><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 |
...