Merge pull request #239 from ga4gh/doc-update

updated domain-entities to complete links needed for remaining TU links.
ga4gh · Dec 5, 2024 · cc7c973 · cc7c973
2 parents b2dc0f8 + d5b1481
commit cc7c973
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diff --git a/docs/source/base-profiles/proposition-profiles.rst b/docs/source/base-profiles/proposition-profiles.rst
@@ -122,3 +122,10 @@ Variant Prognostic Proposition
 
 .. include::  ../def/va-spec/VariantPrognosticProposition.rst
 
+.. _experimental-variant-functional-impact-proposition:
+
+Experimental Variant Functional Impact Proposition
+##################################################
+
+.. include::  ../def/va-spec/ExperimentalVariantFunctionalImpactProposition.rst
+
diff --git a/docs/source/core-information-model/data-types.rst b/docs/source/core-information-model/data-types.rst
@@ -3,37 +3,39 @@
 Data Types
 !!!!!!!!!!
 
-Complex Data Types
-###################
-
-.. _Coding:
-
-Coding
-******
-
-.. include::  ../def/gks-core/Coding.rst
+General Purpose Data Types
+##########################
 
 .. _Extension:
 
 Extension
 *********
 .. include::  ../def/gks-core/Extension.rst
 
+.. _MappableConcept:
 
-.. _RecordMetadata:
+MappableConcept
+***************
 
-RecordMetadata
-**************
+.. include::  ../def/gks-core/MappableConcept.rst
 
-.. include::  ../def/va-spec/RecordMetadata.rst
+.. _ConceptMapping:
 
 ConceptMapping
 **************
 
 .. include::  ../def/gks-core/ConceptMapping.rst
 
-Simple Data Types
-###################
+.. _Coding:
+
+Coding
+******
+
+.. include::  ../def/gks-core/Coding.rst
+
+
+Primitive Data Types
+####################
 
 .. _code:
 

diff --git a/docs/source/core-information-model/entities/domain-entities/conditions/disease.rst b/docs/source/core-information-model/entities/domain-entities/conditions/disease.rst
@@ -3,4 +3,10 @@
 Disease
 !!!!!!!
 
-.. include::  ../../../../../../schema/domain-entities/def/Disease.rst
+We defer to the adopters to use the disease naming authority of their choice 
+(e.g. OMIM, MONDO, etc.) to share a representation of a Disease concept using
+the :ref:`MappableConcept` data type.
+
+NOTE: **conceptType** should be set to "Disease".
+
+.. include::  ../../../../def/gks-core/MappableConcept.rst
diff --git a/docs/source/core-information-model/entities/domain-entities/conditions/index.rst b/docs/source/core-information-model/entities/domain-entities/conditions/index.rst
@@ -6,7 +6,12 @@ Condition
   .. include::  ../../../../def/va-spec/Condition.rst
 
 
-**Subclasses**
+Condition Types
+###############
+
+**Disease** and **Phenotype** are :ref:`MappableConcept` example
+condition types (aka traits) for the atomic representation of a trait.
+MappableConcept may be used for other condition types if appropriate.
 
 .. toctree::
    :titlesonly:

diff --git a/...source/core-information-model/entities/domain-entities/conditions/phenotype.rst b/...source/core-information-model/entities/domain-entities/conditions/phenotype.rst
@@ -3,4 +3,10 @@
 Phenotype
 !!!!!!!!!
 
-.. include::  ../../../../../../schema/domain-entities/def/Phenotype.rst
+We defer to the adopters to use the phenotype naming authority of their choice 
+(e.g. HPO, etc.) to share a representation of a Phenotype concept using
+the :ref:`MappableConcept` data object.
+
+NOTE: **conceptType** should be set to "Phenotype".
+
+.. include::  ../../../../def/gks-core/MappableConcept.rst
diff --git a/docs/source/core-information-model/entities/domain-entities/gene.rst b/docs/source/core-information-model/entities/domain-entities/gene.rst
@@ -3,4 +3,10 @@
 Gene
 !!!!
 
-.. include::  ../../../def/va-spec/Gene.rst  
+We defer to the adopters to use the gene naming authority of their choice 
+(e.g. HGNC, ENTREZ-GENE, etc.) to share a representation of a Gene entity using
+the MappableConcept data object.
+
+NOTE: **conceptType** should be set to "Gene".
+
+.. include::  ../../../../def/gks-core/MappableConcept.rst
diff --git a/docs/source/core-information-model/entities/domain-entities/index.rst b/docs/source/core-information-model/entities/domain-entities/index.rst
@@ -19,7 +19,6 @@ Note that these are minimally specified models at present, which will be evolved
 .. toctree::
    :titlesonly:
 
-   gene
    conditions/index
-   therapeutic-procedures/index
+   therapeutics/index
 
diff --git a/...n-model/entities/domain-entities/therapeutic-procedures/combination-therapy.rst b/...n-model/entities/domain-entities/therapeutic-procedures/combination-therapy.rst
diff --git a/...ore-information-model/entities/domain-entities/therapeutic-procedures/index.rst b/...ore-information-model/entities/domain-entities/therapeutic-procedures/index.rst
diff --git a/...on-model/entities/domain-entities/therapeutic-procedures/therapeutic-action.rst b/...on-model/entities/domain-entities/therapeutic-procedures/therapeutic-action.rst
diff --git a/...ion-model/entities/domain-entities/therapeutic-procedures/therapeutic-agent.rst b/...ion-model/entities/domain-entities/therapeutic-procedures/therapeutic-agent.rst
diff --git a/...ntities/domain-entities/therapeutic-procedures/therapeutic-substitute-group.rst b/...ntities/domain-entities/therapeutic-procedures/therapeutic-substitute-group.rst
diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutics/drug.rst b/docs/source/core-information-model/entities/domain-entities/therapeutics/drug.rst
@@ -0,0 +1,12 @@
+.. _Drug:
+
+Drug
+!!!!
+
+We defer to the adopters to use the drug naming authority of their choice 
+(e.g. NCIT, RXNORM, etc.) to share a representation of a Drug concept using
+the :ref:`MappableConcept` data object.
+
+NOTE: **conceptType** should be set to "Drug".
+
+.. include::  ../../../../def/gks-core/MappableConcept.rst
diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutics/index.rst b/docs/source/core-information-model/entities/domain-entities/therapeutics/index.rst
@@ -0,0 +1,21 @@
+.. _Therapeutic:
+
+Therapeutic
+!!!!!!!!!!!
+
+.. include::  ./../../../def/va-spec/Therapeutic.rst  
+
+Therapeutic Types
+#################
+
+**Drug** and **Procedure** are :ref:`MappableConcept` example
+therapeutic types for the atomic representation of a therapy. 
+MappableConcept may be used for other therapy types if appropriate
+(i.e. behavioral-intervention, etc..).
+
+.. toctree::
+   :titlesonly:
+
+   drug
+   procedure
+   therapy-group
diff --git a/...urce/core-information-model/entities/domain-entities/therapeutics/procedure.rst b/...urce/core-information-model/entities/domain-entities/therapeutics/procedure.rst
@@ -0,0 +1,12 @@
+.. _Procedure:
+
+Procedure
+!!!!!!!!!
+
+We defer to the adopters to use the procedure naming authority of their choice 
+(e.g. NCIT, etc.) to share a representation of a Procedure concept using
+the :ref:`MappableConcept` data object.
+
+NOTE: **conceptType** should be set to "Procedure".
+
+.. include::  ../../../../def/gks-core/MappableConcept.rst
diff --git a/.../core-information-model/entities/domain-entities/therapeutics/therapy-group.rst b/.../core-information-model/entities/domain-entities/therapeutics/therapy-group.rst
@@ -0,0 +1,6 @@
+.. _TherapyGroup:
+
+Therapy Group
+!!!!!!!!!!!!!
+
+.. include:: ../../../../def/va-spec/TherapyGroup.rst