Add GeneDiseaseValidityProposition

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

@@ -0,0 +1,79 @@
+.. 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 that variants affecting a particular Gene are valid for evaluation as causal for some Condition using appropriate variant classification criteria, given a specific mode of inheritance.
+
+**Information Model**
+
+Some GeneDiseaseValidityProposition 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.
+   *  - name
+      -
+      - string
+      - 0..1
+      - A primary name for the entity.
+   *  - description
+      -
+      - string
+      - 0..1
+      - A free-text description of the Entity.
+   *  - aliases
+      -
+                        .. 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.
+   *  - type
+      -
+      - string
+      - 1..1
+      - MUST be "GeneDiseaseValidityProposition".
+   *  - subjectGene
+      -
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 1..1
+      - The Entity or concept about which the Proposition is made.
+   *  - predicate
+      -
+      - string
+      - 1..1
+      - MUST be "variantsInGeneCausalFor".
+   *  - objectCondition
+      -
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 1..1
+      - An Entity or concept that is related to the subject of a Proposition via its predicate.
+   *  - modeOfInheritanceQualifier
+      -
+      - :ref:`MappableConcept` | :ref:`iriReference`
+      - 0..1
+      -

schema/va-spec/base/json/EvidenceLine

@@ -86,6 +86,9 @@
             {
                "$ref": "/ga4gh/schema/va-spec/1.0.1/base/json/ExperimentalVariantFunctionalImpactProposition"
             },
+            {
+               "$ref": "/ga4gh/schema/va-spec/1.0.1/base/json/GeneDiseaseValidityProposition"
+            },
             {
                "$ref": "/ga4gh/schema/va-spec/1.0.1/base/json/VariantClinicalSignificanceProposition"
             },

schema/va-spec/base/json/GeneDiseaseValidityProposition

@@ -0,0 +1,95 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/va-spec/1.0.1/base/json/GeneDiseaseValidityProposition",
+   "title": "GeneDiseaseValidityProposition",
+   "maturity": "draft",
+   "type": "object",
+   "description": "A proposition that variants affecting a particular Gene are valid for evaluation as causal for some Condition using appropriate variant classification criteria, given a specific mode of inheritance.",
+   "properties": {
+      "id": {
+         "type": "string",
+         "description": "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.",
+         "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context."
+      },
+      "name": {
+         "type": "string",
+         "description": "A primary name for the entity."
+      },
+      "description": {
+         "type": "string",
+         "description": "A free-text description of the Entity."
+      },
+      "aliases": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "type": "string"
+         },
+         "description": "Alternative name(s) for the Entity."
+      },
+      "extensions": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "$ref": "/ga4gh/schema/gks-core/1.1.0/json/Extension"
+         },
+         "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
+         "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
+      },
+      "type": {
+         "type": "string",
+         "description": "MUST be \"GeneDiseaseValidityProposition\".",
+         "$comment": "MUST be the name of a concrete class from the data model.",
+         "const": "GeneDiseaseValidityProposition",
+         "default": "GeneDiseaseValidityProposition"
+      },
+      "subjectGene": {
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.1.0/json/MappableConcept"
+            },
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.1.0/json/iriReference"
+            }
+         ],
+         "description": "The Entity or concept about which the Proposition is made.",
+         "$comment": "In profiles for most VA-Spec implementations, the subject will be a some type of genetic variation. However, the Core VA model is domain-agnostic, and supports Propositions about any type of Entity. Some data providers may want to make statements about other entities or concepts that represent evidence for a Propositions about genetic variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)."
+      },
+      "predicate": {
+         "type": "string",
+         "description": "MUST be \"variantsInGeneCausalFor\".",
+         "$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": "variantsInGeneCausalFor",
+         "default": "variantsInGeneCausalFor"
+      },
+      "objectCondition": {
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.1.0/json/MappableConcept"
+            },
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.1.0/json/iriReference"
+            }
+         ],
+         "description": "An Entity or concept that is related to the subject of a Proposition via its predicate.",
+         "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject. When the subject is a genetic variation, the object is often a disease, phenotype, therapeutic intervention, or gene."
+      },
+      "modeOfInheritanceQualifier": {
+         "oneOf": [
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.1.0/json/MappableConcept"
+            },
+            {
+               "$ref": "/ga4gh/schema/gks-core/1.1.0/json/iriReference"
+            }
+         ]
+      }
+   },
+   "required": [
+      "objectCondition",
+      "predicate",
+      "subjectGene",
+      "type"
+   ],
+   "additionalProperties": false
+}

schema/va-spec/base/json/Statement

@@ -87,6 +87,9 @@
             {
                "$ref": "/ga4gh/schema/va-spec/1.0.1/base/json/ExperimentalVariantFunctionalImpactProposition"
             },
+            {
+               "$ref": "/ga4gh/schema/va-spec/1.0.1/base/json/GeneDiseaseValidityProposition"
+            },
             {
                "$ref": "/ga4gh/schema/va-spec/1.0.1/base/json/VariantClinicalSignificanceProposition"
             },

schema/va-spec/base/va-core-source.yaml

@@ -1001,6 +1001,41 @@ $defs:
     - objectTherapeutic
     - conditionQualifier
 
+  GeneDiseaseValidityProposition:
+    inherits: Proposition
+    maturity: draft
+    type: object
+    description: "A proposition that variants affecting a particular Gene are valid for evaluation as causal for some Condition using appropriate variant classification criteria, given a specific mode of inheritance."
+    properties:
+      type:
+        extends: type
+        const: GeneDiseaseValidityProposition
+        default: GeneDiseaseValidityProposition
+        description: MUST be "GeneDiseaseValidityProposition".
+      subjectGene:
+        extends: subject
+        oneOf:
+          - $refCurie: gks.core:MappableConcept
+          - $refCurie: gks.core:iriReference
+      predicate:
+        extends: predicate
+        const: "variantsInGeneCausalFor"
+        default: "variantsInGeneCausalFor"
+        description: MUST be "variantsInGeneCausalFor".
+      objectCondition:
+        extends: object
+        oneOf:
+          - $refCurie: gks.core:MappableConcept
+          - $refCurie: gks.core:iriReference
+      modeOfInheritanceQualifier:
+        oneOf:
+          - $refCurie: gks.core:MappableConcept
+          - $refCurie: gks.core:iriReference
+    required:
+      - predicate
+      - subjectGene
+      - objectCondition
+
   CohortAlleleFrequencyStudyResult:
     inherits: StudyResult
     maturity: trial use