diff --git a/schema/va-spec/aac-2017/def/VariantDiagnosticStudyStatement.rst b/schema/va-spec/aac-2017/def/VariantDiagnosticStudyStatement.rst index 4f9e943..99422b5 100644 --- 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 index 04aec66..41190d3 100644 --- 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 index 55405a2..5026c9d 100644 --- 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 index 262e14c..b50678a 100644 --- 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 index 1e7b45b..49e4942 100644 --- 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 index 4ab8163..9e46bed 100644 --- 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 index 49b2ddf..08886a1 100644 --- 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 index be9708b..a9e2799 100644 --- 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 index 6d01c6d..d64f44d 100644 --- 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 index d0dd253..edcb621 100644 --- 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 index 32bf250..b38f6a9 100644 --- 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 index 9352603..d5a6358 100644 --- 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 index 0722f01..5802907 100644 --- 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 index acce73f..f9109ce 100644 --- 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 index 1aad9bd..509903e 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactProposition.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactProposition.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** @@ -8,7 +8,7 @@ A proposition reporting a conclusion from a single assay or study about the func **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 index 65f4051..cdbd99b 100644 --- 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 index 93f25f6..f823a9c 100644 --- 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 index 43389bc..c58c865 100644 --- 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 index 5693c33..e9b8772 100644 --- 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 index acea200..d289e55 100644 --- 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 index 8cce5b2..aafb59f 100644 --- 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 index d1f4fa5..ec87afe 100644 --- 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 index c297f9a..901481f 100644 --- 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 new file mode 100644 index 0000000..960fe98 --- /dev/null +++ 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 + + ⋮ + - string + - 0..m + - Alternative name(s) for the Entity. + * - extensions + - + .. raw:: html + + ⋮ + - :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 index 083c36d..fbc27d4 100644 --- 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 index 1a727d9..ab4c0cc 100644 --- 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 index 0ca81e7..b88795a 100644 --- 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** diff --git a/schema/va-spec/base/def/VariantDiagnosticProposition.rst b/schema/va-spec/base/def/VariantDiagnosticProposition.rst index 63e5505..5f79ca0 100644 --- a/schema/va-spec/base/def/VariantDiagnosticProposition.rst +++ b/schema/va-spec/base/def/VariantDiagnosticProposition.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** @@ -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:`Proposition`. +Some VariantDiagnosticProposition attributes are inherited from :ref:`SubjectVariantProposition`. .. list-table:: :class: clean-wrap @@ -52,21 +52,16 @@ Some VariantDiagnosticProposition attributes are inherited from :ref:`Propositio - :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 "VariantDiagnosticProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Proposition. * - predicate - - string diff --git a/schema/va-spec/base/def/VariantOncogenicityProposition.rst b/schema/va-spec/base/def/VariantOncogenicityProposition.rst index ee627c4..4237b3d 100644 --- a/schema/va-spec/base/def/VariantOncogenicityProposition.rst +++ b/schema/va-spec/base/def/VariantOncogenicityProposition.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** @@ -8,7 +8,7 @@ A Proposition reporting a conclusion from a single study that supports or refute **Information Model** -Some VariantOncogenicityProposition attributes are inherited from :ref:`Proposition`. +Some VariantOncogenicityProposition attributes are inherited from :ref:`SubjectVariantProposition`. .. list-table:: :class: clean-wrap @@ -52,21 +52,16 @@ Some VariantOncogenicityProposition attributes are inherited from :ref:`Proposit - :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 "VariantOncogenicityProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Proposition. * - predicate - - string diff --git a/schema/va-spec/base/def/VariantPathogenicityProposition.rst b/schema/va-spec/base/def/VariantPathogenicityProposition.rst index 8d6a059..72146bd 100644 --- a/schema/va-spec/base/def/VariantPathogenicityProposition.rst +++ b/schema/va-spec/base/def/VariantPathogenicityProposition.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** @@ -8,7 +8,7 @@ A proposition describing the role of a variant in causing an inherited condition **Information Model** -Some VariantPathogenicityProposition attributes are inherited from :ref:`Proposition`. +Some VariantPathogenicityProposition attributes are inherited from :ref:`SubjectVariantProposition`. .. list-table:: :class: clean-wrap @@ -52,21 +52,16 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`Proposi - :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 "VariantPathogenicityProposition" - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Statement. * - predicate - - string diff --git a/schema/va-spec/base/def/VariantPrognosticProposition.rst b/schema/va-spec/base/def/VariantPrognosticProposition.rst index 63bd84f..0cf0d2c 100644 --- a/schema/va-spec/base/def/VariantPrognosticProposition.rst +++ b/schema/va-spec/base/def/VariantPrognosticProposition.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** @@ -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:`Proposition`. +Some VariantPrognosticProposition attributes are inherited from :ref:`SubjectVariantProposition`. .. list-table:: :class: clean-wrap @@ -52,21 +52,16 @@ Some VariantPrognosticProposition attributes are inherited from :ref:`Propositio - :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 "VariantPrognosticProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Proposition. * - predicate - - string diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseProposition.rst b/schema/va-spec/base/def/VariantTherapeuticResponseProposition.rst index 24a3d60..5a62eb2 100644 --- a/schema/va-spec/base/def/VariantTherapeuticResponseProposition.rst +++ b/schema/va-spec/base/def/VariantTherapeuticResponseProposition.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** @@ -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:`Proposition`. +Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`SubjectVariantProposition`. .. list-table:: :class: clean-wrap @@ -52,21 +52,16 @@ Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`P - :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 "VariantTherapeuticResponseProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Statement. * - predicate - - string diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactProposition b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactProposition index 054f4db..39e5be1 100644 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactProposition +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactProposition @@ -36,17 +36,6 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"ExperimentalVariantFunctionalImpactProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "ExperimentalVariantFunctionalImpactProposition", - "default": "ExperimentalVariantFunctionalImpactProposition" - }, "subjectVariant": { "oneOf": [ { @@ -59,9 +48,16 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" } ], - "description": "A protein or genomic contextual or canonical molecular variant.", + "description": "A variant that is the subject of the Proposition.", "$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)." }, + "type": { + "type": "string", + "description": "MUST be \"ExperimentalVariantFunctionalImpactProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "ExperimentalVariantFunctionalImpactProposition", + "default": "ExperimentalVariantFunctionalImpactProposition" + }, "predicate": { "type": "string", "description": "The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter.", diff --git a/schema/va-spec/base/json/SubjectVariantProposition b/schema/va-spec/base/json/SubjectVariantProposition new file mode 100644 index 0000000..d65f6d9 --- /dev/null +++ b/schema/va-spec/base/json/SubjectVariantProposition @@ -0,0 +1,27 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/SubjectVariantProposition", + "title": "SubjectVariantProposition", + "maturity": "draft", + "description": "A Proposition that has a variant as the subject.", + "oneOf": [ + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactProposition" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticProposition" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantOncogenicityProposition" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticProposition" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseProposition" + } + ] +} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantDiagnosticProposition b/schema/va-spec/base/json/VariantDiagnosticProposition index 9858b9f..6280df2 100644 --- a/schema/va-spec/base/json/VariantDiagnosticProposition +++ b/schema/va-spec/base/json/VariantDiagnosticProposition @@ -36,17 +36,6 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantDiagnosticProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantDiagnosticProposition", - "default": "VariantDiagnosticProposition" - }, "subjectVariant": { "oneOf": [ { @@ -56,12 +45,19 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" } ], "description": "A variant that is the subject of the Proposition.", "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." }, + "type": { + "type": "string", + "description": "MUST be \"VariantDiagnosticProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantDiagnosticProposition", + "default": "VariantDiagnosticProposition" + }, "predicate": { "type": "string", "description": "The relationship declared to hold between the subject and the object of the Statement.", diff --git a/schema/va-spec/base/json/VariantOncogenicityProposition b/schema/va-spec/base/json/VariantOncogenicityProposition index b52a271..17aa043 100644 --- a/schema/va-spec/base/json/VariantOncogenicityProposition +++ b/schema/va-spec/base/json/VariantOncogenicityProposition @@ -36,17 +36,6 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantOncogenicityProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantOncogenicityProposition", - "default": "VariantOncogenicityProposition" - }, "subjectVariant": { "oneOf": [ { @@ -56,12 +45,19 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" } ], "description": "A variant that is the subject of the Proposition.", "$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)." }, + "type": { + "type": "string", + "description": "MUST be \"VariantOncogenicityProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantOncogenicityProposition", + "default": "VariantOncogenicityProposition" + }, "predicate": { "type": "string", "description": "The relationship declared to hold between the subject and the object of the Statement.", diff --git a/schema/va-spec/base/json/VariantPathogenicityProposition b/schema/va-spec/base/json/VariantPathogenicityProposition index 94b6c30..13ed1fc 100644 --- a/schema/va-spec/base/json/VariantPathogenicityProposition +++ b/schema/va-spec/base/json/VariantPathogenicityProposition @@ -36,17 +36,6 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "Must be \"VariantPathogenicityProposition\"", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantPathogenicityProposition", - "default": "VariantPathogenicityProposition" - }, "subjectVariant": { "oneOf": [ { @@ -56,12 +45,19 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" } ], - "description": "A variant that is the subject of the Statement.", + "description": "A variant that is the subject of the Proposition.", "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." }, + "type": { + "type": "string", + "description": "Must be \"VariantPathogenicityProposition\"", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantPathogenicityProposition", + "default": "VariantPathogenicityProposition" + }, "predicate": { "type": "string", "description": "The relationship declared to hold between the subject and the object of the Statement.", diff --git a/schema/va-spec/base/json/VariantPrognosticProposition b/schema/va-spec/base/json/VariantPrognosticProposition index b9db9cd..6298a1f 100644 --- a/schema/va-spec/base/json/VariantPrognosticProposition +++ b/schema/va-spec/base/json/VariantPrognosticProposition @@ -36,17 +36,6 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantPrognosticProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantPrognosticProposition", - "default": "VariantPrognosticProposition" - }, "subjectVariant": { "oneOf": [ { @@ -56,12 +45,19 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" } ], "description": "A variant that is the subject of the Proposition.", "$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)." }, + "type": { + "type": "string", + "description": "MUST be \"VariantPrognosticProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantPrognosticProposition", + "default": "VariantPrognosticProposition" + }, "predicate": { "type": "string", "description": "The relationship declared to hold between the subject and the object of the Statement.", diff --git a/schema/va-spec/base/json/VariantTherapeuticResponseProposition b/schema/va-spec/base/json/VariantTherapeuticResponseProposition index fa95fe3..acd328d 100644 --- a/schema/va-spec/base/json/VariantTherapeuticResponseProposition +++ b/schema/va-spec/base/json/VariantTherapeuticResponseProposition @@ -36,17 +36,6 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantTherapeuticResponseProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantTherapeuticResponseProposition", - "default": "VariantTherapeuticResponseProposition" - }, "subjectVariant": { "oneOf": [ { @@ -56,12 +45,19 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" } ], - "description": "A variant that is the subject of the Statement.", + "description": "A variant that is the subject of the Proposition.", "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." }, + "type": { + "type": "string", + "description": "MUST be \"VariantTherapeuticResponseProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantTherapeuticResponseProposition", + "default": "VariantTherapeuticResponseProposition" + }, "predicate": { "type": "string", "description": "The relationship declared to hold between the subject and the object of the Statement.", diff --git a/schema/va-spec/base/va-spec-source.yaml b/schema/va-spec/base/va-spec-source.yaml index e263a29..18394de 100644 --- a/schema/va-spec/base/va-spec-source.yaml +++ b/schema/va-spec/base/va-spec-source.yaml @@ -226,19 +226,7 @@ $defs: Propositions may be used in two contexts; (1) by Statements that assert them to be true or false, or describe the overall level of confidence/evidence for or against them; (2) by Evidence Lines that report the direction and strength of an evidence-based argument for the Proposition. - oneOf: - - $ref: "#/$defs/ExperimentalVariantFunctionalImpactProposition" - - $ref: "#/$defs/VariantPathogenicityProposition" - - $ref: "#/$defs/VariantDiagnosticProposition" - - $ref: "#/$defs/VariantPrognosticProposition" - - $ref: "#/$defs/VariantOncogenicityProposition" - - $ref: "#/$defs/VariantTherapeuticResponseProposition" heritableProperties: - propositionText: - type: string - description: >- - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for - Breast Cancer". subject: oneOf: - type: object @@ -292,6 +280,28 @@ $defs: - predicate - object + SubjectVariantProposition: + inherits: Proposition + maturity: draft + description: >- + A :ref:`Proposition` that has a variant as the subject. + oneOf: + - $ref: "#/$defs/ExperimentalVariantFunctionalImpactProposition" + - $ref: "#/$defs/VariantPathogenicityProposition" + - $ref: "#/$defs/VariantDiagnosticProposition" + - $ref: "#/$defs/VariantPrognosticProposition" + - $ref: "#/$defs/VariantOncogenicityProposition" + - $ref: "#/$defs/VariantTherapeuticResponseProposition" + heritableProperties: + subjectVariant: + extends: subject + oneOf: + - $ref: "/ga4gh/schema/vrs/2.x/json/MolecularVariation" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: A variant that is the subject of the Proposition. + + # concrete core classes section -- Method, Contribution, Document, Agent, Statement, EvidenceLine, DataSet, StudyGroup Method: type: object @@ -832,7 +842,7 @@ $defs: # Variant Functional Impact Proposition ExperimentalVariantFunctionalImpactProposition: - inherits: Proposition + inherits: SubjectVariantProposition maturity: draft type: object description: >- @@ -844,13 +854,6 @@ $defs: const: "ExperimentalVariantFunctionalImpactProposition" default: "ExperimentalVariantFunctionalImpactProposition" description: MUST be "ExperimentalVariantFunctionalImpactProposition". - subjectVariant: - extends: subject - oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/MolecularVariation" - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: A protein or genomic contextual or canonical molecular variant. predicate: extends: predicate description: >- @@ -878,37 +881,14 @@ $defs: - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - type: object additionalProperties: true - - # impactTypeQualifier: - # description: >- - # A term describing a specific type of functional impact that the variant is determined - # to have on the indicated sequence feature (e.g. decreased activity, dominant negative, - # neomorphic, reduced Ca2+ binding activity). - # $comment: >- - # Implementers may use a set of terms to use here that reflect the specific types of - # functional impact(s) measured by the assay(s) employed. It is recommended that terms - # are drawn from established terminologies where possible. - - # $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - - # # # Matt: At some point we should standardize to a set of permissible values. We could do this from the outset, based on early adopter needs, and growing from there. Or leave unconstrained initially and constrain later. - # # # I seeded an initial proposal that covers specific impact types used in MAVE and CIViC. Note that application/community specific terms these adopters want to use can be captured in the 'classification' slot. - # # # Note also that if there is a way to constrain permissible values when using the MappableConcept pattern, we could do that instead of an enum here. - # # type: string - # # enum: - # # - increased activity/function # maps to CIViC 'gain of function' - # # - decreased activity/function # maps to CIViC 'loss of function' - # # - novel activity/function # maps to CIViC 'neomorphic' - # # - dominant negative activity/function # maps to CIViC 'dominant negative' required: - - subjectVariant - predicate - objectSequenceFeature - studyContextQualifier # Variant Diagnostic Proposition VariantDiagnosticProposition: - inherits: Proposition + inherits: SubjectVariantProposition type: object maturity: draft description: >- @@ -922,13 +902,6 @@ $defs: const: "VariantDiagnosticProposition" default: "VariantDiagnosticProposition" description: MUST be "VariantDiagnosticProposition". - subjectVariant: - extends: subject - oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Variation" - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: A variant that is the subject of the Proposition. predicate: extends: predicate enum: @@ -963,13 +936,12 @@ $defs: diagnostic association in the Proposition. $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" required: - - subjectVariant - predicate - objectCondition # Variant Oncogenicity Proposition VariantOncogenicityProposition: - inherits: Proposition + inherits: SubjectVariantProposition maturity: draft type: object description: >- @@ -982,13 +954,6 @@ $defs: const: "VariantOncogenicityProposition" default: "VariantOncogenicityProposition" description: MUST be "VariantOncogenicityProposition". - subjectVariant: - extends: subject - oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Variation" - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: A variant that is the subject of the Proposition. predicate: extends: predicate enum: @@ -1025,13 +990,12 @@ $defs: role in the Proposition. $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" required: - - subjectVariant - predicate - objectTumorType # Variant Pathogenicity Proposition VariantPathogenicityProposition: - inherits: Proposition + inherits: SubjectVariantProposition maturity: draft type: object description: >- @@ -1042,13 +1006,6 @@ $defs: const: VariantPathogenicityProposition default: VariantPathogenicityProposition description: Must be "VariantPathogenicityProposition" - subjectVariant: - extends: subject - oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Variation" - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: A variant that is the subject of the Statement. predicate: extends: predicate const: isCausalFor @@ -1084,13 +1041,12 @@ $defs: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" required: - - subjectVariant - predicate - objectCondition # Variant Prognostic Proposition VariantPrognosticProposition: - inherits: Proposition + inherits: SubjectVariantProposition type: object maturity: draft description: >- @@ -1103,13 +1059,6 @@ $defs: const: "VariantPrognosticProposition" default: "VariantPrognosticProposition" description: MUST be "VariantPrognosticProposition". - subjectVariant: - extends: subject - oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Variation" - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: A variant that is the subject of the Proposition. predicate: extends: predicate enum: @@ -1144,13 +1093,12 @@ $defs: prognostic association in the Proposition. $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" required: - - subjectVariant - predicate - objectCondition # Variant Therapeutic Response Proposition VariantTherapeuticResponseProposition: - inherits: Proposition + inherits: SubjectVariantProposition maturity: draft type: object description: >- @@ -1163,13 +1111,6 @@ $defs: const: "VariantTherapeuticResponseProposition" default: "VariantTherapeuticResponseProposition" description: MUST be "VariantTherapeuticResponseProposition". - subjectVariant: - extends: subject - oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Variation" - - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: A variant that is the subject of the Statement. predicate: extends: predicate enum: @@ -1213,7 +1154,6 @@ $defs: sensitivity or resistance reported in the Statement. $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" required: - - subjectVariant - predicate - objectTherapeutic - conditionQualifier \ No newline at end of file diff --git a/schema/va-spec/ccv-2022/def/VariantOncogenicityFunctionalImpactEvidenceLine.rst b/schema/va-spec/ccv-2022/def/VariantOncogenicityFunctionalImpactEvidenceLine.rst index 262e14c..b50678a 100644 --- a/schema/va-spec/ccv-2022/def/VariantOncogenicityFunctionalImpactEvidenceLine.rst +++ b/schema/va-spec/ccv-2022/def/VariantOncogenicityFunctionalImpactEvidenceLine.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/ccv-2022/def/VariantOncogenicityStudyStatement.rst b/schema/va-spec/ccv-2022/def/VariantOncogenicityStudyStatement.rst index 2603256..398f59a 100644 --- a/schema/va-spec/ccv-2022/def/VariantOncogenicityStudyStatement.rst +++ b/schema/va-spec/ccv-2022/def/VariantOncogenicityStudyStatement.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**