 |
Page History
| Wiki Markup |
|---|
{scrollbar:icons=false}
h1. { |
| Scrollbar | ||
|---|---|---|
|
page-info |
...
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
...
: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
| | Stanza | id | Entity.entityCode |
...
| No |
...
Stanza
...
name
notes\\ | | Stanza | name | Entity.entityDescription |
...
| No |
...
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2421b381-663e-4cc7-b8fe-92964acee180"><ac:plain-text-body><![CDATA[
...
...
...
notes | | | | Entity.presentation\['textualPresentation'\].text |
...
| No |
...
]]></ac:plain-text-body></ac:structured-macro>
...
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="88e9e139-223f-492f-9532-e55a3a2d4bf9"><ac:plain-text-body><![CDATA[
...
...
...
notes | | | | Entity.presentation\['textualPresentation'\].isPreferred = true |
...
| No |
...
]]></ac:plain-text-body></ac:structured-macro>
...
Stanza
...
alt_id
notes | | Stanza | alt_id | Entity.property.property="alt_id" |
...
| No |
...
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="e0ea57ad-cc04-4a5f-b758-b9f31a6130af"><ac:plain-text-body><![CDATA[
...
...
...
notes | | | | Entity.property\['alt_id'\].propertyId |
...
| No |
...
]]></ac:plain-text-body></ac:structured-macro>
...
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="7f78e9dd-ab5a-496c-8f59-15e7ede088e8"><ac:plain-text-body><![CDATA[
...
...
...
notes | | | | Entity.property\['alt_id'\].text |
...
| No |
...
]]></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
...
...
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
| | Stanza | def.dbxref |
...
None
...
See dbxref
...
Stanza
...
comment
| None | See dbxref | | Stanza | comment | Entity.comment.text |
...
| No |
...
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2fbdd0c9-fea5-4d5a-b09d-0f0bd1adf0da"><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="5e2a0409-386f-4218-a48b-59c55e8b239d"><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="7afad1fb-dc8a-4a8b-8500-7d292d56cf54"><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="fce629aa-bb41-4db7-afa1-bd6bf6015144"><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="f44b4aea-9880-4065-889e-e4bae0f0502d"><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="f2e93e1c-e341-45eb-a576-bae3289521f6"><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
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
| | 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
...
...
| 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
| | 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="fd9d0928-65aa-4605-816d-5c2ed5a01249"><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="faa76da6-6d28-4b21-b469-9621d1a8c3bf"><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="d5c2f8b6-bbbb-48c2-a9fb-6189fa8ca8ab"><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="e28b2a59-8a30-4a6d-8a2d-4995d59bf135"><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="d61e0214-72df-4b6b-928d-f9ae48a00d8e"><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="a5b76ce9-efa3-4e37-9f1e-da3c39b23503"><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="cc92daf5-8b63-405e-8eee-c0d2f30de33b"><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
...
| 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 |
\\
{scrollbar:icons=false} |
