adjust qualifiers per #226

ga4gh · Nov 26, 2024 · 21737e8 · 21737e8
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diff --git a/schema/va-spec/base/def/ClinicalVariantProposition.rst b/schema/va-spec/base/def/ClinicalVariantProposition.rst
@@ -0,0 +1,84 @@
+.. note:: This data class is at a **trial use** maturity level and may \
+    change in future releases. Maturity \
+    levels are described in the :ref:`maturity-model`.
+
+**Computational Definition**
+
+A proposition for use in describing the effect of variants in human subjects.
+
+**Information Model**
+
+Some ClinicalVariantProposition attributes are inherited from :ref:`SubjectVariantProposition`.
+
+.. 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.
+   *  - geneContextQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).
+   *  - alleleOriginQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or another more nuanced concept.
diff --git a/schema/va-spec/base/def/VariantDiagnosticProposition.rst b/schema/va-spec/base/def/VariantDiagnosticProposition.rst
@@ -8,7 +8,7 @@ A Proposition reporting a conclusion from a single study about whether a variant
 
 **Information Model**
 
-Some VariantDiagnosticProposition attributes are inherited from :ref:`SubjectVariantProposition`.
+Some VariantDiagnosticProposition attributes are inherited from :ref:`ClinicalVariantProposition`.
 
 .. list-table::
    :class: clean-wrap
@@ -57,6 +57,16 @@ Some VariantDiagnosticProposition attributes are inherited from :ref:`SubjectVar
       - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference`
       - 1..1
       - A variant that is the subject of the Proposition.
+   *  - geneContextQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).
+   *  - alleleOriginQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or another more nuanced concept.
    *  - type
       - 
       - string
@@ -72,18 +82,3 @@ Some VariantDiagnosticProposition attributes are inherited from :ref:`SubjectVar
       - :ref:`Condition` | :ref:`iriReference`
       - 1..1
       - The disease that is evaluated for diagnosis.
-   *  - alleleOriginQualifier
-      - 
-      - string
-      - 0..1
-      - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).
-   *  - allelePrevalenceQualifier
-      - 
-      - string
-      - 0..1
-      - Reports whether the proposition should be interpreted in the context of the variant being rare or common.
-   *  - geneContextQualifier
-      - 
-      - :ref:`MappableConcept`
-      - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the diagnostic association  in the Proposition.
diff --git a/schema/va-spec/base/def/VariantOncogenicityProposition.rst b/schema/va-spec/base/def/VariantOncogenicityProposition.rst
@@ -8,7 +8,7 @@ A proposition describing the role of a variant in causing a tumor type.
 
 **Information Model**
 
-Some VariantOncogenicityProposition attributes are inherited from :ref:`SubjectVariantProposition`.
+Some VariantOncogenicityProposition attributes are inherited from :ref:`ClinicalVariantProposition`.
 
 .. list-table::
    :class: clean-wrap
@@ -57,6 +57,16 @@ Some VariantOncogenicityProposition attributes are inherited from :ref:`SubjectV
       - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference`
       - 1..1
       - A variant that is the subject of the Proposition.
+   *  - geneContextQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).
+   *  - alleleOriginQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or another more nuanced concept.
    *  - type
       - 
       - string
@@ -72,18 +82,3 @@ Some VariantOncogenicityProposition attributes are inherited from :ref:`SubjectV
       - :ref:`Condition` | :ref:`iriReference`
       - 1..1
       - The tumor type for which the variant impact is evaluated.
-   *  - variantOriginQualifier
-      - 
-      - string
-      - 0..1
-      - Reports whether the proposition should be interpreted in the context of a heritable (germline) variant, an acquired (somatic) mutation, or more nuanced origin.
-   *  - variantPrevalenceQualifier
-      - 
-      - string
-      - 0..1
-      - Reports whether the proposition should be interpreted in the context of the variant being rare, common, or some other expressed form of background population prevalence.
-   *  - geneContextQualifier
-      - 
-      - :ref:`MappableConcept`
-      - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Proposition.
diff --git a/schema/va-spec/base/def/VariantPathogenicityProposition.rst b/schema/va-spec/base/def/VariantPathogenicityProposition.rst
@@ -8,7 +8,7 @@ A proposition describing the role of a variant in causing a heritable condition.
 
 **Information Model**
 
-Some VariantPathogenicityProposition attributes are inherited from :ref:`SubjectVariantProposition`.
+Some VariantPathogenicityProposition attributes are inherited from :ref:`ClinicalVariantProposition`.
 
 .. list-table::
    :class: clean-wrap
@@ -57,6 +57,16 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`Subject
       - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference`
       - 1..1
       - A variant that is the subject of the Proposition.
+   *  - geneContextQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).
+   *  - alleleOriginQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or another more nuanced concept.
    *  - type
       - 
       - string
@@ -74,19 +84,11 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`Subject
       - The :ref:`Condition` for which the variant impact is stated.
    *  - penetranceQualifier
       - 
-      - string
+      - :ref:`MappableConcept`
       - 0..1
       - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. 
    *  - modeOfInheritanceQualifier
       - 
-                        .. 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:`Coding`
-      - 0..m
-      - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify.
-   *  - geneContextQualifier
-      - 
-      - :ref:`MappableConcept` | :ref:`iriReference`
+      - :ref:`MappableConcept`
       - 0..1
-      - Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).
+      - Reports a pattern of inheritance expected for the pathogenic effect of the variant. HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) are recommended to specify.
diff --git a/schema/va-spec/base/def/VariantPrognosticProposition.rst b/schema/va-spec/base/def/VariantPrognosticProposition.rst
@@ -8,7 +8,7 @@ A Proposition reporting a conclusion from a single study about whether a variant
 
 **Information Model**
 
-Some VariantPrognosticProposition attributes are inherited from :ref:`SubjectVariantProposition`.
+Some VariantPrognosticProposition attributes are inherited from :ref:`ClinicalVariantProposition`.
 
 .. list-table::
    :class: clean-wrap
@@ -57,6 +57,16 @@ Some VariantPrognosticProposition attributes are inherited from :ref:`SubjectVar
       - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference`
       - 1..1
       - A variant that is the subject of the Proposition.
+   *  - geneContextQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).
+   *  - alleleOriginQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or another more nuanced concept.
    *  - type
       - 
       - string
@@ -72,18 +82,3 @@ Some VariantPrognosticProposition attributes are inherited from :ref:`SubjectVar
       - :ref:`Condition` | :ref:`iriReference`
       - 1..1
       - The disease that is evaluated for outcome.
-   *  - alleleOriginQualifier
-      - 
-      - string
-      - 0..1
-      - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).
-   *  - allelePrevalenceQualifier
-      - 
-      - string
-      - 0..1
-      - Reports whether the proposition should be interpreted in the context of the variant being rare or common.
-   *  - geneContextQualifier
-      - 
-      - :ref:`MappableConcept`
-      - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the prognostic association  in the Proposition.
diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseProposition.rst b/schema/va-spec/base/def/VariantTherapeuticResponseProposition.rst
@@ -8,7 +8,7 @@ A Statement reporting a conclusion from a single study about the role of a varia
 
 **Information Model**
 
-Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`SubjectVariantProposition`.
+Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`ClinicalVariantProposition`.
 
 .. list-table::
    :class: clean-wrap
@@ -57,6 +57,16 @@ Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`S
       - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference`
       - 1..1
       - A variant that is the subject of the Proposition.
+   *  - geneContextQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).
+   *  - alleleOriginQualifier
+      - 
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or another more nuanced concept.
    *  - type
       - 
       - string
@@ -77,19 +87,3 @@ Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`S
       - :ref:`Condition` | :ref:`iriReference`
       - 1..1
       - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements.
-   *  - alleleOriginQualifier
-      - 
-      - string
-      - 0..1
-      - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).
-   *  - allelePrevalenceQualifier
-      - 
-      - string
-      - 0..1
-      - Reports whether the statement should be interpreted in the context of the variant being rare or common.
-   *  - geneContextQualifier
-      - 
-      - :ref:`MappableConcept`
-      - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement.
-
diff --git a/schema/va-spec/base/json/VariantDiagnosticProposition b/schema/va-spec/base/json/VariantDiagnosticProposition
@@ -51,6 +51,28 @@
          "description": "A variant that is the subject of the Proposition.",
          "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)."
       },
+      "geneContextQualifier": {
+         "description": "Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).",
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept"
+            },
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
+            }
+         ]
+      },
+      "alleleOriginQualifier": {
+         "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or another more nuanced concept.",
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept"
+            },
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
+            }
+         ]
+      },
       "type": {
          "type": "string",
          "description": "MUST be \"VariantDiagnosticProposition\".",
@@ -78,27 +100,6 @@
          ],
          "description": "The disease that is evaluated for diagnosis.",
          "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein."
-      },
-      "alleleOriginQualifier": {
-         "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).",
-         "type": "string",
-         "enum": [
-            "germline",
-            "somatic",
-            "combined"
-         ]
-      },
-      "allelePrevalenceQualifier": {
-         "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.",
-         "type": "string",
-         "enum": [
-            "rare",
-            "common"
-         ]
-      },
-      "geneContextQualifier": {
-         "description": "Reports a gene impacted by the variant, which may contribute to the diagnostic association  in the Proposition.",
-         "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept"
       }
    },
    "required": [