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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 |
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if |
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provided, |
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the |
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value |
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in |
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"default-namespace"; |
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but |
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if |
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not |
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will |
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use |
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filename |
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without |
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the |
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extension. |
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|
| codingScheme.defaultLanguage |
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Hardcoded |
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"en" |
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|
| codingScheme.isNative |
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Hardcoded |
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"true" |
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Stanza | id | Entity.entityCode |
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No |
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notes | ||
Stanza | name | Entity.entityDescription |
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No |
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notes | ||
|
| Entity.presentation |
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['textualPresentation' |
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].text |
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No |
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notes | ||
|
| Entity.presentation |
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['textualPresentation' |
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].isPreferred |
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= |
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true |
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No |
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notes |
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Stanza | alt_id |
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Entity.property.property="alt_id" |
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No |
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notes | ||
|
| Entity.property |
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['alt_id' |
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].propertyId |
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No |
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notes | ||
|
| Entity.property |
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['alt_id' |
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].text |
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No |
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notes |
...
Stanza | is_anonymous |
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Entity.isAnonymous |
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= |
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true |
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No |
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notes |
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Stanza | is_obsolete |
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Entity.isActive |
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= |
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false |
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No |
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notes |
...
Stanza | def | Entity.definition |
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No |
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notes | ||
|
| Entity.definition.isPreferred |
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= |
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true |
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No |
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notes |
...
Stanza | def.dbxref |
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None | See dbxref | |
Stanza | comment | Entity.comment.text |
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No |
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notes | |||
Stanza | subset | property[subset tag] | See subsetdef |
Stanza | syonym | presentation['textualPresentation' |
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].text |
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No |
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notes |
...
Stanza | synonym.scope |
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presentation |
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['textualPresentation' |
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].degreeOfFidelity |
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No |
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notes |
...
Stanza | synonym.type |
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presentation |
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['textualPresentation' |
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].representationalForm |
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No |
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notes |
...
Stanza | synonym.dbxref |
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(see |
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dbxref) |
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No |
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notes |
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Stanza | exact_synonym |
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None | See synonym | |
Stanza | narrow_synonym |
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None | See synonym | |
Stanza | broad_synonym |
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None | See synonym | |
Stanza | xref | Property.['xref' |
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] |
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No |
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notes | |
Stanza | xref_analog |
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None | See synonym | |
Stanza | xref_unk |
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None | No notes | |
Stanza | is_a | AssociationPredicate.['is_a' |
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] |
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Reverse |
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of |
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the |
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source |
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and |
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target. |
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Stanza | is_a.namespace |
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None | If present, |
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the |
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supplied |
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namespace |
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becomes |
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the |
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owning |
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"codingScheme". |
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Stanza | is_a.derived |
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AssociationPredicate.is_a.AssociationSource.AssociationTarget.associationQualifier |
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If |
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present, |
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need |
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to |
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include |
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derived |
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in |
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the |
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supportedAssociationQualifiers |
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section |
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Stanza | intersection_of |
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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" |
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No |
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notes |
...
Stanza | replaced_by |
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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. |
typeDef Stanza | domain | AssociationPredicate.['has_domain' |
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] |
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No |
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notes | ||
typeDef Stanza | range | AssociationPredicate.['has_range' |
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] |
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No |
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notes |
...
typeDef |
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Stanza |
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is_cyclic |
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property |
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['is_cyclic' |
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] |
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No |
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notes |
...
typeDef |
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Stanza |
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is_reflexive |
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property |
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['is_reflexive' |
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] |
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No |
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notes |
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typeDef |
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Stanza |
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is_reflexive |
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AssociationEntity.isReflexive |
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No |
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notes |
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typeDef |
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Stanza |
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is_symmetric |
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property |
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['is_symmetric' |
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] |
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No |
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notes |
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typeDef |
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Stanza |
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is_symmetric |
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association.isSymmetric |
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No |
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notes |
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typeDef |
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Stanza |
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is_transitive |
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property |
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['is_transitive' |
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] |
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No |
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notes |
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typeDef |
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Stanza |
...
is_transitive |
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association.isTransitive |
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No |
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notes |
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typeDef |
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Stanza |
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inverse_of |
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association.inverse |
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No |
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notes |
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instance |
...
stanza |
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id | same rules as general stanza | same rules as general stanza | |
instance stanza | name | same rules as general stanza | same rules as general stanza |
instance stanza | instance_of | AssociationPredicate['has_instance' |
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] |
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No |
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notes | |
instance stanza | instance_of |
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Entity.property.property="" |
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data |
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type |
...
properties |
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go |
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in |
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Coded |
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Entry |
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property section |
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section |
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