Merge branch '1.x' into mbrush-description-text-updates

schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml

@@ -11,7 +11,7 @@ imports:
 $defs:
   CohortAlleleFrequencyStudyResult:
     inherits: va-core:StudyResult
-    maturity: draft
+    maturity: trial use
     type: object
     description: >-
       A StudyResult that reports measures related to the frequency of an Allele in a cohort

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.

schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst

@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. 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**

schema/va-spec/base/def/DataSet.rst

@@ -67,11 +67,8 @@ Some DataSet attributes are inherited from :ref:`gks-core:Entity`.
       - A specific type of data set the DataSet instance represents (e.g. a 'clinical data set', a 'sequencing data set', a 'gene expression data set', a 'genome annotation data set')
    *  - reportedIn
       - 
-                        .. 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:`Document` | :ref:`iriReference`
-      - 0..m
+      - 0..1
       - A document in which the the Method is reported.
    *  - releaseDate
       - 

schema/va-spec/base/def/ExperimentalVariantFunctionalImpactProposition.rst

@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. 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**
@@ -66,7 +66,7 @@ Some ExperimentalVariantFunctionalImpactProposition attributes are inherited fro
       - 
       - string
       - 1..1
-      - The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter.
+      - The relationship this Proposition describes between the subject variant and object sequence feature whose function it may alter.
    *  - objectSequenceFeature
       - 
       - :ref:`iriReference` | :ref:`MappableConcept`

schema/va-spec/base/def/Method.rst

@@ -59,17 +59,11 @@ Some Method attributes are inherited from :ref:`gks-core:Entity`.
       - MUST be "Method".
    *  - subtype
       - 
-                        .. raw:: html
-
-                            <span style="background-color: #D3D3D3; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Draft Maturity Level">D</span>
       - :ref:`MappableConcept`
       - 0..1
       - A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol').
    *  - reportedIn
       - 
-                        .. 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:`Document` | :ref:`iriReference`
-      - 0..m
+      - 0..1
       - A document in which the the Method is reported.

schema/va-spec/base/def/StudyGroup.rst

@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. 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**
@@ -59,22 +59,17 @@ Some StudyGroup attributes are inherited from :ref:`gks-core:Entity`.
       - Must be "StudyGroup"
    *  - memberCount
       - 
+                        .. raw:: html
+
+                            <span style="background-color: #D3D3D3; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Draft Maturity Level">D</span>
       - integer
       - 0..1
       - The total number of individual members in the StudyGroup.
-   *  - isSubsetOf
-      - 
-                        .. 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:`StudyGroup`
-      - 0..m
-      - A larger StudyGroup of which this StudyGroup represents a subset.
    *  - characteristics
       - 
                         .. 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:`Characteristic`
+      - :ref:`MappableConcept`
       - 0..m
       - A feature or role shared by all members of the StudyGroup, representing a criterion for membership in the group.

schema/va-spec/base/def/VariantDiagnosticProposition.rst

@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. 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**
@@ -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.

schema/va-spec/base/def/VariantOncogenicityProposition.rst

@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. 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**
@@ -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.