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="b3d783d7-5445-4faf-9079-0785956be0f4"><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="37e85b20-ac57-4080-ba8d-856b22c8b465"><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="7a204f1a-908c-43a3-af20-7206fac79b1a"><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="50d4540d-e6e8-4775-8b2b-692245f72509"><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="ef965862-3c2f-4a34-8012-05086c174cd6"><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="c4a64ebb-f4c9-48a4-9c44-321297facab0"><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="739d0bfb-a227-4b10-a8ff-dd888866f792"><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="8d7c1024-0f14-48fd-b843-e4ee3692e94f"><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="6f9495f0-6c77-462c-9b68-6a55b0d76c49"><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="2694d42b-94bb-4fd6-b833-85f446ddf0e2"><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="a733e360-b366-4119-a6cc-83fae183acf9"><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="98dec62d-eb65-46a9-b766-a37e1b46de7f"><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="efa82418-1594-4537-a847-2c455fb1a9d6"><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="b78c62a9-52a3-4420-aa6f-a190af65ee8b"><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="286a4843-faae-4b51-8aaf-d1bd56870f66"><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="1dc66c21-e441-480e-ade2-c69df331a6bc"><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="dc1a2e52-44e1-46df-a0ca-1e78062a5213"><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 |