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 |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="e290f208-465b-4b19-aa64-516222bc5061"><ac:plain-text-body><![CDATA[ |
|
|
Entity.presentation['textualPresentation'].text |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="43588d7c-ad90-42de-a377-e757a408e852"><ac:plain-text-body><![CDATA[ |
|
|
Entity.presentation['textualPresentation'].isPreferred = true |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
Stanza |
alt_id |
Entity.property.property="alt_id" |
No notes |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="30a11a92-7a68-48f9-828b-cadf8fb0f4f3"><ac:plain-text-body><![CDATA[ |
|
|
Entity.property['alt_id'].propertyId |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="59fa5435-8079-41bc-8b20-b2bfc6789685"><ac:plain-text-body><![CDATA[ |
|
|
Entity.property['alt_id'].text |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
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 |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="7986abe0-4b73-404a-a72c-a19d5bbea024"><ac:plain-text-body><![CDATA[ |
Stanza |
subset |
property[subset tag] |
See subsetdef |
]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="bb600f4c-37bf-4c17-a9be-3fe7d4a0ed16"><ac:plain-text-body><![CDATA[ |
Stanza |
syonym |
presentation['textualPresentation'].text |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="da272ea3-1f74-45ea-9f12-603f1774d847"><ac:plain-text-body><![CDATA[ |
Stanza |
synonym.scope |
presentation['textualPresentation'].degreeOfFidelity |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="fbb0e3ac-16fe-489c-a5ac-ee3574b46169"><ac:plain-text-body><![CDATA[ |
Stanza |
synonym.type |
presentation['textualPresentation'].representationalForm |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
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 |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="c841f927-b0ec-4620-8098-f54ab0ff05c7"><ac:plain-text-body><![CDATA[ |
Stanza |
xref |
Property.['xref'] |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
Stanza |
xref_analog |
None |
See synonym |
||
Stanza |
xref_unk |
None |
No notes |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="d0f8c970-c8f5-4fa3-8c2b-f6aee4785e5c"><ac:plain-text-body><![CDATA[ |
Stanza |
is_a |
AssociationPredicate.['is_a'] |
Reverse of the source and target. |
]]></ac:plain-text-body></ac:structured-macro> |
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. |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="449833d8-ad81-4107-a294-fe550b12aad1"><ac:plain-text-body><![CDATA[ |
typeDef Stanza |
domain |
AssociationPredicate.['has_domain'] |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="e246534d-51e9-47e9-be8c-563dad0950a6"><ac:plain-text-body><![CDATA[ |
typeDef Stanza |
range |
AssociationPredicate.['has_range'] |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2f613618-7ed5-4c0f-b985-f9be7681a0a2"><ac:plain-text-body><![CDATA[ |
typeDef Stanza |
is_cyclic |
property['is_cyclic'] |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="f94259f6-51b1-4a73-bba2-c7537d718d12"><ac:plain-text-body><![CDATA[ |
typeDef Stanza |
is_reflexive |
property['is_reflexive'] |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
typeDef Stanza |
is_reflexive |
AssociationEntity.isReflexive |
No notes |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2c4810ac-65fc-4c3a-881c-5f826a0efbdc"><ac:plain-text-body><![CDATA[ |
typeDef Stanza |
is_symmetric |
property['is_symmetric'] |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
typeDef Stanza |
is_symmetric |
association.isSymmetric |
No notes |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2087d606-fae4-49c9-9fa4-6c587d3269cd"><ac:plain-text-body><![CDATA[ |
typeDef Stanza |
is_transitive |
property['is_transitive'] |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
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 |
||
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="1be3c719-17a1-489b-a0ae-7073bc6fd75f"><ac:plain-text-body><![CDATA[ |
instance stanza |
instance_of |
AssociationPredicate['has_instance'] |
No notes |
]]></ac:plain-text-body></ac:structured-macro> |
instance stanza |
instance_of |
Entity.property.property="" |
data type properties go in Coded Entry property section |