OBO Mapping |
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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 |
|
|
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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 |
||
|
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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 |
|
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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. |
|
|
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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 |
 |
