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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

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