Merge pull request #220 from ga4gh/subjectVariant-DRY-refactor

DRY refactor SubjectVariant in propositions
ga4gh · Nov 17, 2024 · b35decc · b35decc
2 parents b924df8 + f270c5c
commit b35decc
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diff --git a/schema/va-spec/aac-2017/def/VariantDiagnosticStudyStatement.rst b/schema/va-spec/aac-2017/def/VariantDiagnosticStudyStatement.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/aac-2017/def/VariantPrognosticStudyStatement.rst b/schema/va-spec/aac-2017/def/VariantPrognosticStudyStatement.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/aac-2017/def/VariantTherapeuticResponseStudyStatement.rst b/schema/va-spec/aac-2017/def/VariantTherapeuticResponseStudyStatement.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityFunctionalImpactEvidenceLine.rst b/schema/va-spec/acmg-2015/def/VariantPathogenicityFunctionalImpactEvidenceLine.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/Activity.rst b/schema/va-spec/base/def/Activity.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/Agent.rst b/schema/va-spec/base/def/Agent.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/Characteristic.rst b/schema/va-spec/base/def/Characteristic.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst b/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/Condition.rst b/schema/va-spec/base/def/Condition.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/Contribution.rst b/schema/va-spec/base/def/Contribution.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/DataSet.rst b/schema/va-spec/base/def/DataSet.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/Document.rst b/schema/va-spec/base/def/Document.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/EvidenceLine.rst b/schema/va-spec/base/def/EvidenceLine.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactProposition.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactProposition.rst
@@ -1,14 +1,14 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 
 A proposition reporting a conclusion from a single assay or study about the functional impact of a variant on a sequence feature (typically a gene or gene product).
 
 **Information Model**
 
-Some ExperimentalVariantFunctionalImpactProposition attributes are inherited from :ref:`Proposition`.
+Some ExperimentalVariantFunctionalImpactProposition attributes are inherited from :ref:`SubjectVariantProposition`.
 
 .. list-table::
    :class: clean-wrap
@@ -52,21 +52,16 @@ Some ExperimentalVariantFunctionalImpactProposition attributes are inherited fro
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
-   *  - propositionText
+   *  - subjectVariant
       - 
-      - string
-      - 0..1
-      - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer".
+      - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference`
+      - 1..1
+      - A variant that is the subject of the Proposition.
    *  - type
       - 
       - string
       - 1..1
       - MUST be "ExperimentalVariantFunctionalImpactProposition".
-   *  - subjectVariant
-      - 
-      - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference`
-      - 1..1
-      - A protein or genomic contextual or canonical molecular variant.
    *  - predicate
       - 
       - string

diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/InformationEntity.rst b/schema/va-spec/base/def/InformationEntity.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/Method.rst b/schema/va-spec/base/def/Method.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/Proposition.rst b/schema/va-spec/base/def/Proposition.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 
@@ -57,11 +57,6 @@ Some Proposition attributes are inherited from :ref:`gks-core:Entity`.
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
-   *  - propositionText
-      - 
-      - string
-      - 0..1
-      - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer".
    *  - subject
       - 
       - object

diff --git a/schema/va-spec/base/def/RecordMetadata.rst b/schema/va-spec/base/def/RecordMetadata.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/Statement.rst b/schema/va-spec/base/def/Statement.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/StudyGroup.rst b/schema/va-spec/base/def/StudyGroup.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/StudyResult.rst b/schema/va-spec/base/def/StudyResult.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/SubjectVariantProposition.rst b/schema/va-spec/base/def/SubjectVariantProposition.rst
@@ -0,0 +1,74 @@
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
+**Computational Definition**
+
+A :ref:`Proposition` that has a variant as the subject.
+
+**Information Model**
+
+Some SubjectVariantProposition attributes are inherited from :ref:`Proposition`.
+
+.. list-table::
+   :class: clean-wrap
+   :header-rows: 1
+   :align: left
+   :widths: auto
+
+   *  - Field
+      - Flags
+      - Type
+      - Limits
+      - Description
+   *  - id
+      - 
+      - string
+      - 0..1
+      - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - type
+      - 
+      - string
+      - 1..1
+      - The name of the class that is instantiated by a data object representing the Entity.
+   *  - label
+      - 
+      - string
+      - 0..1
+      - A primary name for the entity.
+   *  - description
+      - 
+      - string
+      - 0..1
+      - A free-text description of the Entity.
+   *  - alternativeLabels
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
+      - string
+      - 0..m
+      - Alternative name(s) for the Entity.
+   *  - extensions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
+      - :ref:`Extension`
+      - 0..m
+      - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
+   *  - predicate
+      - 
+      - string
+      - 1..1
+      - The relationship declared to hold between the subject and the object of the Statement.
+   *  - object
+      - 
+      - object
+      - 1..1
+      - An Entity or concept that is related to the subject of a Proposition via its predicate.
+   *  - subjectVariant
+      - 
+      - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference`
+      - 1..1
+      - A variant that is the subject of the Proposition.
diff --git a/schema/va-spec/base/def/Therapeutic.rst b/schema/va-spec/base/def/Therapeutic.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/TherapyGroup.rst b/schema/va-spec/base/def/TherapyGroup.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**
 

diff --git a/schema/va-spec/base/def/TraitSet.rst b/schema/va-spec/base/def/TraitSet.rst
@@ -1,6 +1,6 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
-    levels are described in the :ref:`maturity-model`.
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
 
 **Computational Definition**