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Page info
title
title

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 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

No notes

Stanza

name

Entity.entityDescription

No notes

 

 

Entity.presentation['textualPresentation'].text

No notes

 

 

Entity.presentation['textualPresentation'].isPreferred = true

No notes

Stanza

alt_id

Entity.property.property="alt_id"

No notes

 

 

Entity.property['alt_id'].propertyId

No notes

 

 

Entity.property['alt_id'].text

No notes

Stanza

is_anonymous

Entity.isAnonymous = true

No notes

Stanza

is_obsolete

Entity.isActive = false

No notes

Stanza

def

Entity.definition

No notes

 

 

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

Stanza

syonym

presentation['textualPresentation'].text

No notes

Stanza

synonym.scope

presentation['textualPresentation'].degreeOfFidelity

No notes

Stanza

synonym.type

presentation['textualPresentation'].representationalForm

No notes

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

Stanza

xref

Property.['xref']

No notes

Stanza

xref_analog

None

See synonym

Stanza

xref_unk

None

No notes

Stanza

is_a

AssociationPredicate.['is_a']

Reverse of the source and target.

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

 

 

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.

typeDef Stanza

domain

AssociationPredicate.['has_domain']

No notes

typeDef Stanza

range

AssociationPredicate.['has_range']

No notes

typeDef Stanza

is_cyclic

property['is_cyclic']

No notes

typeDef Stanza

is_reflexive

property['is_reflexive']

No notes

typeDef Stanza

is_reflexive

AssociationEntity.isReflexive

No notes

typeDef Stanza

is_symmetric

property['is_symmetric']

No notes

typeDef Stanza

is_symmetric

association.isSymmetric

No notes

typeDef Stanza

is_transitive

property['is_transitive']

No notes

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

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

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