Proposition trial use (#227)

* removing RecordMetadata per #225 * EVFI proposition to TU * update Cat-VRS submodule * study group review and TU * test and update CAF to TU
ga4gh · Nov 26, 2024 · fb30f7f · fb30f7f
1 parent 0228579
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diff --git a/schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml b/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

diff --git a/schema/va-spec/base/def/Characteristic.rst b/schema/va-spec/base/def/Characteristic.rst
diff --git a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst b/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**

diff --git a/schema/va-spec/base/def/DataSet.rst b/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
       - 

diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactProposition.rst b/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`

diff --git a/schema/va-spec/base/def/Method.rst b/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.
diff --git a/schema/va-spec/base/def/StudyGroup.rst b/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.
diff --git a/schema/va-spec/base/json/Characteristic b/schema/va-spec/base/json/Characteristic
diff --git a/schema/va-spec/base/json/CohortAlleleFrequencyStudyResult b/schema/va-spec/base/json/CohortAlleleFrequencyStudyResult
@@ -2,7 +2,7 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/CohortAlleleFrequencyStudyResult",
    "title": "CohortAlleleFrequencyStudyResult",
-   "maturity": "draft",
+   "maturity": "trial use",
    "type": "object",
    "description": "A StudyResult that reports measures related to the frequency of an Allele in a cohort",
    "properties": {

diff --git a/schema/va-spec/base/json/DataSet b/schema/va-spec/base/json/DataSet
@@ -51,18 +51,14 @@
          "description": "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": {
-         "type": "array",
-         "ordered": false,
-         "items": {
-            "oneOf": [
-               {
-                  "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Document"
-               },
-               {
-                  "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
-               }
-            ]
-         },
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Document"
+            },
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
+            }
+         ],
          "description": "A document in which the the Method is reported."
       },
       "releaseDate": {

diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactProposition b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactProposition
@@ -2,7 +2,7 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactProposition",
    "title": "ExperimentalVariantFunctionalImpactProposition",
-   "maturity": "draft",
+   "maturity": "trial use",
    "type": "object",
    "description": "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).",
    "properties": {
@@ -60,9 +60,9 @@
       },
       "predicate": {
          "type": "string",
-         "description": "The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter.",
+         "description": "The relationship this Proposition describes between the subject variant and object sequence feature whose function it may alter.",
          "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.",
-         "const": "impactsFunctionOf"
+         "default": "impactsFunctionOf"
       },
       "objectSequenceFeature": {
          "oneOf": [

diff --git a/schema/va-spec/base/json/Method b/schema/va-spec/base/json/Method
@@ -46,23 +46,18 @@
       },
       "subtype": {
          "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept",
-         "maturity": "draft",
-         "$comment": "This attribute can be used to report a specific type for the Method, in cases where a model does not define Method subclasses for this purpose.  Implementers can define their own set of method type codes/terms, to match the needs of their application.\n  reportedIn:",
-         "description": "A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol')."
+         "description": "A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol').",
+         "$comment": "This attribute can be used to report a specific type for the Method, in cases where a model does not define Method subclasses for this purpose.  Implementers can define their own set of method type codes/terms, to match the needs of their application."
       },
       "reportedIn": {
-         "type": "array",
-         "ordered": false,
-         "items": {
-            "oneOf": [
-               {
-                  "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Document"
-               },
-               {
-                  "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
-               }
-            ]
-         },
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Document"
+            },
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
+            }
+         ],
          "description": "A document in which the the Method is reported."
       }
    },

diff --git a/schema/va-spec/base/json/StudyGroup b/schema/va-spec/base/json/StudyGroup
@@ -3,7 +3,7 @@
    "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/StudyGroup",
    "title": "StudyGroup",
    "type": "object",
-   "maturity": "draft",
+   "maturity": "trial use",
    "description": "A collection of individuals or specimens from the same taxonomic class, selected for analysis in a scientific study based on their exhibiting one or more common characteristics  (e.g. species, race, age, gender, disease state, income). May be referred to as a 'cohort' or 'population' in specific research settings.",
    "$comment": "A Study Group may include all participants in a given study, or specific subsets that are designated based on shared roles or characteristics.",
    "properties": {
@@ -45,24 +45,19 @@
          "default": "StudyGroup"
       },
       "memberCount": {
+         "maturity": "draft",
+         "$comment": "this is draft until we see utility in real-world datasets",
          "type": "integer",
          "description": "The total number of individual members in the StudyGroup."
       },
-      "isSubsetOf": {
-         "type": "array",
-         "items": {
-            "$ref": "/ga4gh/schema/va-spec/1.x/base/json/StudyGroup"
-         },
-         "ordered": false,
-         "description": "A larger StudyGroup of which this StudyGroup represents a subset."
-      },
       "characteristics": {
          "type": "array",
          "items": {
-            "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Characteristic"
+            "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept"
          },
          "ordered": false,
-         "description": "A feature or role shared by all members of the StudyGroup, representing a criterion for membership in the group."
+         "description": "A feature or role shared by all members of the StudyGroup, representing a criterion for membership in the group.",
+         "$comment": "We should evaluate this for use with boolean operators before going normative"
       }
    },
    "required": [