Page History
OBO Mapping | |||
OBO Class | OBO Entity | LexGrid Model Element | Notes |
---|---|---|---|
Document Header | format-version | 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 | Not mapped. | |
Document Header | saved-by | Ignored but included if contained in the remark entity. | |
Document Header | auto-generated-by | Ignored but included if contained in the remark entity. | |
Document Header | subsetdef | Not mapped. | |
Document Header | import | Deprecated - Imports are used to assemble a larger document from smaller. | |
Document Header | typeref | Deprecated. | |
Document Header | synonymtypedef | Not mapped. | |
Document Header | idspace | Not mapped.The idspace is a triple - localName, URN and description. | |
Document Header | default-relationship-id-prefix | 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 | |
Stanza | name | Entity.entityDescription | |
| Entity.presentation'textualPresentation'.text | ||
| Entity.presentation'textualPresentation'.isPreferred = true | ||
Stanza | alt_id | ||
|
| Entity.property'alt_id'.propertyId | |
| Entity.property'alt_id'.text | ||
Stanza | is_anonymous | Entity.isAnonymous = true | |
Stanza | is_obsolete | Entity.isActive = false | |
Stanza | def | Entity.definition | |
| Entity.definition.isPreferred = true | ||
Stanza | def.dbxref | See dbxref | |
| |||
Stanza | comment | Entity.comment.text | |
Stanza | subset | propertysubset tag | See subsetdef |
Stanza | syonym | presentation'textualPresentation'.text | |
Stanza | synonym.scope | presentation'textualPresentation'.degreeOfFidelity | |
Stanza | synonym.type | presentation'textualPresentation'.representationalForm | |
Stanza | synonym.dbxref | (see dbxref) | |
Stanza | exact_synonym | See synonym | |
Stanza | narrow_synonym | See synonym | |
Stanza | broad_synonym | See synonym | |
Stanza | xref | Property.'xref' | |
Stanza | xref_analog | See synonym | |
Stanza | xref_unk | ||
| |||
Stanza | is_a | AssociationPredicate.'is_a' | Reverse of the source and target. |
Stanza | is_a.namespace | 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 | Processed the same way that OWL intersection operator is processed. This includes creation of anonymous sets. | |
Stanza | union_of | Same as OWL | |
Stanza | disjoint_from | Same as OWL | |
Stanza | relationship | associations. | |
Stanza | relationship.not_necessary | AssociationTarget..associationQualifier | |
Stanza | relationship.inverse_necessary | AssociationTarget..associationQualifier | |
Stanza | relationship.namespace | If present, the supplied namespace becomes the owning "codingScheme". | |
Stanza | relationship.derived | AssociationTarget..associationQualifier | |
Stanza | relationship.cardinality | AssociationTarget..associationQualifier | |
Stanza | relationship.maxCardinality | AssociationTarget..associationQualifier | |
Stanza | relationship.minCardinality | AssociationTarget..associationQualifier | |
Stanza | is_obsolete | Entity.isActive = false | |
| |||
Stanza | replaced_by |
| |
Stanza | consider | Not Mapped | |
Stanza | use_term | (deprecated) | |
| |||
dbxref | dbxref name | Entity.source |
|
| 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 | Not mapped. | |
dbxref | trailing modifiers | Not mapped. | |
| |||
typeDef Stanza | domain | AssociationPredicate.'has_domain' | |
typeDef Stanza | range | AssociationPredicate.'has_range' | |
typeDef Stanza | is_cyclic | property'is_cyclic' | |
typeDef Stanza | is_reflexive | property'is_reflexive' | |
| AssociationEntity.isReflexive | ||
typeDef Stanza | is_symmetric | property'is_symmetric' | |
| association.isSymmetric | ||
typeDef Stanza | is_transitive | property'is_transitive' | |
| association.isTransitive | ||
typeDef Stanza | inverse_of | association.inverse | |
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 |
instance stanza | instance_of | AssociationPredicate'has_instance' | |
instance stanza | data type properties go in Coded Entry property section |