From 8d153e7904973bfb895baae6373c5dc8016dcb9c Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Thu, 7 Nov 2024 00:17:47 -0500 Subject: [PATCH 01/20] Moved outstanding exp-func-imp PR into this PR with latest reorg of folders --- .../pathogenicity-statement-source.yaml | 12 + schema/va-spec/base/def/Condition.rst | 23 -- ...ntalVariantFunctionalImpactStudyResult.rst | 95 ++++++++ ...VariantFunctionalImpactStudyStatement.rst} | 49 ++-- schema/va-spec/base/def/Therapeutic.rst | 23 -- schema/va-spec/base/def/TherapyGroup.rst | 40 ---- schema/va-spec/base/def/TraitSet.rst | 40 ---- .../def/VariantPathogenicityStatement.rst | 120 ---------- ...riantTherapeuticResponseStudyStatement.rst | 125 ---------- .../exp-func-impact-study-result-source.yaml | 40 ++++ ...xp-func-impact-study-statement-source.yaml | 102 +++++++++ schema/va-spec/base/json/Condition | 15 -- ...rimentalVariantFunctionalImpactStudyResult | 149 ++++++++++++ ...ntalVariantFunctionalImpactStudyStatement} | 97 ++++---- schema/va-spec/base/json/Therapeutic | 15 -- schema/va-spec/base/json/TherapyGroup | 38 --- schema/va-spec/base/json/TraitSet | 38 --- .../base/json/VariantPrognosticStudyStatement | 204 ----------------- .../VariantTherapeuticResponseStudyStatement | 216 ------------------ .../base/pathogenicity-statement-source.yaml | 89 ++++++++ 20 files changed, 556 insertions(+), 974 deletions(-) create mode 100644 schema/va-spec/acmg-2015/pathogenicity-statement-source.yaml delete mode 100644 schema/va-spec/base/def/Condition.rst create mode 100644 schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst rename schema/va-spec/base/def/{VariantPrognosticStudyStatement.rst => ExperimentalVariantFunctionalImpactStudyStatement.rst} (66%) delete mode 100644 schema/va-spec/base/def/Therapeutic.rst delete mode 100644 schema/va-spec/base/def/TherapyGroup.rst delete mode 100644 schema/va-spec/base/def/TraitSet.rst delete mode 100644 schema/va-spec/base/def/VariantPathogenicityStatement.rst delete mode 100644 schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst create mode 100644 schema/va-spec/base/exp-func-impact-study-result-source.yaml create mode 100644 schema/va-spec/base/exp-func-impact-study-statement-source.yaml delete mode 100644 schema/va-spec/base/json/Condition create mode 100644 schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult rename schema/va-spec/base/json/{VariantPathogenicityStatement => ExperimentalVariantFunctionalImpactStudyStatement} (79%) delete mode 100644 schema/va-spec/base/json/Therapeutic delete mode 100644 schema/va-spec/base/json/TherapyGroup delete mode 100644 schema/va-spec/base/json/TraitSet delete mode 100644 schema/va-spec/base/json/VariantPrognosticStudyStatement delete mode 100644 schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement diff --git a/schema/va-spec/acmg-2015/pathogenicity-statement-source.yaml b/schema/va-spec/acmg-2015/pathogenicity-statement-source.yaml new file mode 100644 index 0000000..b063770 --- /dev/null +++ b/schema/va-spec/acmg-2015/pathogenicity-statement-source.yaml @@ -0,0 +1,12 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/acmg-2015/pathogenicity-statement-source.yaml" +title: ACMG 2015 Variant Pathogenicity Statement Standard Profile +strict: true + +imports: + va-spec: ./base/pathogenicity-statement-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: diff --git a/schema/va-spec/base/def/Condition.rst b/schema/va-spec/base/def/Condition.rst deleted file mode 100644 index 0c1fb95..0000000 --- a/schema/va-spec/base/def/Condition.rst +++ /dev/null @@ -1,23 +0,0 @@ - -.. 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 set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement. - -**Information Model** - - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst new file mode 100644 index 0000000..db546ba --- /dev/null +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst @@ -0,0 +1,95 @@ + +.. 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 StudyResult that reports a functional impact score from a variant functional assay or study. + +**Information Model** + +Some ExperimentalVariantFunctionalImpactStudyResult attributes are inherited from :ref:`gks-core:StudyResult`. + +.. list-table:: + :class: clean-wrap + :header-rows: 1 + :align: left + :widths: auto + + * - Field + - 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. + * - label + - string + - 0..1 + - A primary name for the entity. + * - description + - string + - 0..1 + - A free-text description of the Entity. + * - alternativeLabels + - string + - 0..m + - Alternative name(s) for the Entity. + * - extensions + - :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. + * - contributions + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - recordMetadata + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - componentResult + - :ref:`StudyResult` + - 0..m + - Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) . + * - studyGroup + - :ref:`StudyGroup` + - 0..1 + - A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult. + * - ancillaryResults + - object + - 0..1 + - + * - qualityMeasures + - object + - 0..1 + - + * - type + - string + - 1..1 + - MUST be "ExperimentalVariantFunctionalImpactStudyResult". + * - focusVariant + - :ref:`MolecularVariation` | :ref:`iriReference` + - 0..1 + - The genetic variant for which a functional impact score is generated. + * - functionalImpactScore + - number + - 0..1 + - The score of the variant impact measured in the assay or study. + * - specifiedBy + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - The assay that was performed to generate the reported functional impact score. + * - sourceDataSet + - :ref:`DataSet` + - 0..m + - The full data set that provided the reported the functional impact score. diff --git a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst similarity index 66% rename from schema/va-spec/base/def/VariantPrognosticStudyStatement.rst rename to schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst index 41cf0ea..584b90d 100644 --- a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst @@ -1,16 +1,15 @@ -.. 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`. +.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. +A statement 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). **Information Model** -Some VariantPrognosticStudyStatement attributes are inherited from :ref:`gks-core:Statement`. +Some ExperimentalVariantFunctionalImpactStudyStatement attributes are inherited from :ref:`gks-core:Statement`. .. list-table:: :class: clean-wrap @@ -42,10 +41,6 @@ Some VariantPrognosticStudyStatement attributes are inherited from :ref:`gks-cor - :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. - * - specifiedBy - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions - :ref:`Contribution` - 0..m @@ -82,10 +77,6 @@ Some VariantPrognosticStudyStatement attributes are inherited from :ref:`gks-cor - string - 0..1 - A natural-language expression of what a Statement asserts to be true. - * - classification - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines - :ref:`EvidenceLine` - 0..m @@ -93,28 +84,32 @@ Some VariantPrognosticStudyStatement attributes are inherited from :ref:`gks-cor * - type - string - 1..1 - - MUST be "VariantPrognosticStudyStatement". + - MUST be "ExperimentalVariantFunctionalImpactStudyStatement". * - subjectVariant - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - - A variant that is the subject of the Statement. + - A protein or genomic contextual or canonical molecular variant. * - predicate - string - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - :ref:`Condition` | :ref:`iriReference` + - The relationship this Statement describes between the subject Variant and object Sequence Feature whose function it may alter. + * - objectSequenceFeature + - :ref:`iriReference` | :ref:`MappableConcept` - 1..1 - - The disease that is evaluated for outcome. - * - alleleOriginQualifier + - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. + * - studyContextQualifier + - :ref:`Document` | :ref:`iriReference` + - 1..1 + - The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. + * - impactTypeQualifier - string - 0..1 - - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier + - 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). + * - classification - string - 0..1 - - Reports whether the statement should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - :ref:`MappableConcept` + - An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use. + * - specifiedBy + - :ref:`Method` | :ref:`iriReference` - 0..1 - - Reports a gene impacted by the variant, which may contribute to the prognostic association in the Statement. + - The method that specifies how the functional classification is ultimately assigned to the variant, based on interpretation of data from the supporting assay. May include information about thresholds applied on assay variant effect scores to derive the final classification. diff --git a/schema/va-spec/base/def/Therapeutic.rst b/schema/va-spec/base/def/Therapeutic.rst deleted file mode 100644 index 3aab6e1..0000000 --- a/schema/va-spec/base/def/Therapeutic.rst +++ /dev/null @@ -1,23 +0,0 @@ - -.. 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 group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that represents the object of a Therapeutic Response study statement. - -**Information Model** - - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description diff --git a/schema/va-spec/base/def/TherapyGroup.rst b/schema/va-spec/base/def/TherapyGroup.rst deleted file mode 100644 index 063889c..0000000 --- a/schema/va-spec/base/def/TherapyGroup.rst +++ /dev/null @@ -1,40 +0,0 @@ - -.. 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 group of therapies that are applied together in the context of a Therapeutic Response study statement. - -**Information Model** - -Some TherapyGroup attributes are inherited from :ref:`gks-core:Element`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description - * - id - - string - - 0..1 - - The 'logical' identifier of the data element 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. - * - extensions - - :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 - - 0..1 - - The type of the therapy group. - * - therapies - - :ref:`MappableConcept` - - 2..m - - A list of therapies that are applied together in the context of a Therapeutic Response study statement. diff --git a/schema/va-spec/base/def/TraitSet.rst b/schema/va-spec/base/def/TraitSet.rst deleted file mode 100644 index 1405122..0000000 --- a/schema/va-spec/base/def/TraitSet.rst +++ /dev/null @@ -1,40 +0,0 @@ - -.. 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 set of traits that are co-occurring in the context of a Variant Pathogenicity statement. - -**Information Model** - -Some TraitSet attributes are inherited from :ref:`gks-core:Element`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description - * - id - - string - - 0..1 - - The 'logical' identifier of the data element 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. - * - extensions - - :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 - - 0..1 - - The type of the set of traits. - * - traits - - :ref:`MappableConcept` - - 2..m - - A list of traits that are co-occurring in the context of a Variant Pathogenicity statement. diff --git a/schema/va-spec/base/def/VariantPathogenicityStatement.rst b/schema/va-spec/base/def/VariantPathogenicityStatement.rst deleted file mode 100644 index ea0138d..0000000 --- a/schema/va-spec/base/def/VariantPathogenicityStatement.rst +++ /dev/null @@ -1,120 +0,0 @@ - -.. 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 Statement describing the role of a variant in causing an inherited condition. - -**Information Model** - -Some VariantPathogenicityStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - 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. - * - label - - string - - 0..1 - - A primary name for the entity. - * - description - - string - - 0..1 - - A free-text description of the Entity. - * - alternativeLabels - - string - - 0..m - - Alternative name(s) for the Entity. - * - extensions - - :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. - * - specifiedBy - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - string - - 1..1 - - MUST be "VariantPathogenicityStatement". - * - subjectVariant - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Statement. - * - predicate - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The :ref:`Condition` for which the variant impact is stated. - * - penetranceQualifier - - string - - 0..1 - - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. - * - modeOfInheritanceQualifier - - :ref:`Coding` - - 0..m - - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. - * - geneContextQualifier - - :ref:`MappableConcept` | :ref:`iriReference` - - 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). diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst deleted file mode 100644 index e23f64b..0000000 --- a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst +++ /dev/null @@ -1,125 +0,0 @@ - -.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. - -**Information Model** - -Some VariantTherapeuticResponseStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - 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. - * - label - - string - - 0..1 - - A primary name for the entity. - * - description - - string - - 0..1 - - A free-text description of the Entity. - * - alternativeLabels - - string - - 0..m - - Alternative name(s) for the Entity. - * - extensions - - :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. - * - specifiedBy - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - string - - 1..1 - - MUST be "VariantTherapeuticResponseStudyStatement". - * - subjectVariant - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Statement. - * - predicate - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectTherapeutic - - :ref:`Therapeutic` | :ref:`iriReference` - - 1..1 - - A drug administration or other therapeutic procedure that the neoplasm is intended to respond to. - * - conditionQualifier - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements. - * - alleleOriginQualifier - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. - diff --git a/schema/va-spec/base/exp-func-impact-study-result-source.yaml b/schema/va-spec/base/exp-func-impact-study-result-source.yaml new file mode 100644 index 0000000..75b156f --- /dev/null +++ b/schema/va-spec/base/exp-func-impact-study-result-source.yaml @@ -0,0 +1,40 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/exp-func-impact-study-result-source.yaml" +title: Experimental Variant Functional Impact Statement +strict: true + +imports: + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + ExperimentalVariantFunctionalImpactStudyResult: + inherits: gks-core:StudyResult + maturity: trial use + type: object + description: >- + A StudyResult that reports a functional impact score from a variant functional assay or study. + properties: + type: + extends: type + const: "ExperimentalVariantFunctionalImpactStudyResult" + default: "ExperimentalVariantFunctionalImpactStudyResult" + description: MUST be "ExperimentalVariantFunctionalImpactStudyResult". + focusVariant: + extends: focus + oneOf: + - $ref: "/ga4gh/schema/vrs/2.x/json/MolecularVariation" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The genetic variant for which a functional impact score is generated. + functionalImpactScore: + type: number + description: The score of the variant impact measured in the assay or study. + specifiedBy: + extends: specifiedBy + description: >- + The assay that was performed to generate the reported functional impact score. + sourceDataSet: + extends: sourceDataSet + description: >- + The full data set that provided the reported the functional impact score. \ No newline at end of file diff --git a/schema/va-spec/base/exp-func-impact-study-statement-source.yaml b/schema/va-spec/base/exp-func-impact-study-statement-source.yaml new file mode 100644 index 0000000..f60389d --- /dev/null +++ b/schema/va-spec/base/exp-func-impact-study-statement-source.yaml @@ -0,0 +1,102 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/exp-func-impact-study-statement-source.yaml" +title: Experimental Variant Functional Impact Statement +strict: true + +imports: + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + ExperimentalVariantFunctionalImpactStudyStatement: + inherits: gks-core:Statement + maturity: trial use + type: object + description: >- + A statement 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: + type: + extends: type + const: "ExperimentalVariantFunctionalImpactStudyStatement" + default: "ExperimentalVariantFunctionalImpactStudyStatement" + description: MUST be "ExperimentalVariantFunctionalImpactStudyStatement". + 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: >- + The relationship this Statement describes between the subject Variant + and object Sequence Feature whose function it may alter. + const: impactsFunctionOf + objectSequenceFeature: + extends: object + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: "/ga4gh/schema/gks-core/1.x/MappableConcept" # See https://github.com/ga4gh/gks-common/pull/77 + description: >- + The sequence feature (typically a gene or gene product) on whose function the impact + of the subject variant is assessed. + studyContextQualifier: + description: >- + The assay in which the reported variant functional impact was determined - + providing a specific experimental context in which this effect is asserted to hold. + $comment: >- + The attribute is required in order to explicitly specify an assay or study context in + which the reported impact was observed. It's value can be a Document object, or an IRI + pointing to a document that describes the assay/study. This may be a publication, a + database record, or a bespoke document. + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/Document" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + impactTypeQualifier: # This qualifier allows more specific types of impacts to be reported - so the profile supports implementations like CIViC, ClinGen, and I think even some MAVE data. + 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. + + # TO DO: I feel like it would be good to try and standardize the values used here by defining an enum based on early adopter needs, and growing from there. + # I seeded an initial proposal that covers specific impact types used in MAVE and CIViC. Applciation/community specific terms these adopters want to use can be captured in the 'classification' slot. + # But we should consider if this is the best approach. + type: string + enum: + - increased activity # maps to CIViC 'gain of function' + - decreased activity # maps to CIViC 'loss of function' + - novel activity # maps to CIViC 'neomorphic' + - dominant negative activity # maps to CIViC 'dominant negative' + + classification: + extends: classification + description: >- + An term or phrase summarizing the impact reported in the Statement, providing + a functional classification of the subject variant that is familiar for a community of use. + $comment: >- + This is an optional attribute that can be used by data providers to provide a particular + community of users a functional impact classification in familiar terms, + that summarizes/complements the smeantics broken out in the SPOQ attributes of the Statement + (e.g. to mirror established community conventions or reflect language on the data providers + website or documentation). e.g. CIViC docs/web site uses terms like 'unaltered function', + 'gain of function', 'neomorphic', and 'unknown', which could be reropted here. + type: string # Idea here is to make it as easy and flexible possible to add values here for now - since the idea is to support community/application specific terms orf art. If we want to standradize or fomralize these later, we can. + specifiedBy: + extends: specifiedBy + description: >- + The method that specifies how the functional classification is ultimately assigned to + the variant, based on interpretation of data from the supporting assay. May include + information about thresholds applied on assay variant effect scores to derive the + final classification. + required: + - subjectVariant + - predicate + - objectSequenceFeature + - studyContextQualifier \ No newline at end of file diff --git a/schema/va-spec/base/json/Condition b/schema/va-spec/base/json/Condition deleted file mode 100644 index 479190e..0000000 --- a/schema/va-spec/base/json/Condition +++ /dev/null @@ -1,15 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/Condition", - "title": "Condition", - "maturity": "draft", - "description": "A set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/TraitSet" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - ] -} \ No newline at end of file diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult new file mode 100644 index 0000000..b686d92 --- /dev/null +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult @@ -0,0 +1,149 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyResult", + "title": "ExperimentalVariantFunctionalImpactStudyResult", + "maturity": "trial use", + "type": "object", + "description": "A StudyResult that reports a functional impact score from a variant functional assay or study.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "componentResult": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyResult" + }, + "description": "Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) .", + "$comment": "This attribute allows data creators to break down a StudyResult into finer-grained StudyResult instances with a narrower scope. For example, a StudyResult about the frequency of an allele in a global population of individuals can be broken down into separate 'component' Results about distinct subpopulations of individuals in the source data (e.g. frequency of the allele in asian vs african subpopulations, or male vs female subgroups)." + }, + "studyGroup": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyGroup", + "description": "A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult.", + "$comment": "For example, in a StudyResult holding allele frequency data, this attribute points to a StudyGroup object that describes characteristics of the population that the frequency data was generated from (e.g. 'East Asian', 'Female')." + }, + "ancillaryResults": { + "maturity": "draft", + "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", + "type": "object", + "additionalProperties": true + }, + "qualityMeasures": { + "maturity": "draft", + "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", + "type": "object", + "additionalProperties": true + }, + "type": { + "type": "string", + "const": "ExperimentalVariantFunctionalImpactStudyResult", + "default": "ExperimentalVariantFunctionalImpactStudyResult", + "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyResult\"." + }, + "focusVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" + } + ], + "description": "The genetic variant for which a functional impact score is generated.", + "$comment": "The 'focus' of a StudyResult is the what anchors selection of all data items and provenance information that it contains. This focus may be a single participant or subject of a study (e.g. one patient in a clinical study, or one allele in a population frequency analysis). It may be a study group defined as an experimental unit in the study (e.g. a specific treatment arm of a clinical study). Or it may be a variable defined as a unit of analysis in the study (e.g. 'exposure to nicotine' in an analysis correlating this variable with clinical outcomes)." + }, + "functionalImpactScore": { + "type": "number", + "description": "The score of the variant impact measured in the assay or study." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "The assay that was performed to generate the reported functional impact score.", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "sourceDataSet": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/DataSet" + }, + "description": "The full data set that provided the reported the functional impact score. ", + "maximum": 1, + "$comment": "In most cases, a StudyResult will be generated using data from one source dataset - but it is possible multiple datasets related to a single study contain data about a particular focus that get collected into a single StudyResult instance." + } + }, + "required": [ + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantPathogenicityStatement b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement similarity index 79% rename from schema/va-spec/base/json/VariantPathogenicityStatement rename to schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement index 7d5ffb8..db64102 100644 --- a/schema/va-spec/base/json/VariantPathogenicityStatement +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement @@ -1,10 +1,10 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityStatement", - "title": "VariantPathogenicityStatement", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyStatement", + "title": "ExperimentalVariantFunctionalImpactStudyStatement", + "maturity": "trial use", "type": "object", - "maturity": "draft", - "description": "A Statement describing the role of a variant in causing an inherited condition.", + "description": "A statement 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": { "id": { "type": "string", @@ -36,18 +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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, "contributions": { "type": "array", "ordered": false, @@ -116,11 +104,6 @@ "description": "A natural-language expression of what a Statement asserts to be true.", "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, "hasEvidenceLines": { "type": "array", "ordered": false, @@ -132,9 +115,9 @@ }, "type": { "type": "string", - "const": "VariantPathogenicityStatement", - "default": "VariantPathogenicityStatement", - "description": "MUST be \"VariantPathogenicityStatement\"." + "const": "ExperimentalVariantFunctionalImpactStudyStatement", + "default": "ExperimentalVariantFunctionalImpactStudyStatement", + "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyStatement\"." }, "subjectVariant": { "oneOf": [ @@ -145,62 +128,76 @@ "$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 protein or genomic contextual or canonical molecular variant.", "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." }, "predicate": { "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", + "description": "The relationship this Statement describes between the subject Variant and object Sequence Feature whose function it may alter.", "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "const": "isCausalFor" + "const": "impactsFunctionOf" }, - "objectCondition": { + "objectSequenceFeature": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], - "description": "The Condition for which the variant impact is stated.", + "description": "The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed.", "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." }, - "penetranceQualifier": { + "studyContextQualifier": { + "description": "The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.", + "$comment": "The attribute is required in order to explicitly specify an assay or study context in which the reported impact was observed. It's value can be a Document object, or an IRI pointing to a document that describes the assay/study. This may be a publication, a database record, or a bespoke document.", + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "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).", + "$comment": "Implementers may use a set of terms to use here that reflect the specific types of functional impact(s) measured by the assay(s) employed. It is recommended that terms are drawn from established terminologies where possible.", "type": "string", "enum": [ - "high", - "low", - "risk allele" - ], - "description": "Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition." + "increased activity", + "decreased activity", + "novel activity", + "dominant negative activity" + ] }, - "modeOfInheritanceQualifier": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding" - }, - "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify." + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use.", + "$comment": "This is an optional attribute that can be used by data providers to provide a particular community of users a functional impact classification in familiar terms, that summarizes/complements the smeantics broken out in the SPOQ attributes of the Statement (e.g. to mirror established community conventions or reflect language on the data providers website or documentation). e.g. CIViC docs/web site uses terms like 'unaltered function', 'gain of function', 'neomorphic', and 'unknown', which could be reropted here. ", + "type": "string" }, - "geneContextQualifier": { - "description": "Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).", + "specifiedBy": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" }, { "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } - ] + ], + "description": "The method that specifies how the functional classification is ultimately assigned to the variant, based on interpretation of data from the supporting assay. May include information about thresholds applied on assay variant effect scores to derive the final classification.", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." } }, "required": [ - "objectCondition", + "objectSequenceFeature", "predicate", + "studyContextQualifier", "subjectVariant", "type" ], diff --git a/schema/va-spec/base/json/Therapeutic b/schema/va-spec/base/json/Therapeutic deleted file mode 100644 index a39cfc5..0000000 --- a/schema/va-spec/base/json/Therapeutic +++ /dev/null @@ -1,15 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/Therapeutic", - "title": "Therapeutic", - "maturity": "draft", - "description": "A group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that represents the object of a Therapeutic Response study statement.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/TherapyGroup" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - ] -} \ No newline at end of file diff --git a/schema/va-spec/base/json/TherapyGroup b/schema/va-spec/base/json/TherapyGroup deleted file mode 100644 index 0c3b88f..0000000 --- a/schema/va-spec/base/json/TherapyGroup +++ /dev/null @@ -1,38 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/TherapyGroup", - "title": "TherapyGroup", - "type": "object", - "maturity": "draft", - "description": "A group of therapies that are applied together in the context of a Therapeutic Response study statement.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the data element 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." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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": "The type of the therapy group." - }, - "therapies": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "description": "A list of therapies that are applied together in the context of a Therapeutic Response study statement.", - "minItems": 2 - } - }, - "required": [], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/TraitSet b/schema/va-spec/base/json/TraitSet deleted file mode 100644 index 3a71c13..0000000 --- a/schema/va-spec/base/json/TraitSet +++ /dev/null @@ -1,38 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/TraitSet", - "title": "TraitSet", - "type": "object", - "maturity": "draft", - "description": "A set of traits that are co-occurring in the context of a Variant Pathogenicity statement.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "type": { - "type": "string", - "description": "The type of the set of traits." - }, - "traits": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "description": "A list of traits that are co-occurring in the context of a Variant Pathogenicity statement.", - "minItems": 2 - } - }, - "required": [], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantPrognosticStudyStatement b/schema/va-spec/base/json/VariantPrognosticStudyStatement deleted file mode 100644 index bbfcd23..0000000 --- a/schema/va-spec/base/json/VariantPrognosticStudyStatement +++ /dev/null @@ -1,204 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyStatement", - "title": "VariantPrognosticStudyStatement", - "type": "object", - "maturity": "draft", - "description": "A Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantPrognosticStudyStatement", - "default": "VariantPrognosticStudyStatement", - "description": "MUST be \"VariantPrognosticStudyStatement\"." - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "associatedWithBetterOutcomeFor", - "associatedWithWorseOutcomeFor" - ] - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The disease that is evaluated for outcome.", - "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the prognostic association in the Statement.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "objectCondition", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement b/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement deleted file mode 100644 index 72e9774..0000000 --- a/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement +++ /dev/null @@ -1,216 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseStudyStatement", - "title": "VariantTherapeuticResponseStudyStatement", - "maturity": "draft", - "type": "object", - "description": "A Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantTherapeuticResponseStudyStatement", - "default": "VariantTherapeuticResponseStudyStatement", - "description": "MUST be \"VariantTherapeuticResponseStudyStatement\"." - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "predictsSensitivityTo", - "predictsResistanceTo" - ] - }, - "objectTherapeutic": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" - } - ], - "description": "A drug administration or other therapeutic procedure that the neoplasm is intended to respond to.", - "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "conditionQualifier": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. ", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "conditionQualifier", - "objectTherapeutic", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/pathogenicity-statement-source.yaml b/schema/va-spec/base/pathogenicity-statement-source.yaml index c2fb07b..86df472 100644 --- a/schema/va-spec/base/pathogenicity-statement-source.yaml +++ b/schema/va-spec/base/pathogenicity-statement-source.yaml @@ -68,3 +68,92 @@ $defs: - subjectVariant - predicate - objectCondition + +# LB: for this to build we will need to modify gks-core:EvidenceLine to have `heritableProperties` + PathogenicityEvidenceLine: + inherits: gks-core:EvidenceLine + maturity: trial use + type: object + description: >- + An Evidence Line that describes the strength and direction of support provided by one or more + evidence items for or against the pathogenicity of a variant for a particular disease. + properties: + type: + extends: type + const: "pathogenicityEvidenceLine" + default: "PathogenicityEvidenceLine" + description: MUST be "PathogenicityEvidenceLine". + hasEvidenceItems: + extends: hasEvidenceItems + type: array + ordered: false + items: + $ref: "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + description: >- + An Information Entity (e.g. a Functional Impact Study Statement) that was assessed as + evidence in determining the possible pathogenicity of a variant. + directionOfEvidenceProvided: + extends: directionOfEvidenceProvided + description: >- + The direction of support that the Evidence Line is determined to provide for its target + Variant Pathogenicity Proposition (i.e. does the evidence line support or dispute the + pathogenicity of the assessed variant, or remain neutral) + strengthOfEvidenceProvided: # TO DO: Ensure that ten enum below covers terms needed for initial adopters. Merge https://github.com/ga4gh/gks-common/pull/78 which updates the core IM to allow this property to take a string. Think about if we need the PS/BS codes here - as this bakes in direction, and is duplicative as the 'specifiedBy' attribute reports the ACMG criterion applied. + extends: strengthOfEvidenceProvided + type: string + enum: + - PS3_Strong + - PS3_Moderate + - PS3_Supporting + - BS3_Strong + - BS3_Moderate + - BS3_Supporting + description: >- + The strength of support that an Evidence Line is determined to provide for or against + the pathogenicity of the assessed variant. Strength is evaluated relative to the direction + indicated by the directionOfEvidenceProvided attribute. + targetProposition: # TO DO: Merge https://github.com/ga4gh/gks-common/pull/78 adding Proposition class and targetProposition attribute to the core IM to support their use here. + extends: targetProposition + $ref: "#/$defs/VariantPathogenicityProposition" + description: >- + The possible fact toward which the strength and direction of evidence provided by + functional assay data was evaluated (here, a proposition that the assessed variant + may be pathogenic for a particular disease). + specifiedBy: + extends: specifiedBy + description: >- + A method that specifies how evidence items used in the Evidence Line are to be evaluated + and weighed as evidence for or against the pathogenicity of the assessed variant. + # required: # TO DO: decide which if any attributes should be *required* in this profile. + + # Variant Pathogenicity Proposition + VariantPathogenicityProposition: + inherits: gks-core:Proposition + maturity: trial use + type: object + description: >- + A proposition describing the role of a variant in causing an inherited condition. + properties: + type: + extends: type + 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 + objectCondition: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The :ref:`Condition` for which the variant impact is stated. + + # TO DO: decide if we want to include the qualifiers defined on the VarPathStatement class in the VarPathProposition From b5ea9f635e73d1ae034baa514f191f6edbd16aa1 Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Thu, 7 Nov 2024 18:36:04 -0500 Subject: [PATCH 02/20] updates from nov.07.2024 gks-tech sync with MB/AW/LB --- .requirements.txt | 2 +- gks-tech-sync-notes.txt | 19 ++ schema/Makefile | 16 +- schema/va-spec/acmg-2015/Makefile | 44 ++++ .../def/VariantPathogenicityStatement.rst | 22 ++ .../json/VariantPathogenicityStatement | 19 ++ ...athogenicity-statement-profile-source.yaml | 32 +++ .../pathogenicity-statement-source.yaml | 12 - schema/va-spec/acmg-2015/prune.mk | 11 + .../va-spec/base/assay-var-effect-source.yaml | 151 ------------ ...requency-study-result-profile-source.yaml} | 2 +- ...sayVariantEffectMeasurementStudyResult.rst | 96 -------- .../def/CohortAlleleFrequencyStudyResult.rst | 51 ++++- schema/va-spec/base/def/Condition.rst | 22 ++ ...ntalVariantFunctionalImpactStudyResult.rst | 50 +++- ...lVariantFunctionalImpactStudyStatement.rst | 49 +++- .../base/def/PathogenicityEvidenceLine.rst | 126 ++++++++++ schema/va-spec/base/def/Therapeutic.rst | 22 ++ schema/va-spec/base/def/TherapyGroup.rst | 49 ++++ schema/va-spec/base/def/TraitSet.rst | 44 ++++ .../def/VariantDiagnosticStudyStatement.rst | 49 +++- .../def/VariantOncogenicityStudyStatement.rst | 49 +++- .../def/VariantPathogenicityProposition.rst | 79 +++++++ ....rst => VariantPathogenicityStatement.rst} | 94 ++++++-- ...st => VariantPrognosticStudyStatement.rst} | 89 ++++++-- ...riantTherapeuticResponseStudyStatement.rst | 167 ++++++++++++++ ...ostic-study-statement-profile-source.yaml} | 4 +- ...ource.yaml => domain-entities-source.yaml} | 11 +- ...l-impact-study-result-profile-source.yaml} | 4 +- ...mpact-study-statement-profile-source.yaml} | 2 +- schema/va-spec/base/json/Condition | 15 ++ ...tStudyResult => PathogenicityEvidenceLine} | 104 ++++----- schema/va-spec/base/json/Therapeutic | 15 ++ schema/va-spec/base/json/TherapyGroup | 38 +++ schema/va-spec/base/json/TraitSet | 34 +++ .../base/json/VariantPathogenicityProposition | 90 ++++++++ ...tatement => VariantPathogenicityStatement} | 85 ++++--- ...tement => VariantPrognosticStudyStatement} | 84 ++++--- .../VariantTherapeuticResponseStudyStatement | 216 ++++++++++++++++++ ...icity-study-statement-profile-source.yaml} | 4 +- ...genicity-evidenceline-profile-source.yaml} | 67 +----- ...athogenicity-statement-profile-source.yaml | 70 ++++++ ...ostic-study-statement-profile-source.yaml} | 5 +- ...ponse-study-statement-profile-source.yaml} | 4 +- submodules/cat-vrs | 2 +- 45 files changed, 1692 insertions(+), 528 deletions(-) create mode 100644 gks-tech-sync-notes.txt create mode 100644 schema/va-spec/acmg-2015/Makefile create mode 100644 schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst create mode 100644 schema/va-spec/acmg-2015/json/VariantPathogenicityStatement create mode 100644 schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml delete mode 100644 schema/va-spec/acmg-2015/pathogenicity-statement-source.yaml create mode 100644 schema/va-spec/acmg-2015/prune.mk delete mode 100644 schema/va-spec/base/assay-var-effect-source.yaml rename schema/va-spec/base/{caf-study-result-source.yaml => cohort-allele-frequency-study-result-profile-source.yaml} (95%) delete mode 100644 schema/va-spec/base/def/AssayVariantEffectMeasurementStudyResult.rst create mode 100644 schema/va-spec/base/def/Condition.rst create mode 100644 schema/va-spec/base/def/PathogenicityEvidenceLine.rst create mode 100644 schema/va-spec/base/def/Therapeutic.rst create mode 100644 schema/va-spec/base/def/TherapyGroup.rst create mode 100644 schema/va-spec/base/def/TraitSet.rst create mode 100644 schema/va-spec/base/def/VariantPathogenicityProposition.rst rename schema/va-spec/base/def/{AssayVariantEffectClinicalClassificationStatement.rst => VariantPathogenicityStatement.rst} (51%) rename schema/va-spec/base/def/{AssayVariantEffectFunctionalClassificationStatement.rst => VariantPrognosticStudyStatement.rst} (54%) create mode 100644 schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst rename schema/va-spec/base/{diagnostic-study-statement-source.yaml => diagnostic-study-statement-profile-source.yaml} (96%) rename schema/va-spec/base/{shared-concept-source.yaml => domain-entities-source.yaml} (88%) rename schema/va-spec/base/{exp-func-impact-study-result-source.yaml => experimental-functional-impact-study-result-profile-source.yaml} (88%) rename schema/va-spec/base/{exp-func-impact-study-statement-source.yaml => experimental-functional-impact-study-statement-profile-source.yaml} (97%) create mode 100644 schema/va-spec/base/json/Condition rename schema/va-spec/base/json/{AssayVariantEffectMeasurementStudyResult => PathogenicityEvidenceLine} (58%) create mode 100644 schema/va-spec/base/json/Therapeutic create mode 100644 schema/va-spec/base/json/TherapyGroup create mode 100644 schema/va-spec/base/json/TraitSet create mode 100644 schema/va-spec/base/json/VariantPathogenicityProposition rename schema/va-spec/base/json/{AssayVariantEffectClinicalClassificationStatement => VariantPathogenicityStatement} (85%) rename schema/va-spec/base/json/{AssayVariantEffectFunctionalClassificationStatement => VariantPrognosticStudyStatement} (86%) create mode 100644 schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement rename schema/va-spec/base/{oncogenicity-study-statement-source.yaml => oncogenicity-study-statement-profile-source.yaml} (96%) rename schema/va-spec/base/{pathogenicity-statement-source.yaml => pathogenicity-evidenceline-profile-source.yaml} (64%) create mode 100644 schema/va-spec/base/pathogenicity-statement-profile-source.yaml rename schema/va-spec/base/{prognostic-study-statement-source.yaml => prognostic-study-statement-profile-source.yaml} (96%) rename schema/va-spec/base/{therapeutic-response-study-statement-source copy.yaml => therapeutic-response-study-statement-profile-source.yaml} (97%) diff --git a/.requirements.txt b/.requirements.txt index 8e1c969..6d5ac32 100644 --- a/.requirements.txt +++ b/.requirements.txt @@ -2,7 +2,7 @@ pytest sphinx ~= 7.2 sphinx-rtd-theme ~= 1.3 pyyaml -ga4gh.gks.metaschema==0.3.0b14 +ga4gh.gks.metaschema==0.3.0b16 jsonschema referencing jupyterlab diff --git a/gks-tech-sync-notes.txt b/gks-tech-sync-notes.txt new file mode 100644 index 0000000..d4a9ce2 --- /dev/null +++ b/gks-tech-sync-notes.txt @@ -0,0 +1,19 @@ +Notes from gks-tech sync mtg 11/7 + +1. change 'type' to 'groupType' on TherapyGroup +2. remove 'type on TraitSet. Use extensions + +3. keep 'base' +4. rename all files with full names (sans variant) + i.e cohort-allele-frequency-study-result-profile-source.yaml +5. rename shared-concept-source.yaml to domain-entities-source.yaml + +6. delete assay-var-efect-source.yaml (double check nothing was lost) + (convert tests) + +7. pathogenicity-evidenceline-profile-source.yaml (with proposition in it) + +8. make EvidenceLine heritable + + + diff --git a/schema/Makefile b/schema/Makefile index 5b5b3a2..06d8637 100644 --- a/schema/Makefile +++ b/schema/Makefile @@ -1,7 +1,15 @@ -all: va-base +all: base-all acmg-2015-all -va-base: +clean: base-clean acmg-2015-clean + +base-all: (cd va-spec/base; make all) -clean: - (cd va-spec/base; make clean) \ No newline at end of file +acmg-2015-all: + (cd va-spec/acmg-2015; make all) + +base-clean: + (cd va-spec/base; make clean) + +acmg-2015-clean: + (cd va-spec/acmg-2015; make clean) \ No newline at end of file diff --git a/schema/va-spec/acmg-2015/Makefile b/schema/va-spec/acmg-2015/Makefile new file mode 100644 index 0000000..7575c82 --- /dev/null +++ b/schema/va-spec/acmg-2015/Makefile @@ -0,0 +1,44 @@ +.SECONDARY: +.DELETE_ON_ERROR: + +BUILD_DIR := build +DEF_DIR := def +JSON_DIR := json +IMPORT_DIR := import + +vpath %tag $(BUILD_DIR) +vpath %.classes $(BUILD_DIR) + +SOURCES := $(wildcard *-source.yaml) +TAGS := $(SOURCES:-source.yaml=.tag) +IMPORTS := $(wildcard $(IMPORT_DIR)/*-source.yaml) + +all: build-ordered ${TAGS} prune-tag + +build-ordered: | $(BUILD_DIR) + +$(BUILD_DIR): + mkdir $(BUILD_DIR) + +%.tag: %.classes %.json-tag %.defs-tag + touch $(BUILD_DIR)/$@ + +%.classes: %-source.yaml + source2classes $< >${BUILD_DIR}/$@ + +%.json-tag: %-source.yaml ${IMPORTS} + source2splitjs $< + touch $(BUILD_DIR)/$@ + +%.defs-tag: %-source.yaml ${IMPORTS} + y2t $< + touch $(BUILD_DIR)/$@ + +prune-tag: ${TAGS} + $(MAKE) -f prune.mk + touch $(BUILD_DIR)/$@ + +clean: + rm $(BUILD_DIR)/* + rm $(DEF_DIR)/* + rm $(JSON_DIR)/* diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst new file mode 100644 index 0000000..49e4942 --- /dev/null +++ b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst @@ -0,0 +1,22 @@ +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + +**Computational Definition** + +A Statement describing the role of a variant in causing an inherited condition. + +**Information Model** + + +.. list-table:: + :class: clean-wrap + :header-rows: 1 + :align: left + :widths: auto + + * - Field + - Flags + - Type + - Limits + - Description diff --git a/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement b/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement new file mode 100644 index 0000000..8311837 --- /dev/null +++ b/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement @@ -0,0 +1,19 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/acmg-2015/json/VariantPathogenicityStatement", + "title": "VariantPathogenicityStatement", + "maturity": "draft", + "description": "A Statement describing the role of a variant in causing an inherited condition.", + "allOf": [ + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityStatement" + }, + { + "properties": { + "classification": { + "description": "The ACMG 2015 classification of the variant's pathogenicity." + } + } + } + ] +} \ No newline at end of file diff --git a/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml new file mode 100644 index 0000000..5925dec --- /dev/null +++ b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml @@ -0,0 +1,32 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/acmg-2015/pathogenicity-statement-profile-source.yaml" +title: ACMG 2015 Variant Pathogenicity Statement Standard Profile +strict: true + +imports: + va-spec: ../base/pathogenicity-statement-profile-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + VariantPathogenicityStatement: + maturity: draft + description: >- + A Statement describing the role of a variant in causing an inherited condition. + allOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/VariantPathogenicityStatement" + - properties: + classification: + # this is a MappableConcept but we would ideally like to specify a value set with meta characteristics to validate with some consistency + # type: string + # enum: + # - pathogenic + # - likely pathogenic + # - uncertain significance + # - likely benign + # - benign + description: >- + The ACMG 2015 classification of the variant's pathogenicity. + + diff --git a/schema/va-spec/acmg-2015/pathogenicity-statement-source.yaml b/schema/va-spec/acmg-2015/pathogenicity-statement-source.yaml deleted file mode 100644 index b063770..0000000 --- a/schema/va-spec/acmg-2015/pathogenicity-statement-source.yaml +++ /dev/null @@ -1,12 +0,0 @@ -$schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/acmg-2015/pathogenicity-statement-source.yaml" -title: ACMG 2015 Variant Pathogenicity Statement Standard Profile -strict: true - -imports: - va-spec: ./base/pathogenicity-statement-source.yaml - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml - vrs: ../../vrs/vrs-source.yaml - gks-core: ../../gks-core/gks-core-source.yaml - -$defs: diff --git a/schema/va-spec/acmg-2015/prune.mk b/schema/va-spec/acmg-2015/prune.mk new file mode 100644 index 0000000..5d52ce5 --- /dev/null +++ b/schema/va-spec/acmg-2015/prune.mk @@ -0,0 +1,11 @@ +BUILD_DIR := build +SOURCES := $(wildcard *-source.yaml) +CLASS_FILTER_FILES = $(SOURCES:%-source.yaml=${BUILD_DIR}/%.classes) +FILTER_CLASSES := $(shell cat ${CLASS_FILTER_FILES}) +FILTER_JSONS = $(FILTER_CLASSES:%=json/%) +FILTER_DEFS = $(FILTER_CLASSES:%=def/%.rst) + +.DEFAULT: prune + +prune: $(filter-out ${FILTER_JSONS} ${FILTER_DEFS},$(wildcard def/* json/*)) + $(if $^,rm $^) \ No newline at end of file diff --git a/schema/va-spec/base/assay-var-effect-source.yaml b/schema/va-spec/base/assay-var-effect-source.yaml deleted file mode 100644 index 942a5d7..0000000 --- a/schema/va-spec/base/assay-var-effect-source.yaml +++ /dev/null @@ -1,151 +0,0 @@ -$schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/assay-var-effect-source.yaml" -title: VA Spec Assay Variant Effect statement and study result Profiles -strict: true - -imports: - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml - recipes: ../../cat-vrs/recipes-source.yaml - vrs: ../../vrs/vrs-source.yaml - gks-core: ../../gks-core/gks-core-source.yaml - -$defs: - # MaveDB work in progress - AssayVariantEffectFunctionalClassificationStatement: - inherits: gks-core:Statement - maturity: draft - type: object - description: >- - A statement that assigns a functional classification to a variant effect from a functional assay. - properties: - type: - extends: type - const: "AssayVariantEffectFunctionalClassificationStatement" - default: "AssayVariantEffectFunctionalClassificationStatement" - description: MUST be "AssayVariantEffectFunctionalClassificationStatement". - 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 - enum: - - hasAssayVariantEffectFor - objectAssay: - # TODO we may need to model this more specifically as a DomainEntity subtype - extends: object - oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - - $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" - description: >- - The assay that is evaluated for the variant effect. (e.g growth in - haploid cell culture protein stability in fluorescence assay) - classification: - extends: classification - description: >- - The functional classification of the variant effect in the assay. - enum: - - normal - - indeterminate - - abnormal - # method for classification contains info about thresholds for how to classify - specifiedBy: - extends: specifiedBy - description: >- - The method that specifies the functional classification of the variant effect in the assay. - # will will likely need to enhance this a bit due to the complexity of the methods used - required: - - subjectVariant - - predicate - - objectAssay - - classification - - AssayVariantEffectClinicalClassificationStatement: - inherits: gks-core:Statement - maturity: draft - type: object - description: >- - A statement that assigns a clinical strength of evidence to a variant effect from a functional assay. - properties: - type: - extends: type - const: "AssayVariantEffectClinicalClassificationStatement" - default: "AssayVariantEffectClinicalClassificationStatement" - description: MUST be "AssayVariantEffectClinicalClassificationStatement". - 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 - enum: - - hasAssayVariantEffectFor - objectAssay: - # TODO we may need to model this more specifically as a DomainEntity subtype - extends: object - oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - - $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" - description: >- - The assay that is evaluated for the variant effect. (e.g growth in - haploid cell culture protein stability in fluorescence assay) - classification: - extends: classification - description: >- - The clinical strength of evidence of the variant effect in the assay. - enum: - - PS3_Strong - - PS3_Moderate - - PS3_Supporting - - BS3_Strong - - BS3_Moderate - - BS3_Supporting - # method for classification contains info about thresholds for how to classify - specifiedBy: - extends: specifiedBy - description: >- - The method that specifies the clinical strength of evidence of the variant effect in the assay. - # will will likely need to enhance this a bit due to the complexity of the methods used - required: - - subjectVariant - - predicate - - objectAssay - - classification - - AssayVariantEffectMeasurementStudyResult: - inherits: gks-core:StudyResult - maturity: draft - type: object - description: >- - A StudyResult that reports a variant effect score from a functional assay. - properties: - type: - extends: type - const: "AssayVariantEffectMeasurementStudyResult" - default: "AssayVariantEffectMeasurementStudyResult" - description: MUST be "AssayVariantEffectMeasurementStudyResult". - focusVariant: - extends: focus - oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/MolecularVariation" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: The human mapped representation of the variant that is the subject of the Statement. - # derivedFrom: - # #this is the actual assayed variant (e.g. yeast, non-reference, pre-spliced trx, anything you can possibly dream of) - score: - type: number - description: The score of the variant effect in the assay. - specifiedBy: - description: >- - The assay that was used to measure the variant effect with all the various properties - extends: specifiedBy - sourceDataSet: - description: >- - The full data set that this measurement is a part of - extends: sourceDataSet diff --git a/schema/va-spec/base/caf-study-result-source.yaml b/schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml similarity index 95% rename from schema/va-spec/base/caf-study-result-source.yaml rename to schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml index a02f6b6..6ed5e94 100644 --- a/schema/va-spec/base/caf-study-result-source.yaml +++ b/schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml @@ -1,5 +1,5 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/caf-study-result-source.yaml" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/cohort-allele-frequency-study-result-profile-source.yaml" title: Cohort Allele Frequency Study Result Standard Profile strict: true diff --git a/schema/va-spec/base/def/AssayVariantEffectMeasurementStudyResult.rst b/schema/va-spec/base/def/AssayVariantEffectMeasurementStudyResult.rst deleted file mode 100644 index a4ccfef..0000000 --- a/schema/va-spec/base/def/AssayVariantEffectMeasurementStudyResult.rst +++ /dev/null @@ -1,96 +0,0 @@ - -.. 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 StudyResult that reports a variant effect score from a functional assay. - -**Information Model** - -Some AssayVariantEffectMeasurementStudyResult attributes are inherited from :ref:`gks-core:StudyResult`. - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - 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. - * - label - - string - - 0..1 - - A primary name for the entity. - * - description - - string - - 0..1 - - A free-text description of the Entity. - * - alternativeLabels - - string - - 0..m - - Alternative name(s) for the Entity. - * - extensions - - :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. - * - contributions - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - recordMetadata - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - componentResult - - :ref:`StudyResult` - - 0..m - - Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) . - * - studyGroup - - :ref:`StudyGroup` - - 0..1 - - A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult. - * - ancillaryResults - - object - - 0..1 - - - * - qualityMeasures - - object - - 0..1 - - - * - type - - string - - 1..1 - - MUST be "AssayVariantEffectMeasurementStudyResult". - * - focusVariant - - :ref:`MolecularVariation` | :ref:`iriReference` - - 0..1 - - The human mapped representation of the variant that is the subject of the Statement. - * - score - - number - - 0..1 - - The score of the variant effect in the assay. - * - specifiedBy - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - The assay that was used to measure the variant effect with all the various properties - * - sourceDataSet - - :ref:`DataSet` - - 0..m - - The full data set that this measurement is a part of diff --git a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst b/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst index 4c7e638..98a5d68 100644 --- a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst +++ b/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst @@ -1,9 +1,7 @@ - .. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in + significantly in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + **Computational Definition** A StudyResult that reports measures related to the frequency of an Allele in a cohort @@ -19,86 +17,131 @@ Some CohortAlleleFrequencyStudyResult attributes are inherited from :ref:`gks-co :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. * - 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. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - ancillaryResults + - + .. raw:: html + + D - object - 0..1 - * - qualityMeasures + - + .. raw:: html + + D - object - 0..1 - * - type + - - string - 1..1 - MUST be "CohortAlleleFrequencyStudyResult". * - sourceDataSet + - + .. raw:: html + + ⋮ - :ref:`DataSet` - 0..m - The dataset from which the CohortAlleleFrequencyStudyResult was reported. * - focusAllele + - - :ref:`Allele` | string - 1..1 - The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD. * - focusAlleleCount + - - integer - 1..1 - The number of occurrences of the focusAllele in the cohort. * - locusAlleleCount + - - integer - 1..1 - The number of occurrences of all alleles at the locus in the cohort (sometimes referred to as "allele number") * - focusAlleleFrequency + - - number - 1..1 - The frequency of the focusAllele in the cohort. * - cohort + - - :ref:`StudyGroup` - 1..1 - The cohort from which the frequency was derived. * - subCohortFrequency + - + .. raw:: html + + ⋮ - :ref:`CohortAlleleFrequencyStudyResult` - 0..m - A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups. diff --git a/schema/va-spec/base/def/Condition.rst b/schema/va-spec/base/def/Condition.rst new file mode 100644 index 0000000..edcb621 --- /dev/null +++ b/schema/va-spec/base/def/Condition.rst @@ -0,0 +1,22 @@ +.. 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 set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement. + +**Information Model** + + +.. list-table:: + :class: clean-wrap + :header-rows: 1 + :align: left + :widths: auto + + * - Field + - Flags + - Type + - Limits + - Description diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst index db546ba..e329434 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst @@ -1,8 +1,7 @@ - .. 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`. - - + in future releases. Maturity levels are described in + the :ref:`maturity-model`. + **Computational Definition** A StudyResult that reports a functional impact score from a variant functional assay or study. @@ -18,78 +17,121 @@ Some ExperimentalVariantFunctionalImpactStudyResult attributes are inherited fro :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. * - 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. * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - componentResult + - + .. raw:: html + + ⋮ - :ref:`StudyResult` - 0..m - Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) . * - studyGroup + - - :ref:`StudyGroup` - 0..1 - A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult. * - ancillaryResults + - + .. raw:: html + + D - object - 0..1 - * - qualityMeasures + - + .. raw:: html + + D - object - 0..1 - * - type + - - string - 1..1 - MUST be "ExperimentalVariantFunctionalImpactStudyResult". * - focusVariant + - - :ref:`MolecularVariation` | :ref:`iriReference` - 0..1 - The genetic variant for which a functional impact score is generated. * - functionalImpactScore + - - number - 0..1 - The score of the variant impact measured in the assay or study. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - The assay that was performed to generate the reported functional impact score. * - sourceDataSet + - + .. raw:: html + + ⋮ - :ref:`DataSet` - 0..m - The full data set that provided the reported the functional impact score. diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst index 584b90d..f8000c7 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst @@ -1,8 +1,7 @@ - .. 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`. - - + in future releases. Maturity levels are described in + the :ref:`maturity-model`. + **Computational Definition** A statement 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). @@ -18,98 +17,140 @@ Some ExperimentalVariantFunctionalImpactStudyStatement attributes are inherited :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. * - 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. * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - MUST be "ExperimentalVariantFunctionalImpactStudyStatement". * - subjectVariant + - - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A protein or genomic contextual or canonical molecular variant. * - predicate + - - string - 1..1 - The relationship this Statement describes between the subject Variant and object Sequence Feature whose function it may alter. * - objectSequenceFeature + - - :ref:`iriReference` | :ref:`MappableConcept` - 1..1 - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. * - studyContextQualifier + - - :ref:`Document` | :ref:`iriReference` - 1..1 - The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. * - impactTypeQualifier + - - string - 0..1 - 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). * - classification + - - string - 0..1 - An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - The method that specifies how the functional classification is ultimately assigned to the variant, based on interpretation of data from the supporting assay. May include information about thresholds applied on assay variant effect scores to derive the final classification. diff --git a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst new file mode 100644 index 0000000..b50d864 --- /dev/null +++ b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst @@ -0,0 +1,126 @@ +.. 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** + +An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. + +**Information Model** + +Some PathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:EvidenceLine`. + +.. 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. + * - 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. + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - derivedFrom + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - Another Information Entity from which this Information Entity is derived, in whole or in part. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - scoreOfEvidenceProvided + - + - number + - 0..1 + - A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value. + * - type + - + - string + - 1..1 + - MUST be "PathogenicityEvidenceLine". + * - hasEvidenceItems + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - An Information Entity (e.g. a Functional Impact Study Statement) that was assessed as evidence in determining the possible pathogenicity of a variant. + * - directionOfEvidenceProvided + - + - string + - 0..1 + - The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition (i.e. does the evidence line support or dispute the pathogenicity of the assessed variant, or remain neutral) + * - strengthOfEvidenceProvided + - + - string + - 0..1 + - The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. + * - targetProposition + - + - :ref:`VariantPathogenicityProposition` + - 0..1 + - The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant. diff --git a/schema/va-spec/base/def/Therapeutic.rst b/schema/va-spec/base/def/Therapeutic.rst new file mode 100644 index 0000000..fbc27d4 --- /dev/null +++ b/schema/va-spec/base/def/Therapeutic.rst @@ -0,0 +1,22 @@ +.. 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 group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that represents the object of a Therapeutic Response study statement. + +**Information Model** + + +.. list-table:: + :class: clean-wrap + :header-rows: 1 + :align: left + :widths: auto + + * - Field + - Flags + - Type + - Limits + - Description diff --git a/schema/va-spec/base/def/TherapyGroup.rst b/schema/va-spec/base/def/TherapyGroup.rst new file mode 100644 index 0000000..ab4c0cc --- /dev/null +++ b/schema/va-spec/base/def/TherapyGroup.rst @@ -0,0 +1,49 @@ +.. 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 group of therapies that are applied together in the context of a Therapeutic Response study statement. + +**Information Model** + +Some TherapyGroup attributes are inherited from :ref:`gks-core:Element`. + +.. 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 data element 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. + * - 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. + * - groupType + - + - string + - 0..1 + - The type of the therapy group. + * - therapies + - + .. raw:: html + + ⋮ + - :ref:`MappableConcept` + - 2..m + - A list of therapies that are applied together in the context of a Therapeutic Response study statement. diff --git a/schema/va-spec/base/def/TraitSet.rst b/schema/va-spec/base/def/TraitSet.rst new file mode 100644 index 0000000..b88795a --- /dev/null +++ b/schema/va-spec/base/def/TraitSet.rst @@ -0,0 +1,44 @@ +.. 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 set of traits that are co-occurring in the context of a Variant Pathogenicity statement. + +**Information Model** + +Some TraitSet attributes are inherited from :ref:`gks-core:Element`. + +.. 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 data element 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. + * - 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. + * - traits + - + .. raw:: html + + ⋮ + - :ref:`MappableConcept` + - 2..m + - A list of traits that are co-occurring in the context of a Variant Pathogenicity statement. diff --git a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst b/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst index 623e14d..bc7a221 100644 --- a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst +++ b/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst @@ -1,9 +1,7 @@ - .. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in + significantly in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + **Computational Definition** A Statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. @@ -19,102 +17,145 @@ Some VariantDiagnosticStudyStatement attributes are inherited from :ref:`gks-cor :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. * - 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. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification + - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - MUST be "VariantDiagnosticStudyStatement". * - subjectVariant + - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate + - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectCondition + - - :ref:`Condition` | :ref:`iriReference` - 1..1 - The disease that is evaluated for diagnosis. * - alleleOriginQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier + - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Statement. diff --git a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst b/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst index 6b4fc8d..b54fbde 100644 --- a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst +++ b/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst @@ -1,9 +1,7 @@ - .. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in + significantly in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + **Computational Definition** A Statement reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. @@ -19,102 +17,145 @@ Some VariantOncogenicityStudyStatement attributes are inherited from :ref:`gks-c :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. * - 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. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification + - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - MUST be "VariantOncogenicityStudyStatement". * - subjectVariant + - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate + - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectTumorType + - - :ref:`Condition` | :ref:`MappableConcept` - 1..1 - The tumor type for which the variant impact is evaluated. * - alleleOriginQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier + - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Statement. diff --git a/schema/va-spec/base/def/VariantPathogenicityProposition.rst b/schema/va-spec/base/def/VariantPathogenicityProposition.rst new file mode 100644 index 0000000..8b598d6 --- /dev/null +++ b/schema/va-spec/base/def/VariantPathogenicityProposition.rst @@ -0,0 +1,79 @@ +.. 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 describing the role of a variant in causing an inherited condition. + +**Information Model** + +Some VariantPathogenicityProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - 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 + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectCondition + - + - :ref:`Condition` | :ref:`iriReference` + - 1..1 + - The :ref:`Condition` for which the variant impact is stated. diff --git a/schema/va-spec/base/def/AssayVariantEffectClinicalClassificationStatement.rst b/schema/va-spec/base/def/VariantPathogenicityStatement.rst similarity index 51% rename from schema/va-spec/base/def/AssayVariantEffectClinicalClassificationStatement.rst rename to schema/va-spec/base/def/VariantPathogenicityStatement.rst index d24c798..b66de70 100644 --- a/schema/va-spec/base/def/AssayVariantEffectClinicalClassificationStatement.rst +++ b/schema/va-spec/base/def/VariantPathogenicityStatement.rst @@ -1,16 +1,14 @@ - .. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in + significantly in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + **Computational Definition** -A statement that assigns a clinical strength of evidence to a variant effect from a functional assay. +A Statement describing the role of a variant in causing an inherited condition. **Information Model** -Some AssayVariantEffectClinicalClassificationStatement attributes are inherited from :ref:`gks-core:Statement`. +Some VariantPathogenicityStatement attributes are inherited from :ref:`gks-core:Statement`. .. list-table:: :class: clean-wrap @@ -19,90 +17,148 @@ Some AssayVariantEffectClinicalClassificationStatement attributes are inherited :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. * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - - MUST be "AssayVariantEffectClinicalClassificationStatement". + - MUST be "VariantPathogenicityStatement". * - subjectVariant - - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - - A protein or genomic contextual or canonical molecular variant. + - A variant that is the subject of the Statement. * - predicate + - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. - * - objectAssay - - :ref:`iriReference` | :ref:`Coding` - - 1..1 - - The assay that is evaluated for the variant effect. (e.g growth in haploid cell culture protein stability in fluorescence assay) - * - classification - - :ref:`MappableConcept` + * - objectCondition + - + - :ref:`Condition` | :ref:`iriReference` - 1..1 - - The clinical strength of evidence of the variant effect in the assay. - * - specifiedBy - - :ref:`Method` | :ref:`iriReference` + - The :ref:`Condition` for which the variant impact is stated. + * - penetranceQualifier + - + - string + - 0..1 + - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. + * - modeOfInheritanceQualifier + - + .. raw:: html + + ⋮ + - :ref:`Coding` + - 0..m + - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. + * - geneContextQualifier + - + - :ref:`MappableConcept` | :ref:`iriReference` - 0..1 - - The method that specifies the clinical strength of evidence of the variant effect in the assay. + - 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). diff --git a/schema/va-spec/base/def/AssayVariantEffectFunctionalClassificationStatement.rst b/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst similarity index 54% rename from schema/va-spec/base/def/AssayVariantEffectFunctionalClassificationStatement.rst rename to schema/va-spec/base/def/VariantPrognosticStudyStatement.rst index 6987ec3..87b3444 100644 --- a/schema/va-spec/base/def/AssayVariantEffectFunctionalClassificationStatement.rst +++ b/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst @@ -1,16 +1,14 @@ - .. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in + significantly in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + **Computational Definition** -A statement that assigns a functional classification to a variant effect from a functional assay. +A Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. **Information Model** -Some AssayVariantEffectFunctionalClassificationStatement attributes are inherited from :ref:`gks-core:Statement`. +Some VariantPrognosticStudyStatement attributes are inherited from :ref:`gks-core:Statement`. .. list-table:: :class: clean-wrap @@ -19,90 +17,145 @@ Some AssayVariantEffectFunctionalClassificationStatement attributes are inherite :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. * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - - MUST be "AssayVariantEffectFunctionalClassificationStatement". + - MUST be "VariantPrognosticStudyStatement". * - subjectVariant - - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - - A protein or genomic contextual or canonical molecular variant. + - A variant that is the subject of the Statement. * - predicate + - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. - * - objectAssay - - :ref:`iriReference` | :ref:`Coding` + * - objectCondition + - + - :ref:`Condition` | :ref:`iriReference` - 1..1 - - The assay that is evaluated for the variant effect. (e.g growth in haploid cell culture protein stability in fluorescence assay) - * - classification + - The disease that is evaluated for outcome. + * - alleleOriginQualifier + - + - string + - 0..1 + - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). + * - allelePrevalenceQualifier + - + - string + - 0..1 + - Reports whether the statement should be interpreted in the context of the variant being rare or common. + * - geneContextQualifier + - - :ref:`MappableConcept` - - 1..1 - - The functional classification of the variant effect in the assay. - * - specifiedBy - - :ref:`Method` | :ref:`iriReference` - 0..1 - - The method that specifies the functional classification of the variant effect in the assay. + - Reports a gene impacted by the variant, which may contribute to the prognostic association in the Statement. diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst new file mode 100644 index 0000000..d9868df --- /dev/null +++ b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst @@ -0,0 +1,167 @@ +.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. + +**Information Model** + +Some VariantTherapeuticResponseStudyStatement attributes are inherited from :ref:`gks-core:Statement`. + +.. 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. + * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - derivedFrom + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - Another Information Entity from which this Information Entity is derived, in whole or in part. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - direction + - + - string + - 0..1 + - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. + * - strength + - + - :ref:`MappableConcept` + - 0..1 + - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. + * - score + - + - number + - 0..1 + - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. + * - statementText + - + - string + - 0..1 + - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. + * - hasEvidenceLines + - + .. raw:: html + + ⋮ + - :ref:`EvidenceLine` + - 0..m + - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). + * - type + - + - string + - 1..1 + - MUST be "VariantTherapeuticResponseStudyStatement". + * - subjectVariant + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A variant that is the subject of the Statement. + * - predicate + - + - string + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectTherapeutic + - + - :ref:`Therapeutic` | :ref:`iriReference` + - 1..1 + - A drug administration or other therapeutic procedure that the neoplasm is intended to respond to. + * - conditionQualifier + - + - :ref:`Condition` | :ref:`iriReference` + - 1..1 + - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements. + * - alleleOriginQualifier + - + - string + - 0..1 + - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). + * - allelePrevalenceQualifier + - + - string + - 0..1 + - Reports whether the statement should be interpreted in the context of the variant being rare or common. + * - geneContextQualifier + - + - :ref:`MappableConcept` + - 0..1 + - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. + diff --git a/schema/va-spec/base/diagnostic-study-statement-source.yaml b/schema/va-spec/base/diagnostic-study-statement-profile-source.yaml similarity index 96% rename from schema/va-spec/base/diagnostic-study-statement-source.yaml rename to schema/va-spec/base/diagnostic-study-statement-profile-source.yaml index 04d7175..a08f27a 100644 --- a/schema/va-spec/base/diagnostic-study-statement-source.yaml +++ b/schema/va-spec/base/diagnostic-study-statement-profile-source.yaml @@ -1,10 +1,10 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/diagnostic-study-statement-source.yaml" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/diagnostic-study-statement-profile-source.yaml" title: Variant Dx Study Statement Standard Profile strict: true imports: - va-spec: ./shared-concept-source.yaml + domain-entities: ./domain-entities-source.yaml cat-vrs: ../../cat-vrs/cat-vrs-source.yaml vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml diff --git a/schema/va-spec/base/shared-concept-source.yaml b/schema/va-spec/base/domain-entities-source.yaml similarity index 88% rename from schema/va-spec/base/shared-concept-source.yaml rename to schema/va-spec/base/domain-entities-source.yaml index 2d0b95e..e08d8f5 100644 --- a/schema/va-spec/base/shared-concept-source.yaml +++ b/schema/va-spec/base/domain-entities-source.yaml @@ -1,11 +1,9 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/shared-concept-source.yaml" -title: VA Spec Shared Concept Data Structures +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/domain-entities-source.yaml" +title: VA Spec Shared Domain Entity Data Structures strict: true imports: - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml - vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml $defs: @@ -27,9 +25,6 @@ $defs: description: >- A set of traits that are co-occurring in the context of a Variant Pathogenicity statement. properties: - type: - type: string - description: The type of the set of traits. traits: type: array ordered: false @@ -58,7 +53,7 @@ $defs: description: >- A group of therapies that are applied together in the context of a Therapeutic Response study statement. properties: - type: + groupType: type: string description: The type of the therapy group. therapies: diff --git a/schema/va-spec/base/exp-func-impact-study-result-source.yaml b/schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml similarity index 88% rename from schema/va-spec/base/exp-func-impact-study-result-source.yaml rename to schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml index 75b156f..c218e8b 100644 --- a/schema/va-spec/base/exp-func-impact-study-result-source.yaml +++ b/schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml @@ -1,6 +1,6 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/exp-func-impact-study-result-source.yaml" -title: Experimental Variant Functional Impact Statement +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/experimental-functional-impact-study-result-profile-source.yaml" +title: Experimental Variant Functional Impact Study Result Standard Profile strict: true imports: diff --git a/schema/va-spec/base/exp-func-impact-study-statement-source.yaml b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml similarity index 97% rename from schema/va-spec/base/exp-func-impact-study-statement-source.yaml rename to schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml index f60389d..66c9e00 100644 --- a/schema/va-spec/base/exp-func-impact-study-statement-source.yaml +++ b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml @@ -1,5 +1,5 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/exp-func-impact-study-statement-source.yaml" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/experimental-functional-impact-study-statement-profile-source.yaml" title: Experimental Variant Functional Impact Statement strict: true diff --git a/schema/va-spec/base/json/Condition b/schema/va-spec/base/json/Condition new file mode 100644 index 0000000..479190e --- /dev/null +++ b/schema/va-spec/base/json/Condition @@ -0,0 +1,15 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/Condition", + "title": "Condition", + "maturity": "draft", + "description": "A set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement.", + "oneOf": [ + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/TraitSet" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + ] +} \ No newline at end of file diff --git a/schema/va-spec/base/json/AssayVariantEffectMeasurementStudyResult b/schema/va-spec/base/json/PathogenicityEvidenceLine similarity index 58% rename from schema/va-spec/base/json/AssayVariantEffectMeasurementStudyResult rename to schema/va-spec/base/json/PathogenicityEvidenceLine index 736708f..112e5f9 100644 --- a/schema/va-spec/base/json/AssayVariantEffectMeasurementStudyResult +++ b/schema/va-spec/base/json/PathogenicityEvidenceLine @@ -1,10 +1,10 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/AssayVariantEffectMeasurementStudyResult", - "title": "AssayVariantEffectMeasurementStudyResult", - "maturity": "draft", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/PathogenicityEvidenceLine", + "title": "PathogenicityEvidenceLine", + "maturity": "trial use", "type": "object", - "description": "A StudyResult that reports a variant effect score from a functional assay.", + "description": "An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. ", "properties": { "id": { "type": "string", @@ -66,58 +66,64 @@ "description": "Indicates when the information content expressed in the Information Entity was generated.", "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." }, + "derivedFrom": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." + }, "recordMetadata": { "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." }, - "componentResult": { + "scoreOfEvidenceProvided": { + "type": "number", + "description": "A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value." + }, + "type": { + "type": "string", + "const": "pathogenicityEvidenceLine", + "default": "PathogenicityEvidenceLine", + "description": "MUST be \"PathogenicityEvidenceLine\"." + }, + "hasEvidenceItems": { "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyResult" + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" }, - "description": "Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) .", - "$comment": "This attribute allows data creators to break down a StudyResult into finer-grained StudyResult instances with a narrower scope. For example, a StudyResult about the frequency of an allele in a global population of individuals can be broken down into separate 'component' Results about distinct subpopulations of individuals in the source data (e.g. frequency of the allele in asian vs african subpopulations, or male vs female subgroups)." - }, - "studyGroup": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyGroup", - "description": "A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult.", - "$comment": "For example, in a StudyResult holding allele frequency data, this attribute points to a StudyGroup object that describes characteristics of the population that the frequency data was generated from (e.g. 'East Asian', 'Female')." - }, - "ancillaryResults": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true - }, - "qualityMeasures": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true + "description": "An Information Entity (e.g. a Functional Impact Study Statement) that was assessed as evidence in determining the possible pathogenicity of a variant. ", + "$comment": "A given Evidence Line may be supported by one or many individual evidence items. What matters is that all evidence items in a given Evidence Line get collectively assessed and assigned direction and strength as a single argument for or against a target proposition.\nDifferent types and scales of information entity can serve as evidence (experimental measurements or observations, data tables or figures, images, prior assertions, etc.) Only when assessed as evidence do we consider the information to be an 'Evidence Item'. For example, a piece of population frequency data about BRCA2 c.8023A>G becomes an Evidence Item when it is assessed for the support it may offer for a target proposition (e.g. the prospect of the variant\u2019s pathogenicity)." }, - "type": { + "directionOfEvidenceProvided": { "type": "string", - "const": "AssayVariantEffectMeasurementStudyResult", - "default": "AssayVariantEffectMeasurementStudyResult", - "description": "MUST be \"AssayVariantEffectMeasurementStudyResult\"." - }, - "focusVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" - } + "enum": [ + "supports", + "neutral", + "disputes" ], - "description": "The human mapped representation of the variant that is the subject of the Statement.", - "$comment": "The 'focus' of a StudyResult is the what anchors selection of all data items and provenance information that it contains. This focus may be a single participant or subject of a study (e.g. one patient in a clinical study, or one allele in a population frequency analysis). It may be a study group defined as an experimental unit in the study (e.g. a specific treatment arm of a clinical study). Or it may be a variable defined as a unit of analysis in the study (e.g. 'exposure to nicotine' in an analysis correlating this variable with clinical outcomes)." + "description": "The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition (i.e. does the evidence line support or dispute the pathogenicity of the assessed variant, or remain neutral)" }, - "score": { - "type": "number", - "description": "The score of the variant effect in the assay." + "strengthOfEvidenceProvided": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute.", + "$comment": "Values of this attribute can be defined by for a given profile based on domain/application needs, but should be framed in qualitative terms (e.g. 'strong', 'moderate', 'weak'). The 'scoreOfEvidenceProvided' attribute can be used to report quantitative assessments of evidence provided.", + "type": "string", + "enum": [ + "PS3_Strong", + "PS3_Moderate", + "PS3_Supporting", + "BS3_Strong", + "BS3_Moderate", + "BS3_Supporting" + ] + }, + "targetProposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition", + "description": "The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). " }, "specifiedBy": { "oneOf": [ @@ -128,18 +134,8 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], - "description": "The assay that was used to measure the variant effect with all the various properties", + "description": "A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant.", "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "sourceDataSet": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/DataSet" - }, - "description": "The full data set that this measurement is a part of", - "maximum": 1, - "$comment": "In most cases, a StudyResult will be generated using data from one source dataset - but it is possible multiple datasets related to a single study contain data about a particular focus that get collected into a single StudyResult instance." } }, "required": [ diff --git a/schema/va-spec/base/json/Therapeutic b/schema/va-spec/base/json/Therapeutic new file mode 100644 index 0000000..a39cfc5 --- /dev/null +++ b/schema/va-spec/base/json/Therapeutic @@ -0,0 +1,15 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/Therapeutic", + "title": "Therapeutic", + "maturity": "draft", + "description": "A group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that represents the object of a Therapeutic Response study statement.", + "oneOf": [ + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/TherapyGroup" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + ] +} \ No newline at end of file diff --git a/schema/va-spec/base/json/TherapyGroup b/schema/va-spec/base/json/TherapyGroup new file mode 100644 index 0000000..37f59c5 --- /dev/null +++ b/schema/va-spec/base/json/TherapyGroup @@ -0,0 +1,38 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/TherapyGroup", + "title": "TherapyGroup", + "type": "object", + "maturity": "draft", + "description": "A group of therapies that are applied together in the context of a Therapeutic Response study statement.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the data element 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." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "groupType": { + "type": "string", + "description": "The type of the therapy group." + }, + "therapies": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + "description": "A list of therapies that are applied together in the context of a Therapeutic Response study statement.", + "minItems": 2 + } + }, + "required": [], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/TraitSet b/schema/va-spec/base/json/TraitSet new file mode 100644 index 0000000..a19845f --- /dev/null +++ b/schema/va-spec/base/json/TraitSet @@ -0,0 +1,34 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/TraitSet", + "title": "TraitSet", + "type": "object", + "maturity": "draft", + "description": "A set of traits that are co-occurring in the context of a Variant Pathogenicity statement.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "traits": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + "description": "A list of traits that are co-occurring in the context of a Variant Pathogenicity statement.", + "minItems": 2 + } + }, + "required": [], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantPathogenicityProposition b/schema/va-spec/base/json/VariantPathogenicityProposition new file mode 100644 index 0000000..d2fa908 --- /dev/null +++ b/schema/va-spec/base/json/VariantPathogenicityProposition @@ -0,0 +1,90 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition", + "title": "VariantPathogenicityProposition", + "maturity": "trial use", + "type": "object", + "description": "A proposition describing the role of a variant in causing an inherited condition.", + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "propositionText": { + "type": "string", + "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." + }, + "type": { + "type": "string", + "description": "Must be \"VariantPathogenicityProposition\"", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantPathogenicityProposition", + "default": "VariantPathogenicityProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Statement." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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": "isCausalFor" + }, + "objectCondition": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "The Condition for which the variant impact is stated.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein. " + } + }, + "required": [ + "objectCondition", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/AssayVariantEffectClinicalClassificationStatement b/schema/va-spec/base/json/VariantPathogenicityStatement similarity index 85% rename from schema/va-spec/base/json/AssayVariantEffectClinicalClassificationStatement rename to schema/va-spec/base/json/VariantPathogenicityStatement index 70dd678..7d5ffb8 100644 --- a/schema/va-spec/base/json/AssayVariantEffectClinicalClassificationStatement +++ b/schema/va-spec/base/json/VariantPathogenicityStatement @@ -1,10 +1,10 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/AssayVariantEffectClinicalClassificationStatement", - "title": "AssayVariantEffectClinicalClassificationStatement", - "maturity": "draft", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityStatement", + "title": "VariantPathogenicityStatement", "type": "object", - "description": "A statement that assigns a clinical strength of evidence to a variant effect from a functional assay.", + "maturity": "draft", + "description": "A Statement describing the role of a variant in causing an inherited condition.", "properties": { "id": { "type": "string", @@ -36,6 +36,18 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, "contributions": { "type": "array", "ordered": false, @@ -104,6 +116,11 @@ "description": "A natural-language expression of what a Statement asserts to be true.", "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, "hasEvidenceLines": { "type": "array", "ordered": false, @@ -115,9 +132,9 @@ }, "type": { "type": "string", - "const": "AssayVariantEffectClinicalClassificationStatement", - "default": "AssayVariantEffectClinicalClassificationStatement", - "description": "MUST be \"AssayVariantEffectClinicalClassificationStatement\"." + "const": "VariantPathogenicityStatement", + "default": "VariantPathogenicityStatement", + "description": "MUST be \"VariantPathogenicityStatement\"." }, "subjectVariant": { "oneOf": [ @@ -128,61 +145,61 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" } ], - "description": "A protein or genomic contextual or canonical molecular variant.", + "description": "A variant that is the subject of the Statement.", "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." }, "predicate": { "type": "string", "description": "The relationship declared to hold between the subject and the object of the Statement.", "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "hasAssayVariantEffectFor" - ] + "const": "isCausalFor" }, - "objectAssay": { + "objectCondition": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" }, { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" } ], - "description": "The assay that is evaluated for the variant effect. (e.g growth in haploid cell culture protein stability in fluorescence assay)", + "description": "The Condition for which the variant impact is stated.", "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "The clinical strength of evidence of the variant effect in the assay.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification.", + "penetranceQualifier": { + "type": "string", "enum": [ - "PS3_Strong", - "PS3_Moderate", - "PS3_Supporting", - "BS3_Strong", - "BS3_Moderate", - "BS3_Supporting" - ] + "high", + "low", + "risk allele" + ], + "description": "Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition." }, - "specifiedBy": { + "modeOfInheritanceQualifier": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding" + }, + "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify." + }, + "geneContextQualifier": { + "description": "Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).", "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, { "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } - ], - "description": "The method that specifies the clinical strength of evidence of the variant effect in the assay.", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + ] } }, "required": [ - "classification", - "objectAssay", + "objectCondition", "predicate", "subjectVariant", "type" diff --git a/schema/va-spec/base/json/AssayVariantEffectFunctionalClassificationStatement b/schema/va-spec/base/json/VariantPrognosticStudyStatement similarity index 86% rename from schema/va-spec/base/json/AssayVariantEffectFunctionalClassificationStatement rename to schema/va-spec/base/json/VariantPrognosticStudyStatement index a135f7e..bbfcd23 100644 --- a/schema/va-spec/base/json/AssayVariantEffectFunctionalClassificationStatement +++ b/schema/va-spec/base/json/VariantPrognosticStudyStatement @@ -1,10 +1,10 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/AssayVariantEffectFunctionalClassificationStatement", - "title": "AssayVariantEffectFunctionalClassificationStatement", - "maturity": "draft", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyStatement", + "title": "VariantPrognosticStudyStatement", "type": "object", - "description": "A statement that assigns a functional classification to a variant effect from a functional assay.", + "maturity": "draft", + "description": "A Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results.", "properties": { "id": { "type": "string", @@ -36,6 +36,18 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, "contributions": { "type": "array", "ordered": false, @@ -104,6 +116,11 @@ "description": "A natural-language expression of what a Statement asserts to be true.", "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, "hasEvidenceLines": { "type": "array", "ordered": false, @@ -115,9 +132,9 @@ }, "type": { "type": "string", - "const": "AssayVariantEffectFunctionalClassificationStatement", - "default": "AssayVariantEffectFunctionalClassificationStatement", - "description": "MUST be \"AssayVariantEffectFunctionalClassificationStatement\"." + "const": "VariantPrognosticStudyStatement", + "default": "VariantPrognosticStudyStatement", + "description": "MUST be \"VariantPrognosticStudyStatement\"." }, "subjectVariant": { "oneOf": [ @@ -128,10 +145,10 @@ "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" } ], - "description": "A protein or genomic contextual or canonical molecular variant.", + "description": "A variant that is the subject of the Statement.", "$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)." }, "predicate": { @@ -139,47 +156,46 @@ "description": "The relationship declared to hold between the subject and the object of the Statement.", "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", "enum": [ - "hasAssayVariantEffectFor" + "associatedWithBetterOutcomeFor", + "associatedWithWorseOutcomeFor" ] }, - "objectAssay": { + "objectCondition": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" }, { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" } ], - "description": "The assay that is evaluated for the variant effect. (e.g growth in haploid cell culture protein stability in fluorescence assay)", + "description": "The disease that is evaluated for outcome.", "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "The functional classification of the variant effect in the assay.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification.", + "alleleOriginQualifier": { + "type": "string", + "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", "enum": [ - "normal", - "indeterminate", - "abnormal" + "germline", + "somatic", + "combined" ] }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "The method that specifies the functional classification of the variant effect in the assay.", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + "allelePrevalenceQualifier": { + "type": "string", + "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the prognostic association in the Statement.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" } }, "required": [ - "classification", - "objectAssay", + "objectCondition", "predicate", "subjectVariant", "type" diff --git a/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement b/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement new file mode 100644 index 0000000..72e9774 --- /dev/null +++ b/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement @@ -0,0 +1,216 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseStudyStatement", + "title": "VariantTherapeuticResponseStudyStatement", + "maturity": "draft", + "type": "object", + "description": "A Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results.", + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "derivedFrom": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "direction": { + "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", + "type": "string", + "enum": [ + "supports", + "neutral", + "disputes" + ] + }, + "strength": { + "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + "score": { + "type": "number", + "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." + }, + "statementText": { + "type": "string", + "description": "A natural-language expression of what a Statement asserts to be true.", + "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." + }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, + "hasEvidenceLines": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" + }, + "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", + "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." + }, + "type": { + "type": "string", + "const": "VariantTherapeuticResponseStudyStatement", + "default": "VariantTherapeuticResponseStudyStatement", + "description": "MUST be \"VariantTherapeuticResponseStudyStatement\"." + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Statement.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", + "enum": [ + "predictsSensitivityTo", + "predictsResistanceTo" + ] + }, + "objectTherapeutic": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" + } + ], + "description": "A drug administration or other therapeutic procedure that the neoplasm is intended to respond to.", + "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "conditionQualifier": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements." + }, + "alleleOriginQualifier": { + "type": "string", + "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", + "enum": [ + "germline", + "somatic", + "combined" + ] + }, + "allelePrevalenceQualifier": { + "type": "string", + "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. ", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "required": [ + "conditionQualifier", + "objectTherapeutic", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/oncogenicity-study-statement-source.yaml b/schema/va-spec/base/oncogenicity-study-statement-profile-source.yaml similarity index 96% rename from schema/va-spec/base/oncogenicity-study-statement-source.yaml rename to schema/va-spec/base/oncogenicity-study-statement-profile-source.yaml index 12dc3dd..f66e600 100644 --- a/schema/va-spec/base/oncogenicity-study-statement-source.yaml +++ b/schema/va-spec/base/oncogenicity-study-statement-profile-source.yaml @@ -1,10 +1,10 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/oncogenicity-study-statement-source.yaml" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/oncogenicity-study-statement-profile-source.yaml" title: Variant Oncogenicity Study Statement Standard Profile strict: true imports: - va-spec: ./shared-concept-source.yaml + domain-entities: ./domain-entities-source.yaml cat-vrs: ../../cat-vrs/cat-vrs-source.yaml vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml diff --git a/schema/va-spec/base/pathogenicity-statement-source.yaml b/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml similarity index 64% rename from schema/va-spec/base/pathogenicity-statement-source.yaml rename to schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml index 86df472..8c8c071 100644 --- a/schema/va-spec/base/pathogenicity-statement-source.yaml +++ b/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml @@ -1,75 +1,16 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/pathogenicity-statement-source.yaml" -title: Variant Pathogenicity Statement Standard Profile +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/pathogenicity-evidenceline-profile-source.yaml" +title: Variant Pathogenicity EvidenceLine Standard Profile strict: true imports: - va-spec: ./shared-concept-source.yaml + domain-entities: ./domain-entities-source.yaml cat-vrs: ../../cat-vrs/cat-vrs-source.yaml vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml $defs: - # Variant Pathogenicity Statement - VariantPathogenicityStatement: - type: object - maturity: draft - inherits: gks-core:Statement - description: >- - A Statement describing the role of a variant in causing an inherited condition. - properties: - type: - extends: type - const: "VariantPathogenicityStatement" - default: "VariantPathogenicityStatement" - description: MUST be "VariantPathogenicityStatement". - 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 - objectCondition: - extends: object - oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: The :ref:`Condition` for which the variant impact is stated. - penetranceQualifier: - type: string - enum: - - high - - low - - risk allele - description: >- - Reports the penetrance of the pathogenic effect - i.e. the extent to which the - variant impact is expressed by individuals carrying it as a measure of the - proportion of carriers exhibiting the condition. - modeOfInheritanceQualifier: - type: array - ordered: false - items: - $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" - description: >- - Reports a pattern of inheritance expected for the pathogenic effect of the variant. - Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. - geneContextQualifier: - description: >- - Reports the gene through which the pathogenic effect asserted for the variant is mediated - (i.e. it is the variant's impact on this gene that is responsible for causing the condition). - oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - required: - - subjectVariant - - predicate - - objectCondition - -# LB: for this to build we will need to modify gks-core:EvidenceLine to have `heritableProperties` + # Pathogenicity Evidence Line PathogenicityEvidenceLine: inherits: gks-core:EvidenceLine maturity: trial use diff --git a/schema/va-spec/base/pathogenicity-statement-profile-source.yaml b/schema/va-spec/base/pathogenicity-statement-profile-source.yaml new file mode 100644 index 0000000..d67b712 --- /dev/null +++ b/schema/va-spec/base/pathogenicity-statement-profile-source.yaml @@ -0,0 +1,70 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/pathogenicity-statement-profile-source.yaml" +title: Variant Pathogenicity Statement Standard Profile +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Pathogenicity Statement + VariantPathogenicityStatement: + type: object + maturity: draft + inherits: gks-core:Statement + description: >- + A Statement describing the role of a variant in causing an inherited condition. + properties: + type: + extends: type + const: "VariantPathogenicityStatement" + default: "VariantPathogenicityStatement" + description: MUST be "VariantPathogenicityStatement". + 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 + objectCondition: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The :ref:`Condition` for which the variant impact is stated. + penetranceQualifier: + type: string + enum: + - high + - low + - risk allele + description: >- + Reports the penetrance of the pathogenic effect - i.e. the extent to which the + variant impact is expressed by individuals carrying it as a measure of the + proportion of carriers exhibiting the condition. + modeOfInheritanceQualifier: + type: array + ordered: false + items: + $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" + description: >- + Reports a pattern of inheritance expected for the pathogenic effect of the variant. + Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. + geneContextQualifier: + description: >- + Reports the gene through which the pathogenic effect asserted for the variant is mediated + (i.e. it is the variant's impact on this gene that is responsible for causing the condition). + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + required: + - subjectVariant + - predicate + - objectCondition diff --git a/schema/va-spec/base/prognostic-study-statement-source.yaml b/schema/va-spec/base/prognostic-study-statement-profile-source.yaml similarity index 96% rename from schema/va-spec/base/prognostic-study-statement-source.yaml rename to schema/va-spec/base/prognostic-study-statement-profile-source.yaml index 7164c6f..0ffd3a0 100644 --- a/schema/va-spec/base/prognostic-study-statement-source.yaml +++ b/schema/va-spec/base/prognostic-study-statement-profile-source.yaml @@ -1,14 +1,13 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/prognostic-study-statement-source.yaml" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/prognostic-study-statement-profile-source.yaml" title: Variant Prognostic Study Statement Standard Profile strict: true imports: - va-spec: ./shared-concept-source.yaml + domain-entities: ./domain-entities-source.yaml cat-vrs: ../../cat-vrs/cat-vrs-source.yaml vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml - $defs: # Variant Prognostic Study Statement diff --git a/schema/va-spec/base/therapeutic-response-study-statement-source copy.yaml b/schema/va-spec/base/therapeutic-response-study-statement-profile-source.yaml similarity index 97% rename from schema/va-spec/base/therapeutic-response-study-statement-source copy.yaml rename to schema/va-spec/base/therapeutic-response-study-statement-profile-source.yaml index 1af8120..405e882 100644 --- a/schema/va-spec/base/therapeutic-response-study-statement-source copy.yaml +++ b/schema/va-spec/base/therapeutic-response-study-statement-profile-source.yaml @@ -1,10 +1,10 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/therapeutic-response-study-statement-source.yaml" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/therapeutic-response-study-statement-profile-source.yaml" title: Variant Therapeutic Response Study Statement Standard Profile strict: true imports: - va-spec: ./shared-concept-source.yaml + domain-entities: ./domain-entities-source.yaml cat-vrs: ../../cat-vrs/cat-vrs-source.yaml vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml diff --git a/submodules/cat-vrs b/submodules/cat-vrs index b8258e7..3b3d9be 160000 --- a/submodules/cat-vrs +++ b/submodules/cat-vrs @@ -1 +1 @@ -Subproject commit b8258e7bcfb8f52f8fb13d22ad20128dbc7e440c +Subproject commit 3b3d9bee5fd8e8d4fc39c1b1f5aaf5604aecb9c3 From 6d65bfaf905301975a95d5a671afdd0f204c3133 Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Thu, 7 Nov 2024 18:43:42 -0500 Subject: [PATCH 03/20] removed notes file --- gks-tech-sync-notes.txt | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 gks-tech-sync-notes.txt diff --git a/gks-tech-sync-notes.txt b/gks-tech-sync-notes.txt deleted file mode 100644 index d4a9ce2..0000000 --- a/gks-tech-sync-notes.txt +++ /dev/null @@ -1,19 +0,0 @@ -Notes from gks-tech sync mtg 11/7 - -1. change 'type' to 'groupType' on TherapyGroup -2. remove 'type on TraitSet. Use extensions - -3. keep 'base' -4. rename all files with full names (sans variant) - i.e cohort-allele-frequency-study-result-profile-source.yaml -5. rename shared-concept-source.yaml to domain-entities-source.yaml - -6. delete assay-var-efect-source.yaml (double check nothing was lost) - (convert tests) - -7. pathogenicity-evidenceline-profile-source.yaml (with proposition in it) - -8. make EvidenceLine heritable - - - From ff1834bbb89777c232654e5a8a16310bed986a6c Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Fri, 8 Nov 2024 01:03:22 -0500 Subject: [PATCH 04/20] Completed converting pre-existing AVE test cases with new ExpVarFuncImpact profiles. Some questions remain (see comments in test case fixtures) --- ...lVariantFunctionalImpactStudyStatement.rst | 2 +- .../base/def/PathogenicityEvidenceLine.rst | 4 +- .../def/VariantPathogenicityProposition.rst | 18 ++++ ...impact-study-statement-profile-source.yaml | 1 - ...entalVariantFunctionalImpactStudyStatement | 3 +- .../base/json/PathogenicityEvidenceLine | 4 +- .../base/json/VariantPathogenicityProposition | 28 +++++++ ...ogenicity-evidenceline-profile-source.yaml | 35 +++++++- .../fixtures/AVE-clinical-classification.yaml | 84 ++++++++++++------- .../AVE-functional-classification.yaml | 21 +++-- .../fixtures/AVE-functional-study-result.yaml | 10 +-- tests/test_definitions.yaml | 12 +-- 12 files changed, 163 insertions(+), 59 deletions(-) diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst index f8000c7..21b721a 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst @@ -146,7 +146,7 @@ Some ExperimentalVariantFunctionalImpactStudyStatement attributes are inherited - 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). * - classification - - - string + - :ref:`MappableConcept` - 0..1 - An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use. * - specifiedBy diff --git a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst index b50d864..dec16cb 100644 --- a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst +++ b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst @@ -1,5 +1,5 @@ -.. note:: This data class is at a **trial use** maturity level and may change - in future releases. Maturity levels are described in +.. 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/VariantPathogenicityProposition.rst b/schema/va-spec/base/def/VariantPathogenicityProposition.rst index 8b598d6..28f4368 100644 --- a/schema/va-spec/base/def/VariantPathogenicityProposition.rst +++ b/schema/va-spec/base/def/VariantPathogenicityProposition.rst @@ -77,3 +77,21 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`gks-cor - :ref:`Condition` | :ref:`iriReference` - 1..1 - The :ref:`Condition` for which the variant impact is stated. + * - penetranceQualifier + - + - string + - 0..1 + - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. + * - modeOfInheritanceQualifier + - + .. raw:: html + + ⋮ + - :ref:`Coding` + - 0..m + - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. + * - geneContextQualifier + - + - :ref:`MappableConcept` | :ref:`iriReference` + - 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). diff --git a/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml index 66c9e00..923ad73 100644 --- a/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml +++ b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml @@ -87,7 +87,6 @@ $defs: (e.g. to mirror established community conventions or reflect language on the data providers website or documentation). e.g. CIViC docs/web site uses terms like 'unaltered function', 'gain of function', 'neomorphic', and 'unknown', which could be reropted here. - type: string # Idea here is to make it as easy and flexible possible to add values here for now - since the idea is to support community/application specific terms orf art. If we want to standradize or fomralize these later, we can. specifiedBy: extends: specifiedBy description: >- diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement index db64102..8c5971f 100644 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement @@ -178,8 +178,7 @@ "classification": { "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", "description": "An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use.", - "$comment": "This is an optional attribute that can be used by data providers to provide a particular community of users a functional impact classification in familiar terms, that summarizes/complements the smeantics broken out in the SPOQ attributes of the Statement (e.g. to mirror established community conventions or reflect language on the data providers website or documentation). e.g. CIViC docs/web site uses terms like 'unaltered function', 'gain of function', 'neomorphic', and 'unknown', which could be reropted here. ", - "type": "string" + "$comment": "This is an optional attribute that can be used by data providers to provide a particular community of users a functional impact classification in familiar terms, that summarizes/complements the smeantics broken out in the SPOQ attributes of the Statement (e.g. to mirror established community conventions or reflect language on the data providers website or documentation). e.g. CIViC docs/web site uses terms like 'unaltered function', 'gain of function', 'neomorphic', and 'unknown', which could be reropted here. " }, "specifiedBy": { "oneOf": [ diff --git a/schema/va-spec/base/json/PathogenicityEvidenceLine b/schema/va-spec/base/json/PathogenicityEvidenceLine index 112e5f9..02ad1ca 100644 --- a/schema/va-spec/base/json/PathogenicityEvidenceLine +++ b/schema/va-spec/base/json/PathogenicityEvidenceLine @@ -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/PathogenicityEvidenceLine", "title": "PathogenicityEvidenceLine", - "maturity": "trial use", + "maturity": "draft", "type": "object", "description": "An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. ", "properties": { @@ -85,7 +85,7 @@ }, "type": { "type": "string", - "const": "pathogenicityEvidenceLine", + "const": "PathogenicityEvidenceLine", "default": "PathogenicityEvidenceLine", "description": "MUST be \"PathogenicityEvidenceLine\"." }, diff --git a/schema/va-spec/base/json/VariantPathogenicityProposition b/schema/va-spec/base/json/VariantPathogenicityProposition index d2fa908..78dfb6c 100644 --- a/schema/va-spec/base/json/VariantPathogenicityProposition +++ b/schema/va-spec/base/json/VariantPathogenicityProposition @@ -78,6 +78,34 @@ ], "description": "The Condition for which the variant impact is stated.", "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein. " + }, + "penetranceQualifier": { + "type": "string", + "enum": [ + "high", + "low", + "risk allele" + ], + "description": "Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. " + }, + "modeOfInheritanceQualifier": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding" + }, + "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify." + }, + "geneContextQualifier": { + "description": "Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).", + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] } }, "required": [ diff --git a/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml b/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml index 8c8c071..120275d 100644 --- a/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml +++ b/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml @@ -13,7 +13,7 @@ $defs: # Pathogenicity Evidence Line PathogenicityEvidenceLine: inherits: gks-core:EvidenceLine - maturity: trial use + maturity: draft type: object description: >- An Evidence Line that describes the strength and direction of support provided by one or more @@ -21,7 +21,7 @@ $defs: properties: type: extends: type - const: "pathogenicityEvidenceLine" + const: "PathogenicityEvidenceLine" default: "PathogenicityEvidenceLine" description: MUST be "PathogenicityEvidenceLine". hasEvidenceItems: @@ -53,7 +53,7 @@ $defs: The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. - targetProposition: # TO DO: Merge https://github.com/ga4gh/gks-common/pull/78 adding Proposition class and targetProposition attribute to the core IM to support their use here. + targetProposition: extends: targetProposition $ref: "#/$defs/VariantPathogenicityProposition" description: >- @@ -96,5 +96,34 @@ $defs: - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" description: The :ref:`Condition` for which the variant impact is stated. + penetranceQualifier: + type: string + enum: + - high + - low + - risk allele + description: >- + Reports the penetrance of the pathogenic effect - i.e. the extent to which the + variant impact is expressed by individuals carrying it as a measure of the + proportion of carriers exhibiting the condition. + modeOfInheritanceQualifier: + type: array + ordered: false + items: + $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" + description: >- + Reports a pattern of inheritance expected for the pathogenic effect of the variant. + Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. + geneContextQualifier: + description: >- + Reports the gene through which the pathogenic effect asserted for the variant is mediated + (i.e. it is the variant's impact on this gene that is responsible for causing the condition). + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + required: + - subjectVariant + - predicate + - objectCondition # TO DO: decide if we want to include the qualifiers defined on the VarPathStatement class in the VarPathProposition diff --git a/tests/fixtures/AVE-clinical-classification.yaml b/tests/fixtures/AVE-clinical-classification.yaml index ecbdb93..7a28ec2 100644 --- a/tests/fixtures/AVE-clinical-classification.yaml +++ b/tests/fixtures/AVE-clinical-classification.yaml @@ -1,36 +1,60 @@ -type: AssayVariantEffectClinicalClassificationStatement -subjectVariant: - type: CategoricalVariant - constraints: - - type: DefiningAlleleConstraint - allele: - id: ga4gh:VA.t0rDoiIessOWmP0SF0plhXtOwi8TRaZz - type: Allele - location: - type: SequenceLocation - sequenceReference: - refgetAccession: SQ.w7LxW0PSaVPNsPFvOL24weFjHcfaHyOi - type: SequenceReference - start: 10 - end: 11 - sequence: R - state: - type: LiteralSequenceExpression - sequence: T - expressions: - - syntax: hgvs.p - value: NP_000305.3:p.Arg11Thr - relations: - - translates_from - - translates_from_reading_frame -predicate: hasAssayVariantEffectFor -objectAssay: https://github.com/ave-dcd/mave_vocabulary/blob/main/examples/Matreyek_2018.yml -classification: BS3_Supporting +type: PathogenicityEvidenceLine +targetProposition: + type: VariantPathogenicityProposition + subjectVariant: + # LB: Alex, please verify the following... I am using a Cat-VRS: ProteinSequenceConsequence + # I want to review this because there's nothing in this object to tell you that + # It looks identical to the CanonicalAllele except for the data constraints on + # which relations are allowed. + # I think it makes sense for some Recipes to have a more specific object type or subtype property + # maybe something like recipeType: ProteinSequenceConsequence? (recipe is a bit non-computational computationally speaking) + # categoryType or categorySubtype seems better - the focus is on the category portion of CategoricalVariant. + # + # I recognize that computational validation will work fine without this + # but I would imagine it may make debugging validation failures much easier + # if the categoryType or recipeType was stated explicitly in the object. + type: CategoricalVariant + # subtype: ProteinSequenceConsequence or categoryType: ProteinSequenceConsequence + constraints: + - type: DefiningAlleleConstraint + allele: + id: ga4gh:VA.t0rDoiIessOWmP0SF0plhXtOwi8TRaZz + type: Allele + location: + type: SequenceLocation + sequenceReference: + refgetAccession: SQ.w7LxW0PSaVPNsPFvOL24weFjHcfaHyOi + type: SequenceReference + start: 10 + end: 11 + sequence: R + state: + type: LiteralSequenceExpression + sequence: T + expressions: + - syntax: hgvs.p + value: NP_000305.3:p.Arg11Thr + relations: + - translates_from + - translates_from_reading_frame + predicate: isCausalFor + objectCondition: + type: Condition + label: Unspecified + geneContextQualifier: + conceptType: Gene + label: PTEN +# LB: the following objectAssay was in the original test example. I assume it should be dropped, please verify. +# objectAssay: https://github.com/ave-dcd/mave_vocabulary/blob/main/examples/Matreyek_2018.yml + +# LB: strengthOfEvidenceProvided is illogically specified in PathogenicityEvidenceLine +# to conflict with the underlying datatype of MappableConcept +# strengthOfEvidenceProvided: +# label: BS3_Supporting specifiedBy: type: Method subtype: - code: NA - system: Variant Interpretation Guideline + label: Variant Interpretation Guideline reportedIn: - type: Document pmid: 34793697 diff --git a/tests/fixtures/AVE-functional-classification.yaml b/tests/fixtures/AVE-functional-classification.yaml index c9a4b97..be51057 100644 --- a/tests/fixtures/AVE-functional-classification.yaml +++ b/tests/fixtures/AVE-functional-classification.yaml @@ -1,4 +1,4 @@ -type: AssayVariantEffectFunctionalClassificationStatement +type: ExperimentalVariantFunctionalImpactStudyStatement subjectVariant: type: CategoricalVariant constraints: @@ -23,14 +23,23 @@ subjectVariant: relations: - translates_from - translates_from_reading_frame -predicate: hasAssayVariantEffectFor -objectAssay: https://github.com/ave-dcd/mave_vocabulary/blob/main/examples/Matreyek_2018.yml -classification: normal +predicate: impactsFunctionOf +objectSequenceFeature: + id: clinvar-gene:5728 + conceptType: Gene + label: PTEN + mappings: + - coding: + system: https://identifiers.org/ncbigene + code: '5728' + relation: exactMatch +studyContextQualifier: https://github.com/ave-dcd/mave_vocabulary/blob/main/examples/Matreyek_2018.yml +classification: + label: normal specifiedBy: type: Method subtype: - code: NA - system: Variant Interpretation Guideline + label: Variant Interpretation Guideline reportedIn: - type: Document pmid: 29785012 diff --git a/tests/fixtures/AVE-functional-study-result.yaml b/tests/fixtures/AVE-functional-study-result.yaml index 236ce21..0a5edd8 100644 --- a/tests/fixtures/AVE-functional-study-result.yaml +++ b/tests/fixtures/AVE-functional-study-result.yaml @@ -1,4 +1,4 @@ -type: AssayVariantEffectMeasurementStudyResult +type: ExperimentalVariantFunctionalImpactStudyResult focusVariant: id: ga4gh:VA.t0rDoiIessOWmP0SF0plhXtOwi8TRaZz type: Allele @@ -16,20 +16,18 @@ focusVariant: expressions: - syntax: hgvs.p value: NP_000305.3:p.Arg11Thr -score: 1.29395467005388 +functionalImpactScore: 1.29395467005388 specifiedBy: type: Method subtype: - code: NA - system: Experimental Protocol + label: Experimental Protocol reportedIn: - type: Document pmid: 29785012 sourceDataSet: - type: DataSet subtype: - code: NA - system: variant effect data set + label: variant effect data set license: CC0 reportedIn: - type: Document diff --git a/tests/test_definitions.yaml b/tests/test_definitions.yaml index 5e44456..7c6d6aa 100644 --- a/tests/test_definitions.yaml +++ b/tests/test_definitions.yaml @@ -17,9 +17,9 @@ tests: definition: VariantPrognosticStudyStatement - test_file: cohort-allele-freq-test.yaml definition: CohortAlleleFrequencyStudyResult - # - test_file: AVE-functional-classification.yaml - # definition: AssayVariantEffectFunctionalClassificationStatement - # - test_file: AVE-clinical-classification.yaml - # definition: AssayVariantEffectClinicalClassificationStatement - # - test_file: AVE-functional-study-result.yaml - # definition: AssayVariantEffectMeasurementStudyResult \ No newline at end of file + - test_file: AVE-functional-classification.yaml + definition: ExperimentalVariantFunctionalImpactStudyStatement + - test_file: AVE-clinical-classification.yaml + definition: PathogenicityEvidenceLine + - test_file: AVE-functional-study-result.yaml + definition: ExperimentalVariantFunctionalImpactStudyResult \ No newline at end of file From 85acefbdae9a23cebf97ef3c084d96c3d768f9ae Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Fri, 8 Nov 2024 01:12:46 -0500 Subject: [PATCH 05/20] reverted premature`trial use` maturity values to `draft` --- .../def/ExperimentalVariantFunctionalImpactStudyResult.rst | 4 ++-- .../def/ExperimentalVariantFunctionalImpactStudyStatement.rst | 4 ++-- schema/va-spec/base/def/VariantPathogenicityProposition.rst | 4 ++-- ...imental-functional-impact-study-result-profile-source.yaml | 2 +- ...ntal-functional-impact-study-statement-profile-source.yaml | 2 +- .../base/json/ExperimentalVariantFunctionalImpactStudyResult | 2 +- .../json/ExperimentalVariantFunctionalImpactStudyStatement | 2 +- schema/va-spec/base/json/VariantPathogenicityProposition | 2 +- .../base/pathogenicity-evidenceline-profile-source.yaml | 2 +- 9 files changed, 12 insertions(+), 12 deletions(-) diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst index e329434..c6c36f4 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst @@ -1,5 +1,5 @@ -.. note:: This data class is at a **trial use** maturity level and may change - in future releases. Maturity levels are described in +.. 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/ExperimentalVariantFunctionalImpactStudyStatement.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst index 21b721a..1dcc850 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst @@ -1,5 +1,5 @@ -.. note:: This data class is at a **trial use** maturity level and may change - in future releases. Maturity levels are described in +.. 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/VariantPathogenicityProposition.rst b/schema/va-spec/base/def/VariantPathogenicityProposition.rst index 28f4368..9c62f3b 100644 --- a/schema/va-spec/base/def/VariantPathogenicityProposition.rst +++ b/schema/va-spec/base/def/VariantPathogenicityProposition.rst @@ -1,5 +1,5 @@ -.. note:: This data class is at a **trial use** maturity level and may change - in future releases. Maturity levels are described in +.. 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/experimental-functional-impact-study-result-profile-source.yaml b/schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml index c218e8b..1c46777 100644 --- a/schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml +++ b/schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml @@ -11,7 +11,7 @@ imports: $defs: ExperimentalVariantFunctionalImpactStudyResult: inherits: gks-core:StudyResult - maturity: trial use + maturity: draft type: object description: >- A StudyResult that reports a functional impact score from a variant functional assay or study. diff --git a/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml index 923ad73..966f8c9 100644 --- a/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml +++ b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml @@ -11,7 +11,7 @@ imports: $defs: ExperimentalVariantFunctionalImpactStudyStatement: inherits: gks-core:Statement - maturity: trial use + maturity: draft type: object description: >- A statement reporting a conclusion from a single assay or study about the functional diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult index b686d92..7fcd2ea 100644 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult @@ -2,7 +2,7 @@ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyResult", "title": "ExperimentalVariantFunctionalImpactStudyResult", - "maturity": "trial use", + "maturity": "draft", "type": "object", "description": "A StudyResult that reports a functional impact score from a variant functional assay or study.", "properties": { diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement index 8c5971f..4e26039 100644 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement @@ -2,7 +2,7 @@ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyStatement", "title": "ExperimentalVariantFunctionalImpactStudyStatement", - "maturity": "trial use", + "maturity": "draft", "type": "object", "description": "A statement reporting a conclusion from a single assay or study about the functional impact of a variant on a sequence feature (typically a gene or gene product).", "properties": { diff --git a/schema/va-spec/base/json/VariantPathogenicityProposition b/schema/va-spec/base/json/VariantPathogenicityProposition index 78dfb6c..5f13468 100644 --- a/schema/va-spec/base/json/VariantPathogenicityProposition +++ b/schema/va-spec/base/json/VariantPathogenicityProposition @@ -2,7 +2,7 @@ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition", "title": "VariantPathogenicityProposition", - "maturity": "trial use", + "maturity": "draft", "type": "object", "description": "A proposition describing the role of a variant in causing an inherited condition.", "properties": { diff --git a/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml b/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml index 120275d..3315f9b 100644 --- a/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml +++ b/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml @@ -70,7 +70,7 @@ $defs: # Variant Pathogenicity Proposition VariantPathogenicityProposition: inherits: gks-core:Proposition - maturity: trial use + maturity: draft type: object description: >- A proposition describing the role of a variant in causing an inherited condition. From 19f0cdb638c3d3958a4be9f1356c2055dd1fa647 Mon Sep 17 00:00:00 2001 From: Matthew Brush Date: Fri, 8 Nov 2024 08:38:46 -0800 Subject: [PATCH 06/20] Rename pathogenicity-evidenceline-profile-source.yaml to pathogenicity-evidence-line-profile-source.yaml adding dash to evidence-line file name to be consistent with sue of dashes between class names in other profile file names (e.g. study-result) --- ...ource.yaml => pathogenicity-evidence-line-profile-source.yaml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename schema/va-spec/base/{pathogenicity-evidenceline-profile-source.yaml => pathogenicity-evidence-line-profile-source.yaml} (100%) diff --git a/schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml b/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml similarity index 100% rename from schema/va-spec/base/pathogenicity-evidenceline-profile-source.yaml rename to schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml From a793e50b1506bbb58466ba386d853b4f820a63ce Mon Sep 17 00:00:00 2001 From: Matthew Brush Date: Fri, 8 Nov 2024 09:14:39 -0800 Subject: [PATCH 07/20] Update experimental-functional-impact-study-statement-profile-source.yaml Updated comments for discussion/review among developers, based on most recent conversations. --- ...impact-study-statement-profile-source.yaml | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml index 966f8c9..125408c 100644 --- a/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml +++ b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml @@ -39,7 +39,7 @@ $defs: extends: object oneOf: - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - - $ref: "/ga4gh/schema/gks-core/1.x/MappableConcept" # See https://github.com/ga4gh/gks-common/pull/77 + - $ref: "/ga4gh/schema/gks-core/1.x/MappableConcept" # See https://github.com/ga4gh/gks-common/pull/77 - proposes a SequenceFeature domain entity class description: >- The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. @@ -65,22 +65,22 @@ $defs: functional impact(s) measured by the assay(s) employed. It is recommended that terms are drawn from established terminologies where possible. - # TO DO: I feel like it would be good to try and standardize the values used here by defining an enum based on early adopter needs, and growing from there. - # I seeded an initial proposal that covers specific impact types used in MAVE and CIViC. Applciation/community specific terms these adopters want to use can be captured in the 'classification' slot. - # But we should consider if this is the best approach. + # 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 # maps to CIViC 'gain of function' - - decreased activity # maps to CIViC 'loss of function' - - novel activity # maps to CIViC 'neomorphic' - - dominant negative activity # maps to CIViC 'dominant negative' + - 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' - classification: + classification: # this attribute now inherits the data type of 'MappableConcept' from the Core model (rather than simpler 'string' that was originally used) Consider need for a MappableConcept. Consider what tyeps of values would go in this attribute for a FI Statement. And what it would look like if there is no 'code' available. extends: classification description: >- An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use. - $comment: >- + $comment: >- # Matt: update $comment here to reflect outcome of discussion / decisions about what would go here in a FI Statement instance. This is an optional attribute that can be used by data providers to provide a particular community of users a functional impact classification in familiar terms, that summarizes/complements the smeantics broken out in the SPOQ attributes of the Statement @@ -98,4 +98,4 @@ $defs: - subjectVariant - predicate - objectSequenceFeature - - studyContextQualifier \ No newline at end of file + - studyContextQualifier From 7b5072c1cfd2901c6e4a6a5f77a8b3a58f890e2a Mon Sep 17 00:00:00 2001 From: Matthew Brush Date: Fri, 8 Nov 2024 09:56:57 -0800 Subject: [PATCH 08/20] Update pathogenicity-evidence-line-profile-source.yaml - Updated comments/questions about this profile based on outcomes of recent discussions. - made a couple minor improvements to attribute descriptions. --- ...thogenicity-evidence-line-profile-source.yaml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml b/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml index 3315f9b..c51558c 100644 --- a/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml +++ b/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml @@ -31,15 +31,15 @@ $defs: items: $ref: "/ga4gh/schema/gks-core/1.x/json/InformationEntity" description: >- - An Information Entity (e.g. a Functional Impact Study Statement) that was assessed as - evidence in determining the possible pathogenicity of a variant. + An Information Entity that was assessed as evidence in determining the possible + pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Reuslt) directionOfEvidenceProvided: extends: directionOfEvidenceProvided description: >- The direction of support that the Evidence Line is determined to provide for its target - Variant Pathogenicity Proposition (i.e. does the evidence line support or dispute the - pathogenicity of the assessed variant, or remain neutral) - strengthOfEvidenceProvided: # TO DO: Ensure that ten enum below covers terms needed for initial adopters. Merge https://github.com/ga4gh/gks-common/pull/78 which updates the core IM to allow this property to take a string. Think about if we need the PS/BS codes here - as this bakes in direction, and is duplicative as the 'specifiedBy' attribute reports the ACMG criterion applied. + Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the + evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral) + strengthOfEvidenceProvided: # Matt: These ACMG-based values should likely go into a community profile instead of the base profile. Do we add any value constraints in the base profile? And in the AMCF community profile, think about if we need the PS/BS prefixes on values here - as this bakes in direction, and is duplicative as the 'specifiedBy' attribute reports the ACMG criterion applied. extends: strengthOfEvidenceProvided type: string enum: @@ -60,12 +60,12 @@ $defs: The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). - specifiedBy: + specifiedBy: # Matt: Note that in an ACMG community profile, we should consider if/how to ensure values here are one of the ACMG criteria (e.g. PS4, BS3, ...), or the full ACMG Guidelines. extends: specifiedBy description: >- A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant. - # required: # TO DO: decide which if any attributes should be *required* in this profile. + # required: # Matt: decide which if any attributes should be *required* in this profile. None are required in the Core model Evidence Line class. IMO we should not require any here either - as Evidence Lines can be used to report collections of evidence items absent a strength/direction assessment, or strength/direction assessments absent a collection of evidence items, or both. # Variant Pathogenicity Proposition VariantPathogenicityProposition: @@ -125,5 +125,3 @@ $defs: - subjectVariant - predicate - objectCondition - - # TO DO: decide if we want to include the qualifiers defined on the VarPathStatement class in the VarPathProposition From 0bc8f823ea1c233d88b70819873b183d54c15006 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Sat, 9 Nov 2024 10:45:17 -0500 Subject: [PATCH 09/20] rebuild rst --- .../def/VariantPathogenicityStatement.rst | 5 -- .../def/CohortAlleleFrequencyStudyResult.rst | 49 ------------------ schema/va-spec/base/def/Condition.rst | 5 -- ...ntalVariantFunctionalImpactStudyResult.rst | 47 ----------------- ...lVariantFunctionalImpactStudyStatement.rst | 46 ----------------- .../base/def/PathogenicityEvidenceLine.rst | 44 +--------------- schema/va-spec/base/def/Therapeutic.rst | 5 -- schema/va-spec/base/def/TherapyGroup.rst | 15 ------ schema/va-spec/base/def/TraitSet.rst | 14 ------ .../def/VariantDiagnosticStudyStatement.rst | 47 ----------------- .../def/VariantOncogenicityStudyStatement.rst | 47 ----------------- .../def/VariantPathogenicityProposition.rst | 27 ---------- .../def/VariantPathogenicityStatement.rst | 50 ------------------- .../def/VariantPrognosticStudyStatement.rst | 47 ----------------- ...riantTherapeuticResponseStudyStatement.rst | 48 ------------------ 15 files changed, 2 insertions(+), 494 deletions(-) diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst index 49e4942..bdeeaea 100644 --- a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst @@ -1,7 +1,3 @@ -.. 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 Statement describing the role of a variant in causing an inherited condition. @@ -16,7 +12,6 @@ A Statement describing the role of a variant in causing an inherited condition. :widths: auto * - Field - - Flags - Type - Limits - Description diff --git a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst b/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst index 98a5d68..5548822 100644 --- a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst +++ b/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst @@ -1,7 +1,3 @@ -.. 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 StudyResult that reports measures related to the frequency of an Allele in a cohort @@ -17,131 +13,86 @@ Some CohortAlleleFrequencyStudyResult attributes are inherited from :ref:`gks-co :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. * - 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. * - specifiedBy - - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions - - - .. raw:: html - - ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn - - - .. raw:: html - - ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored - - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - recordMetadata - - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - ancillaryResults - - - .. raw:: html - - D - object - 0..1 - * - qualityMeasures - - - .. raw:: html - - D - object - 0..1 - * - type - - - string - 1..1 - MUST be "CohortAlleleFrequencyStudyResult". * - sourceDataSet - - - .. raw:: html - - ⋮ - :ref:`DataSet` - 0..m - The dataset from which the CohortAlleleFrequencyStudyResult was reported. * - focusAllele - - - :ref:`Allele` | string - 1..1 - The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD. * - focusAlleleCount - - - integer - 1..1 - The number of occurrences of the focusAllele in the cohort. * - locusAlleleCount - - - integer - 1..1 - The number of occurrences of all alleles at the locus in the cohort (sometimes referred to as "allele number") * - focusAlleleFrequency - - - number - 1..1 - The frequency of the focusAllele in the cohort. * - cohort - - - :ref:`StudyGroup` - 1..1 - The cohort from which the frequency was derived. * - subCohortFrequency - - - .. raw:: html - - ⋮ - :ref:`CohortAlleleFrequencyStudyResult` - 0..m - A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups. diff --git a/schema/va-spec/base/def/Condition.rst b/schema/va-spec/base/def/Condition.rst index edcb621..9e68ad9 100644 --- a/schema/va-spec/base/def/Condition.rst +++ b/schema/va-spec/base/def/Condition.rst @@ -1,7 +1,3 @@ -.. 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 set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement. @@ -16,7 +12,6 @@ A set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that repr :widths: auto * - Field - - Flags - Type - Limits - Description diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst index c6c36f4..308f9ae 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst @@ -1,7 +1,3 @@ -.. 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 StudyResult that reports a functional impact score from a variant functional assay or study. @@ -17,121 +13,78 @@ Some ExperimentalVariantFunctionalImpactStudyResult attributes are inherited fro :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. * - 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. * - contributions - - - .. raw:: html - - ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn - - - .. raw:: html - - ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored - - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - recordMetadata - - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - componentResult - - - .. raw:: html - - ⋮ - :ref:`StudyResult` - 0..m - Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) . * - studyGroup - - - :ref:`StudyGroup` - 0..1 - A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult. * - ancillaryResults - - - .. raw:: html - - D - object - 0..1 - * - qualityMeasures - - - .. raw:: html - - D - object - 0..1 - * - type - - - string - 1..1 - MUST be "ExperimentalVariantFunctionalImpactStudyResult". * - focusVariant - - - :ref:`MolecularVariation` | :ref:`iriReference` - 0..1 - The genetic variant for which a functional impact score is generated. * - functionalImpactScore - - - number - 0..1 - The score of the variant impact measured in the assay or study. * - specifiedBy - - - :ref:`Method` | :ref:`iriReference` - 0..1 - The assay that was performed to generate the reported functional impact score. * - sourceDataSet - - - .. raw:: html - - ⋮ - :ref:`DataSet` - 0..m - The full data set that provided the reported the functional impact score. diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst index 1dcc850..dd91e1c 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst @@ -1,7 +1,3 @@ -.. 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 statement 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). @@ -17,140 +13,98 @@ Some ExperimentalVariantFunctionalImpactStudyStatement attributes are inherited :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. * - 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. * - contributions - - - .. raw:: html - - ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn - - - .. raw:: html - - ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored - - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom - - - .. raw:: html - - ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata - - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction - - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength - - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score - - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText - - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - hasEvidenceLines - - - .. raw:: html - - ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type - - - string - 1..1 - MUST be "ExperimentalVariantFunctionalImpactStudyStatement". * - subjectVariant - - - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A protein or genomic contextual or canonical molecular variant. * - predicate - - - string - 1..1 - The relationship this Statement describes between the subject Variant and object Sequence Feature whose function it may alter. * - objectSequenceFeature - - - :ref:`iriReference` | :ref:`MappableConcept` - 1..1 - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. * - studyContextQualifier - - - :ref:`Document` | :ref:`iriReference` - 1..1 - The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. * - impactTypeQualifier - - - string - 0..1 - 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). * - classification - - - :ref:`MappableConcept` - 0..1 - An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use. * - specifiedBy - - - :ref:`Method` | :ref:`iriReference` - 0..1 - The method that specifies how the functional classification is ultimately assigned to the variant, based on interpretation of data from the supporting assay. May include information about thresholds applied on assay variant effect scores to derive the final classification. diff --git a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst index dec16cb..a3ff0ce 100644 --- a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst +++ b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst @@ -1,7 +1,3 @@ -.. 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** An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. @@ -17,110 +13,74 @@ Some PathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:Evid :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. * - 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. * - contributions - - - .. raw:: html - - ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn - - - .. raw:: html - - ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored - - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom - - - .. raw:: html - - ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata - - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - scoreOfEvidenceProvided - - - number - 0..1 - A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value. * - type - - - string - 1..1 - MUST be "PathogenicityEvidenceLine". * - hasEvidenceItems - - - .. raw:: html - - ⋮ - :ref:`InformationEntity` - 0..m - - An Information Entity (e.g. a Functional Impact Study Statement) that was assessed as evidence in determining the possible pathogenicity of a variant. + - An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Reuslt) * - directionOfEvidenceProvided - - - string - 0..1 - - The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition (i.e. does the evidence line support or dispute the pathogenicity of the assessed variant, or remain neutral) + - The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral) * - strengthOfEvidenceProvided - - - string - 0..1 - The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. * - targetProposition - - - :ref:`VariantPathogenicityProposition` - 0..1 - The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). * - specifiedBy - - - :ref:`Method` | :ref:`iriReference` - 0..1 - A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant. diff --git a/schema/va-spec/base/def/Therapeutic.rst b/schema/va-spec/base/def/Therapeutic.rst index fbc27d4..c215606 100644 --- a/schema/va-spec/base/def/Therapeutic.rst +++ b/schema/va-spec/base/def/Therapeutic.rst @@ -1,7 +1,3 @@ -.. 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 group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that represents the object of a Therapeutic Response study statement. @@ -16,7 +12,6 @@ A group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that repres :widths: auto * - Field - - Flags - Type - Limits - Description diff --git a/schema/va-spec/base/def/TherapyGroup.rst b/schema/va-spec/base/def/TherapyGroup.rst index ab4c0cc..efd633c 100644 --- a/schema/va-spec/base/def/TherapyGroup.rst +++ b/schema/va-spec/base/def/TherapyGroup.rst @@ -1,7 +1,3 @@ -.. 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 group of therapies that are applied together in the context of a Therapeutic Response study statement. @@ -17,33 +13,22 @@ Some TherapyGroup attributes are inherited from :ref:`gks-core:Element`. :widths: auto * - Field - - Flags - Type - Limits - Description * - id - - - string - 0..1 - The 'logical' identifier of the data element 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. * - 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. * - groupType - - - string - 0..1 - The type of the therapy group. * - therapies - - - .. raw:: html - - ⋮ - :ref:`MappableConcept` - 2..m - A list of therapies that are applied together in the context of a Therapeutic Response study statement. diff --git a/schema/va-spec/base/def/TraitSet.rst b/schema/va-spec/base/def/TraitSet.rst index b88795a..d49ea64 100644 --- a/schema/va-spec/base/def/TraitSet.rst +++ b/schema/va-spec/base/def/TraitSet.rst @@ -1,7 +1,3 @@ -.. 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 set of traits that are co-occurring in the context of a Variant Pathogenicity statement. @@ -17,28 +13,18 @@ Some TraitSet attributes are inherited from :ref:`gks-core:Element`. :widths: auto * - Field - - Flags - Type - Limits - Description * - id - - - string - 0..1 - The 'logical' identifier of the data element 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. * - 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. * - traits - - - .. raw:: html - - ⋮ - :ref:`MappableConcept` - 2..m - A list of traits that are co-occurring in the context of a Variant Pathogenicity statement. diff --git a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst b/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst index bc7a221..a10268b 100644 --- a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst +++ b/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst @@ -1,7 +1,3 @@ -.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. @@ -17,145 +13,102 @@ Some VariantDiagnosticStudyStatement attributes are inherited from :ref:`gks-cor :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. * - 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. * - specifiedBy - - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions - - - .. raw:: html - - ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn - - - .. raw:: html - - ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored - - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom - - - .. raw:: html - - ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata - - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction - - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength - - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score - - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText - - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification - - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines - - - .. raw:: html - - ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type - - - string - 1..1 - MUST be "VariantDiagnosticStudyStatement". * - subjectVariant - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate - - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectCondition - - - :ref:`Condition` | :ref:`iriReference` - 1..1 - The disease that is evaluated for diagnosis. * - alleleOriginQualifier - - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier - - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier - - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Statement. diff --git a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst b/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst index b54fbde..4164dfc 100644 --- a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst +++ b/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst @@ -1,7 +1,3 @@ -.. 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 Statement reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. @@ -17,145 +13,102 @@ Some VariantOncogenicityStudyStatement attributes are inherited from :ref:`gks-c :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. * - 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. * - specifiedBy - - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions - - - .. raw:: html - - ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn - - - .. raw:: html - - ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored - - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom - - - .. raw:: html - - ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata - - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction - - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength - - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score - - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText - - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification - - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines - - - .. raw:: html - - ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type - - - string - 1..1 - MUST be "VariantOncogenicityStudyStatement". * - subjectVariant - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate - - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectTumorType - - - :ref:`Condition` | :ref:`MappableConcept` - 1..1 - The tumor type for which the variant impact is evaluated. * - alleleOriginQualifier - - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier - - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier - - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Statement. diff --git a/schema/va-spec/base/def/VariantPathogenicityProposition.rst b/schema/va-spec/base/def/VariantPathogenicityProposition.rst index 9c62f3b..da9f9c9 100644 --- a/schema/va-spec/base/def/VariantPathogenicityProposition.rst +++ b/schema/va-spec/base/def/VariantPathogenicityProposition.rst @@ -1,7 +1,3 @@ -.. 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 describing the role of a variant in causing an inherited condition. @@ -17,81 +13,58 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`gks-cor :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. * - 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. * - propositionText - - - string - 0..1 - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". * - 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 - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectCondition - - - :ref:`Condition` | :ref:`iriReference` - 1..1 - The :ref:`Condition` for which the variant impact is stated. * - penetranceQualifier - - - string - 0..1 - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. * - modeOfInheritanceQualifier - - - .. raw:: html - - ⋮ - :ref:`Coding` - 0..m - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. * - geneContextQualifier - - - :ref:`MappableConcept` | :ref:`iriReference` - 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). diff --git a/schema/va-spec/base/def/VariantPathogenicityStatement.rst b/schema/va-spec/base/def/VariantPathogenicityStatement.rst index b66de70..07cb4aa 100644 --- a/schema/va-spec/base/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/base/def/VariantPathogenicityStatement.rst @@ -1,7 +1,3 @@ -.. 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 Statement describing the role of a variant in causing an inherited condition. @@ -17,148 +13,102 @@ Some VariantPathogenicityStatement attributes are inherited from :ref:`gks-core: :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. * - 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. * - specifiedBy - - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions - - - .. raw:: html - - ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn - - - .. raw:: html - - ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored - - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom - - - .. raw:: html - - ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata - - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction - - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength - - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score - - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText - - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification - - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines - - - .. raw:: html - - ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type - - - string - 1..1 - MUST be "VariantPathogenicityStatement". * - subjectVariant - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate - - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectCondition - - - :ref:`Condition` | :ref:`iriReference` - 1..1 - The :ref:`Condition` for which the variant impact is stated. * - penetranceQualifier - - - string - 0..1 - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. * - modeOfInheritanceQualifier - - - .. raw:: html - - ⋮ - :ref:`Coding` - 0..m - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. * - geneContextQualifier - - - :ref:`MappableConcept` | :ref:`iriReference` - 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). diff --git a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst b/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst index 87b3444..81bd315 100644 --- a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst +++ b/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst @@ -1,7 +1,3 @@ -.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. @@ -17,145 +13,102 @@ Some VariantPrognosticStudyStatement attributes are inherited from :ref:`gks-cor :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. * - 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. * - specifiedBy - - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions - - - .. raw:: html - - ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn - - - .. raw:: html - - ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored - - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom - - - .. raw:: html - - ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata - - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction - - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength - - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score - - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText - - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification - - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines - - - .. raw:: html - - ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type - - - string - 1..1 - MUST be "VariantPrognosticStudyStatement". * - subjectVariant - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate - - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectCondition - - - :ref:`Condition` | :ref:`iriReference` - 1..1 - The disease that is evaluated for outcome. * - alleleOriginQualifier - - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier - - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier - - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the prognostic association in the Statement. diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst index d9868df..63071b2 100644 --- a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst +++ b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst @@ -1,7 +1,3 @@ -.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. @@ -17,150 +13,106 @@ Some VariantTherapeuticResponseStudyStatement attributes are inherited from :ref :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. * - 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. * - specifiedBy - - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions - - - .. raw:: html - - ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn - - - .. raw:: html - - ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored - - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom - - - .. raw:: html - - ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata - - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction - - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength - - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score - - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText - - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification - - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines - - - .. raw:: html - - ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type - - - string - 1..1 - MUST be "VariantTherapeuticResponseStudyStatement". * - subjectVariant - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate - - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectTherapeutic - - - :ref:`Therapeutic` | :ref:`iriReference` - 1..1 - A drug administration or other therapeutic procedure that the neoplasm is intended to respond to. * - conditionQualifier - - - :ref:`Condition` | :ref:`iriReference` - 1..1 - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements. * - alleleOriginQualifier - - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier - - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier - - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. From e98bda54aa069c57108ed9472b36b72d4e618926 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Sat, 9 Nov 2024 10:53:38 -0500 Subject: [PATCH 10/20] resolves conflicting definition of evidence line property --- .../json/VariantPathogenicityStatement | 12 +++++++++++ ...athogenicity-statement-profile-source.yaml | 17 ++++++++-------- .../base/def/PathogenicityEvidenceLine.rst | 6 +++--- ...entalVariantFunctionalImpactStudyStatement | 8 ++++---- .../base/json/PathogenicityEvidenceLine | 16 +++++---------- ...genicity-evidence-line-profile-source.yaml | 20 +++++++------------ 6 files changed, 40 insertions(+), 39 deletions(-) diff --git a/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement b/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement index 8311837..5396b8d 100644 --- a/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement +++ b/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement @@ -11,6 +11,18 @@ { "properties": { "classification": { + "properties": { + "label": { + "type": "string", + "enum": [ + "pathogenic", + "likely pathogenic", + "uncertain significance", + "likely benign", + "benign" + ] + } + }, "description": "The ACMG 2015 classification of the variant's pathogenicity." } } diff --git a/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml index 5925dec..06b851b 100644 --- a/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml +++ b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml @@ -18,14 +18,15 @@ $defs: - $ref: "/ga4gh/schema/va-spec/1.x/base/VariantPathogenicityStatement" - properties: classification: - # this is a MappableConcept but we would ideally like to specify a value set with meta characteristics to validate with some consistency - # type: string - # enum: - # - pathogenic - # - likely pathogenic - # - uncertain significance - # - likely benign - # - benign + properties: + label: + type: string + enum: + - pathogenic + - likely pathogenic + - uncertain significance + - likely benign + - benign description: >- The ACMG 2015 classification of the variant's pathogenicity. diff --git a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst index a3ff0ce..4361231 100644 --- a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst +++ b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst @@ -67,13 +67,13 @@ Some PathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:Evid * - hasEvidenceItems - :ref:`InformationEntity` - 0..m - - An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Reuslt) + - An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result). * - directionOfEvidenceProvided - string - 0..1 - - The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral) + - The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral) * - strengthOfEvidenceProvided - - string + - {'$ref': '/ga4gh/schema/gks-core/1.x/json/MappableConcept'} - 0..1 - The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. * - targetProposition diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement index 4e26039..5ac9949 100644 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement @@ -169,10 +169,10 @@ "$comment": "Implementers may use a set of terms to use here that reflect the specific types of functional impact(s) measured by the assay(s) employed. It is recommended that terms are drawn from established terminologies where possible.", "type": "string", "enum": [ - "increased activity", - "decreased activity", - "novel activity", - "dominant negative activity" + "increased activity/function", + "decreased activity/function", + "novel activity/function", + "dominant negative activity/function" ] }, "classification": { diff --git a/schema/va-spec/base/json/PathogenicityEvidenceLine b/schema/va-spec/base/json/PathogenicityEvidenceLine index 02ad1ca..de30cde 100644 --- a/schema/va-spec/base/json/PathogenicityEvidenceLine +++ b/schema/va-spec/base/json/PathogenicityEvidenceLine @@ -95,7 +95,7 @@ "items": { "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" }, - "description": "An Information Entity (e.g. a Functional Impact Study Statement) that was assessed as evidence in determining the possible pathogenicity of a variant. ", + "description": "An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result).", "$comment": "A given Evidence Line may be supported by one or many individual evidence items. What matters is that all evidence items in a given Evidence Line get collectively assessed and assigned direction and strength as a single argument for or against a target proposition.\nDifferent types and scales of information entity can serve as evidence (experimental measurements or observations, data tables or figures, images, prior assertions, etc.) Only when assessed as evidence do we consider the information to be an 'Evidence Item'. For example, a piece of population frequency data about BRCA2 c.8023A>G becomes an Evidence Item when it is assessed for the support it may offer for a target proposition (e.g. the prospect of the variant\u2019s pathogenicity)." }, "directionOfEvidenceProvided": { @@ -105,21 +105,15 @@ "neutral", "disputes" ], - "description": "The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition (i.e. does the evidence line support or dispute the pathogenicity of the assessed variant, or remain neutral)" + "description": "The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral)" }, "strengthOfEvidenceProvided": { "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", "description": "The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute.", "$comment": "Values of this attribute can be defined by for a given profile based on domain/application needs, but should be framed in qualitative terms (e.g. 'strong', 'moderate', 'weak'). The 'scoreOfEvidenceProvided' attribute can be used to report quantitative assessments of evidence provided.", - "type": "string", - "enum": [ - "PS3_Strong", - "PS3_Moderate", - "PS3_Supporting", - "BS3_Strong", - "BS3_Moderate", - "BS3_Supporting" - ] + "type": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } }, "targetProposition": { "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition", diff --git a/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml b/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml index c51558c..7f4552b 100644 --- a/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml +++ b/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml @@ -32,23 +32,18 @@ $defs: $ref: "/ga4gh/schema/gks-core/1.x/json/InformationEntity" description: >- An Information Entity that was assessed as evidence in determining the possible - pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Reuslt) + pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result). directionOfEvidenceProvided: extends: directionOfEvidenceProvided description: >- The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the - evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral) - strengthOfEvidenceProvided: # Matt: These ACMG-based values should likely go into a community profile instead of the base profile. Do we add any value constraints in the base profile? And in the AMCF community profile, think about if we need the PS/BS prefixes on values here - as this bakes in direction, and is duplicative as the 'specifiedBy' attribute reports the ACMG criterion applied. + evidence line support or dispute the possible pathogenicity of the subject variant, or + remain neutral) + strengthOfEvidenceProvided: extends: strengthOfEvidenceProvided - type: string - enum: - - PS3_Strong - - PS3_Moderate - - PS3_Supporting - - BS3_Strong - - BS3_Moderate - - BS3_Supporting + type: + $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" description: >- The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction @@ -60,12 +55,11 @@ $defs: The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). - specifiedBy: # Matt: Note that in an ACMG community profile, we should consider if/how to ensure values here are one of the ACMG criteria (e.g. PS4, BS3, ...), or the full ACMG Guidelines. + specifiedBy: extends: specifiedBy description: >- A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant. - # required: # Matt: decide which if any attributes should be *required* in this profile. None are required in the Core model Evidence Line class. IMO we should not require any here either - as Evidence Lines can be used to report collections of evidence items absent a strength/direction assessment, or strength/direction assessments absent a collection of evidence items, or both. # Variant Pathogenicity Proposition VariantPathogenicityProposition: From 8a99ff449fa13c9166f327eb0cb662d5a323d964 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Sat, 9 Nov 2024 11:36:10 -0500 Subject: [PATCH 11/20] update build with newer MSP --- .../def/VariantPathogenicityStatement.rst | 5 ++ .../def/CohortAlleleFrequencyStudyResult.rst | 49 ++++++++++++++++++ schema/va-spec/base/def/Condition.rst | 5 ++ ...ntalVariantFunctionalImpactStudyResult.rst | 47 +++++++++++++++++ ...lVariantFunctionalImpactStudyStatement.rst | 46 +++++++++++++++++ .../base/def/PathogenicityEvidenceLine.rst | 40 +++++++++++++++ schema/va-spec/base/def/Therapeutic.rst | 5 ++ schema/va-spec/base/def/TherapyGroup.rst | 15 ++++++ schema/va-spec/base/def/TraitSet.rst | 14 ++++++ .../def/VariantDiagnosticStudyStatement.rst | 47 +++++++++++++++++ .../def/VariantOncogenicityStudyStatement.rst | 47 +++++++++++++++++ .../def/VariantPathogenicityProposition.rst | 27 ++++++++++ .../def/VariantPathogenicityStatement.rst | 50 +++++++++++++++++++ .../def/VariantPrognosticStudyStatement.rst | 47 +++++++++++++++++ ...riantTherapeuticResponseStudyStatement.rst | 48 ++++++++++++++++++ 15 files changed, 492 insertions(+) diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst index bdeeaea..49e4942 100644 --- a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst @@ -1,3 +1,7 @@ +.. 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 Statement describing the role of a variant in causing an inherited condition. @@ -12,6 +16,7 @@ A Statement describing the role of a variant in causing an inherited condition. :widths: auto * - Field + - Flags - Type - Limits - Description diff --git a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst b/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst index 5548822..98a5d68 100644 --- a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst +++ b/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst @@ -1,3 +1,7 @@ +.. 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 StudyResult that reports measures related to the frequency of an Allele in a cohort @@ -13,86 +17,131 @@ Some CohortAlleleFrequencyStudyResult attributes are inherited from :ref:`gks-co :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. * - 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. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - ancillaryResults + - + .. raw:: html + + D - object - 0..1 - * - qualityMeasures + - + .. raw:: html + + D - object - 0..1 - * - type + - - string - 1..1 - MUST be "CohortAlleleFrequencyStudyResult". * - sourceDataSet + - + .. raw:: html + + ⋮ - :ref:`DataSet` - 0..m - The dataset from which the CohortAlleleFrequencyStudyResult was reported. * - focusAllele + - - :ref:`Allele` | string - 1..1 - The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD. * - focusAlleleCount + - - integer - 1..1 - The number of occurrences of the focusAllele in the cohort. * - locusAlleleCount + - - integer - 1..1 - The number of occurrences of all alleles at the locus in the cohort (sometimes referred to as "allele number") * - focusAlleleFrequency + - - number - 1..1 - The frequency of the focusAllele in the cohort. * - cohort + - - :ref:`StudyGroup` - 1..1 - The cohort from which the frequency was derived. * - subCohortFrequency + - + .. raw:: html + + ⋮ - :ref:`CohortAlleleFrequencyStudyResult` - 0..m - A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups. diff --git a/schema/va-spec/base/def/Condition.rst b/schema/va-spec/base/def/Condition.rst index 9e68ad9..edcb621 100644 --- a/schema/va-spec/base/def/Condition.rst +++ b/schema/va-spec/base/def/Condition.rst @@ -1,3 +1,7 @@ +.. 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 set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement. @@ -12,6 +16,7 @@ A set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that repr :widths: auto * - Field + - Flags - Type - Limits - Description diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst index 308f9ae..c6c36f4 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst @@ -1,3 +1,7 @@ +.. 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 StudyResult that reports a functional impact score from a variant functional assay or study. @@ -13,78 +17,121 @@ Some ExperimentalVariantFunctionalImpactStudyResult attributes are inherited fro :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. * - 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. * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - componentResult + - + .. raw:: html + + ⋮ - :ref:`StudyResult` - 0..m - Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) . * - studyGroup + - - :ref:`StudyGroup` - 0..1 - A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult. * - ancillaryResults + - + .. raw:: html + + D - object - 0..1 - * - qualityMeasures + - + .. raw:: html + + D - object - 0..1 - * - type + - - string - 1..1 - MUST be "ExperimentalVariantFunctionalImpactStudyResult". * - focusVariant + - - :ref:`MolecularVariation` | :ref:`iriReference` - 0..1 - The genetic variant for which a functional impact score is generated. * - functionalImpactScore + - - number - 0..1 - The score of the variant impact measured in the assay or study. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - The assay that was performed to generate the reported functional impact score. * - sourceDataSet + - + .. raw:: html + + ⋮ - :ref:`DataSet` - 0..m - The full data set that provided the reported the functional impact score. diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst index dd91e1c..1dcc850 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst @@ -1,3 +1,7 @@ +.. 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 statement 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). @@ -13,98 +17,140 @@ Some ExperimentalVariantFunctionalImpactStudyStatement attributes are inherited :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. * - 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. * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - MUST be "ExperimentalVariantFunctionalImpactStudyStatement". * - subjectVariant + - - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A protein or genomic contextual or canonical molecular variant. * - predicate + - - string - 1..1 - The relationship this Statement describes between the subject Variant and object Sequence Feature whose function it may alter. * - objectSequenceFeature + - - :ref:`iriReference` | :ref:`MappableConcept` - 1..1 - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. * - studyContextQualifier + - - :ref:`Document` | :ref:`iriReference` - 1..1 - The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. * - impactTypeQualifier + - - string - 0..1 - 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). * - classification + - - :ref:`MappableConcept` - 0..1 - An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - The method that specifies how the functional classification is ultimately assigned to the variant, based on interpretation of data from the supporting assay. May include information about thresholds applied on assay variant effect scores to derive the final classification. diff --git a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst index 4361231..7dbd9f7 100644 --- a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst +++ b/schema/va-spec/base/def/PathogenicityEvidenceLine.rst @@ -1,3 +1,7 @@ +.. 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** An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. @@ -13,74 +17,110 @@ Some PathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:Evid :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. * - 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. * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - scoreOfEvidenceProvided + - - number - 0..1 - A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value. * - type + - - string - 1..1 - MUST be "PathogenicityEvidenceLine". * - hasEvidenceItems + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result). * - directionOfEvidenceProvided + - - string - 0..1 - The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral) * - strengthOfEvidenceProvided + - - {'$ref': '/ga4gh/schema/gks-core/1.x/json/MappableConcept'} - 0..1 - The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. * - targetProposition + - - :ref:`VariantPathogenicityProposition` - 0..1 - The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant. diff --git a/schema/va-spec/base/def/Therapeutic.rst b/schema/va-spec/base/def/Therapeutic.rst index c215606..fbc27d4 100644 --- a/schema/va-spec/base/def/Therapeutic.rst +++ b/schema/va-spec/base/def/Therapeutic.rst @@ -1,3 +1,7 @@ +.. 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 group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that represents the object of a Therapeutic Response study statement. @@ -12,6 +16,7 @@ A group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that repres :widths: auto * - Field + - Flags - Type - Limits - Description diff --git a/schema/va-spec/base/def/TherapyGroup.rst b/schema/va-spec/base/def/TherapyGroup.rst index efd633c..ab4c0cc 100644 --- a/schema/va-spec/base/def/TherapyGroup.rst +++ b/schema/va-spec/base/def/TherapyGroup.rst @@ -1,3 +1,7 @@ +.. 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 group of therapies that are applied together in the context of a Therapeutic Response study statement. @@ -13,22 +17,33 @@ Some TherapyGroup attributes are inherited from :ref:`gks-core:Element`. :widths: auto * - Field + - Flags - Type - Limits - Description * - id + - - string - 0..1 - The 'logical' identifier of the data element 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. * - 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. * - groupType + - - string - 0..1 - The type of the therapy group. * - therapies + - + .. raw:: html + + ⋮ - :ref:`MappableConcept` - 2..m - A list of therapies that are applied together in the context of a Therapeutic Response study statement. diff --git a/schema/va-spec/base/def/TraitSet.rst b/schema/va-spec/base/def/TraitSet.rst index d49ea64..b88795a 100644 --- a/schema/va-spec/base/def/TraitSet.rst +++ b/schema/va-spec/base/def/TraitSet.rst @@ -1,3 +1,7 @@ +.. 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 set of traits that are co-occurring in the context of a Variant Pathogenicity statement. @@ -13,18 +17,28 @@ Some TraitSet attributes are inherited from :ref:`gks-core:Element`. :widths: auto * - Field + - Flags - Type - Limits - Description * - id + - - string - 0..1 - The 'logical' identifier of the data element 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. * - 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. * - traits + - + .. raw:: html + + ⋮ - :ref:`MappableConcept` - 2..m - A list of traits that are co-occurring in the context of a Variant Pathogenicity statement. diff --git a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst b/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst index a10268b..bc7a221 100644 --- a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst +++ b/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst @@ -1,3 +1,7 @@ +.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. @@ -13,102 +17,145 @@ Some VariantDiagnosticStudyStatement attributes are inherited from :ref:`gks-cor :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. * - 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. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification + - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - MUST be "VariantDiagnosticStudyStatement". * - subjectVariant + - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate + - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectCondition + - - :ref:`Condition` | :ref:`iriReference` - 1..1 - The disease that is evaluated for diagnosis. * - alleleOriginQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier + - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Statement. diff --git a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst b/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst index 4164dfc..b54fbde 100644 --- a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst +++ b/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst @@ -1,3 +1,7 @@ +.. 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 Statement reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. @@ -13,102 +17,145 @@ Some VariantOncogenicityStudyStatement attributes are inherited from :ref:`gks-c :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. * - 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. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification + - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - MUST be "VariantOncogenicityStudyStatement". * - subjectVariant + - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate + - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectTumorType + - - :ref:`Condition` | :ref:`MappableConcept` - 1..1 - The tumor type for which the variant impact is evaluated. * - alleleOriginQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier + - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Statement. diff --git a/schema/va-spec/base/def/VariantPathogenicityProposition.rst b/schema/va-spec/base/def/VariantPathogenicityProposition.rst index da9f9c9..9c62f3b 100644 --- a/schema/va-spec/base/def/VariantPathogenicityProposition.rst +++ b/schema/va-spec/base/def/VariantPathogenicityProposition.rst @@ -1,3 +1,7 @@ +.. 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 describing the role of a variant in causing an inherited condition. @@ -13,58 +17,81 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`gks-cor :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. * - 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. * - propositionText + - - string - 0..1 - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". * - 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 - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectCondition + - - :ref:`Condition` | :ref:`iriReference` - 1..1 - The :ref:`Condition` for which the variant impact is stated. * - penetranceQualifier + - - string - 0..1 - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. * - modeOfInheritanceQualifier + - + .. raw:: html + + ⋮ - :ref:`Coding` - 0..m - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. * - geneContextQualifier + - - :ref:`MappableConcept` | :ref:`iriReference` - 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). diff --git a/schema/va-spec/base/def/VariantPathogenicityStatement.rst b/schema/va-spec/base/def/VariantPathogenicityStatement.rst index 07cb4aa..b66de70 100644 --- a/schema/va-spec/base/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/base/def/VariantPathogenicityStatement.rst @@ -1,3 +1,7 @@ +.. 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 Statement describing the role of a variant in causing an inherited condition. @@ -13,102 +17,148 @@ Some VariantPathogenicityStatement attributes are inherited from :ref:`gks-core: :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. * - 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. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification + - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - MUST be "VariantPathogenicityStatement". * - subjectVariant + - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate + - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectCondition + - - :ref:`Condition` | :ref:`iriReference` - 1..1 - The :ref:`Condition` for which the variant impact is stated. * - penetranceQualifier + - - string - 0..1 - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. * - modeOfInheritanceQualifier + - + .. raw:: html + + ⋮ - :ref:`Coding` - 0..m - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. * - geneContextQualifier + - - :ref:`MappableConcept` | :ref:`iriReference` - 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). diff --git a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst b/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst index 81bd315..87b3444 100644 --- a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst +++ b/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst @@ -1,3 +1,7 @@ +.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. @@ -13,102 +17,145 @@ Some VariantPrognosticStudyStatement attributes are inherited from :ref:`gks-cor :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. * - 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. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification + - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - MUST be "VariantPrognosticStudyStatement". * - subjectVariant + - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate + - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectCondition + - - :ref:`Condition` | :ref:`iriReference` - 1..1 - The disease that is evaluated for outcome. * - alleleOriginQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier + - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the prognostic association in the Statement. diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst index 63071b2..d9868df 100644 --- a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst +++ b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst @@ -1,3 +1,7 @@ +.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. @@ -13,106 +17,150 @@ Some VariantTherapeuticResponseStudyStatement attributes are inherited from :ref :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. * - 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. * - specifiedBy + - - :ref:`Method` | :ref:`iriReference` - 0..1 - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions + - + .. raw:: html + + ⋮ - :ref:`Contribution` - 0..m - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. * - reportedIn + - + .. raw:: html + + ⋮ - :ref:`Document` | :ref:`iriReference` - 0..m - A document in which the the Information Entity is reported. * - dateAuthored + - - string - 0..1 - Indicates when the information content expressed in the Information Entity was generated. * - derivedFrom + - + .. raw:: html + + ⋮ - :ref:`InformationEntity` - 0..m - Another Information Entity from which this Information Entity is derived, in whole or in part. * - recordMetadata + - - :ref:`RecordMetadata` - 0..1 - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). * - direction + - - string - 0..1 - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. * - strength + - - :ref:`MappableConcept` - 0..1 - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. * - score + - - number - 0..1 - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. * - statementText + - - string - 0..1 - A natural-language expression of what a Statement asserts to be true. * - classification + - - :ref:`MappableConcept` - 0..1 - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines + - + .. raw:: html + + ⋮ - :ref:`EvidenceLine` - 0..m - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). * - type + - - string - 1..1 - MUST be "VariantTherapeuticResponseStudyStatement". * - subjectVariant + - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - 1..1 - A variant that is the subject of the Statement. * - predicate + - - string - 1..1 - The relationship declared to hold between the subject and the object of the Statement. * - objectTherapeutic + - - :ref:`Therapeutic` | :ref:`iriReference` - 1..1 - A drug administration or other therapeutic procedure that the neoplasm is intended to respond to. * - conditionQualifier + - - :ref:`Condition` | :ref:`iriReference` - 1..1 - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements. * - alleleOriginQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). * - allelePrevalenceQualifier + - - string - 0..1 - Reports whether the statement should be interpreted in the context of the variant being rare or common. * - geneContextQualifier + - - :ref:`MappableConcept` - 0..1 - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. From cd79c0f5e9c8699871958dba94ec3426bca2b713 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Sat, 9 Nov 2024 12:49:48 -0500 Subject: [PATCH 12/20] update fixtures to new mappable concept --- .../fixtures/AVE-clinical-classification.yaml | 2 +- .../fixtures/VA-ClinVar-SCV-Example-001.yaml | 28 ++++-- .../fixtures/VA-ClinVar-SCV-Example-002.yaml | 28 ++++-- tests/fixtures/diagnostic-inline.yaml | 66 +++++++------- tests/fixtures/prognostic-inline.yaml | 66 +++++++------- tests/fixtures/therapeuticAgent.yaml | 10 ++- tests/fixtures/tr-statement-inline.yaml | 86 ++++++++++--------- 7 files changed, 166 insertions(+), 120 deletions(-) diff --git a/tests/fixtures/AVE-clinical-classification.yaml b/tests/fixtures/AVE-clinical-classification.yaml index 7a28ec2..a9a04d7 100644 --- a/tests/fixtures/AVE-clinical-classification.yaml +++ b/tests/fixtures/AVE-clinical-classification.yaml @@ -39,7 +39,7 @@ targetProposition: - translates_from_reading_frame predicate: isCausalFor objectCondition: - type: Condition + conceptType: Condition label: Unspecified geneContextQualifier: conceptType: Gene diff --git a/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml b/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml index 81bd1f9..44d0694 100644 --- a/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml +++ b/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml @@ -45,13 +45,19 @@ objectCondition: predicate: isCausalFor direction: supports strength: - code: cg000021 label: Definitive (ACMG 2015) - system: https://dataexchange.clinicalgenome.org/codes/ + mappings: + - coding: + code: cg000021 + system: https://dataexchange.clinicalgenome.org/codes/ + relation: exactMatch classification: - code: cg000001 label: Pathogenic (ACMG 2015) - system: https://dataexchange.clinicalgenome.org/codes/ + mappings: + - coding: + code: cg000001 + system: https://dataexchange.clinicalgenome.org/codes/ + relation: exactMatch penetranceQualifier: high contributions: - type: Contribution @@ -61,9 +67,12 @@ contributions: label: ClinVar Staff, National Center for Biotechnology Information (NCBI) date: '2018-06-12' activityType: - code: cg000010 label: submitted - system: https://dataexchange.clinicalgenome.org/codes/ + mappings: + - coding: + code: cg000010 + system: https://dataexchange.clinicalgenome.org/codes/ + relation: exactMatch - type: Contribution contributor: - id: clinvar.submitter/500139 @@ -71,9 +80,12 @@ contributions: label: ClinVar Staff, National Center for Biotechnology Information (NCBI) date: '2015-08-20' activityType: - code: cg000011 label: evaluated - system: https://dataexchange.clinicalgenome.org/codes/ + mappings: + - coding: + code: cg000011 + system: https://dataexchange.clinicalgenome.org/codes/ + relation: exactMatch extensions: - name: clinvarActivityLabel value: last evaluated diff --git a/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml b/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml index 4fd5c99..8c6444b 100644 --- a/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml +++ b/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml @@ -14,13 +14,19 @@ objectCondition: predicate: isCausalFor direction: supports strength: - code: cg000022 label: Likely (ACMG 2015) - system: https://dataexchange.clinicalgenome.org/codes/ + mappings: + - coding: + code: cg000022 + system: https://dataexchange.clinicalgenome.org/codes/ + relation: exactMatch classification: - code: cg000002 label: Likely Pathogenic (ACMG 2015) - system: https://dataexchange.clinicalgenome.org/codes/ + mappings: + - coding: + code: cg000002 + system: https://dataexchange.clinicalgenome.org/codes/ + relation: exactMatch description: 'The c.806_808delCCT (p.Ser269del) variant in KCNQ4 has been observed in at least 4 probands with hearing loss (PS4_Supporting; PMID: 23399560, 23443030, LMM unpublished data SCV000967428.1). This variant segregated with hearing loss @@ -40,9 +46,12 @@ contributions: label: ClinGen Hearing Loss Variant Curation Expert Panel date: '2020-05-04' activityType: - code: cg000010 label: submitted - system: https://dataexchange.clinicalgenome.org/codes/ + mappings: + - coding: + code: cg000010 + system: https://dataexchange.clinicalgenome.org/codes/ + relation: exactMatch - type: Contribution contributor: - id: clinvar.submitter/506744 @@ -50,9 +59,12 @@ contributions: label: ClinGen Hearing Loss Variant Curation Expert Panel date: '2019-11-26' activityType: - code: cg000011 label: evaluated - system: https://dataexchange.clinicalgenome.org/codes/ + mappings: + - coding: + code: cg000011 + system: https://dataexchange.clinicalgenome.org/codes/ + relation: exactMatch extensions: - name: clinvarActivityLabel value: last evaluated diff --git a/tests/fixtures/diagnostic-inline.yaml b/tests/fixtures/diagnostic-inline.yaml index 90570bc..e05f1ae 100644 --- a/tests/fixtures/diagnostic-inline.yaml +++ b/tests/fixtures/diagnostic-inline.yaml @@ -3,9 +3,14 @@ type: VariantDiagnosticStudyStatement description: https://civicdb.org/evidence/80/summary direction: supports strength: - code: e000005 - label: clinical cohort evidence - system: https://go.osu.edu/evidence-codes + id: civic.evidenceLevel:B + label: Clinical evidence + mappings: + - coding: + code: e000005 + label: clinical cohort evidence + system: https://go.osu.edu/evidence-codes + relation: exactMatch predicate: isDiagnosticInclusionCriterionFor subjectVariant: id: civic.mpid:12 @@ -85,19 +90,35 @@ geneContextQualifier: id: civic.gid:5 conceptType: Gene label: BRAF - description: "BRAF mutations are found to be recurrent in many cancer types. Of - these, the mutation of valine 600 to glutamic acid (V600E) is the most prevalent. - V600E has been determined to be an activating mutation, and cells that harbor it, - along with other V600 mutations are sensitive to the BRAF inhibitor dabrafenib. It - is also common to use MEK inhibition as a substitute for BRAF inhibitors, and the - MEK inhibitor trametinib has seen some success in BRAF mutant melanomas. BRAF - mutations have also been correlated with poor prognosis in many cancer types, - although there is at least one study that questions this conclusion in papillary - thyroid cancer. Oncogenic BRAF mutations are divided into three categories that - determine their sensitivity to inhibitors. Class 1 BRAF mutations (V600) are - RAS-independent, signal as monomers and are sensitive to current RAF monomer - inhibitors. Class 2 BRAF mutations (K601E, K601N, K601T, L597Q, L597V, G469A, - G469V, G469R, G464V, G464E, and fusions) are RAS-independent, signaling as + mappings: + - coding: + code: ncbigene:673 + system: https://www.ncbi.nlm.nih.gov/gene/ + relation: exactMatch + extensions: + - name: aliases + value: + - B-RAF1 + - B-raf + - BRAF + - BRAF-1 + - BRAF1 + - NS7 + - RAFB1 + - name: description + value: "BRAF mutations are found to be recurrent in many cancer types. Of + these, the mutation of valine 600 to glutamic acid (V600E) is the most prevalent. + V600E has been determined to be an activating mutation, and cells that harbor it, + along with other V600 mutations are sensitive to the BRAF inhibitor dabrafenib. It + is also common to use MEK inhibition as a substitute for BRAF inhibitors, and the + MEK inhibitor trametinib has seen some success in BRAF mutant melanomas. BRAF + mutations have also been correlated with poor prognosis in many cancer types, + although there is at least one study that questions this conclusion in papillary + thyroid cancer. Oncogenic BRAF mutations are divided into three categories that + determine their sensitivity to inhibitors. Class 1 BRAF mutations (V600) are + RAS-independent, signal as monomers and are sensitive to current RAF monomer + inhibitors. Class 2 BRAF mutations (K601E, K601N, K601T, L597Q, L597V, G469A, + G469V, G469R, G464V, G464E, and fusions) are RAS-independent, signaling as constitutive dimers and are resistant to vemurafenib. Such mutants may be sensitive to novel RAF dimer inhibitors or MEK inhibitors. Class 3 BRAF mutations (D287H, V459L, G466V, G466E, G466A, S467L, G469E, N581S, N581I, D594N, D594G, @@ -107,19 +128,6 @@ geneContextQualifier: in melanoma may be treated with MEK inhibitors. In epithelial tumors such as CRC or NSCLC may be effectively treated with combinations that include inhibitors of receptor tyrosine kinase." - mappings: - - coding: - code: ncbigene:673 - system: https://www.ncbi.nlm.nih.gov/gene/ - relation: exactMatch - alternativeLabels: - - B-RAF1 - - B-raf - - BRAF - - BRAF-1 - - BRAF1 - - NS7 - - RAFB1 specifiedBy: id: civic.methods:2019 label: CIViC Curation SOP (2019) diff --git a/tests/fixtures/prognostic-inline.yaml b/tests/fixtures/prognostic-inline.yaml index 0d85cea..ad8e18b 100644 --- a/tests/fixtures/prognostic-inline.yaml +++ b/tests/fixtures/prognostic-inline.yaml @@ -3,9 +3,14 @@ type: VariantPrognosticStudyStatement description: https://civicdb.org/evidence/82/summary direction: supports strength: - code: e000005 - label: clinical cohort evidence - system: https://go.osu.edu/evidence-codes + id: civic.evidenceLevel:B + label: Clinical evidence + mappings: + - coding: + code: e000005 + label: clinical cohort evidence + system: https://go.osu.edu/evidence-codes + relation: exactMatch predicate: associatedWithWorseOutcomeFor subjectVariant: id: civic.mpid:12 @@ -85,19 +90,35 @@ geneContextQualifier: id: civic.gid:5 conceptType: Gene label: BRAF - description: "BRAF mutations are found to be recurrent in many cancer types. Of - these, the mutation of valine 600 to glutamic acid (V600E) is the most prevalent. - V600E has been determined to be an activating mutation, and cells that harbor it, - along with other V600 mutations are sensitive to the BRAF inhibitor dabrafenib. It - is also common to use MEK inhibition as a substitute for BRAF inhibitors, and the - MEK inhibitor trametinib has seen some success in BRAF mutant melanomas. BRAF - mutations have also been correlated with poor prognosis in many cancer types, - although there is at least one study that questions this conclusion in papillary - thyroid cancer. Oncogenic BRAF mutations are divided into three categories that - determine their sensitivity to inhibitors. Class 1 BRAF mutations (V600) are - RAS-independent, signal as monomers and are sensitive to current RAF monomer - inhibitors. Class 2 BRAF mutations (K601E, K601N, K601T, L597Q, L597V, G469A, - G469V, G469R, G464V, G464E, and fusions) are RAS-independent, signaling as + mappings: + - coding: + code: ncbigene:673 + system: https://www.ncbi.nlm.nih.gov/gene/ + relation: exactMatch + extensions: + - name: aliases + value: + - B-RAF1 + - B-raf + - BRAF + - BRAF-1 + - BRAF1 + - NS7 + - RAFB1 + - name: description + value: "BRAF mutations are found to be recurrent in many cancer types. Of + these, the mutation of valine 600 to glutamic acid (V600E) is the most prevalent. + V600E has been determined to be an activating mutation, and cells that harbor it, + along with other V600 mutations are sensitive to the BRAF inhibitor dabrafenib. It + is also common to use MEK inhibition as a substitute for BRAF inhibitors, and the + MEK inhibitor trametinib has seen some success in BRAF mutant melanomas. BRAF + mutations have also been correlated with poor prognosis in many cancer types, + although there is at least one study that questions this conclusion in papillary + thyroid cancer. Oncogenic BRAF mutations are divided into three categories that + determine their sensitivity to inhibitors. Class 1 BRAF mutations (V600) are + RAS-independent, signal as monomers and are sensitive to current RAF monomer + inhibitors. Class 2 BRAF mutations (K601E, K601N, K601T, L597Q, L597V, G469A, + G469V, G469R, G464V, G464E, and fusions) are RAS-independent, signaling as constitutive dimers and are resistant to vemurafenib. Such mutants may be sensitive to novel RAF dimer inhibitors or MEK inhibitors. Class 3 BRAF mutations (D287H, V459L, G466V, G466E, G466A, S467L, G469E, N581S, N581I, D594N, D594G, @@ -107,19 +128,6 @@ geneContextQualifier: in melanoma may be treated with MEK inhibitors. In epithelial tumors such as CRC or NSCLC may be effectively treated with combinations that include inhibitors of receptor tyrosine kinase." - mappings: - - coding: - code: ncbigene:673 - system: https://www.ncbi.nlm.nih.gov/gene/ - relation: exactMatch - alternativeLabels: - - B-RAF1 - - B-raf - - BRAF - - BRAF-1 - - BRAF1 - - NS7 - - RAFB1 specifiedBy: id: civic.methods:2019 label: CIViC Curation SOP (2019) diff --git a/tests/fixtures/therapeuticAgent.yaml b/tests/fixtures/therapeuticAgent.yaml index ab67a83..895120e 100644 --- a/tests/fixtures/therapeuticAgent.yaml +++ b/tests/fixtures/therapeuticAgent.yaml @@ -10,7 +10,9 @@ mappings: code: '1430438' system: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm= relation: exactMatch -alternativeLabels: - - BIBW2992 - - BIBW 2992 - - "(2e)-N-(4-(3-Chloro-4-Fluoroanilino)-7-(((3s)-Oxolan-3-yl)Oxy)Quinoxazolin-6-yl)-4-(Dimethylamino)But-2-Enamide" \ No newline at end of file +extensions: + - name: aliases + value: + - BIBW2992 + - BIBW 2992 + - "(2e)-N-(4-(3-Chloro-4-Fluoroanilino)-7-(((3s)-Oxolan-3-yl)Oxy)Quinoxazolin-6-yl)-4-(Dimethylamino)But-2-Enamide" \ No newline at end of file diff --git a/tests/fixtures/tr-statement-inline.yaml b/tests/fixtures/tr-statement-inline.yaml index 6aac725..f3658d6 100644 --- a/tests/fixtures/tr-statement-inline.yaml +++ b/tests/fixtures/tr-statement-inline.yaml @@ -6,22 +6,27 @@ description: A phase III clinical trial (NCT00949650) found that median progress 95% CI, 0.34 to 0.65; P = 0.001). direction: supports strength: - code: e000005 - label: clinical cohort evidence - system: https://go.osu.edu/evidence-codes + id: civic.evidenceLevel:B + label: Clinical evidence + mappings: + - coding: + code: e000005 + label: clinical cohort evidence + system: https://go.osu.edu/evidence-codes + relation: exactMatch predicate: predictsSensitivityTo subjectVariant: id: civic.mpid:33 type: CategoricalVariant - description: >- - EGFR L858R has long been recognized as a functionally significant mutation in cancer, - and is one of the most prevalent single mutations in lung cancer. Best described in - non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first - and second generation TKI's like gefitinib and neratinib. NSCLC patients with this - mutation treated with TKI's show increased overall and progression-free survival, as - compared to chemotherapy alone. Third generation TKI's are currently in clinical trials - that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in - treating patients that failed to respond to earlier generation TKI therapies. + # description: >- + # EGFR L858R has long been recognized as a functionally significant mutation in cancer, + # and is one of the most prevalent single mutations in lung cancer. Best described in + # non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first + # and second generation TKI's like gefitinib and neratinib. NSCLC patients with this + # mutation treated with TKI's show increased overall and progression-free survival, as + # compared to chemotherapy alone. Third generation TKI's are currently in clinical trials + # that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in + # treating patients that failed to respond to earlier generation TKI therapies. label: EGFR L858R constraints: - type: DefiningAlleleConstraint @@ -31,9 +36,9 @@ subjectVariant: - vrs.json#/ga4gh:VA.3_FsKSUHEdurPIw5gqpw6g0_Ga0TEXQh - vrs.json#/ga4gh:VA.zpv3dW34z8jioKL-NtbGc0fa9clsgAZT - vrs.json#/ga4gh:VA.BJOtfUhZMooMJUO4FjxHXTEimrKXtF0i - alternativeLabels: - - LEU858ARG - - rs121434568 + # alternativeLabels: + # - LEU858ARG + # - rs121434568 mappings: - coding: code: CA126713 @@ -86,10 +91,6 @@ objectTherapeutic: code: '1430438' system: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm= relation: exactMatch - alternativeLabels: - - BIBW2992 - - BIBW 2992 - - "(2e)-N-(4-(3-Chloro-4-Fluoroanilino)-7-(((3s)-Oxolan-3-yl)Oxy)Quinoxazolin-6-yl)-4-(Dimethylamino)But-2-Enamide" conditionQualifier: id: civic.did:30 conceptType: Disease @@ -104,33 +105,36 @@ geneContextQualifier: id: civic.gid:19 conceptType: Gene label: EGFR - description: "EGFR is widely recognized for its importance in cancer. Amplification - and mutations have been shown to be driving events in many cancer types. Its - role in non-small cell lung cancer, glioblastoma and basal-like breast cancers - has spurred many research and drug development efforts. Tyrosine kinase inhibitors - have shown efficacy in EGFR amplfied tumors, most notably gefitinib and erlotinib. - Mutations in EGFR have been shown to confer resistance to these drugs, particularly - the variant T790M, which has been functionally characterized as a resistance - marker for both of these drugs. The later generation TKI's have seen some - success in treating these resistant cases, and targeted sequencing of the - EGFR locus has become a common practice in treatment of non-small cell lung - cancer. \nOverproduction of ligands is another possible mechanism of activation - of EGFR. ERBB ligands include EGF, TGF-a, AREG, EPG, BTC, HB-EGF, EPR and - NRG1-4 (for detailed information please refer to the respective ligand section)." mappings: - coding: code: ncbigene:1956 system: https://www.ncbi.nlm.nih.gov/gene/ relation: exactMatch - alternativeLabels: - - EGFR - - ERBB - - ERBB1 - - ERRP - - HER1 - - NISBD2 - - PIG61 - - mENA + extensions: + - name: aliases + value: + - EGFR + - ERBB + - ERBB1 + - ERRP + - HER1 + - NISBD2 + - PIG61 + - mENA + - name: description + value: "EGFR is widely recognized for its importance in cancer. Amplification + and mutations have been shown to be driving events in many cancer types. Its + role in non-small cell lung cancer, glioblastoma and basal-like breast cancers + has spurred many research and drug development efforts. Tyrosine kinase inhibitors + have shown efficacy in EGFR amplfied tumors, most notably gefitinib and erlotinib. + Mutations in EGFR have been shown to confer resistance to these drugs, particularly + the variant T790M, which has been functionally characterized as a resistance + marker for both of these drugs. The later generation TKI's have seen some + success in treating these resistant cases, and targeted sequencing of the + EGFR locus has become a common practice in treatment of non-small cell lung + cancer. \nOverproduction of ligands is another possible mechanism of activation + of EGFR. ERBB ligands include EGF, TGF-a, AREG, EPG, BTC, HB-EGF, EPR and + NRG1-4 (for detailed information please refer to the respective ligand section)." specifiedBy: id: civic.methods:2019 label: CIViC Curation SOP (2019) From 6e170b3fb30012ee1afda0aa51a648b30fcf222a Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Sat, 9 Nov 2024 21:10:56 -0500 Subject: [PATCH 13/20] add support for namespaced tests --- .../pathogenicity-statement-profile-source.yaml | 2 -- tests/config.py | 7 +++++-- tests/fixtures/VA-ClinVar-SCV-Example-001.yaml | 4 ++-- tests/fixtures/VA-ClinVar-SCV-Example-002.yaml | 4 ++-- tests/test_basic.py | 2 +- tests/test_definitions.yaml | 12 ++++++++++++ tests/test_examples.py | 4 ++-- 7 files changed, 24 insertions(+), 11 deletions(-) diff --git a/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml index 06b851b..bf5cf63 100644 --- a/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml +++ b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml @@ -29,5 +29,3 @@ $defs: - benign description: >- The ACMG 2015 classification of the variant's pathogenicity. - - diff --git a/tests/config.py b/tests/config.py index 8fccbcc..a73a175 100644 --- a/tests/config.py +++ b/tests/config.py @@ -34,10 +34,13 @@ def retrieve_rel_ref(ga4gh_ref: str): content = json.loads(schema_path.read_text()) schema_uri = schema_path.as_uri() content['id'] = schema_uri + schema_idx = schema_path.parts.index('schema') + schema_ns = '.'.join(schema_path.parts[schema_idx+1:-2]) + schema_ns_name = f'{schema_ns}:{schema_path.name}' schema_resource = Resource(contents=content, specification=DRAFT202012) - js_def[schema_path.stem] = content + js_def[schema_ns_name] = content js_registry = js_registry.with_resources([ - (schema_path.name, schema_resource), + (schema_ns_name, schema_resource), (schema_uri, schema_resource) ]) diff --git a/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml b/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml index 44d0694..1217889 100644 --- a/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml +++ b/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml @@ -45,14 +45,14 @@ objectCondition: predicate: isCausalFor direction: supports strength: - label: Definitive (ACMG 2015) + label: definitive mappings: - coding: code: cg000021 system: https://dataexchange.clinicalgenome.org/codes/ relation: exactMatch classification: - label: Pathogenic (ACMG 2015) + label: pathogenic mappings: - coding: code: cg000001 diff --git a/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml b/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml index 8c6444b..750c494 100644 --- a/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml +++ b/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml @@ -14,14 +14,14 @@ objectCondition: predicate: isCausalFor direction: supports strength: - label: Likely (ACMG 2015) + label: likely mappings: - coding: code: cg000022 system: https://dataexchange.clinicalgenome.org/codes/ relation: exactMatch classification: - label: Likely Pathogenic (ACMG 2015) + label: likely pathogenic mappings: - coding: code: cg000002 diff --git a/tests/test_basic.py b/tests/test_basic.py index 04a6e24..63cee2d 100644 --- a/tests/test_basic.py +++ b/tests/test_basic.py @@ -9,4 +9,4 @@ def test_allele_validation(): - assert validator['Allele'].validate(allele) is None + assert validator['vrs:Allele'].validate(allele) is None diff --git a/tests/test_definitions.yaml b/tests/test_definitions.yaml index 7c6d6aa..f6eb738 100644 --- a/tests/test_definitions.yaml +++ b/tests/test_definitions.yaml @@ -1,25 +1,37 @@ tests: - test_file: allele.yaml + namespace: vrs definition: Allele - test_file: allele2.yaml + namespace: vrs definition: Allele - test_file: VA-ClinVar-SCV-Example-001.yaml + namespace: va-spec.acmg-2015 definition: VariantPathogenicityStatement - test_file: VA-ClinVar-SCV-Example-002.yaml + namespace: va-spec.acmg-2015 definition: VariantPathogenicityStatement - test_file: therapeuticAgent.yaml + namespace: gks-core definition: MappableConcept - test_file: tr-statement-inline.yaml + namespace: va-spec.base definition: VariantTherapeuticResponseStudyStatement - test_file: diagnostic-inline.yaml + namespace: va-spec.base definition: VariantDiagnosticStudyStatement - test_file: prognostic-inline.yaml + namespace: va-spec.base definition: VariantPrognosticStudyStatement - test_file: cohort-allele-freq-test.yaml + namespace: va-spec.base definition: CohortAlleleFrequencyStudyResult - test_file: AVE-functional-classification.yaml + namespace: va-spec.base definition: ExperimentalVariantFunctionalImpactStudyStatement - test_file: AVE-clinical-classification.yaml + namespace: va-spec.base definition: PathogenicityEvidenceLine - test_file: AVE-functional-study-result.yaml + namespace: va-spec.base definition: ExperimentalVariantFunctionalImpactStudyResult \ No newline at end of file diff --git a/tests/test_examples.py b/tests/test_examples.py index 669156b..fc84a4d 100644 --- a/tests/test_examples.py +++ b/tests/test_examples.py @@ -9,8 +9,8 @@ def test_examples(): for test in test_spec['tests']: with open(fixtures_path / test['test_file']) as datafile: data = yaml.safe_load(datafile) - - class_validator = validator[test['definition']] + test_cls_name = f"{test['namespace']}:{test['definition']}" + class_validator = validator[test_cls_name] try: assert class_validator.validate(data) is None From e2f87ea71eebb24f014bc7299c21fc479563f090 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Sat, 9 Nov 2024 22:09:28 -0500 Subject: [PATCH 14/20] fix documentation refs for statement profiles --- docs/source/def/cat-vrs | 1 + docs/source/def/gks-core | 1 + docs/source/def/va-spec | 1 + docs/source/def/va-spec.acmg-2015 | 1 + docs/source/def/vrs | 1 + .../standard-profiles/statement-profiles.rst | 15 +++++---------- 6 files changed, 10 insertions(+), 10 deletions(-) create mode 120000 docs/source/def/cat-vrs create mode 120000 docs/source/def/gks-core create mode 120000 docs/source/def/va-spec create mode 120000 docs/source/def/va-spec.acmg-2015 create mode 120000 docs/source/def/vrs diff --git a/docs/source/def/cat-vrs b/docs/source/def/cat-vrs new file mode 120000 index 0000000..e367e2c --- /dev/null +++ b/docs/source/def/cat-vrs @@ -0,0 +1 @@ +../../../schema/cat-vrs/def \ No newline at end of file diff --git a/docs/source/def/gks-core b/docs/source/def/gks-core new file mode 120000 index 0000000..cce93bd --- /dev/null +++ b/docs/source/def/gks-core @@ -0,0 +1 @@ +../../../schema/gks-core/def \ No newline at end of file diff --git a/docs/source/def/va-spec b/docs/source/def/va-spec new file mode 120000 index 0000000..5462653 --- /dev/null +++ b/docs/source/def/va-spec @@ -0,0 +1 @@ +../../../schema/va-spec/base/def \ No newline at end of file diff --git a/docs/source/def/va-spec.acmg-2015 b/docs/source/def/va-spec.acmg-2015 new file mode 120000 index 0000000..921c2c4 --- /dev/null +++ b/docs/source/def/va-spec.acmg-2015 @@ -0,0 +1 @@ +../../../schema/va-spec/acmg-2015/def \ No newline at end of file diff --git a/docs/source/def/vrs b/docs/source/def/vrs new file mode 120000 index 0000000..b977674 --- /dev/null +++ b/docs/source/def/vrs @@ -0,0 +1 @@ +../../../schema/vrs/def \ No newline at end of file diff --git a/docs/source/standard-profiles/statement-profiles.rst b/docs/source/standard-profiles/statement-profiles.rst index aef5fe1..bef5c98 100644 --- a/docs/source/standard-profiles/statement-profiles.rst +++ b/docs/source/standard-profiles/statement-profiles.rst @@ -25,32 +25,27 @@ Below are the **Standard Statement Profiles** currently defined as part of the V Variant Pathogenicity Statement ############################### -An example of data structured using this Standard Profile can be found `here `_. - -.. include:: ../../../schema/profiles/def/VariantPathogenicityStatement.rst - +.. include:: ../def/va-spec/VariantPathogenicityStatement.rst Variant Oncogenicity Study Statement #################################### -.. include:: ../../../schema/profiles/def/VariantOncogenicityStudyStatement.rst - +.. include:: ../def/va-spec/VariantOncogenicityStudyStatement.rst Variant Therapeutic Response Study Statement ############################################# -.. include:: ../../../schema/profiles/def/VariantTherapeuticResponseStudyStatement.rst +.. include:: ../def/va-spec/VariantTherapeuticResponseStudyStatement.rst .. _variant-diagnostic-statement-profile: Variant Diagnostic Study Statement ################################## -.. include:: ../../../schema/profiles/def/VariantDiagnosticStudyStatement.rst - +.. include:: ../def/va-spec/VariantDiagnosticStudyStatement.rst Variant Prognostic Study Statement ################################## -.. include:: ../../../schema/profiles/def/VariantPrognosticStudyStatement.rst +.. include:: ../def/va-spec/VariantPrognosticStudyStatement.rst From c8d15c9bb3167c963142120a67c98a89e403ab75 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Sat, 9 Nov 2024 22:23:56 -0500 Subject: [PATCH 15/20] reorg documentation for base and community profiles --- .../index.rst | 8 ++++---- .../statement-profiles.rst | 0 .../study-result-profiles.rst | 0 docs/source/community-profiles/acmg-2015.rst | 13 +++++++++++++ docs/source/community-profiles/index.rst | 16 ++++++++++++++++ docs/source/index.rst | 7 ++++--- 6 files changed, 37 insertions(+), 7 deletions(-) rename docs/source/{standard-profiles => base-profiles}/index.rst (75%) rename docs/source/{standard-profiles => base-profiles}/statement-profiles.rst (100%) rename docs/source/{standard-profiles => base-profiles}/study-result-profiles.rst (100%) create mode 100644 docs/source/community-profiles/acmg-2015.rst create mode 100644 docs/source/community-profiles/index.rst diff --git a/docs/source/standard-profiles/index.rst b/docs/source/base-profiles/index.rst similarity index 75% rename from docs/source/standard-profiles/index.rst rename to docs/source/base-profiles/index.rst index c114f98..a859d91 100644 --- a/docs/source/standard-profiles/index.rst +++ b/docs/source/base-profiles/index.rst @@ -1,11 +1,11 @@ -.. _standard-profiles: +.. _base-profiles: -Standard Profiles -!!!!!!!!!!!!!!!!! +Base Profiles +!!!!!!!!!!!!! ``PREREQUISITES:`` :ref:`Introduction `, :ref:`Core Information Model ` -**VA Standard Profiles** are the end product of the VA Modeling Framework, providing standard models that will be used by the GA4GH community to store and exchange variant data. They are built as specializations of the :ref:`Statement`, :ref:`Study Result`, or :ref:`EvidenceLine` classes in the Core-IM, each supporting a specific type of knowledge about genetic variation. +**VA Base Profiles** are the end product of the VA Modeling Framework for exchanging variant knowledge. They are built as specializations of the :ref:`Statement`, :ref:`Study Result`, or :ref:`EvidenceLine` classes in the Core-IM, each supporting a specific type of knowledge about genetic variation. * **Statement Profiles** are used to represent discrete assertions of general **knowledge** about a variant (e.g. a pathogenicity classification). diff --git a/docs/source/standard-profiles/statement-profiles.rst b/docs/source/base-profiles/statement-profiles.rst similarity index 100% rename from docs/source/standard-profiles/statement-profiles.rst rename to docs/source/base-profiles/statement-profiles.rst diff --git a/docs/source/standard-profiles/study-result-profiles.rst b/docs/source/base-profiles/study-result-profiles.rst similarity index 100% rename from docs/source/standard-profiles/study-result-profiles.rst rename to docs/source/base-profiles/study-result-profiles.rst diff --git a/docs/source/community-profiles/acmg-2015.rst b/docs/source/community-profiles/acmg-2015.rst new file mode 100644 index 0000000..6a4d5ad --- /dev/null +++ b/docs/source/community-profiles/acmg-2015.rst @@ -0,0 +1,13 @@ +.. _acmg-2015: + +ACMG/AMP 2015 Community Profiles +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +Below are the **ACMG/AMP 2015 Community Profiles**. + +.. _acmg-2015-statement-profile: + +Variant Pathogenicity Statement (ACMG 2015) +########################################### + +.. include:: ../def/va-spec.acmg-2015/VariantPathogenicityStatement.rst diff --git a/docs/source/community-profiles/index.rst b/docs/source/community-profiles/index.rst new file mode 100644 index 0000000..ee47e2c --- /dev/null +++ b/docs/source/community-profiles/index.rst @@ -0,0 +1,16 @@ +.. _community-profiles: + +Community Profiles +!!!!!!!!!!!!!!!!!! + +``PREREQUISITES:`` :ref:`Introduction `, :ref:`Core Information Model ` + +**VA Community Profiles** are constrained specializations of :ref:`base-profiles`. + + * **ACMG/AMP 2015 Profiles** are used to represent data from the ACMG 2015 variant pathogenicity guidelines. + +.. toctree:: + :maxdepth: 4 + :titlesonly: + + acmg-2015 diff --git a/docs/source/index.rst b/docs/source/index.rst index 2119286..952d76e 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -15,8 +15,8 @@ Readers may wish to review this :ref:`annotated data example ` Detailed descriptions and implementation guidance for the classes and attributes in the foundational Core-IM. -* :ref:`Standard Profiles ` - Detailed descriptions and implementation guidance for Statement and Study Result Profiles provided as standards for representing variant knowledge. +* :ref:`Base Profiles ` + Detailed descriptions and implementation guidance for Statement and Study Result Profiles for representing variant knowledge. * :ref:`Profiling Methodology ` Instructions and resources for creating or expanding Statement and Study Result Profiles through the SEPIO profiling process. * :ref:`Modeling Foundations ` @@ -40,7 +40,8 @@ If you have questions or feedback, please reach out to the VA Team on `Slack Date: Sat, 9 Nov 2024 22:38:30 -0500 Subject: [PATCH 16/20] draft solution to ga4gh/gks-metaschema#35 --- .../def/VariantPathogenicityStatement.rst | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst index 49e4942..eb328f9 100644 --- a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst @@ -6,17 +6,11 @@ A Statement describing the role of a variant in causing an inherited condition. -**Information Model** +**Profile Conditions** +This class adds the following conditions to the :ref:`variant-pathogenicity-statement-profile`: -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description +- `VariantPathogenicityStatement.classification` is additionally defined as + *The ACMG 2015 classification of the variant's pathogenicity*. + - `.classification.label` is constrained to values `pathogenic`, `likely pathogenic`, + `uncertain significance`, `likely benign`, and `benign`. From 62a96471dc0eeedd662a25ec93a4286b84519af7 Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Tue, 12 Nov 2024 11:32:35 -0500 Subject: [PATCH 17/20] Replace Stmt SPOQ attribs with Proposition. --- .../def/VariantPathogenicityStatement.rst | 18 +- .../json/VariantPathogenicityStatement | 2 +- ...athogenicity-statement-profile-source.yaml | 2 +- ...ariantFunctionalImpactStudyProposition.rst | 89 +++++++ ...lVariantFunctionalImpactStudyStatement.rst | 46 +--- .../def/VariantDiagnosticStudyProposition.rst | 94 +++++++ .../def/VariantDiagnosticStudyStatement.rst | 31 +-- .../VariantOncogenicityStudyProposition.rst | 94 +++++++ .../def/VariantOncogenicityStudyStatement.rst | 31 +-- ...t => VariantPathogenicityEvidenceLine.rst} | 4 +- .../def/VariantPathogenicityStatement.rst | 34 +-- .../def/VariantPrognosticStudyProposition.rst | 94 +++++++ .../def/VariantPrognosticStudyStatement.rst | 31 +-- ...antTherapeuticResponseStudyProposition.rst | 100 ++++++++ ...riantTherapeuticResponseStudyStatement.rst | 37 +-- .../def/XCohortAlleleFrequencyStudyResult.rst | 147 +++++++++++ ...ariantFunctionalImpactStudyProposition.rst | 89 +++++++ ...ntalVariantFunctionalImpactStudyResult.rst | 137 ++++++++++ ...lVariantFunctionalImpactStudyStatement.rst | 136 ++++++++++ .../XVariantDiagnosticStudyProposition.rst | 94 +++++++ .../def/XVariantDiagnosticStudyStatement.rst | 136 ++++++++++ .../XVariantOncogenicityStudyProposition.rst | 94 +++++++ .../XVariantOncogenicityStudyStatement.rst | 136 ++++++++++ .../def/XVariantPathogenicityEvidenceLine.rst | 126 +++++++++ .../def/XVariantPathogenicityProposition.rst | 97 +++++++ .../def/XVariantPathogenicityStatement.rst | 136 ++++++++++ .../XVariantPrognosticStudyProposition.rst | 94 +++++++ .../def/XVariantPrognosticStudyStatement.rst | 136 ++++++++++ ...antTherapeuticResponseStudyProposition.rst | 100 ++++++++ ...riantTherapeuticResponseStudyStatement.rst | 136 ++++++++++ ...stic-study-proposition-profile-source.yaml | 72 ++++++ ...nostic-study-statement-profile-source.yaml | 52 +--- ...pact-study-proposition-profile-source.yaml | 81 ++++++ ...al-impact-study-result-profile-source.yaml | 1 - ...impact-study-statement-profile-source.yaml | 105 ++------ ...talVariantFunctionalImpactStudyProposition | 115 +++++++++ ...entalVariantFunctionalImpactStudyStatement | 98 ++----- .../json/VariantDiagnosticStudyProposition | 115 +++++++++ .../base/json/VariantDiagnosticStudyStatement | 64 +---- .../json/VariantOncogenicityStudyProposition | 116 +++++++++ .../json/VariantOncogenicityStudyStatement | 65 +---- ...eLine => VariantPathogenicityEvidenceLine} | 10 +- .../base/json/VariantPathogenicityProposition | 5 +- .../base/json/VariantPathogenicityStatement | 68 +---- .../json/VariantPrognosticStudyProposition | 115 +++++++++ .../base/json/VariantPrognosticStudyStatement | 64 +---- ...VariantTherapeuticResponseStudyProposition | 127 +++++++++ .../VariantTherapeuticResponseStudyStatement | 76 +----- .../json/XCohortAlleleFrequencyStudyResult | 165 ++++++++++++ ...talVariantFunctionalImpactStudyProposition | 115 +++++++++ ...rimentalVariantFunctionalImpactStudyResult | 149 +++++++++++ ...entalVariantFunctionalImpactStudyStatement | 150 +++++++++++ .../json/XVariantDiagnosticStudyProposition | 115 +++++++++ .../json/XVariantDiagnosticStudyStatement | 150 +++++++++++ .../json/XVariantOncogenicityStudyProposition | 116 +++++++++ .../json/XVariantOncogenicityStudyStatement | 150 +++++++++++ .../json/XVariantPathogenicityEvidenceLine | 139 ++++++++++ .../json/XVariantPathogenicityProposition | 119 +++++++++ .../base/json/XVariantPathogenicityStatement | 150 +++++++++++ .../json/XVariantPrognosticStudyProposition | 115 +++++++++ .../json/XVariantPrognosticStudyStatement | 150 +++++++++++ ...VariantTherapeuticResponseStudyProposition | 127 +++++++++ .../XVariantTherapeuticResponseStudyStatement | 150 +++++++++++ ...city-study-proposition-profile-source.yaml | 73 ++++++ ...nicity-study-statement-profile-source.yaml | 55 +--- ...genicity-evidence-line-profile-source.yaml | 71 +----- ...hogenicity-proposition-profile-source.yaml | 70 +++++ ...athogenicity-statement-profile-source.yaml | 52 +--- ...stic-study-proposition-profile-source.yaml | 71 ++++++ ...nostic-study-statement-profile-source.yaml | 52 +--- ...onse-study-proposition-profile-source.yaml | 81 ++++++ ...sponse-study-statement-profile-source.yaml | 64 +---- ...ohort-allele-frequency-profile-source.yaml | 61 +++++ ...iant-functional-impact-profile-source.yaml | 152 +++++++++++ ...riant-diagnostic-study-profile-source.yaml | 97 +++++++ ...ant-oncogenicity-study-profile-source.yaml | 97 +++++++ ...-variant-pathogenicity-profile-source.yaml | 142 +++++++++++ ...riant-prognostic-study-profile-source.yaml | 95 +++++++ ...apeutic-response-study-profile-source.yaml | 99 ++++++++ submodules/cat-vrs | 2 +- .../fixtures/AVE-clinical-classification.yaml | 2 +- .../AVE-functional-classification.yaml | 72 +++--- .../fixtures/VA-ClinVar-SCV-Example-001.yaml | 90 +++---- .../fixtures/VA-ClinVar-SCV-Example-002.yaml | 26 +- tests/fixtures/diagnostic-inline.yaml | 232 ++++++++--------- tests/fixtures/prognostic-inline.yaml | 232 ++++++++--------- tests/fixtures/tr-statement-inline.yaml | 240 +++++++++--------- tests/test_definitions.yaml | 6 +- 88 files changed, 6729 insertions(+), 1415 deletions(-) create mode 100644 schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyProposition.rst create mode 100644 schema/va-spec/base/def/VariantDiagnosticStudyProposition.rst create mode 100644 schema/va-spec/base/def/VariantOncogenicityStudyProposition.rst rename schema/va-spec/base/def/{PathogenicityEvidenceLine.rst => VariantPathogenicityEvidenceLine.rst} (97%) create mode 100644 schema/va-spec/base/def/VariantPrognosticStudyProposition.rst create mode 100644 schema/va-spec/base/def/VariantTherapeuticResponseStudyProposition.rst create mode 100644 schema/va-spec/base/def/XCohortAlleleFrequencyStudyResult.rst create mode 100644 schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyProposition.rst create mode 100644 schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyResult.rst create mode 100644 schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyStatement.rst create mode 100644 schema/va-spec/base/def/XVariantDiagnosticStudyProposition.rst create mode 100644 schema/va-spec/base/def/XVariantDiagnosticStudyStatement.rst create mode 100644 schema/va-spec/base/def/XVariantOncogenicityStudyProposition.rst create mode 100644 schema/va-spec/base/def/XVariantOncogenicityStudyStatement.rst create mode 100644 schema/va-spec/base/def/XVariantPathogenicityEvidenceLine.rst create mode 100644 schema/va-spec/base/def/XVariantPathogenicityProposition.rst create mode 100644 schema/va-spec/base/def/XVariantPathogenicityStatement.rst create mode 100644 schema/va-spec/base/def/XVariantPrognosticStudyProposition.rst create mode 100644 schema/va-spec/base/def/XVariantPrognosticStudyStatement.rst create mode 100644 schema/va-spec/base/def/XVariantTherapeuticResponseStudyProposition.rst create mode 100644 schema/va-spec/base/def/XVariantTherapeuticResponseStudyStatement.rst create mode 100644 schema/va-spec/base/diagnostic-study-proposition-profile-source.yaml create mode 100644 schema/va-spec/base/experimental-functional-impact-study-proposition-profile-source.yaml create mode 100644 schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyProposition create mode 100644 schema/va-spec/base/json/VariantDiagnosticStudyProposition create mode 100644 schema/va-spec/base/json/VariantOncogenicityStudyProposition rename schema/va-spec/base/json/{PathogenicityEvidenceLine => VariantPathogenicityEvidenceLine} (96%) create mode 100644 schema/va-spec/base/json/VariantPrognosticStudyProposition create mode 100644 schema/va-spec/base/json/VariantTherapeuticResponseStudyProposition create mode 100644 schema/va-spec/base/json/XCohortAlleleFrequencyStudyResult create mode 100644 schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyProposition create mode 100644 schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyResult create mode 100644 schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyStatement create mode 100644 schema/va-spec/base/json/XVariantDiagnosticStudyProposition create mode 100644 schema/va-spec/base/json/XVariantDiagnosticStudyStatement create mode 100644 schema/va-spec/base/json/XVariantOncogenicityStudyProposition create mode 100644 schema/va-spec/base/json/XVariantOncogenicityStudyStatement create mode 100644 schema/va-spec/base/json/XVariantPathogenicityEvidenceLine create mode 100644 schema/va-spec/base/json/XVariantPathogenicityProposition create mode 100644 schema/va-spec/base/json/XVariantPathogenicityStatement create mode 100644 schema/va-spec/base/json/XVariantPrognosticStudyProposition create mode 100644 schema/va-spec/base/json/XVariantPrognosticStudyStatement create mode 100644 schema/va-spec/base/json/XVariantTherapeuticResponseStudyProposition create mode 100644 schema/va-spec/base/json/XVariantTherapeuticResponseStudyStatement create mode 100644 schema/va-spec/base/oncogenicity-study-proposition-profile-source.yaml create mode 100644 schema/va-spec/base/pathogenicity-proposition-profile-source.yaml create mode 100644 schema/va-spec/base/prognostic-study-proposition-profile-source.yaml create mode 100644 schema/va-spec/base/therapeutic-response-study-proposition-profile-source.yaml create mode 100644 schema/va-spec/base/x-cohort-allele-frequency-profile-source.yaml create mode 100644 schema/va-spec/base/x-experimental-variant-functional-impact-profile-source.yaml create mode 100644 schema/va-spec/base/x-variant-diagnostic-study-profile-source.yaml create mode 100644 schema/va-spec/base/x-variant-oncogenicity-study-profile-source.yaml create mode 100644 schema/va-spec/base/x-variant-pathogenicity-profile-source.yaml create mode 100644 schema/va-spec/base/x-variant-prognostic-study-profile-source.yaml create mode 100644 schema/va-spec/base/x-variant-therapeutic-response-study-profile-source.yaml diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst index eb328f9..49e4942 100644 --- a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst @@ -6,11 +6,17 @@ A Statement describing the role of a variant in causing an inherited condition. -**Profile Conditions** +**Information Model** -This class adds the following conditions to the :ref:`variant-pathogenicity-statement-profile`: -- `VariantPathogenicityStatement.classification` is additionally defined as - *The ACMG 2015 classification of the variant's pathogenicity*. - - `.classification.label` is constrained to values `pathogenic`, `likely pathogenic`, - `uncertain significance`, `likely benign`, and `benign`. +.. list-table:: + :class: clean-wrap + :header-rows: 1 + :align: left + :widths: auto + + * - Field + - Flags + - Type + - Limits + - Description diff --git a/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement b/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement index 5396b8d..01f9a2f 100644 --- a/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement +++ b/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement @@ -6,7 +6,7 @@ "description": "A Statement describing the role of a variant in causing an inherited condition.", "allOf": [ { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityStatement" + "$ref": "/ga4gh/schema/gks-core/1.x/json/Statement" }, { "properties": { diff --git a/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml index bf5cf63..84e418e 100644 --- a/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml +++ b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml @@ -15,7 +15,7 @@ $defs: description: >- A Statement describing the role of a variant in causing an inherited condition. allOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/VariantPathogenicityStatement" + - $ref: "/ga4gh/schema/gks-core/1.x/Statement" - properties: classification: properties: diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyProposition.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyProposition.rst new file mode 100644 index 0000000..691ee85 --- /dev/null +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyProposition.rst @@ -0,0 +1,89 @@ +.. 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 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). + +**Information Model** + +Some ExperimentalVariantFunctionalImpactStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - type + - + - string + - 1..1 + - MUST be "ExperimentalVariantFunctionalImpactStudyProposition". + * - subjectVariant + - + - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A protein or genomic contextual or canonical molecular variant. + * - predicate + - + - string + - 1..1 + - The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter. + * - objectSequenceFeature + - + - :ref:`iriReference` | :ref:`MappableConcept` + - 1..1 + - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. + * - studyContextQualifier + - + - :ref:`Document` | :ref:`iriReference` + - 1..1 + - The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. + * - impactTypeQualifier + - + - string + - 0..1 + - 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). diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst index 1dcc850..29c0f70 100644 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst +++ b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst @@ -52,6 +52,11 @@ Some ExperimentalVariantFunctionalImpactStudyStatement attributes are inherited - :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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity * - contributions - .. raw:: html @@ -106,6 +111,11 @@ Some ExperimentalVariantFunctionalImpactStudyStatement attributes are inherited - string - 0..1 - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines - .. raw:: html @@ -119,38 +129,8 @@ Some ExperimentalVariantFunctionalImpactStudyStatement attributes are inherited - string - 1..1 - MUST be "ExperimentalVariantFunctionalImpactStudyStatement". - * - subjectVariant - - - - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A protein or genomic contextual or canonical molecular variant. - * - predicate + * - proposition - - - string + - :ref:`ExperimentalVariantFunctionalImpactStudyProposition` - 1..1 - - The relationship this Statement describes between the subject Variant and object Sequence Feature whose function it may alter. - * - objectSequenceFeature - - - - :ref:`iriReference` | :ref:`MappableConcept` - - 1..1 - - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. - * - studyContextQualifier - - - - :ref:`Document` | :ref:`iriReference` - - 1..1 - - The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. - * - impactTypeQualifier - - - - string - - 0..1 - - 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). - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - The method that specifies how the functional classification is ultimately assigned to the variant, based on interpretation of data from the supporting assay. May include information about thresholds applied on assay variant effect scores to derive the final classification. + - The proposition for which the study provides evidence - that the subject variant impacts the function of the object sequence feature. diff --git a/schema/va-spec/base/def/VariantDiagnosticStudyProposition.rst b/schema/va-spec/base/def/VariantDiagnosticStudyProposition.rst new file mode 100644 index 0000000..583dc69 --- /dev/null +++ b/schema/va-spec/base/def/VariantDiagnosticStudyProposition.rst @@ -0,0 +1,94 @@ +.. 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 reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. + +**Information Model** + +Some VariantDiagnosticStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - type + - + - string + - 1..1 + - MUST be "VariantDiagnosticStudyProposition". + * - subjectVariant + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A variant that is the subject of the Proposition. + * - predicate + - + - string + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectCondition + - + - :ref:`Condition` | :ref:`iriReference` + - 1..1 + - The disease that is evaluated for diagnosis. + * - alleleOriginQualifier + - + - string + - 0..1 + - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). + * - allelePrevalenceQualifier + - + - string + - 0..1 + - Reports whether the proposition should be interpreted in the context of the variant being rare or common. + * - geneContextQualifier + - + - :ref:`MappableConcept` + - 0..1 + - Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Proposition. diff --git a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst b/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst index bc7a221..f0fae69 100644 --- a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst +++ b/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst @@ -129,33 +129,8 @@ Some VariantDiagnosticStudyStatement attributes are inherited from :ref:`gks-cor - string - 1..1 - MUST be "VariantDiagnosticStudyStatement". - * - subjectVariant + * - proposition - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - :ref:`VariantDiagnosticStudyProposition` - 1..1 - - A variant that is the subject of the Statement. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The disease that is evaluated for diagnosis. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Statement. + - The proposition for which the study provides evidence - that the subject variant is associated with the object disease. diff --git a/schema/va-spec/base/def/VariantOncogenicityStudyProposition.rst b/schema/va-spec/base/def/VariantOncogenicityStudyProposition.rst new file mode 100644 index 0000000..7c47fb5 --- /dev/null +++ b/schema/va-spec/base/def/VariantOncogenicityStudyProposition.rst @@ -0,0 +1,94 @@ +.. 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 reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. + +**Information Model** + +Some VariantOncogenicityStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - type + - + - string + - 1..1 + - MUST be "VariantOncogenicityStudyProposition". + * - subjectVariant + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A variant that is the subject of the Proposition. + * - predicate + - + - string + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectTumorType + - + - :ref:`Condition` | :ref:`MappableConcept` + - 1..1 + - The tumor type for which the variant impact is evaluated. + * - 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 oncogenic role in the Proposition. diff --git a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst b/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst index b54fbde..0e60b61 100644 --- a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst +++ b/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst @@ -129,33 +129,8 @@ Some VariantOncogenicityStudyStatement attributes are inherited from :ref:`gks-c - string - 1..1 - MUST be "VariantOncogenicityStudyStatement". - * - subjectVariant + * - proposition - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - :ref:`VariantOncogenicityStudyProposition` - 1..1 - - A variant that is the subject of the Statement. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectTumorType - - - - :ref:`Condition` | :ref:`MappableConcept` - - 1..1 - - The tumor type for which the variant impact is evaluated. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Statement. + - The proposition for which the study provides evidence - that the subject variant is associated with the object tumor type. diff --git a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst b/schema/va-spec/base/def/VariantPathogenicityEvidenceLine.rst similarity index 97% rename from schema/va-spec/base/def/PathogenicityEvidenceLine.rst rename to schema/va-spec/base/def/VariantPathogenicityEvidenceLine.rst index 7dbd9f7..43b6b82 100644 --- a/schema/va-spec/base/def/PathogenicityEvidenceLine.rst +++ b/schema/va-spec/base/def/VariantPathogenicityEvidenceLine.rst @@ -8,7 +8,7 @@ An Evidence Line that describes the strength and direction of support provided b **Information Model** -Some PathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:EvidenceLine`. +Some VariantPathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:EvidenceLine`. .. list-table:: :class: clean-wrap @@ -95,7 +95,7 @@ Some PathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:Evid - - string - 1..1 - - MUST be "PathogenicityEvidenceLine". + - MUST be "VariantPathogenicityEvidenceLine". * - hasEvidenceItems - .. raw:: html diff --git a/schema/va-spec/base/def/VariantPathogenicityStatement.rst b/schema/va-spec/base/def/VariantPathogenicityStatement.rst index b66de70..3a5d785 100644 --- a/schema/va-spec/base/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/base/def/VariantPathogenicityStatement.rst @@ -129,36 +129,8 @@ Some VariantPathogenicityStatement attributes are inherited from :ref:`gks-core: - string - 1..1 - MUST be "VariantPathogenicityStatement". - * - subjectVariant + * - proposition - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - :ref:`VariantPathogenicityProposition` - 1..1 - - A variant that is the subject of the Statement. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The :ref:`Condition` for which the variant impact is stated. - * - penetranceQualifier - - - - string - - 0..1 - - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. - * - modeOfInheritanceQualifier - - - .. raw:: html - - ⋮ - - :ref:`Coding` - - 0..m - - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. - * - geneContextQualifier - - - - :ref:`MappableConcept` | :ref:`iriReference` - - 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). + - The proposition that the subject variant is associated with the object disease. diff --git a/schema/va-spec/base/def/VariantPrognosticStudyProposition.rst b/schema/va-spec/base/def/VariantPrognosticStudyProposition.rst new file mode 100644 index 0000000..4945d8a --- /dev/null +++ b/schema/va-spec/base/def/VariantPrognosticStudyProposition.rst @@ -0,0 +1,94 @@ +.. 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 reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. + +**Information Model** + +Some VariantPrognosticStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - type + - + - string + - 1..1 + - MUST be "VariantPrognosticStudyProposition". + * - subjectVariant + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A variant that is the subject of the Proposition. + * - predicate + - + - string + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectCondition + - + - :ref:`Condition` | :ref:`iriReference` + - 1..1 + - The disease that is evaluated for outcome. + * - alleleOriginQualifier + - + - string + - 0..1 + - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). + * - allelePrevalenceQualifier + - + - string + - 0..1 + - Reports whether the proposition should be interpreted in the context of the variant being rare or common. + * - geneContextQualifier + - + - :ref:`MappableConcept` + - 0..1 + - Reports a gene impacted by the variant, which may contribute to the prognostic association in the Proposition. diff --git a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst b/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst index 87b3444..ce58488 100644 --- a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst +++ b/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst @@ -129,33 +129,8 @@ Some VariantPrognosticStudyStatement attributes are inherited from :ref:`gks-cor - string - 1..1 - MUST be "VariantPrognosticStudyStatement". - * - subjectVariant + * - proposition - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - :ref:`VariantPrognosticStudyProposition` - 1..1 - - A variant that is the subject of the Statement. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The disease that is evaluated for outcome. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the prognostic association in the Statement. + - The proposition for which the study provides evidence - that the subject variant is associated with the object disease outcome. diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseStudyProposition.rst b/schema/va-spec/base/def/VariantTherapeuticResponseStudyProposition.rst new file mode 100644 index 0000000..b1be3ea --- /dev/null +++ b/schema/va-spec/base/def/VariantTherapeuticResponseStudyProposition.rst @@ -0,0 +1,100 @@ +.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. + +**Information Model** + +Some VariantTherapeuticResponseStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - type + - + - string + - 1..1 + - MUST be "VariantTherapeuticResponseStudyProposition". + * - subjectVariant + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A variant that is the subject of the Statement. + * - predicate + - + - string + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectTherapeutic + - + - :ref:`Therapeutic` | :ref:`iriReference` + - 1..1 + - A drug administration or other therapeutic procedure that the neoplasm is intended to respond to. + * - conditionQualifier + - + - :ref:`Condition` | :ref:`iriReference` + - 1..1 + - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements. + * - alleleOriginQualifier + - + - string + - 0..1 + - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). + * - allelePrevalenceQualifier + - + - string + - 0..1 + - Reports whether the statement should be interpreted in the context of the variant being rare or common. + * - geneContextQualifier + - + - :ref:`MappableConcept` + - 0..1 + - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. + diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst index d9868df..022623b 100644 --- a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst +++ b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst @@ -129,39 +129,8 @@ Some VariantTherapeuticResponseStudyStatement attributes are inherited from :ref - string - 1..1 - MUST be "VariantTherapeuticResponseStudyStatement". - * - subjectVariant + * - proposition - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - :ref:`VariantTherapeuticResponseStudyProposition` - 1..1 - - A variant that is the subject of the Statement. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectTherapeutic - - - - :ref:`Therapeutic` | :ref:`iriReference` - - 1..1 - - A drug administration or other therapeutic procedure that the neoplasm is intended to respond to. - * - conditionQualifier - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. - + - Reports the conclusion of the study, which is that the subject variant is associated with therapeutic sensitivity or resistance to the object therapeutic. diff --git a/schema/va-spec/base/def/XCohortAlleleFrequencyStudyResult.rst b/schema/va-spec/base/def/XCohortAlleleFrequencyStudyResult.rst new file mode 100644 index 0000000..5c9b612 --- /dev/null +++ b/schema/va-spec/base/def/XCohortAlleleFrequencyStudyResult.rst @@ -0,0 +1,147 @@ +.. 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 StudyResult that reports measures related to the frequency of an Allele in a cohort + +**Information Model** + +Some XCohortAlleleFrequencyStudyResult attributes are inherited from :ref:`gks-core:StudyResult`. + +.. 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. + * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - ancillaryResults + - + .. raw:: html + + D + - object + - 0..1 + - + * - qualityMeasures + - + .. raw:: html + + D + - object + - 0..1 + - + * - type + - + - string + - 1..1 + - MUST be "CohortAlleleFrequencyStudyResult". + * - sourceDataSet + - + .. raw:: html + + ⋮ + - :ref:`DataSet` + - 0..m + - The dataset from which the CohortAlleleFrequencyStudyResult was reported. + * - focusAllele + - + - :ref:`Allele` | string + - 1..1 + - The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD. + * - focusAlleleCount + - + - integer + - 1..1 + - The number of occurrences of the focusAllele in the cohort. + * - locusAlleleCount + - + - integer + - 1..1 + - The number of occurrences of all alleles at the locus in the cohort (sometimes referred to as "allele number") + * - focusAlleleFrequency + - + - number + - 1..1 + - The frequency of the focusAllele in the cohort. + * - cohort + - + - :ref:`StudyGroup` + - 1..1 + - The cohort from which the frequency was derived. + * - subCohortFrequency + - + .. raw:: html + + ⋮ + - :ref:`XCohortAlleleFrequencyStudyResult` + - 0..m + - A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups. diff --git a/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyProposition.rst b/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyProposition.rst new file mode 100644 index 0000000..6a3c07e --- /dev/null +++ b/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyProposition.rst @@ -0,0 +1,89 @@ +.. 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 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). + +**Information Model** + +Some XExperimentalVariantFunctionalImpactStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - type + - + - string + - 1..1 + - MUST be "ExperimentalVariantFunctionalImpactStudyProposition". + * - subjectVariant + - + - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A protein or genomic contextual or canonical molecular variant. + * - predicate + - + - string + - 1..1 + - The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter. + * - objectSequenceFeature + - + - :ref:`iriReference` | :ref:`MappableConcept` + - 1..1 + - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. + * - studyContextQualifier + - + - :ref:`Document` | :ref:`iriReference` + - 1..1 + - The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. + * - impactTypeQualifier + - + - string + - 0..1 + - 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). diff --git a/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyResult.rst b/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyResult.rst new file mode 100644 index 0000000..373acd3 --- /dev/null +++ b/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyResult.rst @@ -0,0 +1,137 @@ +.. 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 StudyResult that reports a functional impact score from a variant functional assay or study. + +**Information Model** + +Some XExperimentalVariantFunctionalImpactStudyResult attributes are inherited from :ref:`gks-core:StudyResult`. + +.. 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. + * - 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. + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - componentResult + - + .. raw:: html + + ⋮ + - :ref:`StudyResult` + - 0..m + - Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) . + * - studyGroup + - + - :ref:`StudyGroup` + - 0..1 + - A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult. + * - ancillaryResults + - + .. raw:: html + + D + - object + - 0..1 + - + * - qualityMeasures + - + .. raw:: html + + D + - object + - 0..1 + - + * - type + - + - string + - 1..1 + - MUST be "ExperimentalVariantFunctionalImpactStudyResult". + * - focusVariant + - + - :ref:`MolecularVariation` | :ref:`iriReference` + - 0..1 + - The genetic variant for which a functional impact score is generated. + * - functionalImpactScore + - + - number + - 0..1 + - The score of the variant impact measured in the assay or study. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - The assay that was performed to generate the reported functional impact score. + * - sourceDataSet + - + .. raw:: html + + ⋮ + - :ref:`DataSet` + - 0..m + - The full data set that provided the reported the functional impact score. diff --git a/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyStatement.rst b/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyStatement.rst new file mode 100644 index 0000000..6868001 --- /dev/null +++ b/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyStatement.rst @@ -0,0 +1,136 @@ +.. 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 statement 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). + +**Information Model** + +Some XExperimentalVariantFunctionalImpactStudyStatement attributes are inherited from :ref:`gks-core:Statement`. + +.. 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. + * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - derivedFrom + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - Another Information Entity from which this Information Entity is derived, in whole or in part. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - direction + - + - string + - 0..1 + - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. + * - strength + - + - :ref:`MappableConcept` + - 0..1 + - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. + * - score + - + - number + - 0..1 + - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. + * - statementText + - + - string + - 0..1 + - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. + * - hasEvidenceLines + - + .. raw:: html + + ⋮ + - :ref:`EvidenceLine` + - 0..m + - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). + * - type + - + - string + - 1..1 + - MUST be "ExperimentalVariantFunctionalImpactStudyStatement". + * - proposition + - + - :ref:`XExperimentalVariantFunctionalImpactStudyProposition` + - 1..1 + - The proposition for which the study provides evidence - that the subject variant impacts the function of the object sequence feature. diff --git a/schema/va-spec/base/def/XVariantDiagnosticStudyProposition.rst b/schema/va-spec/base/def/XVariantDiagnosticStudyProposition.rst new file mode 100644 index 0000000..8ba075b --- /dev/null +++ b/schema/va-spec/base/def/XVariantDiagnosticStudyProposition.rst @@ -0,0 +1,94 @@ +.. 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 reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. + +**Information Model** + +Some XVariantDiagnosticStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - type + - + - string + - 1..1 + - MUST be "VariantDiagnosticStudyProposition". + * - subjectVariant + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A variant that is the subject of the Proposition. + * - predicate + - + - string + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectCondition + - + - :ref:`Condition` | :ref:`iriReference` + - 1..1 + - The disease that is evaluated for diagnosis. + * - alleleOriginQualifier + - + - string + - 0..1 + - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). + * - allelePrevalenceQualifier + - + - string + - 0..1 + - Reports whether the proposition should be interpreted in the context of the variant being rare or common. + * - geneContextQualifier + - + - :ref:`MappableConcept` + - 0..1 + - Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Proposition. diff --git a/schema/va-spec/base/def/XVariantDiagnosticStudyStatement.rst b/schema/va-spec/base/def/XVariantDiagnosticStudyStatement.rst new file mode 100644 index 0000000..aaa2348 --- /dev/null +++ b/schema/va-spec/base/def/XVariantDiagnosticStudyStatement.rst @@ -0,0 +1,136 @@ +.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. + +**Information Model** + +Some XVariantDiagnosticStudyStatement attributes are inherited from :ref:`gks-core:Statement`. + +.. 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. + * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - derivedFrom + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - Another Information Entity from which this Information Entity is derived, in whole or in part. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - direction + - + - string + - 0..1 + - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. + * - strength + - + - :ref:`MappableConcept` + - 0..1 + - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. + * - score + - + - number + - 0..1 + - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. + * - statementText + - + - string + - 0..1 + - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. + * - hasEvidenceLines + - + .. raw:: html + + ⋮ + - :ref:`EvidenceLine` + - 0..m + - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). + * - type + - + - string + - 1..1 + - MUST be "VariantDiagnosticStudyStatement". + * - proposition + - + - :ref:`XVariantDiagnosticStudyProposition` + - 1..1 + - The proposition for which the study provides evidence - that the subject variant is associated with the object disease. diff --git a/schema/va-spec/base/def/XVariantOncogenicityStudyProposition.rst b/schema/va-spec/base/def/XVariantOncogenicityStudyProposition.rst new file mode 100644 index 0000000..9f7d2de --- /dev/null +++ b/schema/va-spec/base/def/XVariantOncogenicityStudyProposition.rst @@ -0,0 +1,94 @@ +.. 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 reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. + +**Information Model** + +Some XVariantOncogenicityStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - type + - + - string + - 1..1 + - MUST be "VariantOncogenicityStudyProposition". + * - subjectVariant + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A variant that is the subject of the Proposition. + * - predicate + - + - string + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectTumorType + - + - :ref:`Condition` | :ref:`MappableConcept` + - 1..1 + - The tumor type for which the variant impact is evaluated. + * - 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 oncogenic role in the Proposition. diff --git a/schema/va-spec/base/def/XVariantOncogenicityStudyStatement.rst b/schema/va-spec/base/def/XVariantOncogenicityStudyStatement.rst new file mode 100644 index 0000000..66d55ce --- /dev/null +++ b/schema/va-spec/base/def/XVariantOncogenicityStudyStatement.rst @@ -0,0 +1,136 @@ +.. 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 Statement reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. + +**Information Model** + +Some XVariantOncogenicityStudyStatement attributes are inherited from :ref:`gks-core:Statement`. + +.. 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. + * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - derivedFrom + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - Another Information Entity from which this Information Entity is derived, in whole or in part. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - direction + - + - string + - 0..1 + - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. + * - strength + - + - :ref:`MappableConcept` + - 0..1 + - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. + * - score + - + - number + - 0..1 + - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. + * - statementText + - + - string + - 0..1 + - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. + * - hasEvidenceLines + - + .. raw:: html + + ⋮ + - :ref:`EvidenceLine` + - 0..m + - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). + * - type + - + - string + - 1..1 + - MUST be "VariantOncogenicityStudyStatement". + * - proposition + - + - :ref:`XVariantOncogenicityStudyProposition` + - 1..1 + - The proposition for which the study provides evidence - that the subject variant is associated with the object tumor type. diff --git a/schema/va-spec/base/def/XVariantPathogenicityEvidenceLine.rst b/schema/va-spec/base/def/XVariantPathogenicityEvidenceLine.rst new file mode 100644 index 0000000..d559f99 --- /dev/null +++ b/schema/va-spec/base/def/XVariantPathogenicityEvidenceLine.rst @@ -0,0 +1,126 @@ +.. 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** + +An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. + +**Information Model** + +Some XVariantPathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:EvidenceLine`. + +.. 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. + * - 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. + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - derivedFrom + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - Another Information Entity from which this Information Entity is derived, in whole or in part. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - scoreOfEvidenceProvided + - + - number + - 0..1 + - A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value. + * - type + - + - string + - 1..1 + - MUST be "VariantPathogenicityEvidenceLine". + * - hasEvidenceItems + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result). + * - directionOfEvidenceProvided + - + - string + - 0..1 + - The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral) + * - strengthOfEvidenceProvided + - + - {'$ref': '/ga4gh/schema/gks-core/1.x/json/MappableConcept'} + - 0..1 + - The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. + * - targetProposition + - + - :ref:`XVariantPathogenicityProposition` + - 0..1 + - The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant. diff --git a/schema/va-spec/base/def/XVariantPathogenicityProposition.rst b/schema/va-spec/base/def/XVariantPathogenicityProposition.rst new file mode 100644 index 0000000..4837b60 --- /dev/null +++ b/schema/va-spec/base/def/XVariantPathogenicityProposition.rst @@ -0,0 +1,97 @@ +.. 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 describing the role of a variant in causing an inherited condition. + +**Information Model** + +Some XVariantPathogenicityProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - 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 + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectCondition + - + - :ref:`Condition` | :ref:`iriReference` + - 1..1 + - The :ref:`Condition` for which the variant impact is stated. + * - penetranceQualifier + - + - string + - 0..1 + - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. + * - modeOfInheritanceQualifier + - + .. raw:: html + + ⋮ + - :ref:`Coding` + - 0..m + - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. + * - geneContextQualifier + - + - :ref:`MappableConcept` | :ref:`iriReference` + - 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). diff --git a/schema/va-spec/base/def/XVariantPathogenicityStatement.rst b/schema/va-spec/base/def/XVariantPathogenicityStatement.rst new file mode 100644 index 0000000..12a57b7 --- /dev/null +++ b/schema/va-spec/base/def/XVariantPathogenicityStatement.rst @@ -0,0 +1,136 @@ +.. 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 Statement describing the role of a variant in causing an inherited condition. + +**Information Model** + +Some XVariantPathogenicityStatement attributes are inherited from :ref:`gks-core:Statement`. + +.. 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. + * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - derivedFrom + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - Another Information Entity from which this Information Entity is derived, in whole or in part. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - direction + - + - string + - 0..1 + - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. + * - strength + - + - :ref:`MappableConcept` + - 0..1 + - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. + * - score + - + - number + - 0..1 + - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. + * - statementText + - + - string + - 0..1 + - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. + * - hasEvidenceLines + - + .. raw:: html + + ⋮ + - :ref:`EvidenceLine` + - 0..m + - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). + * - type + - + - string + - 1..1 + - MUST be "VariantPathogenicityStatement". + * - proposition + - + - :ref:`XVariantPathogenicityProposition` + - 1..1 + - The proposition that the subject variant is associated with the object disease. diff --git a/schema/va-spec/base/def/XVariantPrognosticStudyProposition.rst b/schema/va-spec/base/def/XVariantPrognosticStudyProposition.rst new file mode 100644 index 0000000..d9a353f --- /dev/null +++ b/schema/va-spec/base/def/XVariantPrognosticStudyProposition.rst @@ -0,0 +1,94 @@ +.. 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 reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. + +**Information Model** + +Some XVariantPrognosticStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - type + - + - string + - 1..1 + - MUST be "VariantPrognosticStudyProposition". + * - subjectVariant + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A variant that is the subject of the Proposition. + * - predicate + - + - string + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectCondition + - + - :ref:`Condition` | :ref:`iriReference` + - 1..1 + - The disease that is evaluated for outcome. + * - alleleOriginQualifier + - + - string + - 0..1 + - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). + * - allelePrevalenceQualifier + - + - string + - 0..1 + - Reports whether the proposition should be interpreted in the context of the variant being rare or common. + * - geneContextQualifier + - + - :ref:`MappableConcept` + - 0..1 + - Reports a gene impacted by the variant, which may contribute to the prognostic association in the Proposition. diff --git a/schema/va-spec/base/def/XVariantPrognosticStudyStatement.rst b/schema/va-spec/base/def/XVariantPrognosticStudyStatement.rst new file mode 100644 index 0000000..7fa323c --- /dev/null +++ b/schema/va-spec/base/def/XVariantPrognosticStudyStatement.rst @@ -0,0 +1,136 @@ +.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. + +**Information Model** + +Some XVariantPrognosticStudyStatement attributes are inherited from :ref:`gks-core:Statement`. + +.. 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. + * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - derivedFrom + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - Another Information Entity from which this Information Entity is derived, in whole or in part. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - direction + - + - string + - 0..1 + - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. + * - strength + - + - :ref:`MappableConcept` + - 0..1 + - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. + * - score + - + - number + - 0..1 + - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. + * - statementText + - + - string + - 0..1 + - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. + * - hasEvidenceLines + - + .. raw:: html + + ⋮ + - :ref:`EvidenceLine` + - 0..m + - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). + * - type + - + - string + - 1..1 + - MUST be "VariantPrognosticStudyStatement". + * - proposition + - + - :ref:`XVariantPrognosticStudyProposition` + - 1..1 + - The proposition for which the study provides evidence - that the subject variant is associated with the object disease outcome. diff --git a/schema/va-spec/base/def/XVariantTherapeuticResponseStudyProposition.rst b/schema/va-spec/base/def/XVariantTherapeuticResponseStudyProposition.rst new file mode 100644 index 0000000..f025b2b --- /dev/null +++ b/schema/va-spec/base/def/XVariantTherapeuticResponseStudyProposition.rst @@ -0,0 +1,100 @@ +.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. + +**Information Model** + +Some XVariantTherapeuticResponseStudyProposition attributes are inherited from :ref:`gks-core: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. + * - 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. + * - type + - + - string + - 1..1 + - Must be "Proposition" + * - propositionText + - + - string + - 0..1 + - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". + * - subjectVariant + - + - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` + - 1..1 + - A variant that is the subject of the Statement. + * - predicate + - + - string + - 1..1 + - The relationship declared to hold between the subject and the object of the Statement. + * - objectTherapeutic + - + - :ref:`Therapeutic` | :ref:`iriReference` + - 1..1 + - A drug administration or other therapeutic procedure that the neoplasm is intended to respond to. + * - conditionQualifier + - + - :ref:`Condition` | :ref:`iriReference` + - 1..1 + - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements. + * - alleleOriginQualifier + - + - string + - 0..1 + - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). + * - allelePrevalenceQualifier + - + - string + - 0..1 + - Reports whether the statement should be interpreted in the context of the variant being rare or common. + * - geneContextQualifier + - + - :ref:`MappableConcept` + - 0..1 + - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. + diff --git a/schema/va-spec/base/def/XVariantTherapeuticResponseStudyStatement.rst b/schema/va-spec/base/def/XVariantTherapeuticResponseStudyStatement.rst new file mode 100644 index 0000000..e0da1e2 --- /dev/null +++ b/schema/va-spec/base/def/XVariantTherapeuticResponseStudyStatement.rst @@ -0,0 +1,136 @@ +.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. + +**Information Model** + +Some XVariantTherapeuticResponseStudyStatement attributes are inherited from :ref:`gks-core:Statement`. + +.. 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. + * - 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. + * - specifiedBy + - + - :ref:`Method` | :ref:`iriReference` + - 0..1 + - A specification that describes all or part of the process that led to creation of the Information Entity + * - contributions + - + .. raw:: html + + ⋮ + - :ref:`Contribution` + - 0..m + - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. + * - reportedIn + - + .. raw:: html + + ⋮ + - :ref:`Document` | :ref:`iriReference` + - 0..m + - A document in which the the Information Entity is reported. + * - dateAuthored + - + - string + - 0..1 + - Indicates when the information content expressed in the Information Entity was generated. + * - derivedFrom + - + .. raw:: html + + ⋮ + - :ref:`InformationEntity` + - 0..m + - Another Information Entity from which this Information Entity is derived, in whole or in part. + * - recordMetadata + - + - :ref:`RecordMetadata` + - 0..1 + - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). + * - direction + - + - string + - 0..1 + - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. + * - strength + - + - :ref:`MappableConcept` + - 0..1 + - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. + * - score + - + - number + - 0..1 + - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. + * - statementText + - + - string + - 0..1 + - A natural-language expression of what a Statement asserts to be true. + * - classification + - + - :ref:`MappableConcept` + - 0..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. + * - hasEvidenceLines + - + .. raw:: html + + ⋮ + - :ref:`EvidenceLine` + - 0..m + - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). + * - type + - + - string + - 1..1 + - MUST be "VariantTherapeuticResponseStudyStatement". + * - proposition + - + - :ref:`XVariantTherapeuticResponseStudyProposition` + - 1..1 + - Reports the conclusion of the study, which is that the subject variant is associated with therapeutic sensitivity or resistance to the object therapeutic. diff --git a/schema/va-spec/base/diagnostic-study-proposition-profile-source.yaml b/schema/va-spec/base/diagnostic-study-proposition-profile-source.yaml new file mode 100644 index 0000000..0d26d11 --- /dev/null +++ b/schema/va-spec/base/diagnostic-study-proposition-profile-source.yaml @@ -0,0 +1,72 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/diagnostic-study-proposition-profile-source.yaml" +title: Variant Dx Study Proposition Standard Profile +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Diagnostic Study Statement + VariantDiagnosticStudyProposition: + inherits: gks-core:Proposition + type: object + maturity: draft + description: >- + A Proposition reporting a conclusion from a single study about whether a variant + is associated with a disease (a diagnostic inclusion criterion), or absence of a + disease (diagnostic exclusion criterion) - based on interpretation of the study's + results. + properties: + type: + extends: type + const: "VariantDiagnosticStudyProposition" + default: "VariantDiagnosticStudyProposition" + description: MUST be "VariantDiagnosticStudyProposition". + 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: + - isDiagnosticInclusionCriterionFor + - isDiagnosticExclusionCriterionFor + objectCondition: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The disease that is evaluated for diagnosis. + alleleOriginQualifier: + description: >- + Reports whether the proposition should be interpreted in the context of an inherited + (germline) variant, an acquired (somatic) mutation, or both (combined). + type: string + enum: + - germline + - somatic + - combined + allelePrevalenceQualifier: + description: >- + Reports whether the proposition should be interpreted in the context of the variant + being rare or common. + type: string + enum: + - rare + - common + geneContextQualifier: + description: >- + Reports a gene impacted by the variant, which may contribute to the + diagnostic association in the Proposition. + $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + required: + - subjectVariant + - predicate + - objectCondition \ No newline at end of file diff --git a/schema/va-spec/base/diagnostic-study-statement-profile-source.yaml b/schema/va-spec/base/diagnostic-study-statement-profile-source.yaml index a08f27a..63ad2a9 100644 --- a/schema/va-spec/base/diagnostic-study-statement-profile-source.yaml +++ b/schema/va-spec/base/diagnostic-study-statement-profile-source.yaml @@ -4,9 +4,7 @@ title: Variant Dx Study Statement Standard Profile strict: true imports: - domain-entities: ./domain-entities-source.yaml - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml - vrs: ../../vrs/vrs-source.yaml + va-dx-prop: ./diagnostic-study-proposition-profile-source.yaml gks-core: ../../gks-core/gks-core-source.yaml $defs: @@ -26,47 +24,11 @@ $defs: const: "VariantDiagnosticStudyStatement" default: "VariantDiagnosticStudyStatement" description: MUST be "VariantDiagnosticStudyStatement". - 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: - - isDiagnosticInclusionCriterionFor - - isDiagnosticExclusionCriterionFor - objectCondition: - extends: object - oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: The disease that is evaluated for diagnosis. - alleleOriginQualifier: + proposition: + extends: proposition + $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticStudyProposition" description: >- - Reports whether the statement should be interpreted in the context of an inherited - (germline) variant, an acquired (somatic) mutation, or both (combined). - type: string - enum: - - germline - - somatic - - combined - allelePrevalenceQualifier: - description: >- - Reports whether the statement should be interpreted in the context of the variant - being rare or common. - type: string - enum: - - rare - - common - geneContextQualifier: - description: >- - Reports a gene impacted by the variant, which may contribute to the - diagnostic association in the Statement. - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + The proposition for which the study provides evidence - that the subject variant + is associated with the object disease. required: - - subjectVariant - - predicate - - objectCondition \ No newline at end of file + - proposition \ No newline at end of file diff --git a/schema/va-spec/base/experimental-functional-impact-study-proposition-profile-source.yaml b/schema/va-spec/base/experimental-functional-impact-study-proposition-profile-source.yaml new file mode 100644 index 0000000..7be26ec --- /dev/null +++ b/schema/va-spec/base/experimental-functional-impact-study-proposition-profile-source.yaml @@ -0,0 +1,81 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/experimental-functional-impact-study-proposition-profile-source.yaml" +title: Experimental Variant Functional Impact Study Proposition +strict: true + +imports: + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + ExperimentalVariantFunctionalImpactStudyProposition: + inherits: gks-core:Proposition + maturity: draft + 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: + type: + extends: type + const: "ExperimentalVariantFunctionalImpactStudyProposition" + default: "ExperimentalVariantFunctionalImpactStudyProposition" + description: MUST be "ExperimentalVariantFunctionalImpactStudyProposition". + 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: >- + The relationship this Proposition describes between the subject Variant + and object Sequence Feature whose function it may alter. + const: impactsFunctionOf + objectSequenceFeature: + extends: object + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: "/ga4gh/schema/gks-core/1.x/MappableConcept" # See https://github.com/ga4gh/gks-common/pull/77 - proposes a SequenceFeature domain entity class + description: >- + The sequence feature (typically a gene or gene product) on whose function the impact + of the subject variant is assessed. + studyContextQualifier: + description: >- + The assay in which the reported variant functional impact was determined - + providing a specific experimental context in which this effect is asserted to hold. + $comment: >- + The attribute is required in order to explicitly specify an assay or study context in + which the reported impact was observed. It's value can be a Document object, or an IRI + pointing to a document that describes the assay/study. This may be a publication, a + database record, or a bespoke document. + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/Document" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + impactTypeQualifier: # This qualifier allows more specific types of impacts to be reported - so the profile supports implementations like CIViC, ClinGen, and I think even some MAVE data. + 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. + + # 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 diff --git a/schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml b/schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml index 1c46777..dc589f9 100644 --- a/schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml +++ b/schema/va-spec/base/experimental-functional-impact-study-result-profile-source.yaml @@ -4,7 +4,6 @@ title: Experimental Variant Functional Impact Study Result Standard Profile strict: true imports: - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml diff --git a/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml index 125408c..2cd2003 100644 --- a/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml +++ b/schema/va-spec/base/experimental-functional-impact-study-statement-profile-source.yaml @@ -1,11 +1,10 @@ $schema: "https://json-schema.org/draft/2020-12/schema" $id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/experimental-functional-impact-study-statement-profile-source.yaml" -title: Experimental Variant Functional Impact Statement +title: Experimental Variant Functional Impact Study Statement strict: true imports: - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml - vrs: ../../vrs/vrs-source.yaml + va-expfunc-prop: ./experimental-functional-impact-study-proposition-profile-source.yaml gks-core: ../../gks-core/gks-core-source.yaml $defs: @@ -22,80 +21,30 @@ $defs: const: "ExperimentalVariantFunctionalImpactStudyStatement" default: "ExperimentalVariantFunctionalImpactStudyStatement" description: MUST be "ExperimentalVariantFunctionalImpactStudyStatement". - 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 + proposition: + extends: proposition + $ref: "/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyProposition" description: >- - The relationship this Statement describes between the subject Variant - and object Sequence Feature whose function it may alter. - const: impactsFunctionOf - objectSequenceFeature: - extends: object - oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - - $ref: "/ga4gh/schema/gks-core/1.x/MappableConcept" # See https://github.com/ga4gh/gks-common/pull/77 - proposes a SequenceFeature domain entity class - description: >- - The sequence feature (typically a gene or gene product) on whose function the impact - of the subject variant is assessed. - studyContextQualifier: - description: >- - The assay in which the reported variant functional impact was determined - - providing a specific experimental context in which this effect is asserted to hold. - $comment: >- - The attribute is required in order to explicitly specify an assay or study context in - which the reported impact was observed. It's value can be a Document object, or an IRI - pointing to a document that describes the assay/study. This may be a publication, a - database record, or a bespoke document. - oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/Document" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - impactTypeQualifier: # This qualifier allows more specific types of impacts to be reported - so the profile supports implementations like CIViC, ClinGen, and I think even some MAVE data. - 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. - - # 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' - - classification: # this attribute now inherits the data type of 'MappableConcept' from the Core model (rather than simpler 'string' that was originally used) Consider need for a MappableConcept. Consider what tyeps of values would go in this attribute for a FI Statement. And what it would look like if there is no 'code' available. - extends: classification - description: >- - An term or phrase summarizing the impact reported in the Statement, providing - a functional classification of the subject variant that is familiar for a community of use. - $comment: >- # Matt: update $comment here to reflect outcome of discussion / decisions about what would go here in a FI Statement instance. - This is an optional attribute that can be used by data providers to provide a particular - community of users a functional impact classification in familiar terms, - that summarizes/complements the smeantics broken out in the SPOQ attributes of the Statement - (e.g. to mirror established community conventions or reflect language on the data providers - website or documentation). e.g. CIViC docs/web site uses terms like 'unaltered function', - 'gain of function', 'neomorphic', and 'unknown', which could be reropted here. - specifiedBy: - extends: specifiedBy - description: >- - The method that specifies how the functional classification is ultimately assigned to - the variant, based on interpretation of data from the supporting assay. May include - information about thresholds applied on assay variant effect scores to derive the - final classification. + The proposition for which the study provides evidence - that the subject variant + impacts the function of the object sequence feature. + # classification: # this attribute now inherits the data type of 'MappableConcept' from the Core model (rather than simpler 'string' that was originally used) Consider need for a MappableConcept. Consider what tyeps of values would go in this attribute for a FI Statement. And what it would look like if there is no 'code' available. + # extends: classification + # description: >- + # An term or phrase summarizing the impact reported in the Statement, providing + # a functional classification of the subject variant that is familiar for a community of use. + # $comment: >- # Matt: update $comment here to reflect outcome of discussion / decisions about what would go here in a FI Statement instance. + # This is an optional attribute that can be used by data providers to provide a particular + # community of users a functional impact classification in familiar terms, + # that summarizes/complements the smeantics broken out in the SPOQ attributes of the Statement + # (e.g. to mirror established community conventions or reflect language on the data providers + # website or documentation). e.g. CIViC docs/web site uses terms like 'unaltered function', + # 'gain of function', 'neomorphic', and 'unknown', which could be reropted here. + # specifiedBy: + # extends: specifiedBy + # description: >- + # The method that specifies how the functional classification is ultimately assigned to + # the variant, based on interpretation of data from the supporting assay. May include + # information about thresholds applied on assay variant effect scores to derive the + # final classification. required: - - subjectVariant - - predicate - - objectSequenceFeature - - studyContextQualifier + - proposition diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyProposition b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyProposition new file mode 100644 index 0000000..8173594 --- /dev/null +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyProposition @@ -0,0 +1,115 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyProposition", + "title": "ExperimentalVariantFunctionalImpactStudyProposition", + "maturity": "draft", + "type": "object", + "description": "A proposition reporting a conclusion from a single assay or study about the functional impact of a variant on a sequence feature (typically a gene or gene product).", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "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 \"ExperimentalVariantFunctionalImpactStudyProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "ExperimentalVariantFunctionalImpactStudyProposition", + "default": "ExperimentalVariantFunctionalImpactStudyProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" + } + ], + "description": "A protein or genomic contextual or canonical molecular variant.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter.", + "$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" + }, + "objectSequenceFeature": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "studyContextQualifier": { + "description": "The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.", + "$comment": "The attribute is required in order to explicitly specify an assay or study context in which the reported impact was observed. It's value can be a Document object, or an IRI pointing to a document that describes the assay/study. This may be a publication, a database record, or a bespoke document.", + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "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).", + "$comment": "Implementers may use a set of terms to use here that reflect the specific types of functional impact(s) measured by the assay(s) employed. It is recommended that terms are drawn from established terminologies where possible.", + "type": "string", + "enum": [ + "increased activity/function", + "decreased activity/function", + "novel activity/function", + "dominant negative activity/function" + ] + } + }, + "required": [ + "objectSequenceFeature", + "predicate", + "studyContextQualifier", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement index 5ac9949..8764e0a 100644 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement @@ -36,6 +36,18 @@ "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, "contributions": { "type": "array", "ordered": false, @@ -104,6 +116,11 @@ "description": "A natural-language expression of what a Statement asserts to be true.", "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, "hasEvidenceLines": { "type": "array", "ordered": false, @@ -119,85 +136,14 @@ "default": "ExperimentalVariantFunctionalImpactStudyStatement", "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyStatement\"." }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" - } - ], - "description": "A protein or genomic contextual or canonical molecular variant.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship this Statement describes between the subject Variant and object Sequence Feature whose function it may alter.", - "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "const": "impactsFunctionOf" - }, - "objectSequenceFeature": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed.", - "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "studyContextQualifier": { - "description": "The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.", - "$comment": "The attribute is required in order to explicitly specify an assay or study context in which the reported impact was observed. It's value can be a Document object, or an IRI pointing to a document that describes the assay/study. This may be a publication, a database record, or a bespoke document.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "impactTypeQualifier": { - "description": "A term describing a specific type of functional impact that the variant is determined to have on the indicated sequence feature (e.g. decreased activity, dominant negative, neomorphic, reduced Ca2+ binding activity).", - "$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.", - "type": "string", - "enum": [ - "increased activity/function", - "decreased activity/function", - "novel activity/function", - "dominant negative activity/function" - ] - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "An term or phrase summarizing the impact reported in the Statement, providing a functional classification of the subject variant that is familiar for a community of use.", - "$comment": "This is an optional attribute that can be used by data providers to provide a particular community of users a functional impact classification in familiar terms, that summarizes/complements the smeantics broken out in the SPOQ attributes of the Statement (e.g. to mirror established community conventions or reflect language on the data providers website or documentation). e.g. CIViC docs/web site uses terms like 'unaltered function', 'gain of function', 'neomorphic', and 'unknown', which could be reropted here. " - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "The method that specifies how the functional classification is ultimately assigned to the variant, based on interpretation of data from the supporting assay. May include information about thresholds applied on assay variant effect scores to derive the final classification.", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyProposition", + "description": "The proposition for which the study provides evidence - that the subject variant impacts the function of the object sequence feature.", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " } }, "required": [ - "objectSequenceFeature", - "predicate", - "studyContextQualifier", - "subjectVariant", + "proposition", "type" ], "additionalProperties": false diff --git a/schema/va-spec/base/json/VariantDiagnosticStudyProposition b/schema/va-spec/base/json/VariantDiagnosticStudyProposition new file mode 100644 index 0000000..0d22a15 --- /dev/null +++ b/schema/va-spec/base/json/VariantDiagnosticStudyProposition @@ -0,0 +1,115 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticStudyProposition", + "title": "VariantDiagnosticStudyProposition", + "type": "object", + "maturity": "draft", + "description": "A Proposition reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "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 \"VariantDiagnosticStudyProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantDiagnosticStudyProposition", + "default": "VariantDiagnosticStudyProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Proposition.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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.", + "enum": [ + "isDiagnosticInclusionCriterionFor", + "isDiagnosticExclusionCriterionFor" + ] + }, + "objectCondition": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "The disease that is evaluated for diagnosis.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "alleleOriginQualifier": { + "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", + "type": "string", + "enum": [ + "germline", + "somatic", + "combined" + ] + }, + "allelePrevalenceQualifier": { + "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", + "type": "string", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Proposition.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "required": [ + "objectCondition", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantDiagnosticStudyStatement b/schema/va-spec/base/json/VariantDiagnosticStudyStatement index 16b733a..7b629bf 100644 --- a/schema/va-spec/base/json/VariantDiagnosticStudyStatement +++ b/schema/va-spec/base/json/VariantDiagnosticStudyStatement @@ -136,68 +136,14 @@ "default": "VariantDiagnosticStudyStatement", "description": "MUST be \"VariantDiagnosticStudyStatement\"." }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "isDiagnosticInclusionCriterionFor", - "isDiagnosticExclusionCriterionFor" - ] - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The disease that is evaluated for diagnosis.", - "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "type": "string", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", - "type": "string", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Statement.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticStudyProposition", + "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object disease. ", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " } }, "required": [ - "objectCondition", - "predicate", - "subjectVariant", + "proposition", "type" ], "additionalProperties": false diff --git a/schema/va-spec/base/json/VariantOncogenicityStudyProposition b/schema/va-spec/base/json/VariantOncogenicityStudyProposition new file mode 100644 index 0000000..5e318eb --- /dev/null +++ b/schema/va-spec/base/json/VariantOncogenicityStudyProposition @@ -0,0 +1,116 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantOncogenicityStudyProposition", + "title": "VariantOncogenicityStudyProposition", + "maturity": "draft", + "type": "object", + "description": "A Proposition reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "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 \"VariantOncogenicityStudyProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantOncogenicityStudyProposition", + "default": "VariantOncogenicityStudyProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Proposition.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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.", + "enum": [ + "isOncogenicFor", + "isProtectiveFor", + "isPredisposingFor" + ] + }, + "objectTumorType": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "The tumor type for which the variant impact is evaluated.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "alleleOriginQualifier": { + "type": "string", + "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", + "enum": [ + "germline", + "somatic", + "combined" + ] + }, + "allelePrevalenceQualifier": { + "type": "string", + "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Proposition.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "required": [ + "objectTumorType", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantOncogenicityStudyStatement b/schema/va-spec/base/json/VariantOncogenicityStudyStatement index 4ff7358..4ebc0fa 100644 --- a/schema/va-spec/base/json/VariantOncogenicityStudyStatement +++ b/schema/va-spec/base/json/VariantOncogenicityStudyStatement @@ -136,69 +136,14 @@ "default": "VariantOncogenicityStudyStatement", "description": "MUST be \"VariantOncogenicityStudyStatement\"." }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "isOncogenicFor", - "isProtectiveFor", - "isPredisposingFor" - ] - }, - "objectTumorType": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The tumor type for which the variant impact is evaluated.", - "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Statement.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantOncogenicityStudyProposition", + "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object tumor type.", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " } }, "required": [ - "objectTumorType", - "predicate", - "subjectVariant", + "proposition", "type" ], "additionalProperties": false diff --git a/schema/va-spec/base/json/PathogenicityEvidenceLine b/schema/va-spec/base/json/VariantPathogenicityEvidenceLine similarity index 96% rename from schema/va-spec/base/json/PathogenicityEvidenceLine rename to schema/va-spec/base/json/VariantPathogenicityEvidenceLine index de30cde..06965ef 100644 --- a/schema/va-spec/base/json/PathogenicityEvidenceLine +++ b/schema/va-spec/base/json/VariantPathogenicityEvidenceLine @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/PathogenicityEvidenceLine", - "title": "PathogenicityEvidenceLine", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityEvidenceLine", + "title": "VariantPathogenicityEvidenceLine", "maturity": "draft", "type": "object", "description": "An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. ", @@ -85,9 +85,9 @@ }, "type": { "type": "string", - "const": "PathogenicityEvidenceLine", - "default": "PathogenicityEvidenceLine", - "description": "MUST be \"PathogenicityEvidenceLine\"." + "const": "VariantPathogenicityEvidenceLine", + "default": "VariantPathogenicityEvidenceLine", + "description": "MUST be \"VariantPathogenicityEvidenceLine\"." }, "hasEvidenceItems": { "type": "array", diff --git a/schema/va-spec/base/json/VariantPathogenicityProposition b/schema/va-spec/base/json/VariantPathogenicityProposition index 5f13468..94b6c30 100644 --- a/schema/va-spec/base/json/VariantPathogenicityProposition +++ b/schema/va-spec/base/json/VariantPathogenicityProposition @@ -59,7 +59,8 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" } ], - "description": "A variant that is the subject of the Statement." + "description": "A variant that is the subject of the Statement.", + "$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)." }, "predicate": { "type": "string", @@ -77,7 +78,7 @@ } ], "description": "The Condition for which the variant impact is stated.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein. " + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." }, "penetranceQualifier": { "type": "string", diff --git a/schema/va-spec/base/json/VariantPathogenicityStatement b/schema/va-spec/base/json/VariantPathogenicityStatement index 7d5ffb8..07053ff 100644 --- a/schema/va-spec/base/json/VariantPathogenicityStatement +++ b/schema/va-spec/base/json/VariantPathogenicityStatement @@ -136,72 +136,14 @@ "default": "VariantPathogenicityStatement", "description": "MUST be \"VariantPathogenicityStatement\"." }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "const": "isCausalFor" - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The Condition for which the variant impact is stated.", - "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "penetranceQualifier": { - "type": "string", - "enum": [ - "high", - "low", - "risk allele" - ], - "description": "Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition." - }, - "modeOfInheritanceQualifier": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding" - }, - "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify." - }, - "geneContextQualifier": { - "description": "Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).", - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition", + "description": "The proposition that the subject variant is associated with the object disease.", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " } }, "required": [ - "objectCondition", - "predicate", - "subjectVariant", + "proposition", "type" ], "additionalProperties": false diff --git a/schema/va-spec/base/json/VariantPrognosticStudyProposition b/schema/va-spec/base/json/VariantPrognosticStudyProposition new file mode 100644 index 0000000..42e3eec --- /dev/null +++ b/schema/va-spec/base/json/VariantPrognosticStudyProposition @@ -0,0 +1,115 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyProposition", + "title": "VariantPrognosticStudyProposition", + "type": "object", + "maturity": "draft", + "description": "A Proposition reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "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 \"VariantPrognosticStudyProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantPrognosticStudyProposition", + "default": "VariantPrognosticStudyProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Proposition.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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.", + "enum": [ + "associatedWithBetterOutcomeFor", + "associatedWithWorseOutcomeFor" + ] + }, + "objectCondition": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "The disease that is evaluated for outcome.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "alleleOriginQualifier": { + "type": "string", + "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", + "enum": [ + "germline", + "somatic", + "combined" + ] + }, + "allelePrevalenceQualifier": { + "type": "string", + "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the prognostic association in the Proposition.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "required": [ + "objectCondition", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantPrognosticStudyStatement b/schema/va-spec/base/json/VariantPrognosticStudyStatement index bbfcd23..df99c24 100644 --- a/schema/va-spec/base/json/VariantPrognosticStudyStatement +++ b/schema/va-spec/base/json/VariantPrognosticStudyStatement @@ -136,68 +136,14 @@ "default": "VariantPrognosticStudyStatement", "description": "MUST be \"VariantPrognosticStudyStatement\"." }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "associatedWithBetterOutcomeFor", - "associatedWithWorseOutcomeFor" - ] - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The disease that is evaluated for outcome.", - "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the prognostic association in the Statement.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyProposition", + "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object disease outcome.", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " } }, "required": [ - "objectCondition", - "predicate", - "subjectVariant", + "proposition", "type" ], "additionalProperties": false diff --git a/schema/va-spec/base/json/VariantTherapeuticResponseStudyProposition b/schema/va-spec/base/json/VariantTherapeuticResponseStudyProposition new file mode 100644 index 0000000..e417df2 --- /dev/null +++ b/schema/va-spec/base/json/VariantTherapeuticResponseStudyProposition @@ -0,0 +1,127 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseStudyProposition", + "title": "VariantTherapeuticResponseStudyProposition", + "maturity": "draft", + "type": "object", + "description": "A Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "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 \"VariantTherapeuticResponseStudyProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantTherapeuticResponseStudyProposition", + "default": "VariantTherapeuticResponseStudyProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Statement.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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.", + "enum": [ + "predictsSensitivityTo", + "predictsResistanceTo" + ] + }, + "objectTherapeutic": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" + } + ], + "description": "A drug administration or other therapeutic procedure that the neoplasm is intended to respond to.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "conditionQualifier": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements." + }, + "alleleOriginQualifier": { + "type": "string", + "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", + "enum": [ + "germline", + "somatic", + "combined" + ] + }, + "allelePrevalenceQualifier": { + "type": "string", + "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. ", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "required": [ + "conditionQualifier", + "objectTherapeutic", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement b/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement index 72e9774..0c24bf8 100644 --- a/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement +++ b/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement @@ -136,80 +136,14 @@ "default": "VariantTherapeuticResponseStudyStatement", "description": "MUST be \"VariantTherapeuticResponseStudyStatement\"." }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Statement (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "predictsSensitivityTo", - "predictsResistanceTo" - ] - }, - "objectTherapeutic": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" - } - ], - "description": "A drug administration or other therapeutic procedure that the neoplasm is intended to respond to.", - "$comment": "The object of a Statement can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "conditionQualifier": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. ", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseStudyProposition", + "description": "Reports the conclusion of the study, which is that the subject variant is associated with therapeutic sensitivity or resistance to the object therapeutic.", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " } }, "required": [ - "conditionQualifier", - "objectTherapeutic", - "predicate", - "subjectVariant", + "proposition", "type" ], "additionalProperties": false diff --git a/schema/va-spec/base/json/XCohortAlleleFrequencyStudyResult b/schema/va-spec/base/json/XCohortAlleleFrequencyStudyResult new file mode 100644 index 0000000..f0e6339 --- /dev/null +++ b/schema/va-spec/base/json/XCohortAlleleFrequencyStudyResult @@ -0,0 +1,165 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XCohortAlleleFrequencyStudyResult", + "title": "XCohortAlleleFrequencyStudyResult", + "maturity": "draft", + "type": "object", + "description": "A StudyResult that reports measures related to the frequency of an Allele in a cohort", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "ancillaryResults": { + "maturity": "draft", + "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", + "type": "object", + "additionalProperties": true + }, + "qualityMeasures": { + "maturity": "draft", + "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", + "type": "object", + "additionalProperties": true + }, + "type": { + "type": "string", + "const": "CohortAlleleFrequencyStudyResult", + "default": "CohortAlleleFrequencyStudyResult", + "description": "MUST be \"CohortAlleleFrequencyStudyResult\"." + }, + "sourceDataSet": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/DataSet" + }, + "description": "The dataset from which the CohortAlleleFrequencyStudyResult was reported.", + "maximum": 1, + "$comment": "In most cases, a StudyResult will be generated using data from one source dataset - but it is possible multiple datasets related to a single study contain data about a particular focus that get collected into a single StudyResult instance.", + "additionalProperties": false + }, + "focusAllele": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" + }, + { + "type": "string", + "format": "uri-reference", + "description": "The Allele for which frequency results are reported." + } + ], + "description": "The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD.", + "$comment": "The 'focus' of a StudyResult is the what anchors selection of all data items and provenance information that it contains. This focus may be a single participant or subject of a study (e.g. one patient in a clinical study, or one allele in a population frequency analysis). It may be a study group defined as an experimental unit in the study (e.g. a specific treatment arm of a clinical study). Or it may be a variable defined as a unit of analysis in the study (e.g. 'exposure to nicotine' in an analysis correlating this variable with clinical outcomes)." + }, + "focusAlleleCount": { + "type": "integer", + "description": "The number of occurrences of the focusAllele in the cohort." + }, + "locusAlleleCount": { + "type": "integer", + "description": "The number of occurrences of all alleles at the locus in the cohort (sometimes referred to as \"allele number\")" + }, + "focusAlleleFrequency": { + "type": "number", + "description": "The frequency of the focusAllele in the cohort." + }, + "cohort": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyGroup", + "description": "The cohort from which the frequency was derived.", + "$comment": "For example, in a StudyResult holding allele frequency data, this attribute points to a StudyGroup object that describes characteristics of the population that the frequency data was generated from (e.g. 'East Asian', 'Female')." + }, + "subCohortFrequency": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XCohortAlleleFrequencyStudyResult" + }, + "description": "A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups.", + "$comment": "This attribute allows data creators to break down a StudyResult into finer-grained StudyResult instances with a narrower scope. For example, a StudyResult about the frequency of an allele in a global population of individuals can be broken down into separate 'component' Results about distinct subpopulations of individuals in the source data (e.g. frequency of the allele in asian vs african subpopulations, or male vs female subgroups)." + } + }, + "required": [ + "cohort", + "focusAllele", + "focusAlleleCount", + "focusAlleleFrequency", + "locusAlleleCount", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyProposition b/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyProposition new file mode 100644 index 0000000..cb8f097 --- /dev/null +++ b/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyProposition @@ -0,0 +1,115 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XExperimentalVariantFunctionalImpactStudyProposition", + "title": "XExperimentalVariantFunctionalImpactStudyProposition", + "maturity": "draft", + "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": { + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "propositionText": { + "type": "string", + "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." + }, + "type": { + "type": "string", + "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "ExperimentalVariantFunctionalImpactStudyProposition", + "default": "ExperimentalVariantFunctionalImpactStudyProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" + } + ], + "description": "A protein or genomic contextual or canonical molecular variant.", + "$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)." + }, + "predicate": { + "type": "string", + "description": "The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter.", + "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", + "const": "impactsFunctionOf" + }, + "objectSequenceFeature": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "studyContextQualifier": { + "description": "The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.", + "$comment": "The attribute is required in order to explicitly specify an assay or study context in which the reported impact was observed. It's value can be a Document object, or an IRI pointing to a document that describes the assay/study. This may be a publication, a database record, or a bespoke document.", + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "impactTypeQualifier": { + "description": "A term describing a specific type of functional impact that the variant is determined to have on the indicated sequence feature (e.g. decreased activity, dominant negative, neomorphic, reduced Ca2+ binding activity).", + "$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.", + "type": "string", + "enum": [ + "increased activity/function", + "decreased activity/function", + "novel activity/function", + "dominant negative activity/function" + ] + } + }, + "required": [ + "objectSequenceFeature", + "predicate", + "studyContextQualifier", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyResult b/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyResult new file mode 100644 index 0000000..39ac885 --- /dev/null +++ b/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyResult @@ -0,0 +1,149 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XExperimentalVariantFunctionalImpactStudyResult", + "title": "XExperimentalVariantFunctionalImpactStudyResult", + "maturity": "draft", + "type": "object", + "description": "A StudyResult that reports a functional impact score from a variant functional assay or study.", + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "componentResult": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyResult" + }, + "description": "Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) .", + "$comment": "This attribute allows data creators to break down a StudyResult into finer-grained StudyResult instances with a narrower scope. For example, a StudyResult about the frequency of an allele in a global population of individuals can be broken down into separate 'component' Results about distinct subpopulations of individuals in the source data (e.g. frequency of the allele in asian vs african subpopulations, or male vs female subgroups)." + }, + "studyGroup": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyGroup", + "description": "A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult.", + "$comment": "For example, in a StudyResult holding allele frequency data, this attribute points to a StudyGroup object that describes characteristics of the population that the frequency data was generated from (e.g. 'East Asian', 'Female')." + }, + "ancillaryResults": { + "maturity": "draft", + "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", + "type": "object", + "additionalProperties": true + }, + "qualityMeasures": { + "maturity": "draft", + "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", + "type": "object", + "additionalProperties": true + }, + "type": { + "type": "string", + "const": "ExperimentalVariantFunctionalImpactStudyResult", + "default": "ExperimentalVariantFunctionalImpactStudyResult", + "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyResult\"." + }, + "focusVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" + } + ], + "description": "The genetic variant for which a functional impact score is generated.", + "$comment": "The 'focus' of a StudyResult is the what anchors selection of all data items and provenance information that it contains. This focus may be a single participant or subject of a study (e.g. one patient in a clinical study, or one allele in a population frequency analysis). It may be a study group defined as an experimental unit in the study (e.g. a specific treatment arm of a clinical study). Or it may be a variable defined as a unit of analysis in the study (e.g. 'exposure to nicotine' in an analysis correlating this variable with clinical outcomes)." + }, + "functionalImpactScore": { + "type": "number", + "description": "The score of the variant impact measured in the assay or study." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "The assay that was performed to generate the reported functional impact score.", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "sourceDataSet": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/DataSet" + }, + "description": "The full data set that provided the reported the functional impact score. ", + "maximum": 1, + "$comment": "In most cases, a StudyResult will be generated using data from one source dataset - but it is possible multiple datasets related to a single study contain data about a particular focus that get collected into a single StudyResult instance." + } + }, + "required": [ + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyStatement b/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyStatement new file mode 100644 index 0000000..e369207 --- /dev/null +++ b/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyStatement @@ -0,0 +1,150 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XExperimentalVariantFunctionalImpactStudyStatement", + "title": "XExperimentalVariantFunctionalImpactStudyStatement", + "maturity": "draft", + "type": "object", + "description": "A statement 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": { + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "derivedFrom": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "direction": { + "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", + "type": "string", + "enum": [ + "supports", + "neutral", + "disputes" + ] + }, + "strength": { + "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + "score": { + "type": "number", + "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." + }, + "statementText": { + "type": "string", + "description": "A natural-language expression of what a Statement asserts to be true.", + "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." + }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, + "hasEvidenceLines": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" + }, + "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", + "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." + }, + "type": { + "type": "string", + "const": "ExperimentalVariantFunctionalImpactStudyStatement", + "default": "ExperimentalVariantFunctionalImpactStudyStatement", + "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyStatement\"." + }, + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XExperimentalVariantFunctionalImpactStudyProposition", + "description": "The proposition for which the study provides evidence - that the subject variant impacts the function of the object sequence feature.", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " + } + }, + "required": [ + "proposition", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantDiagnosticStudyProposition b/schema/va-spec/base/json/XVariantDiagnosticStudyProposition new file mode 100644 index 0000000..56a00f5 --- /dev/null +++ b/schema/va-spec/base/json/XVariantDiagnosticStudyProposition @@ -0,0 +1,115 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantDiagnosticStudyProposition", + "title": "XVariantDiagnosticStudyProposition", + "type": "object", + "maturity": "draft", + "description": "A Proposition reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "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 \"VariantDiagnosticStudyProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantDiagnosticStudyProposition", + "default": "VariantDiagnosticStudyProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Proposition.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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.", + "enum": [ + "isDiagnosticInclusionCriterionFor", + "isDiagnosticExclusionCriterionFor" + ] + }, + "objectCondition": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "The disease that is evaluated for diagnosis.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "alleleOriginQualifier": { + "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", + "type": "string", + "enum": [ + "germline", + "somatic", + "combined" + ] + }, + "allelePrevalenceQualifier": { + "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", + "type": "string", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Proposition.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "required": [ + "objectCondition", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantDiagnosticStudyStatement b/schema/va-spec/base/json/XVariantDiagnosticStudyStatement new file mode 100644 index 0000000..e96b791 --- /dev/null +++ b/schema/va-spec/base/json/XVariantDiagnosticStudyStatement @@ -0,0 +1,150 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantDiagnosticStudyStatement", + "title": "XVariantDiagnosticStudyStatement", + "type": "object", + "maturity": "draft", + "description": "A Statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results.", + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "derivedFrom": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "direction": { + "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", + "type": "string", + "enum": [ + "supports", + "neutral", + "disputes" + ] + }, + "strength": { + "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + "score": { + "type": "number", + "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." + }, + "statementText": { + "type": "string", + "description": "A natural-language expression of what a Statement asserts to be true.", + "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." + }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, + "hasEvidenceLines": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" + }, + "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", + "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." + }, + "type": { + "type": "string", + "const": "VariantDiagnosticStudyStatement", + "default": "VariantDiagnosticStudyStatement", + "description": "MUST be \"VariantDiagnosticStudyStatement\"." + }, + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantDiagnosticStudyProposition", + "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object disease. ", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " + } + }, + "required": [ + "proposition", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantOncogenicityStudyProposition b/schema/va-spec/base/json/XVariantOncogenicityStudyProposition new file mode 100644 index 0000000..ea93602 --- /dev/null +++ b/schema/va-spec/base/json/XVariantOncogenicityStudyProposition @@ -0,0 +1,116 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantOncogenicityStudyProposition", + "title": "XVariantOncogenicityStudyProposition", + "maturity": "draft", + "type": "object", + "description": "A Proposition reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "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 \"VariantOncogenicityStudyProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantOncogenicityStudyProposition", + "default": "VariantOncogenicityStudyProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Proposition.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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.", + "enum": [ + "isOncogenicFor", + "isProtectiveFor", + "isPredisposingFor" + ] + }, + "objectTumorType": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "The tumor type for which the variant impact is evaluated.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "alleleOriginQualifier": { + "type": "string", + "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", + "enum": [ + "germline", + "somatic", + "combined" + ] + }, + "allelePrevalenceQualifier": { + "type": "string", + "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Proposition.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "required": [ + "objectTumorType", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantOncogenicityStudyStatement b/schema/va-spec/base/json/XVariantOncogenicityStudyStatement new file mode 100644 index 0000000..7cbfebf --- /dev/null +++ b/schema/va-spec/base/json/XVariantOncogenicityStudyStatement @@ -0,0 +1,150 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantOncogenicityStudyStatement", + "title": "XVariantOncogenicityStudyStatement", + "maturity": "draft", + "type": "object", + "description": "A Statement reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results.", + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "derivedFrom": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "direction": { + "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", + "type": "string", + "enum": [ + "supports", + "neutral", + "disputes" + ] + }, + "strength": { + "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + "score": { + "type": "number", + "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." + }, + "statementText": { + "type": "string", + "description": "A natural-language expression of what a Statement asserts to be true.", + "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." + }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, + "hasEvidenceLines": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" + }, + "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", + "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." + }, + "type": { + "type": "string", + "const": "VariantOncogenicityStudyStatement", + "default": "VariantOncogenicityStudyStatement", + "description": "MUST be \"VariantOncogenicityStudyStatement\"." + }, + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantOncogenicityStudyProposition", + "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object tumor type.", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " + } + }, + "required": [ + "proposition", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPathogenicityEvidenceLine b/schema/va-spec/base/json/XVariantPathogenicityEvidenceLine new file mode 100644 index 0000000..92a178d --- /dev/null +++ b/schema/va-spec/base/json/XVariantPathogenicityEvidenceLine @@ -0,0 +1,139 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityEvidenceLine", + "title": "XVariantPathogenicityEvidenceLine", + "maturity": "draft", + "type": "object", + "description": "An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. ", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "derivedFrom": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "scoreOfEvidenceProvided": { + "type": "number", + "description": "A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value." + }, + "type": { + "type": "string", + "const": "VariantPathogenicityEvidenceLine", + "default": "VariantPathogenicityEvidenceLine", + "description": "MUST be \"VariantPathogenicityEvidenceLine\"." + }, + "hasEvidenceItems": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result).", + "$comment": "A given Evidence Line may be supported by one or many individual evidence items. What matters is that all evidence items in a given Evidence Line get collectively assessed and assigned direction and strength as a single argument for or against a target proposition.\nDifferent types and scales of information entity can serve as evidence (experimental measurements or observations, data tables or figures, images, prior assertions, etc.) Only when assessed as evidence do we consider the information to be an 'Evidence Item'. For example, a piece of population frequency data about BRCA2 c.8023A>G becomes an Evidence Item when it is assessed for the support it may offer for a target proposition (e.g. the prospect of the variant\u2019s pathogenicity)." + }, + "directionOfEvidenceProvided": { + "type": "string", + "enum": [ + "supports", + "neutral", + "disputes" + ], + "description": "The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral)" + }, + "strengthOfEvidenceProvided": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute.", + "$comment": "Values of this attribute can be defined by for a given profile based on domain/application needs, but should be framed in qualitative terms (e.g. 'strong', 'moderate', 'weak'). The 'scoreOfEvidenceProvided' attribute can be used to report quantitative assessments of evidence provided.", + "type": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "targetProposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityProposition", + "description": "The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). " + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant.", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + } + }, + "required": [ + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPathogenicityProposition b/schema/va-spec/base/json/XVariantPathogenicityProposition new file mode 100644 index 0000000..58658c5 --- /dev/null +++ b/schema/va-spec/base/json/XVariantPathogenicityProposition @@ -0,0 +1,119 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityProposition", + "title": "XVariantPathogenicityProposition", + "maturity": "draft", + "type": "object", + "description": "A proposition describing the role of a variant in causing an inherited condition.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "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\"", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantPathogenicityProposition", + "default": "VariantPathogenicityProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Statement.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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": "isCausalFor" + }, + "objectCondition": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "The Condition for which the variant impact is stated.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "penetranceQualifier": { + "type": "string", + "enum": [ + "high", + "low", + "risk allele" + ], + "description": "Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. " + }, + "modeOfInheritanceQualifier": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding" + }, + "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify." + }, + "geneContextQualifier": { + "description": "Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).", + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + } + }, + "required": [ + "objectCondition", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPathogenicityStatement b/schema/va-spec/base/json/XVariantPathogenicityStatement new file mode 100644 index 0000000..63cc4c9 --- /dev/null +++ b/schema/va-spec/base/json/XVariantPathogenicityStatement @@ -0,0 +1,150 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityStatement", + "title": "XVariantPathogenicityStatement", + "type": "object", + "maturity": "draft", + "description": "A Statement describing the role of a variant in causing an inherited condition.", + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "derivedFrom": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "direction": { + "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", + "type": "string", + "enum": [ + "supports", + "neutral", + "disputes" + ] + }, + "strength": { + "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + "score": { + "type": "number", + "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." + }, + "statementText": { + "type": "string", + "description": "A natural-language expression of what a Statement asserts to be true.", + "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." + }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, + "hasEvidenceLines": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" + }, + "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", + "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." + }, + "type": { + "type": "string", + "const": "VariantPathogenicityStatement", + "default": "VariantPathogenicityStatement", + "description": "MUST be \"VariantPathogenicityStatement\"." + }, + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityProposition", + "description": "The proposition that the subject variant is associated with the object disease.", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " + } + }, + "required": [ + "proposition", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPrognosticStudyProposition b/schema/va-spec/base/json/XVariantPrognosticStudyProposition new file mode 100644 index 0000000..dfd0497 --- /dev/null +++ b/schema/va-spec/base/json/XVariantPrognosticStudyProposition @@ -0,0 +1,115 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPrognosticStudyProposition", + "title": "XVariantPrognosticStudyProposition", + "type": "object", + "maturity": "draft", + "description": "A Proposition reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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." + }, + "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 \"VariantPrognosticStudyProposition\".", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "VariantPrognosticStudyProposition", + "default": "VariantPrognosticStudyProposition" + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Proposition.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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.", + "enum": [ + "associatedWithBetterOutcomeFor", + "associatedWithWorseOutcomeFor" + ] + }, + "objectCondition": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "The disease that is evaluated for outcome.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "alleleOriginQualifier": { + "type": "string", + "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", + "enum": [ + "germline", + "somatic", + "combined" + ] + }, + "allelePrevalenceQualifier": { + "type": "string", + "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the prognostic association in the Proposition.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "required": [ + "objectCondition", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPrognosticStudyStatement b/schema/va-spec/base/json/XVariantPrognosticStudyStatement new file mode 100644 index 0000000..f4cb933 --- /dev/null +++ b/schema/va-spec/base/json/XVariantPrognosticStudyStatement @@ -0,0 +1,150 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPrognosticStudyStatement", + "title": "XVariantPrognosticStudyStatement", + "type": "object", + "maturity": "draft", + "description": "A Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results.", + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "derivedFrom": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "direction": { + "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", + "type": "string", + "enum": [ + "supports", + "neutral", + "disputes" + ] + }, + "strength": { + "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + "score": { + "type": "number", + "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." + }, + "statementText": { + "type": "string", + "description": "A natural-language expression of what a Statement asserts to be true.", + "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." + }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, + "hasEvidenceLines": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" + }, + "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", + "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." + }, + "type": { + "type": "string", + "const": "VariantPrognosticStudyStatement", + "default": "VariantPrognosticStudyStatement", + "description": "MUST be \"VariantPrognosticStudyStatement\"." + }, + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantPrognosticStudyProposition", + "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object disease outcome.", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " + } + }, + "required": [ + "proposition", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantTherapeuticResponseStudyProposition b/schema/va-spec/base/json/XVariantTherapeuticResponseStudyProposition new file mode 100644 index 0000000..8b1b74d --- /dev/null +++ b/schema/va-spec/base/json/XVariantTherapeuticResponseStudyProposition @@ -0,0 +1,127 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantTherapeuticResponseStudyProposition", + "title": "XVariantTherapeuticResponseStudyProposition", + "maturity": "draft", + "type": "object", + "description": "A Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results.", + "properties": { + "id": { + "type": "string", + "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", + "$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." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" + }, + "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", + "$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 \"Proposition\"", + "$comment": "MUST be the label of a concrete class from the data model.", + "const": "Proposition", + "default": "Proposition" + }, + "propositionText": { + "type": "string", + "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." + }, + "subjectVariant": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + } + ], + "description": "A variant that is the subject of the Statement.", + "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." + }, + "predicate": { + "type": "string", + "description": "The relationship declared to hold between the subject and the object of the Statement.", + "$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.", + "enum": [ + "predictsSensitivityTo", + "predictsResistanceTo" + ] + }, + "objectTherapeutic": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" + } + ], + "description": "A drug administration or other therapeutic procedure that the neoplasm is intended to respond to.", + "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." + }, + "conditionQualifier": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + }, + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" + } + ], + "description": "Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements." + }, + "alleleOriginQualifier": { + "type": "string", + "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", + "enum": [ + "germline", + "somatic", + "combined" + ] + }, + "allelePrevalenceQualifier": { + "type": "string", + "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", + "enum": [ + "rare", + "common" + ] + }, + "geneContextQualifier": { + "description": "Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. ", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + } + }, + "required": [ + "conditionQualifier", + "objectTherapeutic", + "predicate", + "subjectVariant", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantTherapeuticResponseStudyStatement b/schema/va-spec/base/json/XVariantTherapeuticResponseStudyStatement new file mode 100644 index 0000000..2c627d1 --- /dev/null +++ b/schema/va-spec/base/json/XVariantTherapeuticResponseStudyStatement @@ -0,0 +1,150 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantTherapeuticResponseStudyStatement", + "title": "XVariantTherapeuticResponseStudyStatement", + "maturity": "draft", + "type": "object", + "description": "A Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results.", + "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.", + "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." + }, + "label": { + "type": "string", + "description": "A primary name for the entity." + }, + "description": { + "type": "string", + "description": "A free-text description of the Entity." + }, + "alternativeLabels": { + "type": "array", + "ordered": false, + "items": { + "type": "string" + }, + "description": "Alternative name(s) for the Entity." + }, + "extensions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/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.", + "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." + }, + "specifiedBy": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ], + "description": "A specification that describes all or part of the process that led to creation of the Information Entity", + "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + }, + "contributions": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" + }, + "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", + "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." + }, + "reportedIn": { + "type": "array", + "ordered": false, + "items": { + "oneOf": [ + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" + }, + { + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + } + ] + }, + "description": "A document in which the the Information Entity is reported." + }, + "dateAuthored": { + "type": "string", + "format": "datetime", + "description": "Indicates when the information content expressed in the Information Entity was generated.", + "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." + }, + "derivedFrom": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + }, + "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." + }, + "recordMetadata": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", + "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", + "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." + }, + "direction": { + "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", + "type": "string", + "enum": [ + "supports", + "neutral", + "disputes" + ] + }, + "strength": { + "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + }, + "score": { + "type": "number", + "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", + "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." + }, + "statementText": { + "type": "string", + "description": "A natural-language expression of what a Statement asserts to be true.", + "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." + }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + }, + "hasEvidenceLines": { + "type": "array", + "ordered": false, + "items": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" + }, + "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", + "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." + }, + "type": { + "type": "string", + "const": "VariantTherapeuticResponseStudyStatement", + "default": "VariantTherapeuticResponseStudyStatement", + "description": "MUST be \"VariantTherapeuticResponseStudyStatement\"." + }, + "proposition": { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantTherapeuticResponseStudyProposition", + "description": "Reports the conclusion of the study, which is that the subject variant is associated with therapeutic sensitivity or resistance to the object therapeutic. ", + "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " + } + }, + "required": [ + "proposition", + "type" + ], + "additionalProperties": false +} \ No newline at end of file diff --git a/schema/va-spec/base/oncogenicity-study-proposition-profile-source.yaml b/schema/va-spec/base/oncogenicity-study-proposition-profile-source.yaml new file mode 100644 index 0000000..6f689c8 --- /dev/null +++ b/schema/va-spec/base/oncogenicity-study-proposition-profile-source.yaml @@ -0,0 +1,73 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/oncogenicity-study-proposition-profile-source.yaml" +title: Variant Oncogenicity Study Proposition Standard Profile +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Oncogenicity Study Proposition + VariantOncogenicityStudyProposition: + inherits: gks-core:Proposition + maturity: draft + type: object + description: >- + A Proposition reporting a conclusion from a single study that supports or refutes a + variant's effect on oncogenesis for a specific tumor type - based on interpretation + of the study's results. + properties: + type: + extends: type + const: "VariantOncogenicityStudyProposition" + default: "VariantOncogenicityStudyProposition" + description: MUST be "VariantOncogenicityStudyProposition". + 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: + - isOncogenicFor + - isProtectiveFor + - isPredisposingFor + objectTumorType: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + description: >- + The tumor type for which the variant impact is evaluated. + alleleOriginQualifier: + type: string + description: >- + Reports whether the proposition should be interpreted in the context of an inherited + (germline) variant, an acquired (somatic) mutation, or both (combined). + enum: + - germline + - somatic + - combined + allelePrevalenceQualifier: + type: string + description: >- + Reports whether the proposition should be interpreted in the context of the variant + being rare or common. + enum: + - rare + - common + geneContextQualifier: + description: >- + Reports a gene impacted by the variant, which may contribute to the oncogenic + role in the Proposition. + $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + required: + - subjectVariant + - predicate + - objectTumorType \ No newline at end of file diff --git a/schema/va-spec/base/oncogenicity-study-statement-profile-source.yaml b/schema/va-spec/base/oncogenicity-study-statement-profile-source.yaml index f66e600..2f0b8d8 100644 --- a/schema/va-spec/base/oncogenicity-study-statement-profile-source.yaml +++ b/schema/va-spec/base/oncogenicity-study-statement-profile-source.yaml @@ -4,12 +4,9 @@ title: Variant Oncogenicity Study Statement Standard Profile strict: true imports: - domain-entities: ./domain-entities-source.yaml - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml - vrs: ../../vrs/vrs-source.yaml + va-onc-prop: ./oncogenicity-study-proposition-profile-source.yaml gks-core: ../../gks-core/gks-core-source.yaml - $defs: # Variant Oncogenicity Study Statement VariantOncogenicityStudyStatement: @@ -26,49 +23,11 @@ $defs: const: "VariantOncogenicityStudyStatement" default: "VariantOncogenicityStudyStatement" description: MUST be "VariantOncogenicityStudyStatement". - 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: - - isOncogenicFor - - isProtectiveFor - - isPredisposingFor - objectTumorType: - extends: object - oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - description: >- - The tumor type for which the variant impact is evaluated. - alleleOriginQualifier: - type: string - description: >- - Reports whether the statement should be interpreted in the context of an inherited - (germline) variant, an acquired (somatic) mutation, or both (combined). - enum: - - germline - - somatic - - combined - allelePrevalenceQualifier: - type: string - description: >- - Reports whether the statement should be interpreted in the context of the variant - being rare or common. - enum: - - rare - - common - geneContextQualifier: + proposition: + extends: proposition + $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantOncogenicityStudyProposition" description: >- - Reports a gene impacted by the variant, which may contribute to the oncogenic - role in the Statement. - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + The proposition for which the study provides evidence - that the subject variant + is associated with the object tumor type. required: - - subjectVariant - - predicate - - objectTumorType \ No newline at end of file + - proposition \ No newline at end of file diff --git a/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml b/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml index 7f4552b..b248c76 100644 --- a/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml +++ b/schema/va-spec/base/pathogenicity-evidence-line-profile-source.yaml @@ -4,14 +4,15 @@ title: Variant Pathogenicity EvidenceLine Standard Profile strict: true imports: + va-path-prop: ./pathogenicity-proposition-profile-source.yaml domain-entities: ./domain-entities-source.yaml cat-vrs: ../../cat-vrs/cat-vrs-source.yaml vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml $defs: - # Pathogenicity Evidence Line - PathogenicityEvidenceLine: + # Variant Pathogenicity Evidence Line + VariantPathogenicityEvidenceLine: inherits: gks-core:EvidenceLine maturity: draft type: object @@ -21,9 +22,9 @@ $defs: properties: type: extends: type - const: "PathogenicityEvidenceLine" - default: "PathogenicityEvidenceLine" - description: MUST be "PathogenicityEvidenceLine". + const: "VariantPathogenicityEvidenceLine" + default: "VariantPathogenicityEvidenceLine" + description: MUST be "VariantPathogenicityEvidenceLine". hasEvidenceItems: extends: hasEvidenceItems type: array @@ -50,7 +51,7 @@ $defs: indicated by the directionOfEvidenceProvided attribute. targetProposition: extends: targetProposition - $ref: "#/$defs/VariantPathogenicityProposition" + $ref: "/ga4gh/schema/va-path-prop/1.x/base/json/VariantPathogenicityProposition" description: >- The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant @@ -61,61 +62,3 @@ $defs: A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant. - # Variant Pathogenicity Proposition - VariantPathogenicityProposition: - inherits: gks-core:Proposition - maturity: draft - type: object - description: >- - A proposition describing the role of a variant in causing an inherited condition. - properties: - type: - extends: type - 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 - objectCondition: - extends: object - oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: The :ref:`Condition` for which the variant impact is stated. - penetranceQualifier: - type: string - enum: - - high - - low - - risk allele - description: >- - Reports the penetrance of the pathogenic effect - i.e. the extent to which the - variant impact is expressed by individuals carrying it as a measure of the - proportion of carriers exhibiting the condition. - modeOfInheritanceQualifier: - type: array - ordered: false - items: - $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" - description: >- - Reports a pattern of inheritance expected for the pathogenic effect of the variant. - Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. - geneContextQualifier: - description: >- - Reports the gene through which the pathogenic effect asserted for the variant is mediated - (i.e. it is the variant's impact on this gene that is responsible for causing the condition). - oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - required: - - subjectVariant - - predicate - - objectCondition diff --git a/schema/va-spec/base/pathogenicity-proposition-profile-source.yaml b/schema/va-spec/base/pathogenicity-proposition-profile-source.yaml new file mode 100644 index 0000000..e4ae286 --- /dev/null +++ b/schema/va-spec/base/pathogenicity-proposition-profile-source.yaml @@ -0,0 +1,70 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/pathogenicity-proposition-profile-source.yaml" +title: Variant Pathogenicity Proposition Standard Profile +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Pathogenicity Proposition + VariantPathogenicityProposition: + inherits: gks-core:Proposition + maturity: draft + type: object + description: >- + A proposition describing the role of a variant in causing an inherited condition. + properties: + type: + extends: type + 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 + objectCondition: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The :ref:`Condition` for which the variant impact is stated. + penetranceQualifier: + type: string + enum: + - high + - low + - risk allele + description: >- + Reports the penetrance of the pathogenic effect - i.e. the extent to which the + variant impact is expressed by individuals carrying it as a measure of the + proportion of carriers exhibiting the condition. + modeOfInheritanceQualifier: + type: array + ordered: false + items: + $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" + description: >- + Reports a pattern of inheritance expected for the pathogenic effect of the variant. + Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. + geneContextQualifier: + description: >- + Reports the gene through which the pathogenic effect asserted for the variant is mediated + (i.e. it is the variant's impact on this gene that is responsible for causing the condition). + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + required: + - subjectVariant + - predicate + - objectCondition diff --git a/schema/va-spec/base/pathogenicity-statement-profile-source.yaml b/schema/va-spec/base/pathogenicity-statement-profile-source.yaml index d67b712..89f44b5 100644 --- a/schema/va-spec/base/pathogenicity-statement-profile-source.yaml +++ b/schema/va-spec/base/pathogenicity-statement-profile-source.yaml @@ -4,9 +4,7 @@ title: Variant Pathogenicity Statement Standard Profile strict: true imports: - domain-entities: ./domain-entities-source.yaml - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml - vrs: ../../vrs/vrs-source.yaml + va-path-prop: ./pathogenicity-proposition-profile-source.yaml gks-core: ../../gks-core/gks-core-source.yaml $defs: @@ -23,48 +21,10 @@ $defs: const: "VariantPathogenicityStatement" default: "VariantPathogenicityStatement" description: MUST be "VariantPathogenicityStatement". - 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 - objectCondition: - extends: object - oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: The :ref:`Condition` for which the variant impact is stated. - penetranceQualifier: - type: string - enum: - - high - - low - - risk allele + proposition: + extends: proposition + $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition" description: >- - Reports the penetrance of the pathogenic effect - i.e. the extent to which the - variant impact is expressed by individuals carrying it as a measure of the - proportion of carriers exhibiting the condition. - modeOfInheritanceQualifier: - type: array - ordered: false - items: - $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" - description: >- - Reports a pattern of inheritance expected for the pathogenic effect of the variant. - Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. - geneContextQualifier: - description: >- - Reports the gene through which the pathogenic effect asserted for the variant is mediated - (i.e. it is the variant's impact on this gene that is responsible for causing the condition). - oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + The proposition that the subject variant is associated with the object disease. required: - - subjectVariant - - predicate - - objectCondition + - proposition diff --git a/schema/va-spec/base/prognostic-study-proposition-profile-source.yaml b/schema/va-spec/base/prognostic-study-proposition-profile-source.yaml new file mode 100644 index 0000000..99699db --- /dev/null +++ b/schema/va-spec/base/prognostic-study-proposition-profile-source.yaml @@ -0,0 +1,71 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/prognostic-study-proposition-profile-source.yaml" +title: Variant Prognostic Study Proposition Standard Profile +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Prognostic Study Proposition + VariantPrognosticStudyProposition: + inherits: gks-core:Proposition + type: object + maturity: draft + description: >- + A Proposition reporting a conclusion from a single study about whether a variant + is associated with an improved or worse outcome for a disease - based on + interpretation of the study's results. + properties: + type: + extends: type + const: "VariantPrognosticStudyProposition" + default: "VariantPrognosticStudyProposition" + description: MUST be "VariantPrognosticStudyProposition". + 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: + - associatedWithBetterOutcomeFor + - associatedWithWorseOutcomeFor + objectCondition: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The disease that is evaluated for outcome. + alleleOriginQualifier: + type: string + description: >- + Reports whether the proposition should be interpreted in the context of an inherited + (germline) variant, an acquired (somatic) mutation, or both (combined). + enum: + - germline + - somatic + - combined + allelePrevalenceQualifier: + type: string + description: >- + Reports whether the proposition should be interpreted in the context of the variant + being rare or common. + enum: + - rare + - common + geneContextQualifier: + description: >- + Reports a gene impacted by the variant, which may contribute to the + prognostic association in the Proposition. + $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + required: + - subjectVariant + - predicate + - objectCondition diff --git a/schema/va-spec/base/prognostic-study-statement-profile-source.yaml b/schema/va-spec/base/prognostic-study-statement-profile-source.yaml index 0ffd3a0..6cca9e2 100644 --- a/schema/va-spec/base/prognostic-study-statement-profile-source.yaml +++ b/schema/va-spec/base/prognostic-study-statement-profile-source.yaml @@ -4,9 +4,7 @@ title: Variant Prognostic Study Statement Standard Profile strict: true imports: - domain-entities: ./domain-entities-source.yaml - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml - vrs: ../../vrs/vrs-source.yaml + va-prog-prop: ./prognostic-study-proposition-profile-source.yaml gks-core: ../../gks-core/gks-core-source.yaml $defs: @@ -25,47 +23,11 @@ $defs: const: "VariantPrognosticStudyStatement" default: "VariantPrognosticStudyStatement" description: MUST be "VariantPrognosticStudyStatement". - 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: - - associatedWithBetterOutcomeFor - - associatedWithWorseOutcomeFor - objectCondition: - extends: object - oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - description: The disease that is evaluated for outcome. - alleleOriginQualifier: - type: string + proposition: + extends: proposition + $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyProposition" description: >- - Reports whether the statement should be interpreted in the context of an inherited - (germline) variant, an acquired (somatic) mutation, or both (combined). - enum: - - germline - - somatic - - combined - allelePrevalenceQualifier: - type: string - description: >- - Reports whether the statement should be interpreted in the context of the variant - being rare or common. - enum: - - rare - - common - geneContextQualifier: - description: >- - Reports a gene impacted by the variant, which may contribute to the - prognostic association in the Statement. - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + The proposition for which the study provides evidence - that the subject variant + is associated with the object disease outcome. required: - - subjectVariant - - predicate - - objectCondition + - proposition diff --git a/schema/va-spec/base/therapeutic-response-study-proposition-profile-source.yaml b/schema/va-spec/base/therapeutic-response-study-proposition-profile-source.yaml new file mode 100644 index 0000000..daa1954 --- /dev/null +++ b/schema/va-spec/base/therapeutic-response-study-proposition-profile-source.yaml @@ -0,0 +1,81 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/therapeutic-response-study-proposition-profile-source.yaml" +title: Variant Therapeutic Response Study Proposition Standard Profile +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Therapeutic Response Study Proposition + VariantTherapeuticResponseStudyProposition: + inherits: gks-core:Proposition + maturity: draft + type: object + description: >- + A Statement reporting a conclusion from a single study about the role of a variant + in modulating the response of a neoplasm to drug administration or other therapeutic + procedures - based on interpretation of the study's results. + properties: + type: + extends: type + const: "VariantTherapeuticResponseStudyProposition" + default: "VariantTherapeuticResponseStudyProposition" + description: MUST be "VariantTherapeuticResponseStudyProposition". + 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: + - predictsSensitivityTo + - predictsResistanceTo + objectTherapeutic: + description: A drug administration or other therapeutic procedure that the neoplasm + is intended to respond to. + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + conditionQualifier: + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: >- + Reports the disease context in which the variant's association with therapeutic + sensitivity or resistance is evaluated. Note that this is a required qualifier in + therapeutic response statements. + alleleOriginQualifier: + type: string + description: >- + Reports whether the statement should be interpreted in the context of an inherited + (germline) variant, an acquired (somatic) mutation, or both (combined). + enum: + - germline + - somatic + - combined + allelePrevalenceQualifier: + type: string + description: >- + Reports whether the statement should be interpreted in the context of the variant + being rare or common. + enum: + - rare + - common + geneContextQualifier: + description: > + Reports a gene impacted by the variant, which may contribute to the therapeutic + 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/base/therapeutic-response-study-statement-profile-source.yaml b/schema/va-spec/base/therapeutic-response-study-statement-profile-source.yaml index 405e882..1c1275e 100644 --- a/schema/va-spec/base/therapeutic-response-study-statement-profile-source.yaml +++ b/schema/va-spec/base/therapeutic-response-study-statement-profile-source.yaml @@ -4,9 +4,7 @@ title: Variant Therapeutic Response Study Statement Standard Profile strict: true imports: - domain-entities: ./domain-entities-source.yaml - cat-vrs: ../../cat-vrs/cat-vrs-source.yaml - vrs: ../../vrs/vrs-source.yaml + va-tr-prop: ./therapeutic-response-study-proposition-profile-source.yaml gks-core: ../../gks-core/gks-core-source.yaml $defs: @@ -25,57 +23,11 @@ $defs: const: "VariantTherapeuticResponseStudyStatement" default: "VariantTherapeuticResponseStudyStatement" description: MUST be "VariantTherapeuticResponseStudyStatement". - 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: - - predictsSensitivityTo - - predictsResistanceTo - objectTherapeutic: - description: A drug administration or other therapeutic procedure that the neoplasm - is intended to respond to. - extends: object - oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - conditionQualifier: - oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + proposition: + extends: proposition + # LB: should this be a oneOf and include the option for an IRI reference? + $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseStudyProposition" description: >- - Reports the disease context in which the variant's association with therapeutic - sensitivity or resistance is evaluated. Note that this is a required qualifier in - therapeutic response statements. - alleleOriginQualifier: - type: string - description: >- - Reports whether the statement should be interpreted in the context of an inherited - (germline) variant, an acquired (somatic) mutation, or both (combined). - enum: - - germline - - somatic - - combined - allelePrevalenceQualifier: - type: string - description: >- - Reports whether the statement should be interpreted in the context of the variant - being rare or common. - enum: - - rare - - common - geneContextQualifier: - description: > - Reports a gene impacted by the variant, which may contribute to the therapeutic - sensitivity or resistance reported in the Statement. - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - required: - - subjectVariant - - predicate - - objectTherapeutic - - conditionQualifier + Reports the conclusion of the study, which is that the subject variant is + associated with therapeutic sensitivity or resistance to the object therapeutic. + diff --git a/schema/va-spec/base/x-cohort-allele-frequency-profile-source.yaml b/schema/va-spec/base/x-cohort-allele-frequency-profile-source.yaml new file mode 100644 index 0000000..4fbadd3 --- /dev/null +++ b/schema/va-spec/base/x-cohort-allele-frequency-profile-source.yaml @@ -0,0 +1,61 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/x-cohort-allele-frequency-study-result-profile-source.yaml" +title: Cohort Allele Frequency Base Profiles +strict: true + +imports: + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + XCohortAlleleFrequencyStudyResult: + inherits: gks-core:StudyResult + maturity: draft + type: object + description: >- + A StudyResult that reports measures related to the frequency of an Allele in a cohort + properties: + type: + extends: type + const: "CohortAlleleFrequencyStudyResult" + default: "CohortAlleleFrequencyStudyResult" + description: MUST be "CohortAlleleFrequencyStudyResult". + sourceDataSet: + extends: sourceDataSet + description: The dataset from which the CohortAlleleFrequencyStudyResult was reported. + additionalProperties: false + focusAllele: + extends: focus + oneOf: + - $ref: "/ga4gh/schema/vrs/2.x/json/Allele" + - type: string + format: uri-reference + description: The Allele for which frequency results are reported. + focusAlleleCount: + type: integer + description: The number of occurrences of the focusAllele in the cohort. + locusAlleleCount: + type: integer + description: >- + The number of occurrences of all alleles at the locus in the cohort + (sometimes referred to as "allele number") + focusAlleleFrequency: + type: number + description: The frequency of the focusAllele in the cohort. + cohort: + extends: studyGroup + description: The cohort from which the frequency was derived. + subCohortFrequency: + extends: componentResult + description: >- + A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. + This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. + This enables, for example, the description of different ancestry groups and sexes among those ancestry groups. + items: + $ref: "#/$defs/XCohortAlleleFrequencyStudyResult" + required: + - focusAllele + - focusAlleleCount + - locusAlleleCount + - focusAlleleFrequency + - cohort diff --git a/schema/va-spec/base/x-experimental-variant-functional-impact-profile-source.yaml b/schema/va-spec/base/x-experimental-variant-functional-impact-profile-source.yaml new file mode 100644 index 0000000..dbfba22 --- /dev/null +++ b/schema/va-spec/base/x-experimental-variant-functional-impact-profile-source.yaml @@ -0,0 +1,152 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/x-experimental-variant-functional-impact-profile-source.yaml" +title: Experimental Variant Functional Impact Base Profiles +strict: true + +imports: + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + XExperimentalVariantFunctionalImpactStudyProposition: + inherits: gks-core:Proposition + maturity: draft + 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: + type: + extends: type + const: "ExperimentalVariantFunctionalImpactStudyProposition" + default: "ExperimentalVariantFunctionalImpactStudyProposition" + description: MUST be "ExperimentalVariantFunctionalImpactStudyProposition". + 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: >- + The relationship this Proposition describes between the subject Variant + and object Sequence Feature whose function it may alter. + const: impactsFunctionOf + objectSequenceFeature: + extends: object + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: "/ga4gh/schema/gks-core/1.x/MappableConcept" # See https://github.com/ga4gh/gks-common/pull/77 - proposes a SequenceFeature domain entity class + description: >- + The sequence feature (typically a gene or gene product) on whose function the impact + of the subject variant is assessed. + studyContextQualifier: + description: >- + The assay in which the reported variant functional impact was determined - + providing a specific experimental context in which this effect is asserted to hold. + $comment: >- + The attribute is required in order to explicitly specify an assay or study context in + which the reported impact was observed. It's value can be a Document object, or an IRI + pointing to a document that describes the assay/study. This may be a publication, a + database record, or a bespoke document. + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/Document" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + impactTypeQualifier: # This qualifier allows more specific types of impacts to be reported - so the profile supports implementations like CIViC, ClinGen, and I think even some MAVE data. + 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. + + # 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 + + XExperimentalVariantFunctionalImpactStudyResult: + inherits: gks-core:StudyResult + maturity: draft + type: object + description: >- + A StudyResult that reports a functional impact score from a variant functional assay or study. + properties: + type: + extends: type + const: "ExperimentalVariantFunctionalImpactStudyResult" + default: "ExperimentalVariantFunctionalImpactStudyResult" + description: MUST be "ExperimentalVariantFunctionalImpactStudyResult". + focusVariant: + extends: focus + oneOf: + - $ref: "/ga4gh/schema/vrs/2.x/json/MolecularVariation" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The genetic variant for which a functional impact score is generated. + functionalImpactScore: + type: number + description: The score of the variant impact measured in the assay or study. + specifiedBy: + extends: specifiedBy + description: >- + The assay that was performed to generate the reported functional impact score. + sourceDataSet: + extends: sourceDataSet + description: >- + The full data set that provided the reported the functional impact score. + + XExperimentalVariantFunctionalImpactStudyStatement: + inherits: gks-core:Statement + maturity: draft + type: object + description: >- + A statement 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: + type: + extends: type + const: "ExperimentalVariantFunctionalImpactStudyStatement" + default: "ExperimentalVariantFunctionalImpactStudyStatement" + description: MUST be "ExperimentalVariantFunctionalImpactStudyStatement". + proposition: + extends: proposition + $ref: "#/$defs/XExperimentalVariantFunctionalImpactStudyProposition" + description: >- + The proposition for which the study provides evidence - that the subject variant + impacts the function of the object sequence feature. + # classification: # this attribute now inherits the data type of 'MappableConcept' from the Core model (rather than simpler 'string' that was originally used) Consider need for a MappableConcept. Consider what tyeps of values would go in this attribute for a FI Statement. And what it would look like if there is no 'code' available. + # extends: classification + # description: >- + # An term or phrase summarizing the impact reported in the Statement, providing + # a functional classification of the subject variant that is familiar for a community of use. + # $comment: >- # Matt: update $comment here to reflect outcome of discussion / decisions about what would go here in a FI Statement instance. + # This is an optional attribute that can be used by data providers to provide a particular + # community of users a functional impact classification in familiar terms, + # that summarizes/complements the smeantics broken out in the SPOQ attributes of the Statement + # (e.g. to mirror established community conventions or reflect language on the data providers + # website or documentation). e.g. CIViC docs/web site uses terms like 'unaltered function', + # 'gain of function', 'neomorphic', and 'unknown', which could be reropted here. + # specifiedBy: + # extends: specifiedBy + # description: >- + # The method that specifies how the functional classification is ultimately assigned to + # the variant, based on interpretation of data from the supporting assay. May include + # information about thresholds applied on assay variant effect scores to derive the + # final classification. + required: + - proposition \ No newline at end of file diff --git a/schema/va-spec/base/x-variant-diagnostic-study-profile-source.yaml b/schema/va-spec/base/x-variant-diagnostic-study-profile-source.yaml new file mode 100644 index 0000000..f729afd --- /dev/null +++ b/schema/va-spec/base/x-variant-diagnostic-study-profile-source.yaml @@ -0,0 +1,97 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/x-variant-diagnostic-study-profile-source.yaml" +title: Variant Diagnostic Study Base Profiles +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Diagnostic Study Statement + XVariantDiagnosticStudyProposition: + inherits: gks-core:Proposition + type: object + maturity: draft + description: >- + A Proposition reporting a conclusion from a single study about whether a variant + is associated with a disease (a diagnostic inclusion criterion), or absence of a + disease (diagnostic exclusion criterion) - based on interpretation of the study's + results. + properties: + type: + extends: type + const: "VariantDiagnosticStudyProposition" + default: "VariantDiagnosticStudyProposition" + description: MUST be "VariantDiagnosticStudyProposition". + 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: + - isDiagnosticInclusionCriterionFor + - isDiagnosticExclusionCriterionFor + objectCondition: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The disease that is evaluated for diagnosis. + alleleOriginQualifier: + description: >- + Reports whether the proposition should be interpreted in the context of an inherited + (germline) variant, an acquired (somatic) mutation, or both (combined). + type: string + enum: + - germline + - somatic + - combined + allelePrevalenceQualifier: + description: >- + Reports whether the proposition should be interpreted in the context of the variant + being rare or common. + type: string + enum: + - rare + - common + geneContextQualifier: + description: >- + Reports a gene impacted by the variant, which may contribute to the + diagnostic association in the Proposition. + $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + required: + - subjectVariant + - predicate + - objectCondition + + # Variant Diagnostic Study Statement + XVariantDiagnosticStudyStatement: + inherits: gks-core:Statement + type: object + maturity: draft + description: >- + A Statement reporting a conclusion from a single study about whether a variant + is associated with a disease (a diagnostic inclusion criterion), or absence of a + disease (diagnostic exclusion criterion) - based on interpretation of the study's + results. + properties: + type: + extends: type + const: "VariantDiagnosticStudyStatement" + default: "VariantDiagnosticStudyStatement" + description: MUST be "VariantDiagnosticStudyStatement". + proposition: + extends: proposition + $ref: "#/$defs/XVariantDiagnosticStudyProposition" + description: >- + The proposition for which the study provides evidence - that the subject variant + is associated with the object disease. + required: + - proposition \ No newline at end of file diff --git a/schema/va-spec/base/x-variant-oncogenicity-study-profile-source.yaml b/schema/va-spec/base/x-variant-oncogenicity-study-profile-source.yaml new file mode 100644 index 0000000..2e16217 --- /dev/null +++ b/schema/va-spec/base/x-variant-oncogenicity-study-profile-source.yaml @@ -0,0 +1,97 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/x-variant-oncogenicity-study-profile-source.yaml" +title: Variant Oncogenicity Study Base Profiles +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Oncogenicity Study Proposition + XVariantOncogenicityStudyProposition: + inherits: gks-core:Proposition + maturity: draft + type: object + description: >- + A Proposition reporting a conclusion from a single study that supports or refutes a + variant's effect on oncogenesis for a specific tumor type - based on interpretation + of the study's results. + properties: + type: + extends: type + const: "VariantOncogenicityStudyProposition" + default: "VariantOncogenicityStudyProposition" + description: MUST be "VariantOncogenicityStudyProposition". + 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: + - isOncogenicFor + - isProtectiveFor + - isPredisposingFor + objectTumorType: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + description: >- + The tumor type for which the variant impact is evaluated. + alleleOriginQualifier: + type: string + description: >- + Reports whether the proposition should be interpreted in the context of an inherited + (germline) variant, an acquired (somatic) mutation, or both (combined). + enum: + - germline + - somatic + - combined + allelePrevalenceQualifier: + type: string + description: >- + Reports whether the proposition should be interpreted in the context of the variant + being rare or common. + enum: + - rare + - common + geneContextQualifier: + description: >- + Reports a gene impacted by the variant, which may contribute to the oncogenic + role in the Proposition. + $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + required: + - subjectVariant + - predicate + - objectTumorType + + # Variant Oncogenicity Study Statement + XVariantOncogenicityStudyStatement: + inherits: gks-core:Statement + maturity: draft + type: object + description: >- + A Statement reporting a conclusion from a single study that supports or refutes a + variant's effect on oncogenesis for a specific tumor type - based on interpretation + of the study's results. + properties: + type: + extends: type + const: "VariantOncogenicityStudyStatement" + default: "VariantOncogenicityStudyStatement" + description: MUST be "VariantOncogenicityStudyStatement". + proposition: + extends: proposition + $ref: "#/$defs/XVariantOncogenicityStudyProposition" + description: >- + The proposition for which the study provides evidence - that the subject variant + is associated with the object tumor type. + required: + - proposition \ No newline at end of file diff --git a/schema/va-spec/base/x-variant-pathogenicity-profile-source.yaml b/schema/va-spec/base/x-variant-pathogenicity-profile-source.yaml new file mode 100644 index 0000000..388544a --- /dev/null +++ b/schema/va-spec/base/x-variant-pathogenicity-profile-source.yaml @@ -0,0 +1,142 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/x-variant-pathogenicity-profile-source.yaml" +title: Variant Pathogenicity Base Profiles +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Pathogenicity Evidence Line + XVariantPathogenicityEvidenceLine: + inherits: gks-core:EvidenceLine + maturity: draft + type: object + description: >- + An Evidence Line that describes the strength and direction of support provided by one or more + evidence items for or against the pathogenicity of a variant for a particular disease. + properties: + type: + extends: type + const: "VariantPathogenicityEvidenceLine" + default: "VariantPathogenicityEvidenceLine" + description: MUST be "VariantPathogenicityEvidenceLine". + hasEvidenceItems: + extends: hasEvidenceItems + type: array + ordered: false + items: + $ref: "/ga4gh/schema/gks-core/1.x/json/InformationEntity" + description: >- + An Information Entity that was assessed as evidence in determining the possible + pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result). + directionOfEvidenceProvided: + extends: directionOfEvidenceProvided + description: >- + The direction of support that the Evidence Line is determined to provide for its target + Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the + evidence line support or dispute the possible pathogenicity of the subject variant, or + remain neutral) + strengthOfEvidenceProvided: + extends: strengthOfEvidenceProvided + type: + $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + description: >- + The strength of support that an Evidence Line is determined to provide for or against + the pathogenicity of the assessed variant. Strength is evaluated relative to the direction + indicated by the directionOfEvidenceProvided attribute. + targetProposition: + extends: targetProposition + $ref: "#/$defs/XVariantPathogenicityProposition" + description: >- + The possible fact toward which the strength and direction of evidence provided by + functional assay data was evaluated (here, a proposition that the assessed variant + may be pathogenic for a particular disease). + specifiedBy: + extends: specifiedBy + description: >- + A method that specifies how evidence items used in the Evidence Line are to be evaluated + and weighed as evidence for or against the pathogenicity of the assessed variant. + + # Variant Pathogenicity Proposition + XVariantPathogenicityProposition: + inherits: gks-core:Proposition + maturity: draft + type: object + description: >- + A proposition describing the role of a variant in causing an inherited condition. + properties: + type: + extends: type + 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 + objectCondition: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The :ref:`Condition` for which the variant impact is stated. + penetranceQualifier: + type: string + enum: + - high + - low + - risk allele + description: >- + Reports the penetrance of the pathogenic effect - i.e. the extent to which the + variant impact is expressed by individuals carrying it as a measure of the + proportion of carriers exhibiting the condition. + modeOfInheritanceQualifier: + type: array + ordered: false + items: + $ref: "/ga4gh/schema/gks-core/1.x/json/Coding" + description: >- + Reports a pattern of inheritance expected for the pathogenic effect of the variant. + Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. + geneContextQualifier: + description: >- + Reports the gene through which the pathogenic effect asserted for the variant is mediated + (i.e. it is the variant's impact on this gene that is responsible for causing the condition). + oneOf: + - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + required: + - subjectVariant + - predicate + - objectCondition + + # Variant Pathogenicity Statement + XVariantPathogenicityStatement: + type: object + maturity: draft + inherits: gks-core:Statement + description: >- + A Statement describing the role of a variant in causing an inherited condition. + properties: + type: + extends: type + const: "VariantPathogenicityStatement" + default: "VariantPathogenicityStatement" + description: MUST be "VariantPathogenicityStatement". + proposition: + extends: proposition + $ref: "#/$defs/XVariantPathogenicityProposition" + description: >- + The proposition that the subject variant is associated with the object disease. + required: + - proposition \ No newline at end of file diff --git a/schema/va-spec/base/x-variant-prognostic-study-profile-source.yaml b/schema/va-spec/base/x-variant-prognostic-study-profile-source.yaml new file mode 100644 index 0000000..dba95ff --- /dev/null +++ b/schema/va-spec/base/x-variant-prognostic-study-profile-source.yaml @@ -0,0 +1,95 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/x-variant-prognostic-study-profile-source.yaml" +title: Variant Prognostic Study Base Profiles +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Prognostic Study Proposition + XVariantPrognosticStudyProposition: + inherits: gks-core:Proposition + type: object + maturity: draft + description: >- + A Proposition reporting a conclusion from a single study about whether a variant + is associated with an improved or worse outcome for a disease - based on + interpretation of the study's results. + properties: + type: + extends: type + const: "VariantPrognosticStudyProposition" + default: "VariantPrognosticStudyProposition" + description: MUST be "VariantPrognosticStudyProposition". + 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: + - associatedWithBetterOutcomeFor + - associatedWithWorseOutcomeFor + objectCondition: + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: The disease that is evaluated for outcome. + alleleOriginQualifier: + type: string + description: >- + Reports whether the proposition should be interpreted in the context of an inherited + (germline) variant, an acquired (somatic) mutation, or both (combined). + enum: + - germline + - somatic + - combined + allelePrevalenceQualifier: + type: string + description: >- + Reports whether the proposition should be interpreted in the context of the variant + being rare or common. + enum: + - rare + - common + geneContextQualifier: + description: >- + Reports a gene impacted by the variant, which may contribute to the + prognostic association in the Proposition. + $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + required: + - subjectVariant + - predicate + - objectCondition + + # Variant Prognostic Study Statement + XVariantPrognosticStudyStatement: + inherits: gks-core:Statement + type: object + maturity: draft + description: >- + A Statement reporting a conclusion from a single study about whether a variant + is associated with an improved or worse outcome for a disease - based on + interpretation of the study's results. + properties: + type: + extends: type + const: "VariantPrognosticStudyStatement" + default: "VariantPrognosticStudyStatement" + description: MUST be "VariantPrognosticStudyStatement". + proposition: + extends: proposition + $ref: "#/$defs/XVariantPrognosticStudyProposition" + description: >- + The proposition for which the study provides evidence - that the subject variant + is associated with the object disease outcome. + required: + - proposition \ No newline at end of file diff --git a/schema/va-spec/base/x-variant-therapeutic-response-study-profile-source.yaml b/schema/va-spec/base/x-variant-therapeutic-response-study-profile-source.yaml new file mode 100644 index 0000000..6c63d71 --- /dev/null +++ b/schema/va-spec/base/x-variant-therapeutic-response-study-profile-source.yaml @@ -0,0 +1,99 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/x-variatn-therapeutic-response-study-profile-source.yaml" +title: Variant Therapeutic Response Study Base Profiles +strict: true + +imports: + domain-entities: ./domain-entities-source.yaml + cat-vrs: ../../cat-vrs/cat-vrs-source.yaml + vrs: ../../vrs/vrs-source.yaml + gks-core: ../../gks-core/gks-core-source.yaml + +$defs: + # Variant Therapeutic Response Study Proposition + XVariantTherapeuticResponseStudyProposition: + inherits: gks-core:Proposition + maturity: draft + type: object + description: >- + A Statement reporting a conclusion from a single study about the role of a variant + in modulating the response of a neoplasm to drug administration or other therapeutic + procedures - based on interpretation of the study's results. + properties: + 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: + - predictsSensitivityTo + - predictsResistanceTo + objectTherapeutic: + description: A drug administration or other therapeutic procedure that the neoplasm + is intended to respond to. + extends: object + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + conditionQualifier: + oneOf: + - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" + - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + description: >- + Reports the disease context in which the variant's association with therapeutic + sensitivity or resistance is evaluated. Note that this is a required qualifier in + therapeutic response statements. + alleleOriginQualifier: + type: string + description: >- + Reports whether the statement should be interpreted in the context of an inherited + (germline) variant, an acquired (somatic) mutation, or both (combined). + enum: + - germline + - somatic + - combined + allelePrevalenceQualifier: + type: string + description: >- + Reports whether the statement should be interpreted in the context of the variant + being rare or common. + enum: + - rare + - common + geneContextQualifier: + description: > + Reports a gene impacted by the variant, which may contribute to the therapeutic + sensitivity or resistance reported in the Statement. + $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + required: + - subjectVariant + - predicate + - objectTherapeutic + - conditionQualifier + + # Variant Therapeutic Response Study Statement + XVariantTherapeuticResponseStudyStatement: + inherits: gks-core:Statement + maturity: draft + type: object + description: >- + A Statement reporting a conclusion from a single study about the role of a variant + in modulating the response of a neoplasm to drug administration or other therapeutic + procedures - based on interpretation of the study's results. + properties: + type: + extends: type + const: "VariantTherapeuticResponseStudyStatement" + default: "VariantTherapeuticResponseStudyStatement" + description: MUST be "VariantTherapeuticResponseStudyStatement". + proposition: + extends: proposition + # LB: should this be a oneOf and include the option for an IRI reference? + $ref: "#/$defs/XVariantTherapeuticResponseStudyProposition" + description: >- + Reports the conclusion of the study, which is that the subject variant is + associated with therapeutic sensitivity or resistance to the object therapeutic. \ No newline at end of file diff --git a/submodules/cat-vrs b/submodules/cat-vrs index 3b3d9be..25fc036 160000 --- a/submodules/cat-vrs +++ b/submodules/cat-vrs @@ -1 +1 @@ -Subproject commit 3b3d9bee5fd8e8d4fc39c1b1f5aaf5604aecb9c3 +Subproject commit 25fc036fab59275ff5cc4c75708419c95166421f diff --git a/tests/fixtures/AVE-clinical-classification.yaml b/tests/fixtures/AVE-clinical-classification.yaml index a9a04d7..b2cb96f 100644 --- a/tests/fixtures/AVE-clinical-classification.yaml +++ b/tests/fixtures/AVE-clinical-classification.yaml @@ -1,4 +1,4 @@ -type: PathogenicityEvidenceLine +type: VariantPathogenicityEvidenceLine targetProposition: type: VariantPathogenicityProposition subjectVariant: diff --git a/tests/fixtures/AVE-functional-classification.yaml b/tests/fixtures/AVE-functional-classification.yaml index be51057..854590e 100644 --- a/tests/fixtures/AVE-functional-classification.yaml +++ b/tests/fixtures/AVE-functional-classification.yaml @@ -1,39 +1,41 @@ type: ExperimentalVariantFunctionalImpactStudyStatement -subjectVariant: - type: CategoricalVariant - constraints: - - type: DefiningAlleleConstraint - allele: - id: ga4gh:VA.t0rDoiIessOWmP0SF0plhXtOwi8TRaZz - type: Allele - location: - type: SequenceLocation - sequenceReference: - refgetAccession: SQ.w7LxW0PSaVPNsPFvOL24weFjHcfaHyOi - type: SequenceReference - start: 10 - end: 11 - sequence: R - state: - type: LiteralSequenceExpression - sequence: T - expressions: - - syntax: hgvs.p - value: NP_000305.3:p.Arg11Thr - relations: - - translates_from - - translates_from_reading_frame -predicate: impactsFunctionOf -objectSequenceFeature: - id: clinvar-gene:5728 - conceptType: Gene - label: PTEN - mappings: - - coding: - system: https://identifiers.org/ncbigene - code: '5728' - relation: exactMatch -studyContextQualifier: https://github.com/ave-dcd/mave_vocabulary/blob/main/examples/Matreyek_2018.yml +proposition: + type: ExperimentalVariantFunctionalImpactStudyProposition + subjectVariant: + type: CategoricalVariant + constraints: + - type: DefiningAlleleConstraint + allele: + id: ga4gh:VA.t0rDoiIessOWmP0SF0plhXtOwi8TRaZz + type: Allele + location: + type: SequenceLocation + sequenceReference: + refgetAccession: SQ.w7LxW0PSaVPNsPFvOL24weFjHcfaHyOi + type: SequenceReference + start: 10 + end: 11 + sequence: R + state: + type: LiteralSequenceExpression + sequence: T + expressions: + - syntax: hgvs.p + value: NP_000305.3:p.Arg11Thr + relations: + - translates_from + - translates_from_reading_frame + predicate: impactsFunctionOf + objectSequenceFeature: + id: clinvar-gene:5728 + conceptType: Gene + label: PTEN + mappings: + - coding: + system: https://identifiers.org/ncbigene + code: '5728' + relation: exactMatch + studyContextQualifier: https://github.com/ave-dcd/mave_vocabulary/blob/main/examples/Matreyek_2018.yml classification: label: normal specifiedBy: diff --git a/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml b/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml index 1217889..2eed644 100644 --- a/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml +++ b/tests/fixtures/VA-ClinVar-SCV-Example-001.yaml @@ -1,48 +1,51 @@ id: SCV000778434.1 type: VariantPathogenicityStatement -subjectVariant: - id: clinvar/208366 - type: CategoricalVariant - constraints: - - type: DefiningAlleleConstraint - allele: - id: ga4gh:VA.Ti7zPciQelW7jTfgg-uzjZpxosnGzROK - digest: Ti7zPciQelW7jTfgg-uzjZpxosnGzROK - type: Allele - location: - id: ga4gh:VSL.5lPU1ZzNnkDe-9ltOWXvcp2td9sM9CHr - digest: 5lPU1ZzNnkDe-9ltOWXvcp2td9sM9CHr - type: SequenceLocation - sequenceReference: - id: NC_000001.11 - type: SequenceReference - refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO - label: NC_000001.11 - start: 40819438 - end: 40819446 - state: - repeatSubunitLength: 3 - type: ReferenceLengthExpression - length: 5 - expressions: - - syntax: hgvs.g - value: NC_000001.11:g.40819441CCT[1] - - syntax: spdi - value: NC_000001.11:40819438:CTCCTCCT:CTCCT - relations: - - liftover_to - - transcribes_to - label: NM_004700.4(KCNQ4):c.803CCT[1] (p.Ser269del) -objectCondition: - id: clinvar.trait/939 - conceptType: Disease - label: Autosomal dominant nonsyndromic hearing loss 2A - mappings: - - coding: - code: C2677637 - system: https://www.ncbi.nlm.nih.gov/medgen/ - relation: exactMatch -predicate: isCausalFor +proposition: + type: VariantPathogenicityProposition + subjectVariant: + id: clinvar/208366 + type: CategoricalVariant + constraints: + - type: DefiningAlleleConstraint + allele: + id: ga4gh:VA.Ti7zPciQelW7jTfgg-uzjZpxosnGzROK + digest: Ti7zPciQelW7jTfgg-uzjZpxosnGzROK + type: Allele + location: + id: ga4gh:VSL.5lPU1ZzNnkDe-9ltOWXvcp2td9sM9CHr + digest: 5lPU1ZzNnkDe-9ltOWXvcp2td9sM9CHr + type: SequenceLocation + sequenceReference: + id: NC_000001.11 + type: SequenceReference + refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO + label: NC_000001.11 + start: 40819438 + end: 40819446 + state: + repeatSubunitLength: 3 + type: ReferenceLengthExpression + length: 5 + expressions: + - syntax: hgvs.g + value: NC_000001.11:g.40819441CCT[1] + - syntax: spdi + value: NC_000001.11:40819438:CTCCTCCT:CTCCT + relations: + - liftover_to + - transcribes_to + label: NM_004700.4(KCNQ4):c.803CCT[1] (p.Ser269del) + objectCondition: + id: clinvar.trait/939 + conceptType: Disease + label: Autosomal dominant nonsyndromic hearing loss 2A + mappings: + - coding: + code: C2677637 + system: https://www.ncbi.nlm.nih.gov/medgen/ + relation: exactMatch + predicate: isCausalFor + penetranceQualifier: high direction: supports strength: label: definitive @@ -58,7 +61,6 @@ classification: code: cg000001 system: https://dataexchange.clinicalgenome.org/codes/ relation: exactMatch -penetranceQualifier: high contributions: - type: Contribution contributor: diff --git a/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml b/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml index 750c494..d3f3a5e 100644 --- a/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml +++ b/tests/fixtures/VA-ClinVar-SCV-Example-002.yaml @@ -1,17 +1,19 @@ id: SCV001245167.1 type: VariantPathogenicityStatement -subjectVariant: catvars-mvp.jsonc#/208366 # NOQA: IRI resolution not tested; inline - # version of this object tested in SCV example 1 -objectCondition: - id: clinvarTrait:9544 # This ID syntax is clinvar.trait/9544 in example 1. Both OK. - conceptType: Disease - label: Nonsyndromic genetic hearing loss - mappings: - - coding: - system: https://www.ncbi.nlm.nih.gov/medgen/ - code: CN043648 - relation: exactMatch -predicate: isCausalFor +proposition: + type: VariantPathogenicityProposition + subjectVariant: catvars-mvp.jsonc#/208366 # NOQA: IRI resolution not tested; inline + # version of this object tested in SCV example 1 + objectCondition: + id: clinvarTrait:9544 # This ID syntax is clinvar.trait/9544 in example 1. Both OK. + conceptType: Disease + label: Nonsyndromic genetic hearing loss + mappings: + - coding: + system: https://www.ncbi.nlm.nih.gov/medgen/ + code: CN043648 + relation: exactMatch + predicate: isCausalFor direction: supports strength: label: likely diff --git a/tests/fixtures/diagnostic-inline.yaml b/tests/fixtures/diagnostic-inline.yaml index e05f1ae..1b1a2ca 100644 --- a/tests/fixtures/diagnostic-inline.yaml +++ b/tests/fixtures/diagnostic-inline.yaml @@ -11,123 +11,125 @@ strength: label: clinical cohort evidence system: https://go.osu.edu/evidence-codes relation: exactMatch -predicate: isDiagnosticInclusionCriterionFor -subjectVariant: - id: civic.mpid:12 - type: CategoricalVariant - description: >- - BRAF V600E has been shown to be recurrent in many cancer types. It is one of the - most widely studied variants in cancer. This variant is correlated with poor - prognosis in certain cancer types, including colorectal cancer and papillary thyroid - cancer. The targeted therapeutic dabrafenib has been shown to be effective in - clinical trials with an array of BRAF mutations and cancer types. Dabrafenib has - also shown to be effective when combined with the MEK inhibitor trametinib in - colorectal cancer and melanoma. However, in patients with TP53, CDKN2A and KRAS - mutations, dabrafenib resistance has been reported. Ipilimumab, regorafenib, - vemurafenib, and a number of combination therapies have been successful in treating - V600E mutations. However, cetuximab and panitumumab have been largely shown to be - ineffective without supplementary treatment. - label: BRAF V600E - constraints: - - type: "DefiningAlleleConstraint" - allele: vrs.json#/ga4gh:VA.j4XnsLZcdzDIYa5pvvXM7t1wn9OITr0L - members: - - vrs.json#/ga4gh:VA.Otc5ovrw906Ack087o1fhegB4jDRqCAe - alternativeLabels: - - VAL600GLU - - V640E - - VAL640GLU - mappings: - - coding: - code: CA123643 - system: https://reg.clinicalgenome.org/ - relation: relatedMatch - - coding: - code: '13961' - system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ - relation: relatedMatch +proposition: + type: VariantDiagnosticStudyProposition + predicate: isDiagnosticInclusionCriterionFor + subjectVariant: + id: civic.mpid:12 + type: CategoricalVariant + description: >- + BRAF V600E has been shown to be recurrent in many cancer types. It is one of the + most widely studied variants in cancer. This variant is correlated with poor + prognosis in certain cancer types, including colorectal cancer and papillary thyroid + cancer. The targeted therapeutic dabrafenib has been shown to be effective in + clinical trials with an array of BRAF mutations and cancer types. Dabrafenib has + also shown to be effective when combined with the MEK inhibitor trametinib in + colorectal cancer and melanoma. However, in patients with TP53, CDKN2A and KRAS + mutations, dabrafenib resistance has been reported. Ipilimumab, regorafenib, + vemurafenib, and a number of combination therapies have been successful in treating + V600E mutations. However, cetuximab and panitumumab have been largely shown to be + ineffective without supplementary treatment. + label: BRAF V600E + constraints: + - type: "DefiningAlleleConstraint" + allele: vrs.json#/ga4gh:VA.j4XnsLZcdzDIYa5pvvXM7t1wn9OITr0L + members: + - vrs.json#/ga4gh:VA.Otc5ovrw906Ack087o1fhegB4jDRqCAe + alternativeLabels: + - VAL600GLU + - V640E + - VAL640GLU + mappings: + - coding: + code: CA123643 + system: https://reg.clinicalgenome.org/ + relation: relatedMatch + - coding: + code: '13961' + system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ + relation: relatedMatch + - coding: + code: '376069' + system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ + relation: relatedMatch + - coding: + code: '12' + system: https://civicdb.org/variants/ + relation: exactMatch + - coding: + code: rs113488022 + system: https://www.ncbi.nlm.nih.gov/snp/ + relation: relatedMatch + extensions: + - name: CIViC representative coordinate + value: + chromosome: '7' + start: 140453136 + stop: 140453136 + reference_bases: A + variant_bases: T + representative_transcript: ENST00000288602.6 + ensembl_version: 75 + reference_build: GRCh37 + - name: CIViC Molecular Profile Score + value: 1378.5 + - name: Variant type + value: + code: SO:0001583 + system: http://www.sequenceontology.org/browser/current_release/term/ + label: missense_variant + objectCondition: + id: civic.did:156 + conceptType: Disease + label: Thyroid Gland Papillary Carcinoma + mappings: + - coding: + code: DOID:3969 + system: https://www.disease-ontology.org/ + relation: exactMatch + alleleOriginQualifier: somatic + geneContextQualifier: + id: civic.gid:5 + conceptType: Gene + label: BRAF + mappings: - coding: - code: '376069' - system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ - relation: relatedMatch - - coding: - code: '12' - system: https://civicdb.org/variants/ + code: ncbigene:673 + system: https://www.ncbi.nlm.nih.gov/gene/ relation: exactMatch - - coding: - code: rs113488022 - system: https://www.ncbi.nlm.nih.gov/snp/ - relation: relatedMatch - extensions: - - name: CIViC representative coordinate - value: - chromosome: '7' - start: 140453136 - stop: 140453136 - reference_bases: A - variant_bases: T - representative_transcript: ENST00000288602.6 - ensembl_version: 75 - reference_build: GRCh37 - - name: CIViC Molecular Profile Score - value: 1378.5 - - name: Variant type - value: - code: SO:0001583 - system: http://www.sequenceontology.org/browser/current_release/term/ - label: missense_variant -objectCondition: - id: civic.did:156 - conceptType: Disease - label: Thyroid Gland Papillary Carcinoma - mappings: - - coding: - code: DOID:3969 - system: https://www.disease-ontology.org/ - relation: exactMatch -alleleOriginQualifier: somatic -geneContextQualifier: - id: civic.gid:5 - conceptType: Gene - label: BRAF - mappings: - - coding: - code: ncbigene:673 - system: https://www.ncbi.nlm.nih.gov/gene/ - relation: exactMatch - extensions: - - name: aliases - value: - - B-RAF1 - - B-raf - - BRAF - - BRAF-1 - - BRAF1 - - NS7 - - RAFB1 - - name: description - value: "BRAF mutations are found to be recurrent in many cancer types. Of - these, the mutation of valine 600 to glutamic acid (V600E) is the most prevalent. - V600E has been determined to be an activating mutation, and cells that harbor it, - along with other V600 mutations are sensitive to the BRAF inhibitor dabrafenib. It - is also common to use MEK inhibition as a substitute for BRAF inhibitors, and the - MEK inhibitor trametinib has seen some success in BRAF mutant melanomas. BRAF - mutations have also been correlated with poor prognosis in many cancer types, - although there is at least one study that questions this conclusion in papillary - thyroid cancer. Oncogenic BRAF mutations are divided into three categories that - determine their sensitivity to inhibitors. Class 1 BRAF mutations (V600) are - RAS-independent, signal as monomers and are sensitive to current RAF monomer - inhibitors. Class 2 BRAF mutations (K601E, K601N, K601T, L597Q, L597V, G469A, - G469V, G469R, G464V, G464E, and fusions) are RAS-independent, signaling as - constitutive dimers and are resistant to vemurafenib. Such mutants may be - sensitive to novel RAF dimer inhibitors or MEK inhibitors. Class 3 BRAF mutations - (D287H, V459L, G466V, G466E, G466A, S467L, G469E, N581S, N581I, D594N, D594G, - D594A, D594H, F595L, G596D, and G596R) with low or absent kinase activity are - RAS-dependent and they activate ERK by increasing their binding to activated RAS - and wild-type CRAF. Class 3 BRAF mutations coexist with mutations in RAS or NF1 - in melanoma may be treated with MEK inhibitors. In epithelial tumors such as CRC - or NSCLC may be effectively treated with combinations that include inhibitors of - receptor tyrosine kinase." + extensions: + - name: aliases + value: + - B-RAF1 + - B-raf + - BRAF + - BRAF-1 + - BRAF1 + - NS7 + - RAFB1 + - name: description + value: "BRAF mutations are found to be recurrent in many cancer types. Of + these, the mutation of valine 600 to glutamic acid (V600E) is the most prevalent. + V600E has been determined to be an activating mutation, and cells that harbor it, + along with other V600 mutations are sensitive to the BRAF inhibitor dabrafenib. It + is also common to use MEK inhibition as a substitute for BRAF inhibitors, and the + MEK inhibitor trametinib has seen some success in BRAF mutant melanomas. BRAF + mutations have also been correlated with poor prognosis in many cancer types, + although there is at least one study that questions this conclusion in papillary + thyroid cancer. Oncogenic BRAF mutations are divided into three categories that + determine their sensitivity to inhibitors. Class 1 BRAF mutations (V600) are + RAS-independent, signal as monomers and are sensitive to current RAF monomer + inhibitors. Class 2 BRAF mutations (K601E, K601N, K601T, L597Q, L597V, G469A, + G469V, G469R, G464V, G464E, and fusions) are RAS-independent, signaling as + constitutive dimers and are resistant to vemurafenib. Such mutants may be + sensitive to novel RAF dimer inhibitors or MEK inhibitors. Class 3 BRAF mutations + (D287H, V459L, G466V, G466E, G466A, S467L, G469E, N581S, N581I, D594N, D594G, + D594A, D594H, F595L, G596D, and G596R) with low or absent kinase activity are + RAS-dependent and they activate ERK by increasing their binding to activated RAS + and wild-type CRAF. Class 3 BRAF mutations coexist with mutations in RAS or NF1 + in melanoma may be treated with MEK inhibitors. In epithelial tumors such as CRC + or NSCLC may be effectively treated with combinations that include inhibitors of + receptor tyrosine kinase." specifiedBy: id: civic.methods:2019 label: CIViC Curation SOP (2019) diff --git a/tests/fixtures/prognostic-inline.yaml b/tests/fixtures/prognostic-inline.yaml index ad8e18b..9ee4b12 100644 --- a/tests/fixtures/prognostic-inline.yaml +++ b/tests/fixtures/prognostic-inline.yaml @@ -11,123 +11,125 @@ strength: label: clinical cohort evidence system: https://go.osu.edu/evidence-codes relation: exactMatch -predicate: associatedWithWorseOutcomeFor -subjectVariant: - id: civic.mpid:12 - type: CategoricalVariant - description: >- - BRAF V600E has been shown to be recurrent in many cancer types. It is one of the - most widely studied variants in cancer. This variant is correlated with poor - prognosis in certain cancer types, including colorectal cancer and papillary thyroid - cancer. The targeted therapeutic dabrafenib has been shown to be effective in - clinical trials with an array of BRAF mutations and cancer types. Dabrafenib has - also shown to be effective when combined with the MEK inhibitor trametinib in - colorectal cancer and melanoma. However, in patients with TP53, CDKN2A and KRAS - mutations, dabrafenib resistance has been reported. Ipilimumab, regorafenib, - vemurafenib, and a number of combination therapies have been successful in treating - V600E mutations. However, cetuximab and panitumumab have been largely shown to be - ineffective without supplementary treatment. - label: BRAF V600E - constraints: - - type: "DefiningAlleleConstraint" - allele: vrs.json#/ga4gh:VA.j4XnsLZcdzDIYa5pvvXM7t1wn9OITr0L - members: - - vrs.json#/ga4gh:VA.Otc5ovrw906Ack087o1fhegB4jDRqCAe - alternativeLabels: - - VAL600GLU - - V640E - - VAL640GLU - mappings: - - coding: - code: CA123643 - system: https://reg.clinicalgenome.org/ - relation: relatedMatch - - coding: - code: '13961' - system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ - relation: relatedMatch +proposition: + type: VariantPrognosticStudyProposition + predicate: associatedWithWorseOutcomeFor + subjectVariant: + id: civic.mpid:12 + type: CategoricalVariant + description: >- + BRAF V600E has been shown to be recurrent in many cancer types. It is one of the + most widely studied variants in cancer. This variant is correlated with poor + prognosis in certain cancer types, including colorectal cancer and papillary thyroid + cancer. The targeted therapeutic dabrafenib has been shown to be effective in + clinical trials with an array of BRAF mutations and cancer types. Dabrafenib has + also shown to be effective when combined with the MEK inhibitor trametinib in + colorectal cancer and melanoma. However, in patients with TP53, CDKN2A and KRAS + mutations, dabrafenib resistance has been reported. Ipilimumab, regorafenib, + vemurafenib, and a number of combination therapies have been successful in treating + V600E mutations. However, cetuximab and panitumumab have been largely shown to be + ineffective without supplementary treatment. + label: BRAF V600E + constraints: + - type: "DefiningAlleleConstraint" + allele: vrs.json#/ga4gh:VA.j4XnsLZcdzDIYa5pvvXM7t1wn9OITr0L + members: + - vrs.json#/ga4gh:VA.Otc5ovrw906Ack087o1fhegB4jDRqCAe + alternativeLabels: + - VAL600GLU + - V640E + - VAL640GLU + mappings: + - coding: + code: CA123643 + system: https://reg.clinicalgenome.org/ + relation: relatedMatch + - coding: + code: '13961' + system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ + relation: relatedMatch + - coding: + code: '376069' + system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ + relation: relatedMatch + - coding: + code: '12' + system: https://civicdb.org/variants/ + relation: exactMatch + - coding: + code: rs113488022 + system: https://www.ncbi.nlm.nih.gov/snp/ + relation: relatedMatch + extensions: + - name: CIViC representative coordinate + value: + chromosome: '7' + start: 140453136 + stop: 140453136 + reference_bases: A + variant_bases: T + representative_transcript: ENST00000288602.6 + ensembl_version: 75 + reference_build: GRCh37 + - name: CIViC Molecular Profile Score + value: 1378.5 + - name: Variant type + value: + code: SO:0001583 + system: http://www.sequenceontology.org/browser/current_release/term/ + label: missense_variant + objectCondition: + id: civic.did:7 + conceptType: Disease + label: Melanoma + mappings: + - coding: + code: DOID:1909 + system: https://www.disease-ontology.org/ + relation: exactMatch + alleleOriginQualifier: somatic + geneContextQualifier: + id: civic.gid:5 + conceptType: Gene + label: BRAF + mappings: - coding: - code: '376069' - system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ - relation: relatedMatch - - coding: - code: '12' - system: https://civicdb.org/variants/ + code: ncbigene:673 + system: https://www.ncbi.nlm.nih.gov/gene/ relation: exactMatch - - coding: - code: rs113488022 - system: https://www.ncbi.nlm.nih.gov/snp/ - relation: relatedMatch - extensions: - - name: CIViC representative coordinate - value: - chromosome: '7' - start: 140453136 - stop: 140453136 - reference_bases: A - variant_bases: T - representative_transcript: ENST00000288602.6 - ensembl_version: 75 - reference_build: GRCh37 - - name: CIViC Molecular Profile Score - value: 1378.5 - - name: Variant type - value: - code: SO:0001583 - system: http://www.sequenceontology.org/browser/current_release/term/ - label: missense_variant -objectCondition: - id: civic.did:7 - conceptType: Disease - label: Melanoma - mappings: - - coding: - code: DOID:1909 - system: https://www.disease-ontology.org/ - relation: exactMatch -alleleOriginQualifier: somatic -geneContextQualifier: - id: civic.gid:5 - conceptType: Gene - label: BRAF - mappings: - - coding: - code: ncbigene:673 - system: https://www.ncbi.nlm.nih.gov/gene/ - relation: exactMatch - extensions: - - name: aliases - value: - - B-RAF1 - - B-raf - - BRAF - - BRAF-1 - - BRAF1 - - NS7 - - RAFB1 - - name: description - value: "BRAF mutations are found to be recurrent in many cancer types. Of - these, the mutation of valine 600 to glutamic acid (V600E) is the most prevalent. - V600E has been determined to be an activating mutation, and cells that harbor it, - along with other V600 mutations are sensitive to the BRAF inhibitor dabrafenib. It - is also common to use MEK inhibition as a substitute for BRAF inhibitors, and the - MEK inhibitor trametinib has seen some success in BRAF mutant melanomas. BRAF - mutations have also been correlated with poor prognosis in many cancer types, - although there is at least one study that questions this conclusion in papillary - thyroid cancer. Oncogenic BRAF mutations are divided into three categories that - determine their sensitivity to inhibitors. Class 1 BRAF mutations (V600) are - RAS-independent, signal as monomers and are sensitive to current RAF monomer - inhibitors. Class 2 BRAF mutations (K601E, K601N, K601T, L597Q, L597V, G469A, - G469V, G469R, G464V, G464E, and fusions) are RAS-independent, signaling as - constitutive dimers and are resistant to vemurafenib. Such mutants may be - sensitive to novel RAF dimer inhibitors or MEK inhibitors. Class 3 BRAF mutations - (D287H, V459L, G466V, G466E, G466A, S467L, G469E, N581S, N581I, D594N, D594G, - D594A, D594H, F595L, G596D, and G596R) with low or absent kinase activity are - RAS-dependent and they activate ERK by increasing their binding to activated RAS - and wild-type CRAF. Class 3 BRAF mutations coexist with mutations in RAS or NF1 - in melanoma may be treated with MEK inhibitors. In epithelial tumors such as CRC - or NSCLC may be effectively treated with combinations that include inhibitors of - receptor tyrosine kinase." + extensions: + - name: aliases + value: + - B-RAF1 + - B-raf + - BRAF + - BRAF-1 + - BRAF1 + - NS7 + - RAFB1 + - name: description + value: "BRAF mutations are found to be recurrent in many cancer types. Of + these, the mutation of valine 600 to glutamic acid (V600E) is the most prevalent. + V600E has been determined to be an activating mutation, and cells that harbor it, + along with other V600 mutations are sensitive to the BRAF inhibitor dabrafenib. It + is also common to use MEK inhibition as a substitute for BRAF inhibitors, and the + MEK inhibitor trametinib has seen some success in BRAF mutant melanomas. BRAF + mutations have also been correlated with poor prognosis in many cancer types, + although there is at least one study that questions this conclusion in papillary + thyroid cancer. Oncogenic BRAF mutations are divided into three categories that + determine their sensitivity to inhibitors. Class 1 BRAF mutations (V600) are + RAS-independent, signal as monomers and are sensitive to current RAF monomer + inhibitors. Class 2 BRAF mutations (K601E, K601N, K601T, L597Q, L597V, G469A, + G469V, G469R, G464V, G464E, and fusions) are RAS-independent, signaling as + constitutive dimers and are resistant to vemurafenib. Such mutants may be + sensitive to novel RAF dimer inhibitors or MEK inhibitors. Class 3 BRAF mutations + (D287H, V459L, G466V, G466E, G466A, S467L, G469E, N581S, N581I, D594N, D594G, + D594A, D594H, F595L, G596D, and G596R) with low or absent kinase activity are + RAS-dependent and they activate ERK by increasing their binding to activated RAS + and wild-type CRAF. Class 3 BRAF mutations coexist with mutations in RAS or NF1 + in melanoma may be treated with MEK inhibitors. In epithelial tumors such as CRC + or NSCLC may be effectively treated with combinations that include inhibitors of + receptor tyrosine kinase." specifiedBy: id: civic.methods:2019 label: CIViC Curation SOP (2019) diff --git a/tests/fixtures/tr-statement-inline.yaml b/tests/fixtures/tr-statement-inline.yaml index f3658d6..e4bd0bf 100644 --- a/tests/fixtures/tr-statement-inline.yaml +++ b/tests/fixtures/tr-statement-inline.yaml @@ -14,127 +14,129 @@ strength: label: clinical cohort evidence system: https://go.osu.edu/evidence-codes relation: exactMatch -predicate: predictsSensitivityTo -subjectVariant: - id: civic.mpid:33 - type: CategoricalVariant - # description: >- - # EGFR L858R has long been recognized as a functionally significant mutation in cancer, - # and is one of the most prevalent single mutations in lung cancer. Best described in - # non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first - # and second generation TKI's like gefitinib and neratinib. NSCLC patients with this - # mutation treated with TKI's show increased overall and progression-free survival, as - # compared to chemotherapy alone. Third generation TKI's are currently in clinical trials - # that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in - # treating patients that failed to respond to earlier generation TKI therapies. - label: EGFR L858R - constraints: - - type: DefiningAlleleConstraint - allele: vrs.json#/ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA - members: - - vrs.json#/ga4gh:VA.7jX7fHgVEqx4C4jMRyZOH0ZBHnLn7_gJ - - vrs.json#/ga4gh:VA.3_FsKSUHEdurPIw5gqpw6g0_Ga0TEXQh - - vrs.json#/ga4gh:VA.zpv3dW34z8jioKL-NtbGc0fa9clsgAZT - - vrs.json#/ga4gh:VA.BJOtfUhZMooMJUO4FjxHXTEimrKXtF0i - # alternativeLabels: - # - LEU858ARG - # - rs121434568 - mappings: - - coding: - code: CA126713 - system: https://reg.clinicalgenome.org/ - relation: relatedMatch - - coding: - code: '16609' - system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ - relation: relatedMatch - - coding: - code: '376282' - system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ - relation: relatedMatch - - coding: - code: '376280' - system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ - relation: relatedMatch - - coding: - code: rs121434568 - system: https://www.ncbi.nlm.nih.gov/snp/ - relation: relatedMatch - extensions: - - name: CIViC representative coordinate - value: - chromosome: '7' - start: 55259515 - stop: 55259515 - reference_bases: T - variant_bases: G - representative_transcript: ENST00000275493.2 - ensembl_version: 75 - reference_build: GRCh37 - - name: CIViC Molecular Profile Score - value: 379 - - name: Variant type - value: - code: SO:0001583 - system: http://www.sequenceontology.org/browser/current_release/term/ - label: missense_variant -objectTherapeutic: - id: civic.tid:146 - conceptType: Drug - label: Afatinib - mappings: +proposition: + type: VariantTherapeuticResponseStudyProposition + predicate: predictsSensitivityTo + subjectVariant: + id: civic.mpid:33 + type: CategoricalVariant + # description: >- + # EGFR L858R has long been recognized as a functionally significant mutation in cancer, + # and is one of the most prevalent single mutations in lung cancer. Best described in + # non-small cell lung cancer (NSCLC), the mutation seems to confer sensitivity to first + # and second generation TKI's like gefitinib and neratinib. NSCLC patients with this + # mutation treated with TKI's show increased overall and progression-free survival, as + # compared to chemotherapy alone. Third generation TKI's are currently in clinical trials + # that specifically focus on mutant forms of EGFR, a few of which have shown efficacy in + # treating patients that failed to respond to earlier generation TKI therapies. + label: EGFR L858R + constraints: + - type: DefiningAlleleConstraint + allele: vrs.json#/ga4gh:VA.kgjrhgf84CEndyLjKdAO0RxN-e3pJjxA + members: + - vrs.json#/ga4gh:VA.7jX7fHgVEqx4C4jMRyZOH0ZBHnLn7_gJ + - vrs.json#/ga4gh:VA.3_FsKSUHEdurPIw5gqpw6g0_Ga0TEXQh + - vrs.json#/ga4gh:VA.zpv3dW34z8jioKL-NtbGc0fa9clsgAZT + - vrs.json#/ga4gh:VA.BJOtfUhZMooMJUO4FjxHXTEimrKXtF0i + # alternativeLabels: + # - LEU858ARG + # - rs121434568 + mappings: + - coding: + code: CA126713 + system: https://reg.clinicalgenome.org/ + relation: relatedMatch + - coding: + code: '16609' + system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ + relation: relatedMatch + - coding: + code: '376282' + system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ + relation: relatedMatch + - coding: + code: '376280' + system: https://www.ncbi.nlm.nih.gov/clinvar/variation/ + relation: relatedMatch + - coding: + code: rs121434568 + system: https://www.ncbi.nlm.nih.gov/snp/ + relation: relatedMatch + extensions: + - name: CIViC representative coordinate + value: + chromosome: '7' + start: 55259515 + stop: 55259515 + reference_bases: T + variant_bases: G + representative_transcript: ENST00000275493.2 + ensembl_version: 75 + reference_build: GRCh37 + - name: CIViC Molecular Profile Score + value: 379 + - name: Variant type + value: + code: SO:0001583 + system: http://www.sequenceontology.org/browser/current_release/term/ + label: missense_variant + objectTherapeutic: + id: civic.tid:146 + conceptType: Drug + label: Afatinib + mappings: + - coding: + code: C66940 + system: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code= + relation: exactMatch + - coding: + code: '1430438' + system: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm= + relation: exactMatch + conditionQualifier: + id: civic.did:30 + conceptType: Disease + label: Lung Adenocarcinoma + mappings: + - coding: + code: DOID:3910 + system: https://www.disease-ontology.org/ + relation: exactMatch + alleleOriginQualifier: somatic + geneContextQualifier: + id: civic.gid:19 + conceptType: Gene + label: EGFR + mappings: - coding: - code: C66940 - system: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code= + code: ncbigene:1956 + system: https://www.ncbi.nlm.nih.gov/gene/ relation: exactMatch - - coding: - code: '1430438' - system: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm= - relation: exactMatch -conditionQualifier: - id: civic.did:30 - conceptType: Disease - label: Lung Adenocarcinoma - mappings: - - coding: - code: DOID:3910 - system: https://www.disease-ontology.org/ - relation: exactMatch -alleleOriginQualifier: somatic -geneContextQualifier: - id: civic.gid:19 - conceptType: Gene - label: EGFR - mappings: - - coding: - code: ncbigene:1956 - system: https://www.ncbi.nlm.nih.gov/gene/ - relation: exactMatch - extensions: - - name: aliases - value: - - EGFR - - ERBB - - ERBB1 - - ERRP - - HER1 - - NISBD2 - - PIG61 - - mENA - - name: description - value: "EGFR is widely recognized for its importance in cancer. Amplification - and mutations have been shown to be driving events in many cancer types. Its - role in non-small cell lung cancer, glioblastoma and basal-like breast cancers - has spurred many research and drug development efforts. Tyrosine kinase inhibitors - have shown efficacy in EGFR amplfied tumors, most notably gefitinib and erlotinib. - Mutations in EGFR have been shown to confer resistance to these drugs, particularly - the variant T790M, which has been functionally characterized as a resistance - marker for both of these drugs. The later generation TKI's have seen some - success in treating these resistant cases, and targeted sequencing of the - EGFR locus has become a common practice in treatment of non-small cell lung - cancer. \nOverproduction of ligands is another possible mechanism of activation - of EGFR. ERBB ligands include EGF, TGF-a, AREG, EPG, BTC, HB-EGF, EPR and - NRG1-4 (for detailed information please refer to the respective ligand section)." + extensions: + - name: aliases + value: + - EGFR + - ERBB + - ERBB1 + - ERRP + - HER1 + - NISBD2 + - PIG61 + - mENA + - name: description + value: "EGFR is widely recognized for its importance in cancer. Amplification + and mutations have been shown to be driving events in many cancer types. Its + role in non-small cell lung cancer, glioblastoma and basal-like breast cancers + has spurred many research and drug development efforts. Tyrosine kinase inhibitors + have shown efficacy in EGFR amplfied tumors, most notably gefitinib and erlotinib. + Mutations in EGFR have been shown to confer resistance to these drugs, particularly + the variant T790M, which has been functionally characterized as a resistance + marker for both of these drugs. The later generation TKI's have seen some + success in treating these resistant cases, and targeted sequencing of the + EGFR locus has become a common practice in treatment of non-small cell lung + cancer. \nOverproduction of ligands is another possible mechanism of activation + of EGFR. ERBB ligands include EGF, TGF-a, AREG, EPG, BTC, HB-EGF, EPR and + NRG1-4 (for detailed information please refer to the respective ligand section)." specifiedBy: id: civic.methods:2019 label: CIViC Curation SOP (2019) diff --git a/tests/test_definitions.yaml b/tests/test_definitions.yaml index f6eb738..503b958 100644 --- a/tests/test_definitions.yaml +++ b/tests/test_definitions.yaml @@ -6,10 +6,10 @@ tests: namespace: vrs definition: Allele - test_file: VA-ClinVar-SCV-Example-001.yaml - namespace: va-spec.acmg-2015 + namespace: va-spec.base definition: VariantPathogenicityStatement - test_file: VA-ClinVar-SCV-Example-002.yaml - namespace: va-spec.acmg-2015 + namespace: va-spec.base definition: VariantPathogenicityStatement - test_file: therapeuticAgent.yaml namespace: gks-core @@ -31,7 +31,7 @@ tests: definition: ExperimentalVariantFunctionalImpactStudyStatement - test_file: AVE-clinical-classification.yaml namespace: va-spec.base - definition: PathogenicityEvidenceLine + definition: VariantPathogenicityEvidenceLine - test_file: AVE-functional-study-result.yaml namespace: va-spec.base definition: ExperimentalVariantFunctionalImpactStudyResult \ No newline at end of file From af94fe36cbac6e954d87a5c9c3a4169936c992ee Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Tue, 12 Nov 2024 11:39:57 -0500 Subject: [PATCH 18/20] add back lost proposal from AHW on community docs --- .../def/VariantPathogenicityStatement.rst | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst index 49e4942..322f32e 100644 --- a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst @@ -9,14 +9,7 @@ A Statement describing the role of a variant in causing an inherited condition. **Information Model** -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description +- `VariantPathogenicityStatement.classification` is additionally defined as + *The ACMG 2015 classification of the variant's pathogenicity*. + - `.classification.label` is constrained to values `pathogenic`, `likely pathogenic`, + `uncertain significance`, `likely benign`, and `benign`. \ No newline at end of file From 6fcbfef802c8e12a54900c8a563ed1e941b33df5 Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Tue, 12 Nov 2024 12:00:14 -0500 Subject: [PATCH 19/20] draft changes to acmg-2015 func-imp-evid-line --- ...hogenicityFunctionalImpactEvidenceLine.rst | 22 +++++++++++++ ... example-rst-output-for-allof-classes.rst} | 3 +- ...tPathogenicityFunctionalImpactEvidenceLine | 29 +++++++++++++++++ .../json/VariantPathogenicityStatement | 31 ------------------ ...athogenicity-statement-profile-source.yaml | 32 ++++++++++--------- .../def/VariantPathogenicityStatement.rst | 10 +++--- .../base/json/VariantPathogenicityStatement | 23 ++++++++++--- ...athogenicity-statement-profile-source.yaml | 12 +++++++ 8 files changed, 105 insertions(+), 57 deletions(-) create mode 100644 schema/va-spec/acmg-2015/def/VariantPathogenicityFunctionalImpactEvidenceLine.rst rename schema/va-spec/acmg-2015/{def/VariantPathogenicityStatement.rst => example-rst-output-for-allof-classes.rst} (82%) create mode 100644 schema/va-spec/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine delete mode 100644 schema/va-spec/acmg-2015/json/VariantPathogenicityStatement diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityFunctionalImpactEvidenceLine.rst b/schema/va-spec/acmg-2015/def/VariantPathogenicityFunctionalImpactEvidenceLine.rst new file mode 100644 index 0000000..b50678a --- /dev/null +++ b/schema/va-spec/acmg-2015/def/VariantPathogenicityFunctionalImpactEvidenceLine.rst @@ -0,0 +1,22 @@ +.. 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** + +An Evidence Line providing information about the functional impact of a variant on a gene or gene product. + +**Information Model** + + +.. list-table:: + :class: clean-wrap + :header-rows: 1 + :align: left + :widths: auto + + * - Field + - Flags + - Type + - Limits + - Description diff --git a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst b/schema/va-spec/acmg-2015/example-rst-output-for-allof-classes.rst similarity index 82% rename from schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst rename to schema/va-spec/acmg-2015/example-rst-output-for-allof-classes.rst index 322f32e..2025c0d 100644 --- a/schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/acmg-2015/example-rst-output-for-allof-classes.rst @@ -6,8 +6,9 @@ A Statement describing the role of a variant in causing an inherited condition. -**Information Model** +**Profile Conditions** +This class adds the following conditions to the :ref:`variant-pathogenicity-evidence-line-profile`: - `VariantPathogenicityStatement.classification` is additionally defined as *The ACMG 2015 classification of the variant's pathogenicity*. diff --git a/schema/va-spec/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine b/schema/va-spec/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine new file mode 100644 index 0000000..bfab18b --- /dev/null +++ b/schema/va-spec/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine @@ -0,0 +1,29 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine", + "title": "VariantPathogenicityFunctionalImpactEvidenceLine", + "maturity": "draft", + "description": "An Evidence Line providing information about the functional impact of a variant on a gene or gene product.", + "allOf": [ + { + "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityEvidenceLine" + }, + { + "properties": { + "strengthOfEvidenceProvided": { + "extends": "strengthOfEvidenceProvided", + "type": "string", + "enum": [ + "PS3_Strong", + "PS3_Moderate", + "PS3_Supporting", + "BS3_Strong", + "BS3_Moderate", + "BS3_Supporting" + ], + "description": "The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. " + } + } + } + ] +} \ No newline at end of file diff --git a/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement b/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement deleted file mode 100644 index 01f9a2f..0000000 --- a/schema/va-spec/acmg-2015/json/VariantPathogenicityStatement +++ /dev/null @@ -1,31 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/acmg-2015/json/VariantPathogenicityStatement", - "title": "VariantPathogenicityStatement", - "maturity": "draft", - "description": "A Statement describing the role of a variant in causing an inherited condition.", - "allOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Statement" - }, - { - "properties": { - "classification": { - "properties": { - "label": { - "type": "string", - "enum": [ - "pathogenic", - "likely pathogenic", - "uncertain significance", - "likely benign", - "benign" - ] - } - }, - "description": "The ACMG 2015 classification of the variant's pathogenicity." - } - } - } - ] -} \ No newline at end of file diff --git a/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml index 84e418e..7659ecf 100644 --- a/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml +++ b/schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml @@ -4,28 +4,30 @@ title: ACMG 2015 Variant Pathogenicity Statement Standard Profile strict: true imports: - va-spec: ../base/pathogenicity-statement-profile-source.yaml + va-spec: ../base/pathogenicity-evidence-line-profile-source.yaml cat-vrs: ../../cat-vrs/cat-vrs-source.yaml vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml $defs: - VariantPathogenicityStatement: + VariantPathogenicityFunctionalImpactEvidenceLine: maturity: draft description: >- - A Statement describing the role of a variant in causing an inherited condition. + An Evidence Line providing information about the functional impact of a variant on a gene or gene product. allOf: - - $ref: "/ga4gh/schema/gks-core/1.x/Statement" + - $ref: "/ga4gh/schema/va-spec/1.x/base/VariantPathogenicityEvidenceLine" - properties: - classification: - properties: - label: - type: string - enum: - - pathogenic - - likely pathogenic - - uncertain significance - - likely benign - - benign + strengthOfEvidenceProvided: # TO DO: Ensure that the enum below covers terms needed for initial adopters. Merge https://github.com/ga4gh/gks-core/pull/78 which updates the core IM to allow this property to take a string so we can define the enum here. Think about if we need the 'PS'/'BS' parts of enum value labels - as this bakes in direction, and is duplicative as the 'specifiedBy' attribute reports the ACMG criterion applied. + extends: strengthOfEvidenceProvided + type: string # Note that in the core model, the data type for this attribute was changed to be a MappableConcept. How then can we define a set of allowable values? Do we even want to do this in the base profile at all (maybe this constraint goes in a Community Profile)? + enum: + - PS3_Strong + - PS3_Moderate + - PS3_Supporting + - BS3_Strong + - BS3_Moderate + - BS3_Supporting description: >- - The ACMG 2015 classification of the variant's pathogenicity. + The strength of support that an Evidence Line is determined to provide for or against + the pathogenicity of the assessed variant. Strength is evaluated relative to the direction + indicated by the directionOfEvidenceProvided attribute. diff --git a/schema/va-spec/base/def/VariantPathogenicityStatement.rst b/schema/va-spec/base/def/VariantPathogenicityStatement.rst index 3a5d785..7311257 100644 --- a/schema/va-spec/base/def/VariantPathogenicityStatement.rst +++ b/schema/va-spec/base/def/VariantPathogenicityStatement.rst @@ -111,11 +111,6 @@ Some VariantPathogenicityStatement attributes are inherited from :ref:`gks-core: - string - 0..1 - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. * - hasEvidenceLines - .. raw:: html @@ -134,3 +129,8 @@ Some VariantPathogenicityStatement attributes are inherited from :ref:`gks-core: - :ref:`VariantPathogenicityProposition` - 1..1 - The proposition that the subject variant is associated with the object disease. + * - classification + - + - :ref:`MappableConcept` + - 1..1 + - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. diff --git a/schema/va-spec/base/json/VariantPathogenicityStatement b/schema/va-spec/base/json/VariantPathogenicityStatement index 07053ff..65fa5aa 100644 --- a/schema/va-spec/base/json/VariantPathogenicityStatement +++ b/schema/va-spec/base/json/VariantPathogenicityStatement @@ -116,11 +116,6 @@ "description": "A natural-language expression of what a Statement asserts to be true.", "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, "hasEvidenceLines": { "type": "array", "ordered": false, @@ -140,9 +135,27 @@ "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition", "description": "The proposition that the subject variant is associated with the object disease.", "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " + }, + "classification": { + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", + "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", + "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification.", + "properties": { + "label": { + "type": "string", + "enum": [ + "pathogenic", + "likely pathogenic", + "uncertain significance", + "likely benign", + "benign" + ] + } + } } }, "required": [ + "classification", "proposition", "type" ], diff --git a/schema/va-spec/base/pathogenicity-statement-profile-source.yaml b/schema/va-spec/base/pathogenicity-statement-profile-source.yaml index 89f44b5..8d58834 100644 --- a/schema/va-spec/base/pathogenicity-statement-profile-source.yaml +++ b/schema/va-spec/base/pathogenicity-statement-profile-source.yaml @@ -26,5 +26,17 @@ $defs: $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition" description: >- The proposition that the subject variant is associated with the object disease. + classification: + extends: classification + properties: + label: + type: string + enum: + - pathogenic + - likely pathogenic + - uncertain significance + - likely benign + - benign required: - proposition + - classification From c7a1ef14e510c7d63cf90410330c3187c2f46c8e Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Tue, 12 Nov 2024 17:42:17 -0500 Subject: [PATCH 20/20] clean schema folders --- ...hogenicityFunctionalImpactEvidenceLine.rst | 22 --- ...tPathogenicityFunctionalImpactEvidenceLine | 29 --- .../def/CohortAlleleFrequencyStudyResult.rst | 147 ---------------- schema/va-spec/base/def/Condition.rst | 22 --- ...ariantFunctionalImpactStudyProposition.rst | 89 ---------- ...ntalVariantFunctionalImpactStudyResult.rst | 137 --------------- ...lVariantFunctionalImpactStudyStatement.rst | 136 --------------- schema/va-spec/base/def/Therapeutic.rst | 22 --- schema/va-spec/base/def/TherapyGroup.rst | 49 ------ schema/va-spec/base/def/TraitSet.rst | 44 ----- .../def/VariantDiagnosticStudyProposition.rst | 94 ---------- .../def/VariantDiagnosticStudyStatement.rst | 136 --------------- .../VariantOncogenicityStudyProposition.rst | 94 ---------- .../def/VariantOncogenicityStudyStatement.rst | 136 --------------- .../def/VariantPathogenicityEvidenceLine.rst | 126 ------------- .../def/VariantPathogenicityProposition.rst | 97 ---------- .../def/VariantPathogenicityStatement.rst | 136 --------------- .../def/VariantPrognosticStudyProposition.rst | 94 ---------- .../def/VariantPrognosticStudyStatement.rst | 136 --------------- ...antTherapeuticResponseStudyProposition.rst | 100 ----------- ...riantTherapeuticResponseStudyStatement.rst | 136 --------------- .../def/XCohortAlleleFrequencyStudyResult.rst | 147 ---------------- ...ariantFunctionalImpactStudyProposition.rst | 89 ---------- ...ntalVariantFunctionalImpactStudyResult.rst | 137 --------------- ...lVariantFunctionalImpactStudyStatement.rst | 136 --------------- .../XVariantDiagnosticStudyProposition.rst | 94 ---------- .../def/XVariantDiagnosticStudyStatement.rst | 136 --------------- .../XVariantOncogenicityStudyProposition.rst | 94 ---------- .../XVariantOncogenicityStudyStatement.rst | 136 --------------- .../def/XVariantPathogenicityEvidenceLine.rst | 126 ------------- .../def/XVariantPathogenicityProposition.rst | 97 ---------- .../def/XVariantPathogenicityStatement.rst | 136 --------------- .../XVariantPrognosticStudyProposition.rst | 94 ---------- .../def/XVariantPrognosticStudyStatement.rst | 136 --------------- ...antTherapeuticResponseStudyProposition.rst | 100 ----------- ...riantTherapeuticResponseStudyStatement.rst | 136 --------------- .../json/CohortAlleleFrequencyStudyResult | 165 ------------------ schema/va-spec/base/json/Condition | 15 -- ...talVariantFunctionalImpactStudyProposition | 115 ------------ ...rimentalVariantFunctionalImpactStudyResult | 149 ---------------- ...entalVariantFunctionalImpactStudyStatement | 150 ---------------- schema/va-spec/base/json/Therapeutic | 15 -- schema/va-spec/base/json/TherapyGroup | 38 ---- schema/va-spec/base/json/TraitSet | 34 ---- .../json/VariantDiagnosticStudyProposition | 115 ------------ .../base/json/VariantDiagnosticStudyStatement | 150 ---------------- .../json/VariantOncogenicityStudyProposition | 116 ------------ .../json/VariantOncogenicityStudyStatement | 150 ---------------- .../json/VariantPathogenicityEvidenceLine | 139 --------------- .../base/json/VariantPathogenicityProposition | 119 ------------- .../base/json/VariantPathogenicityStatement | 163 ----------------- .../json/VariantPrognosticStudyProposition | 115 ------------ .../base/json/VariantPrognosticStudyStatement | 150 ---------------- ...VariantTherapeuticResponseStudyProposition | 127 -------------- .../VariantTherapeuticResponseStudyStatement | 150 ---------------- .../json/XCohortAlleleFrequencyStudyResult | 165 ------------------ ...talVariantFunctionalImpactStudyProposition | 115 ------------ ...rimentalVariantFunctionalImpactStudyResult | 149 ---------------- ...entalVariantFunctionalImpactStudyStatement | 150 ---------------- .../json/XVariantDiagnosticStudyProposition | 115 ------------ .../json/XVariantDiagnosticStudyStatement | 150 ---------------- .../json/XVariantOncogenicityStudyProposition | 116 ------------ .../json/XVariantOncogenicityStudyStatement | 150 ---------------- .../json/XVariantPathogenicityEvidenceLine | 139 --------------- .../json/XVariantPathogenicityProposition | 119 ------------- .../base/json/XVariantPathogenicityStatement | 150 ---------------- .../json/XVariantPrognosticStudyProposition | 115 ------------ .../json/XVariantPrognosticStudyStatement | 150 ---------------- ...VariantTherapeuticResponseStudyProposition | 127 -------------- .../XVariantTherapeuticResponseStudyStatement | 150 ---------------- 70 files changed, 8011 deletions(-) delete mode 100644 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b50678a..0000000 --- a/schema/va-spec/acmg-2015/def/VariantPathogenicityFunctionalImpactEvidenceLine.rst +++ /dev/null @@ -1,22 +0,0 @@ -.. 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** - -An Evidence Line providing information about the functional impact of a variant on a gene or gene product. - -**Information Model** - - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description diff --git a/schema/va-spec/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine b/schema/va-spec/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine deleted file mode 100644 index bfab18b..0000000 --- a/schema/va-spec/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine +++ /dev/null @@ -1,29 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/acmg-2015/json/VariantPathogenicityFunctionalImpactEvidenceLine", - "title": "VariantPathogenicityFunctionalImpactEvidenceLine", - "maturity": "draft", - "description": "An Evidence Line providing information about the functional impact of a variant on a gene or gene product.", - "allOf": [ - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityEvidenceLine" - }, - { - "properties": { - "strengthOfEvidenceProvided": { - "extends": "strengthOfEvidenceProvided", - "type": "string", - "enum": [ - "PS3_Strong", - "PS3_Moderate", - "PS3_Supporting", - "BS3_Strong", - "BS3_Moderate", - "BS3_Supporting" - ], - "description": "The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. " - } - } - } - ] -} \ No newline at end of file diff --git a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst b/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst deleted file mode 100644 index 98a5d68..0000000 --- a/schema/va-spec/base/def/CohortAlleleFrequencyStudyResult.rst +++ /dev/null @@ -1,147 +0,0 @@ -.. 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 StudyResult that reports measures related to the frequency of an Allele in a cohort - -**Information Model** - -Some CohortAlleleFrequencyStudyResult attributes are inherited from :ref:`gks-core:StudyResult`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - ancillaryResults - - - .. raw:: html - - D - - object - - 0..1 - - - * - qualityMeasures - - - .. raw:: html - - D - - object - - 0..1 - - - * - type - - - - string - - 1..1 - - MUST be "CohortAlleleFrequencyStudyResult". - * - sourceDataSet - - - .. raw:: html - - ⋮ - - :ref:`DataSet` - - 0..m - - The dataset from which the CohortAlleleFrequencyStudyResult was reported. - * - focusAllele - - - - :ref:`Allele` | string - - 1..1 - - The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD. - * - focusAlleleCount - - - - integer - - 1..1 - - The number of occurrences of the focusAllele in the cohort. - * - locusAlleleCount - - - - integer - - 1..1 - - The number of occurrences of all alleles at the locus in the cohort (sometimes referred to as "allele number") - * - focusAlleleFrequency - - - - number - - 1..1 - - The frequency of the focusAllele in the cohort. - * - cohort - - - - :ref:`StudyGroup` - - 1..1 - - The cohort from which the frequency was derived. - * - subCohortFrequency - - - .. raw:: html - - ⋮ - - :ref:`CohortAlleleFrequencyStudyResult` - - 0..m - - A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups. diff --git a/schema/va-spec/base/def/Condition.rst b/schema/va-spec/base/def/Condition.rst deleted file mode 100644 index edcb621..0000000 --- a/schema/va-spec/base/def/Condition.rst +++ /dev/null @@ -1,22 +0,0 @@ -.. 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 set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement. - -**Information Model** - - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyProposition.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyProposition.rst deleted file mode 100644 index 691ee85..0000000 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyProposition.rst +++ /dev/null @@ -1,89 +0,0 @@ -.. 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 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). - -**Information Model** - -Some ExperimentalVariantFunctionalImpactStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - type - - - - string - - 1..1 - - MUST be "ExperimentalVariantFunctionalImpactStudyProposition". - * - subjectVariant - - - - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A protein or genomic contextual or canonical molecular variant. - * - predicate - - - - string - - 1..1 - - The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter. - * - objectSequenceFeature - - - - :ref:`iriReference` | :ref:`MappableConcept` - - 1..1 - - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. - * - studyContextQualifier - - - - :ref:`Document` | :ref:`iriReference` - - 1..1 - - The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. - * - impactTypeQualifier - - - - string - - 0..1 - - 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). diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst deleted file mode 100644 index c6c36f4..0000000 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyResult.rst +++ /dev/null @@ -1,137 +0,0 @@ -.. 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 StudyResult that reports a functional impact score from a variant functional assay or study. - -**Information Model** - -Some ExperimentalVariantFunctionalImpactStudyResult attributes are inherited from :ref:`gks-core:StudyResult`. - -.. 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. - * - 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. - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - componentResult - - - .. raw:: html - - ⋮ - - :ref:`StudyResult` - - 0..m - - Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) . - * - studyGroup - - - - :ref:`StudyGroup` - - 0..1 - - A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult. - * - ancillaryResults - - - .. raw:: html - - D - - object - - 0..1 - - - * - qualityMeasures - - - .. raw:: html - - D - - object - - 0..1 - - - * - type - - - - string - - 1..1 - - MUST be "ExperimentalVariantFunctionalImpactStudyResult". - * - focusVariant - - - - :ref:`MolecularVariation` | :ref:`iriReference` - - 0..1 - - The genetic variant for which a functional impact score is generated. - * - functionalImpactScore - - - - number - - 0..1 - - The score of the variant impact measured in the assay or study. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - The assay that was performed to generate the reported functional impact score. - * - sourceDataSet - - - .. raw:: html - - ⋮ - - :ref:`DataSet` - - 0..m - - The full data set that provided the reported the functional impact score. diff --git a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst b/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst deleted file mode 100644 index 29c0f70..0000000 --- a/schema/va-spec/base/def/ExperimentalVariantFunctionalImpactStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 statement 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). - -**Information Model** - -Some ExperimentalVariantFunctionalImpactStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "ExperimentalVariantFunctionalImpactStudyStatement". - * - proposition - - - - :ref:`ExperimentalVariantFunctionalImpactStudyProposition` - - 1..1 - - The proposition for which the study provides evidence - that the subject variant impacts the function of the object sequence feature. diff --git a/schema/va-spec/base/def/Therapeutic.rst b/schema/va-spec/base/def/Therapeutic.rst deleted file mode 100644 index fbc27d4..0000000 --- a/schema/va-spec/base/def/Therapeutic.rst +++ /dev/null @@ -1,22 +0,0 @@ -.. 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 group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that represents the object of a Therapeutic Response study statement. - -**Information Model** - - -.. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Flags - - Type - - Limits - - Description diff --git a/schema/va-spec/base/def/TherapyGroup.rst b/schema/va-spec/base/def/TherapyGroup.rst deleted file mode 100644 index ab4c0cc..0000000 --- a/schema/va-spec/base/def/TherapyGroup.rst +++ /dev/null @@ -1,49 +0,0 @@ -.. 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 group of therapies that are applied together in the context of a Therapeutic Response study statement. - -**Information Model** - -Some TherapyGroup attributes are inherited from :ref:`gks-core:Element`. - -.. 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 data element 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. - * - 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. - * - groupType - - - - string - - 0..1 - - The type of the therapy group. - * - therapies - - - .. raw:: html - - ⋮ - - :ref:`MappableConcept` - - 2..m - - A list of therapies that are applied together in the context of a Therapeutic Response study statement. diff --git a/schema/va-spec/base/def/TraitSet.rst b/schema/va-spec/base/def/TraitSet.rst deleted file mode 100644 index b88795a..0000000 --- a/schema/va-spec/base/def/TraitSet.rst +++ /dev/null @@ -1,44 +0,0 @@ -.. 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 set of traits that are co-occurring in the context of a Variant Pathogenicity statement. - -**Information Model** - -Some TraitSet attributes are inherited from :ref:`gks-core:Element`. - -.. 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 data element 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. - * - 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. - * - traits - - - .. raw:: html - - ⋮ - - :ref:`MappableConcept` - - 2..m - - A list of traits that are co-occurring in the context of a Variant Pathogenicity statement. diff --git a/schema/va-spec/base/def/VariantDiagnosticStudyProposition.rst b/schema/va-spec/base/def/VariantDiagnosticStudyProposition.rst deleted file mode 100644 index 583dc69..0000000 --- a/schema/va-spec/base/def/VariantDiagnosticStudyProposition.rst +++ /dev/null @@ -1,94 +0,0 @@ -.. 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 reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. - -**Information Model** - -Some VariantDiagnosticStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - type - - - - string - - 1..1 - - MUST be "VariantDiagnosticStudyProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Proposition. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The disease that is evaluated for diagnosis. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the proposition should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Proposition. diff --git a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst b/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst deleted file mode 100644 index f0fae69..0000000 --- a/schema/va-spec/base/def/VariantDiagnosticStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. - -**Information Model** - -Some VariantDiagnosticStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantDiagnosticStudyStatement". - * - proposition - - - - :ref:`VariantDiagnosticStudyProposition` - - 1..1 - - The proposition for which the study provides evidence - that the subject variant is associated with the object disease. diff --git a/schema/va-spec/base/def/VariantOncogenicityStudyProposition.rst b/schema/va-spec/base/def/VariantOncogenicityStudyProposition.rst deleted file mode 100644 index 7c47fb5..0000000 --- a/schema/va-spec/base/def/VariantOncogenicityStudyProposition.rst +++ /dev/null @@ -1,94 +0,0 @@ -.. 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 reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. - -**Information Model** - -Some VariantOncogenicityStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - type - - - - string - - 1..1 - - MUST be "VariantOncogenicityStudyProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Proposition. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectTumorType - - - - :ref:`Condition` | :ref:`MappableConcept` - - 1..1 - - The tumor type for which the variant impact is evaluated. - * - 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 oncogenic role in the Proposition. diff --git a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst b/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst deleted file mode 100644 index 0e60b61..0000000 --- a/schema/va-spec/base/def/VariantOncogenicityStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. - -**Information Model** - -Some VariantOncogenicityStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantOncogenicityStudyStatement". - * - proposition - - - - :ref:`VariantOncogenicityStudyProposition` - - 1..1 - - The proposition for which the study provides evidence - that the subject variant is associated with the object tumor type. diff --git a/schema/va-spec/base/def/VariantPathogenicityEvidenceLine.rst b/schema/va-spec/base/def/VariantPathogenicityEvidenceLine.rst deleted file mode 100644 index 43b6b82..0000000 --- a/schema/va-spec/base/def/VariantPathogenicityEvidenceLine.rst +++ /dev/null @@ -1,126 +0,0 @@ -.. 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** - -An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. - -**Information Model** - -Some VariantPathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:EvidenceLine`. - -.. 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. - * - 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. - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - scoreOfEvidenceProvided - - - - number - - 0..1 - - A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value. - * - type - - - - string - - 1..1 - - MUST be "VariantPathogenicityEvidenceLine". - * - hasEvidenceItems - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result). - * - directionOfEvidenceProvided - - - - string - - 0..1 - - The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral) - * - strengthOfEvidenceProvided - - - - {'$ref': '/ga4gh/schema/gks-core/1.x/json/MappableConcept'} - - 0..1 - - The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. - * - targetProposition - - - - :ref:`VariantPathogenicityProposition` - - 0..1 - - The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant. diff --git a/schema/va-spec/base/def/VariantPathogenicityProposition.rst b/schema/va-spec/base/def/VariantPathogenicityProposition.rst deleted file mode 100644 index 9c62f3b..0000000 --- a/schema/va-spec/base/def/VariantPathogenicityProposition.rst +++ /dev/null @@ -1,97 +0,0 @@ -.. 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 describing the role of a variant in causing an inherited condition. - -**Information Model** - -Some VariantPathogenicityProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - 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 - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The :ref:`Condition` for which the variant impact is stated. - * - penetranceQualifier - - - - string - - 0..1 - - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. - * - modeOfInheritanceQualifier - - - .. raw:: html - - ⋮ - - :ref:`Coding` - - 0..m - - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. - * - geneContextQualifier - - - - :ref:`MappableConcept` | :ref:`iriReference` - - 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). diff --git a/schema/va-spec/base/def/VariantPathogenicityStatement.rst b/schema/va-spec/base/def/VariantPathogenicityStatement.rst deleted file mode 100644 index 7311257..0000000 --- a/schema/va-spec/base/def/VariantPathogenicityStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement describing the role of a variant in causing an inherited condition. - -**Information Model** - -Some VariantPathogenicityStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantPathogenicityStatement". - * - proposition - - - - :ref:`VariantPathogenicityProposition` - - 1..1 - - The proposition that the subject variant is associated with the object disease. - * - classification - - - - :ref:`MappableConcept` - - 1..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. diff --git a/schema/va-spec/base/def/VariantPrognosticStudyProposition.rst b/schema/va-spec/base/def/VariantPrognosticStudyProposition.rst deleted file mode 100644 index 4945d8a..0000000 --- a/schema/va-spec/base/def/VariantPrognosticStudyProposition.rst +++ /dev/null @@ -1,94 +0,0 @@ -.. 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 reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. - -**Information Model** - -Some VariantPrognosticStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - type - - - - string - - 1..1 - - MUST be "VariantPrognosticStudyProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Proposition. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The disease that is evaluated for outcome. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the proposition should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the prognostic association in the Proposition. diff --git a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst b/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst deleted file mode 100644 index ce58488..0000000 --- a/schema/va-spec/base/def/VariantPrognosticStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. - -**Information Model** - -Some VariantPrognosticStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantPrognosticStudyStatement". - * - proposition - - - - :ref:`VariantPrognosticStudyProposition` - - 1..1 - - The proposition for which the study provides evidence - that the subject variant is associated with the object disease outcome. diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseStudyProposition.rst b/schema/va-spec/base/def/VariantTherapeuticResponseStudyProposition.rst deleted file mode 100644 index b1be3ea..0000000 --- a/schema/va-spec/base/def/VariantTherapeuticResponseStudyProposition.rst +++ /dev/null @@ -1,100 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. - -**Information Model** - -Some VariantTherapeuticResponseStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - type - - - - string - - 1..1 - - MUST be "VariantTherapeuticResponseStudyProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Statement. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectTherapeutic - - - - :ref:`Therapeutic` | :ref:`iriReference` - - 1..1 - - A drug administration or other therapeutic procedure that the neoplasm is intended to respond to. - * - conditionQualifier - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. - diff --git a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst b/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst deleted file mode 100644 index 022623b..0000000 --- a/schema/va-spec/base/def/VariantTherapeuticResponseStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. - -**Information Model** - -Some VariantTherapeuticResponseStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantTherapeuticResponseStudyStatement". - * - proposition - - - - :ref:`VariantTherapeuticResponseStudyProposition` - - 1..1 - - Reports the conclusion of the study, which is that the subject variant is associated with therapeutic sensitivity or resistance to the object therapeutic. diff --git a/schema/va-spec/base/def/XCohortAlleleFrequencyStudyResult.rst b/schema/va-spec/base/def/XCohortAlleleFrequencyStudyResult.rst deleted file mode 100644 index 5c9b612..0000000 --- a/schema/va-spec/base/def/XCohortAlleleFrequencyStudyResult.rst +++ /dev/null @@ -1,147 +0,0 @@ -.. 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 StudyResult that reports measures related to the frequency of an Allele in a cohort - -**Information Model** - -Some XCohortAlleleFrequencyStudyResult attributes are inherited from :ref:`gks-core:StudyResult`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - ancillaryResults - - - .. raw:: html - - D - - object - - 0..1 - - - * - qualityMeasures - - - .. raw:: html - - D - - object - - 0..1 - - - * - type - - - - string - - 1..1 - - MUST be "CohortAlleleFrequencyStudyResult". - * - sourceDataSet - - - .. raw:: html - - ⋮ - - :ref:`DataSet` - - 0..m - - The dataset from which the CohortAlleleFrequencyStudyResult was reported. - * - focusAllele - - - - :ref:`Allele` | string - - 1..1 - - The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD. - * - focusAlleleCount - - - - integer - - 1..1 - - The number of occurrences of the focusAllele in the cohort. - * - locusAlleleCount - - - - integer - - 1..1 - - The number of occurrences of all alleles at the locus in the cohort (sometimes referred to as "allele number") - * - focusAlleleFrequency - - - - number - - 1..1 - - The frequency of the focusAllele in the cohort. - * - cohort - - - - :ref:`StudyGroup` - - 1..1 - - The cohort from which the frequency was derived. - * - subCohortFrequency - - - .. raw:: html - - ⋮ - - :ref:`XCohortAlleleFrequencyStudyResult` - - 0..m - - A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups. diff --git a/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyProposition.rst b/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyProposition.rst deleted file mode 100644 index 6a3c07e..0000000 --- a/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyProposition.rst +++ /dev/null @@ -1,89 +0,0 @@ -.. 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 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). - -**Information Model** - -Some XExperimentalVariantFunctionalImpactStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - type - - - - string - - 1..1 - - MUST be "ExperimentalVariantFunctionalImpactStudyProposition". - * - subjectVariant - - - - :ref:`MolecularVariation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A protein or genomic contextual or canonical molecular variant. - * - predicate - - - - string - - 1..1 - - The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter. - * - objectSequenceFeature - - - - :ref:`iriReference` | :ref:`MappableConcept` - - 1..1 - - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed. - * - studyContextQualifier - - - - :ref:`Document` | :ref:`iriReference` - - 1..1 - - The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. - * - impactTypeQualifier - - - - string - - 0..1 - - 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). diff --git a/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyResult.rst b/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyResult.rst deleted file mode 100644 index 373acd3..0000000 --- a/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyResult.rst +++ /dev/null @@ -1,137 +0,0 @@ -.. 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 StudyResult that reports a functional impact score from a variant functional assay or study. - -**Information Model** - -Some XExperimentalVariantFunctionalImpactStudyResult attributes are inherited from :ref:`gks-core:StudyResult`. - -.. 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. - * - 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. - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - componentResult - - - .. raw:: html - - ⋮ - - :ref:`StudyResult` - - 0..m - - Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) . - * - studyGroup - - - - :ref:`StudyGroup` - - 0..1 - - A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult. - * - ancillaryResults - - - .. raw:: html - - D - - object - - 0..1 - - - * - qualityMeasures - - - .. raw:: html - - D - - object - - 0..1 - - - * - type - - - - string - - 1..1 - - MUST be "ExperimentalVariantFunctionalImpactStudyResult". - * - focusVariant - - - - :ref:`MolecularVariation` | :ref:`iriReference` - - 0..1 - - The genetic variant for which a functional impact score is generated. - * - functionalImpactScore - - - - number - - 0..1 - - The score of the variant impact measured in the assay or study. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - The assay that was performed to generate the reported functional impact score. - * - sourceDataSet - - - .. raw:: html - - ⋮ - - :ref:`DataSet` - - 0..m - - The full data set that provided the reported the functional impact score. diff --git a/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyStatement.rst b/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyStatement.rst deleted file mode 100644 index 6868001..0000000 --- a/schema/va-spec/base/def/XExperimentalVariantFunctionalImpactStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 statement 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). - -**Information Model** - -Some XExperimentalVariantFunctionalImpactStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "ExperimentalVariantFunctionalImpactStudyStatement". - * - proposition - - - - :ref:`XExperimentalVariantFunctionalImpactStudyProposition` - - 1..1 - - The proposition for which the study provides evidence - that the subject variant impacts the function of the object sequence feature. diff --git a/schema/va-spec/base/def/XVariantDiagnosticStudyProposition.rst b/schema/va-spec/base/def/XVariantDiagnosticStudyProposition.rst deleted file mode 100644 index 8ba075b..0000000 --- a/schema/va-spec/base/def/XVariantDiagnosticStudyProposition.rst +++ /dev/null @@ -1,94 +0,0 @@ -.. 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 reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. - -**Information Model** - -Some XVariantDiagnosticStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - type - - - - string - - 1..1 - - MUST be "VariantDiagnosticStudyProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Proposition. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The disease that is evaluated for diagnosis. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the proposition should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Proposition. diff --git a/schema/va-spec/base/def/XVariantDiagnosticStudyStatement.rst b/schema/va-spec/base/def/XVariantDiagnosticStudyStatement.rst deleted file mode 100644 index aaa2348..0000000 --- a/schema/va-spec/base/def/XVariantDiagnosticStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results. - -**Information Model** - -Some XVariantDiagnosticStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantDiagnosticStudyStatement". - * - proposition - - - - :ref:`XVariantDiagnosticStudyProposition` - - 1..1 - - The proposition for which the study provides evidence - that the subject variant is associated with the object disease. diff --git a/schema/va-spec/base/def/XVariantOncogenicityStudyProposition.rst b/schema/va-spec/base/def/XVariantOncogenicityStudyProposition.rst deleted file mode 100644 index 9f7d2de..0000000 --- a/schema/va-spec/base/def/XVariantOncogenicityStudyProposition.rst +++ /dev/null @@ -1,94 +0,0 @@ -.. 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 reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. - -**Information Model** - -Some XVariantOncogenicityStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - type - - - - string - - 1..1 - - MUST be "VariantOncogenicityStudyProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Proposition. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectTumorType - - - - :ref:`Condition` | :ref:`MappableConcept` - - 1..1 - - The tumor type for which the variant impact is evaluated. - * - 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 oncogenic role in the Proposition. diff --git a/schema/va-spec/base/def/XVariantOncogenicityStudyStatement.rst b/schema/va-spec/base/def/XVariantOncogenicityStudyStatement.rst deleted file mode 100644 index 66d55ce..0000000 --- a/schema/va-spec/base/def/XVariantOncogenicityStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results. - -**Information Model** - -Some XVariantOncogenicityStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantOncogenicityStudyStatement". - * - proposition - - - - :ref:`XVariantOncogenicityStudyProposition` - - 1..1 - - The proposition for which the study provides evidence - that the subject variant is associated with the object tumor type. diff --git a/schema/va-spec/base/def/XVariantPathogenicityEvidenceLine.rst b/schema/va-spec/base/def/XVariantPathogenicityEvidenceLine.rst deleted file mode 100644 index d559f99..0000000 --- a/schema/va-spec/base/def/XVariantPathogenicityEvidenceLine.rst +++ /dev/null @@ -1,126 +0,0 @@ -.. 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** - -An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. - -**Information Model** - -Some XVariantPathogenicityEvidenceLine attributes are inherited from :ref:`gks-core:EvidenceLine`. - -.. 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. - * - 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. - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - scoreOfEvidenceProvided - - - - number - - 0..1 - - A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value. - * - type - - - - string - - 1..1 - - MUST be "VariantPathogenicityEvidenceLine". - * - hasEvidenceItems - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result). - * - directionOfEvidenceProvided - - - - string - - 0..1 - - The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral) - * - strengthOfEvidenceProvided - - - - {'$ref': '/ga4gh/schema/gks-core/1.x/json/MappableConcept'} - - 0..1 - - The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute. - * - targetProposition - - - - :ref:`XVariantPathogenicityProposition` - - 0..1 - - The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant. diff --git a/schema/va-spec/base/def/XVariantPathogenicityProposition.rst b/schema/va-spec/base/def/XVariantPathogenicityProposition.rst deleted file mode 100644 index 4837b60..0000000 --- a/schema/va-spec/base/def/XVariantPathogenicityProposition.rst +++ /dev/null @@ -1,97 +0,0 @@ -.. 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 describing the role of a variant in causing an inherited condition. - -**Information Model** - -Some XVariantPathogenicityProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - 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 - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The :ref:`Condition` for which the variant impact is stated. - * - penetranceQualifier - - - - string - - 0..1 - - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. - * - modeOfInheritanceQualifier - - - .. raw:: html - - ⋮ - - :ref:`Coding` - - 0..m - - Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify. - * - geneContextQualifier - - - - :ref:`MappableConcept` | :ref:`iriReference` - - 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). diff --git a/schema/va-spec/base/def/XVariantPathogenicityStatement.rst b/schema/va-spec/base/def/XVariantPathogenicityStatement.rst deleted file mode 100644 index 12a57b7..0000000 --- a/schema/va-spec/base/def/XVariantPathogenicityStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement describing the role of a variant in causing an inherited condition. - -**Information Model** - -Some XVariantPathogenicityStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantPathogenicityStatement". - * - proposition - - - - :ref:`XVariantPathogenicityProposition` - - 1..1 - - The proposition that the subject variant is associated with the object disease. diff --git a/schema/va-spec/base/def/XVariantPrognosticStudyProposition.rst b/schema/va-spec/base/def/XVariantPrognosticStudyProposition.rst deleted file mode 100644 index d9a353f..0000000 --- a/schema/va-spec/base/def/XVariantPrognosticStudyProposition.rst +++ /dev/null @@ -1,94 +0,0 @@ -.. 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 reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. - -**Information Model** - -Some XVariantPrognosticStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - type - - - - string - - 1..1 - - MUST be "VariantPrognosticStudyProposition". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Proposition. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectCondition - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - The disease that is evaluated for outcome. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the proposition should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the prognostic association in the Proposition. diff --git a/schema/va-spec/base/def/XVariantPrognosticStudyStatement.rst b/schema/va-spec/base/def/XVariantPrognosticStudyStatement.rst deleted file mode 100644 index 7fa323c..0000000 --- a/schema/va-spec/base/def/XVariantPrognosticStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results. - -**Information Model** - -Some XVariantPrognosticStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantPrognosticStudyStatement". - * - proposition - - - - :ref:`XVariantPrognosticStudyProposition` - - 1..1 - - The proposition for which the study provides evidence - that the subject variant is associated with the object disease outcome. diff --git a/schema/va-spec/base/def/XVariantTherapeuticResponseStudyProposition.rst b/schema/va-spec/base/def/XVariantTherapeuticResponseStudyProposition.rst deleted file mode 100644 index f025b2b..0000000 --- a/schema/va-spec/base/def/XVariantTherapeuticResponseStudyProposition.rst +++ /dev/null @@ -1,100 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. - -**Information Model** - -Some XVariantTherapeuticResponseStudyProposition attributes are inherited from :ref:`gks-core: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. - * - 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. - * - type - - - - string - - 1..1 - - Must be "Proposition" - * - propositionText - - - - string - - 0..1 - - A natural-language expression of the Proposition's meaning. e.g. "BRCA2 c.8023A>G is pathogenic for Breast Cancer". - * - subjectVariant - - - - :ref:`Variation` | :ref:`CategoricalVariant` | :ref:`iriReference` - - 1..1 - - A variant that is the subject of the Statement. - * - predicate - - - - string - - 1..1 - - The relationship declared to hold between the subject and the object of the Statement. - * - objectTherapeutic - - - - :ref:`Therapeutic` | :ref:`iriReference` - - 1..1 - - A drug administration or other therapeutic procedure that the neoplasm is intended to respond to. - * - conditionQualifier - - - - :ref:`Condition` | :ref:`iriReference` - - 1..1 - - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements. - * - alleleOriginQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined). - * - allelePrevalenceQualifier - - - - string - - 0..1 - - Reports whether the statement should be interpreted in the context of the variant being rare or common. - * - geneContextQualifier - - - - :ref:`MappableConcept` - - 0..1 - - Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. - diff --git a/schema/va-spec/base/def/XVariantTherapeuticResponseStudyStatement.rst b/schema/va-spec/base/def/XVariantTherapeuticResponseStudyStatement.rst deleted file mode 100644 index e0da1e2..0000000 --- a/schema/va-spec/base/def/XVariantTherapeuticResponseStudyStatement.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. 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 Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results. - -**Information Model** - -Some XVariantTherapeuticResponseStudyStatement attributes are inherited from :ref:`gks-core:Statement`. - -.. 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. - * - 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. - * - specifiedBy - - - - :ref:`Method` | :ref:`iriReference` - - 0..1 - - A specification that describes all or part of the process that led to creation of the Information Entity - * - contributions - - - .. raw:: html - - ⋮ - - :ref:`Contribution` - - 0..m - - Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity. - * - reportedIn - - - .. raw:: html - - ⋮ - - :ref:`Document` | :ref:`iriReference` - - 0..m - - A document in which the the Information Entity is reported. - * - dateAuthored - - - - string - - 0..1 - - Indicates when the information content expressed in the Information Entity was generated. - * - derivedFrom - - - .. raw:: html - - ⋮ - - :ref:`InformationEntity` - - 0..m - - Another Information Entity from which this Information Entity is derived, in whole or in part. - * - recordMetadata - - - - :ref:`RecordMetadata` - - 0..1 - - Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries). - * - direction - - - - string - - 0..1 - - A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates. - * - strength - - - - :ref:`MappableConcept` - - 0..1 - - A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it. - * - score - - - - number - - 0..1 - - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. - * - statementText - - - - string - - 0..1 - - A natural-language expression of what a Statement asserts to be true. - * - classification - - - - :ref:`MappableConcept` - - 0..1 - - A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject. - * - hasEvidenceLines - - - .. raw:: html - - ⋮ - - :ref:`EvidenceLine` - - 0..m - - An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items). - * - type - - - - string - - 1..1 - - MUST be "VariantTherapeuticResponseStudyStatement". - * - proposition - - - - :ref:`XVariantTherapeuticResponseStudyProposition` - - 1..1 - - Reports the conclusion of the study, which is that the subject variant is associated with therapeutic sensitivity or resistance to the object therapeutic. diff --git a/schema/va-spec/base/json/CohortAlleleFrequencyStudyResult b/schema/va-spec/base/json/CohortAlleleFrequencyStudyResult deleted file mode 100644 index a4d4435..0000000 --- a/schema/va-spec/base/json/CohortAlleleFrequencyStudyResult +++ /dev/null @@ -1,165 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/CohortAlleleFrequencyStudyResult", - "title": "CohortAlleleFrequencyStudyResult", - "maturity": "draft", - "type": "object", - "description": "A StudyResult that reports measures related to the frequency of an Allele in a cohort", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "ancillaryResults": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true - }, - "qualityMeasures": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true - }, - "type": { - "type": "string", - "const": "CohortAlleleFrequencyStudyResult", - "default": "CohortAlleleFrequencyStudyResult", - "description": "MUST be \"CohortAlleleFrequencyStudyResult\"." - }, - "sourceDataSet": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/DataSet" - }, - "description": "The dataset from which the CohortAlleleFrequencyStudyResult was reported.", - "maximum": 1, - "$comment": "In most cases, a StudyResult will be generated using data from one source dataset - but it is possible multiple datasets related to a single study contain data about a particular focus that get collected into a single StudyResult instance.", - "additionalProperties": false - }, - "focusAllele": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" - }, - { - "type": "string", - "format": "uri-reference", - "description": "The Allele for which frequency results are reported." - } - ], - "description": "The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD.", - "$comment": "The 'focus' of a StudyResult is the what anchors selection of all data items and provenance information that it contains. This focus may be a single participant or subject of a study (e.g. one patient in a clinical study, or one allele in a population frequency analysis). It may be a study group defined as an experimental unit in the study (e.g. a specific treatment arm of a clinical study). Or it may be a variable defined as a unit of analysis in the study (e.g. 'exposure to nicotine' in an analysis correlating this variable with clinical outcomes)." - }, - "focusAlleleCount": { - "type": "integer", - "description": "The number of occurrences of the focusAllele in the cohort." - }, - "locusAlleleCount": { - "type": "integer", - "description": "The number of occurrences of all alleles at the locus in the cohort (sometimes referred to as \"allele number\")" - }, - "focusAlleleFrequency": { - "type": "number", - "description": "The frequency of the focusAllele in the cohort." - }, - "cohort": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyGroup", - "description": "The cohort from which the frequency was derived.", - "$comment": "For example, in a StudyResult holding allele frequency data, this attribute points to a StudyGroup object that describes characteristics of the population that the frequency data was generated from (e.g. 'East Asian', 'Female')." - }, - "subCohortFrequency": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/CohortAlleleFrequencyStudyResult" - }, - "description": "A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups.", - "$comment": "This attribute allows data creators to break down a StudyResult into finer-grained StudyResult instances with a narrower scope. For example, a StudyResult about the frequency of an allele in a global population of individuals can be broken down into separate 'component' Results about distinct subpopulations of individuals in the source data (e.g. frequency of the allele in asian vs african subpopulations, or male vs female subgroups)." - } - }, - "required": [ - "cohort", - "focusAllele", - "focusAlleleCount", - "focusAlleleFrequency", - "locusAlleleCount", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/Condition b/schema/va-spec/base/json/Condition deleted file mode 100644 index 479190e..0000000 --- a/schema/va-spec/base/json/Condition +++ /dev/null @@ -1,15 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/Condition", - "title": "Condition", - "maturity": "draft", - "description": "A set of trais (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/TraitSet" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - ] -} \ No newline at end of file diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyProposition b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyProposition deleted file mode 100644 index 8173594..0000000 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyProposition +++ /dev/null @@ -1,115 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyProposition", - "title": "ExperimentalVariantFunctionalImpactStudyProposition", - "maturity": "draft", - "type": "object", - "description": "A proposition reporting a conclusion from a single assay or study about the functional impact of a variant on a sequence feature (typically a gene or gene product).", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "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 \"ExperimentalVariantFunctionalImpactStudyProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "ExperimentalVariantFunctionalImpactStudyProposition", - "default": "ExperimentalVariantFunctionalImpactStudyProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" - } - ], - "description": "A protein or genomic contextual or canonical molecular variant.", - "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." - }, - "predicate": { - "type": "string", - "description": "The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter.", - "$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" - }, - "objectSequenceFeature": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "studyContextQualifier": { - "description": "The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.", - "$comment": "The attribute is required in order to explicitly specify an assay or study context in which the reported impact was observed. It's value can be a Document object, or an IRI pointing to a document that describes the assay/study. This may be a publication, a database record, or a bespoke document.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "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).", - "$comment": "Implementers may use a set of terms to use here that reflect the specific types of functional impact(s) measured by the assay(s) employed. It is recommended that terms are drawn from established terminologies where possible.", - "type": "string", - "enum": [ - "increased activity/function", - "decreased activity/function", - "novel activity/function", - "dominant negative activity/function" - ] - } - }, - "required": [ - "objectSequenceFeature", - "predicate", - "studyContextQualifier", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult deleted file mode 100644 index 7fcd2ea..0000000 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult +++ /dev/null @@ -1,149 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyResult", - "title": "ExperimentalVariantFunctionalImpactStudyResult", - "maturity": "draft", - "type": "object", - "description": "A StudyResult that reports a functional impact score from a variant functional assay or study.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "componentResult": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyResult" - }, - "description": "Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) .", - "$comment": "This attribute allows data creators to break down a StudyResult into finer-grained StudyResult instances with a narrower scope. For example, a StudyResult about the frequency of an allele in a global population of individuals can be broken down into separate 'component' Results about distinct subpopulations of individuals in the source data (e.g. frequency of the allele in asian vs african subpopulations, or male vs female subgroups)." - }, - "studyGroup": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyGroup", - "description": "A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult.", - "$comment": "For example, in a StudyResult holding allele frequency data, this attribute points to a StudyGroup object that describes characteristics of the population that the frequency data was generated from (e.g. 'East Asian', 'Female')." - }, - "ancillaryResults": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true - }, - "qualityMeasures": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true - }, - "type": { - "type": "string", - "const": "ExperimentalVariantFunctionalImpactStudyResult", - "default": "ExperimentalVariantFunctionalImpactStudyResult", - "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyResult\"." - }, - "focusVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" - } - ], - "description": "The genetic variant for which a functional impact score is generated.", - "$comment": "The 'focus' of a StudyResult is the what anchors selection of all data items and provenance information that it contains. This focus may be a single participant or subject of a study (e.g. one patient in a clinical study, or one allele in a population frequency analysis). It may be a study group defined as an experimental unit in the study (e.g. a specific treatment arm of a clinical study). Or it may be a variable defined as a unit of analysis in the study (e.g. 'exposure to nicotine' in an analysis correlating this variable with clinical outcomes)." - }, - "functionalImpactScore": { - "type": "number", - "description": "The score of the variant impact measured in the assay or study." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "The assay that was performed to generate the reported functional impact score.", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "sourceDataSet": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/DataSet" - }, - "description": "The full data set that provided the reported the functional impact score. ", - "maximum": 1, - "$comment": "In most cases, a StudyResult will be generated using data from one source dataset - but it is possible multiple datasets related to a single study contain data about a particular focus that get collected into a single StudyResult instance." - } - }, - "required": [ - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement deleted file mode 100644 index 8764e0a..0000000 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyStatement", - "title": "ExperimentalVariantFunctionalImpactStudyStatement", - "maturity": "draft", - "type": "object", - "description": "A statement reporting a conclusion from a single assay or study about the functional impact of a variant on a sequence feature (typically a gene or gene product).", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "ExperimentalVariantFunctionalImpactStudyStatement", - "default": "ExperimentalVariantFunctionalImpactStudyStatement", - "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/ExperimentalVariantFunctionalImpactStudyProposition", - "description": "The proposition for which the study provides evidence - that the subject variant impacts the function of the object sequence feature.", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/Therapeutic b/schema/va-spec/base/json/Therapeutic deleted file mode 100644 index a39cfc5..0000000 --- a/schema/va-spec/base/json/Therapeutic +++ /dev/null @@ -1,15 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/Therapeutic", - "title": "Therapeutic", - "maturity": "draft", - "description": "A group of therapies (TherapyGroup) or a single therapy (Drug, etc.) that represents the object of a Therapeutic Response study statement.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/TherapyGroup" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - ] -} \ No newline at end of file diff --git a/schema/va-spec/base/json/TherapyGroup b/schema/va-spec/base/json/TherapyGroup deleted file mode 100644 index 37f59c5..0000000 --- a/schema/va-spec/base/json/TherapyGroup +++ /dev/null @@ -1,38 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/TherapyGroup", - "title": "TherapyGroup", - "type": "object", - "maturity": "draft", - "description": "A group of therapies that are applied together in the context of a Therapeutic Response study statement.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the data element 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." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "groupType": { - "type": "string", - "description": "The type of the therapy group." - }, - "therapies": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "description": "A list of therapies that are applied together in the context of a Therapeutic Response study statement.", - "minItems": 2 - } - }, - "required": [], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/TraitSet b/schema/va-spec/base/json/TraitSet deleted file mode 100644 index a19845f..0000000 --- a/schema/va-spec/base/json/TraitSet +++ /dev/null @@ -1,34 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/TraitSet", - "title": "TraitSet", - "type": "object", - "maturity": "draft", - "description": "A set of traits that are co-occurring in the context of a Variant Pathogenicity statement.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "traits": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "description": "A list of traits that are co-occurring in the context of a Variant Pathogenicity statement.", - "minItems": 2 - } - }, - "required": [], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantDiagnosticStudyProposition b/schema/va-spec/base/json/VariantDiagnosticStudyProposition deleted file mode 100644 index 0d22a15..0000000 --- a/schema/va-spec/base/json/VariantDiagnosticStudyProposition +++ /dev/null @@ -1,115 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticStudyProposition", - "title": "VariantDiagnosticStudyProposition", - "type": "object", - "maturity": "draft", - "description": "A Proposition reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantDiagnosticStudyProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantDiagnosticStudyProposition", - "default": "VariantDiagnosticStudyProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Proposition.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "isDiagnosticInclusionCriterionFor", - "isDiagnosticExclusionCriterionFor" - ] - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The disease that is evaluated for diagnosis.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "type": "string", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", - "type": "string", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Proposition.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "objectCondition", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantDiagnosticStudyStatement b/schema/va-spec/base/json/VariantDiagnosticStudyStatement deleted file mode 100644 index 7b629bf..0000000 --- a/schema/va-spec/base/json/VariantDiagnosticStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticStudyStatement", - "title": "VariantDiagnosticStudyStatement", - "type": "object", - "maturity": "draft", - "description": "A Statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantDiagnosticStudyStatement", - "default": "VariantDiagnosticStudyStatement", - "description": "MUST be \"VariantDiagnosticStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticStudyProposition", - "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object disease. ", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantOncogenicityStudyProposition b/schema/va-spec/base/json/VariantOncogenicityStudyProposition deleted file mode 100644 index 5e318eb..0000000 --- a/schema/va-spec/base/json/VariantOncogenicityStudyProposition +++ /dev/null @@ -1,116 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantOncogenicityStudyProposition", - "title": "VariantOncogenicityStudyProposition", - "maturity": "draft", - "type": "object", - "description": "A Proposition reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantOncogenicityStudyProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantOncogenicityStudyProposition", - "default": "VariantOncogenicityStudyProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Proposition.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "isOncogenicFor", - "isProtectiveFor", - "isPredisposingFor" - ] - }, - "objectTumorType": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The tumor type for which the variant impact is evaluated.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Proposition.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "objectTumorType", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantOncogenicityStudyStatement b/schema/va-spec/base/json/VariantOncogenicityStudyStatement deleted file mode 100644 index 4ebc0fa..0000000 --- a/schema/va-spec/base/json/VariantOncogenicityStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantOncogenicityStudyStatement", - "title": "VariantOncogenicityStudyStatement", - "maturity": "draft", - "type": "object", - "description": "A Statement reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantOncogenicityStudyStatement", - "default": "VariantOncogenicityStudyStatement", - "description": "MUST be \"VariantOncogenicityStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantOncogenicityStudyProposition", - "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object tumor type.", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantPathogenicityEvidenceLine b/schema/va-spec/base/json/VariantPathogenicityEvidenceLine deleted file mode 100644 index 06965ef..0000000 --- a/schema/va-spec/base/json/VariantPathogenicityEvidenceLine +++ /dev/null @@ -1,139 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityEvidenceLine", - "title": "VariantPathogenicityEvidenceLine", - "maturity": "draft", - "type": "object", - "description": "An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. ", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "scoreOfEvidenceProvided": { - "type": "number", - "description": "A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value." - }, - "type": { - "type": "string", - "const": "VariantPathogenicityEvidenceLine", - "default": "VariantPathogenicityEvidenceLine", - "description": "MUST be \"VariantPathogenicityEvidenceLine\"." - }, - "hasEvidenceItems": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result).", - "$comment": "A given Evidence Line may be supported by one or many individual evidence items. What matters is that all evidence items in a given Evidence Line get collectively assessed and assigned direction and strength as a single argument for or against a target proposition.\nDifferent types and scales of information entity can serve as evidence (experimental measurements or observations, data tables or figures, images, prior assertions, etc.) Only when assessed as evidence do we consider the information to be an 'Evidence Item'. For example, a piece of population frequency data about BRCA2 c.8023A>G becomes an Evidence Item when it is assessed for the support it may offer for a target proposition (e.g. the prospect of the variant\u2019s pathogenicity)." - }, - "directionOfEvidenceProvided": { - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ], - "description": "The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral)" - }, - "strengthOfEvidenceProvided": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute.", - "$comment": "Values of this attribute can be defined by for a given profile based on domain/application needs, but should be framed in qualitative terms (e.g. 'strong', 'moderate', 'weak'). The 'scoreOfEvidenceProvided' attribute can be used to report quantitative assessments of evidence provided.", - "type": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "targetProposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition", - "description": "The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). " - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant.", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - } - }, - "required": [ - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantPathogenicityProposition b/schema/va-spec/base/json/VariantPathogenicityProposition deleted file mode 100644 index 94b6c30..0000000 --- a/schema/va-spec/base/json/VariantPathogenicityProposition +++ /dev/null @@ -1,119 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition", - "title": "VariantPathogenicityProposition", - "maturity": "draft", - "type": "object", - "description": "A proposition describing the role of a variant in causing an inherited condition.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "Must be \"VariantPathogenicityProposition\"", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantPathogenicityProposition", - "default": "VariantPathogenicityProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "const": "isCausalFor" - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The Condition for which the variant impact is stated.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "penetranceQualifier": { - "type": "string", - "enum": [ - "high", - "low", - "risk allele" - ], - "description": "Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. " - }, - "modeOfInheritanceQualifier": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding" - }, - "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify." - }, - "geneContextQualifier": { - "description": "Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).", - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - } - }, - "required": [ - "objectCondition", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantPathogenicityStatement b/schema/va-spec/base/json/VariantPathogenicityStatement deleted file mode 100644 index 65fa5aa..0000000 --- a/schema/va-spec/base/json/VariantPathogenicityStatement +++ /dev/null @@ -1,163 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityStatement", - "title": "VariantPathogenicityStatement", - "type": "object", - "maturity": "draft", - "description": "A Statement describing the role of a variant in causing an inherited condition.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantPathogenicityStatement", - "default": "VariantPathogenicityStatement", - "description": "MUST be \"VariantPathogenicityStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityProposition", - "description": "The proposition that the subject variant is associated with the object disease.", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification.", - "properties": { - "label": { - "type": "string", - "enum": [ - "pathogenic", - "likely pathogenic", - "uncertain significance", - "likely benign", - "benign" - ] - } - } - } - }, - "required": [ - "classification", - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantPrognosticStudyProposition b/schema/va-spec/base/json/VariantPrognosticStudyProposition deleted file mode 100644 index 42e3eec..0000000 --- a/schema/va-spec/base/json/VariantPrognosticStudyProposition +++ /dev/null @@ -1,115 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyProposition", - "title": "VariantPrognosticStudyProposition", - "type": "object", - "maturity": "draft", - "description": "A Proposition reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantPrognosticStudyProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantPrognosticStudyProposition", - "default": "VariantPrognosticStudyProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Proposition.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "associatedWithBetterOutcomeFor", - "associatedWithWorseOutcomeFor" - ] - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The disease that is evaluated for outcome.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the prognostic association in the Proposition.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "objectCondition", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantPrognosticStudyStatement b/schema/va-spec/base/json/VariantPrognosticStudyStatement deleted file mode 100644 index df99c24..0000000 --- a/schema/va-spec/base/json/VariantPrognosticStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyStatement", - "title": "VariantPrognosticStudyStatement", - "type": "object", - "maturity": "draft", - "description": "A Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantPrognosticStudyStatement", - "default": "VariantPrognosticStudyStatement", - "description": "MUST be \"VariantPrognosticStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyProposition", - "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object disease outcome.", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantTherapeuticResponseStudyProposition b/schema/va-spec/base/json/VariantTherapeuticResponseStudyProposition deleted file mode 100644 index e417df2..0000000 --- a/schema/va-spec/base/json/VariantTherapeuticResponseStudyProposition +++ /dev/null @@ -1,127 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseStudyProposition", - "title": "VariantTherapeuticResponseStudyProposition", - "maturity": "draft", - "type": "object", - "description": "A Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantTherapeuticResponseStudyProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantTherapeuticResponseStudyProposition", - "default": "VariantTherapeuticResponseStudyProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "predictsSensitivityTo", - "predictsResistanceTo" - ] - }, - "objectTherapeutic": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" - } - ], - "description": "A drug administration or other therapeutic procedure that the neoplasm is intended to respond to.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "conditionQualifier": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. ", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "conditionQualifier", - "objectTherapeutic", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement b/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement deleted file mode 100644 index 0c24bf8..0000000 --- a/schema/va-spec/base/json/VariantTherapeuticResponseStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseStudyStatement", - "title": "VariantTherapeuticResponseStudyStatement", - "maturity": "draft", - "type": "object", - "description": "A Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantTherapeuticResponseStudyStatement", - "default": "VariantTherapeuticResponseStudyStatement", - "description": "MUST be \"VariantTherapeuticResponseStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseStudyProposition", - "description": "Reports the conclusion of the study, which is that the subject variant is associated with therapeutic sensitivity or resistance to the object therapeutic.", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XCohortAlleleFrequencyStudyResult b/schema/va-spec/base/json/XCohortAlleleFrequencyStudyResult deleted file mode 100644 index f0e6339..0000000 --- a/schema/va-spec/base/json/XCohortAlleleFrequencyStudyResult +++ /dev/null @@ -1,165 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XCohortAlleleFrequencyStudyResult", - "title": "XCohortAlleleFrequencyStudyResult", - "maturity": "draft", - "type": "object", - "description": "A StudyResult that reports measures related to the frequency of an Allele in a cohort", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "ancillaryResults": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true - }, - "qualityMeasures": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true - }, - "type": { - "type": "string", - "const": "CohortAlleleFrequencyStudyResult", - "default": "CohortAlleleFrequencyStudyResult", - "description": "MUST be \"CohortAlleleFrequencyStudyResult\"." - }, - "sourceDataSet": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/DataSet" - }, - "description": "The dataset from which the CohortAlleleFrequencyStudyResult was reported.", - "maximum": 1, - "$comment": "In most cases, a StudyResult will be generated using data from one source dataset - but it is possible multiple datasets related to a single study contain data about a particular focus that get collected into a single StudyResult instance.", - "additionalProperties": false - }, - "focusAllele": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" - }, - { - "type": "string", - "format": "uri-reference", - "description": "The Allele for which frequency results are reported." - } - ], - "description": "The specific subject or experimental unit in a Study that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD.", - "$comment": "The 'focus' of a StudyResult is the what anchors selection of all data items and provenance information that it contains. This focus may be a single participant or subject of a study (e.g. one patient in a clinical study, or one allele in a population frequency analysis). It may be a study group defined as an experimental unit in the study (e.g. a specific treatment arm of a clinical study). Or it may be a variable defined as a unit of analysis in the study (e.g. 'exposure to nicotine' in an analysis correlating this variable with clinical outcomes)." - }, - "focusAlleleCount": { - "type": "integer", - "description": "The number of occurrences of the focusAllele in the cohort." - }, - "locusAlleleCount": { - "type": "integer", - "description": "The number of occurrences of all alleles at the locus in the cohort (sometimes referred to as \"allele number\")" - }, - "focusAlleleFrequency": { - "type": "number", - "description": "The frequency of the focusAllele in the cohort." - }, - "cohort": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyGroup", - "description": "The cohort from which the frequency was derived.", - "$comment": "For example, in a StudyResult holding allele frequency data, this attribute points to a StudyGroup object that describes characteristics of the population that the frequency data was generated from (e.g. 'East Asian', 'Female')." - }, - "subCohortFrequency": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XCohortAlleleFrequencyStudyResult" - }, - "description": "A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. This creates a recursive relationship and subcohorts can be further subdivided into more subcohorts. This enables, for example, the description of different ancestry groups and sexes among those ancestry groups.", - "$comment": "This attribute allows data creators to break down a StudyResult into finer-grained StudyResult instances with a narrower scope. For example, a StudyResult about the frequency of an allele in a global population of individuals can be broken down into separate 'component' Results about distinct subpopulations of individuals in the source data (e.g. frequency of the allele in asian vs african subpopulations, or male vs female subgroups)." - } - }, - "required": [ - "cohort", - "focusAllele", - "focusAlleleCount", - "focusAlleleFrequency", - "locusAlleleCount", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyProposition b/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyProposition deleted file mode 100644 index cb8f097..0000000 --- a/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyProposition +++ /dev/null @@ -1,115 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XExperimentalVariantFunctionalImpactStudyProposition", - "title": "XExperimentalVariantFunctionalImpactStudyProposition", - "maturity": "draft", - "type": "object", - "description": "A proposition reporting a conclusion from a single assay or study about the functional impact of a variant on a sequence feature (typically a gene or gene product).", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "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 \"ExperimentalVariantFunctionalImpactStudyProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "ExperimentalVariantFunctionalImpactStudyProposition", - "default": "ExperimentalVariantFunctionalImpactStudyProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" - } - ], - "description": "A protein or genomic contextual or canonical molecular variant.", - "$comment": "While the Core Information Model is domain-agnostic, and supports Statements about any type of Entity, for most VA-Spec implementations the subject will be a some type of genetic or molecular variation. But data creators may want to make statements about other entities or concepts that represent evidence for a Statement about variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)." - }, - "predicate": { - "type": "string", - "description": "The relationship this Proposition describes between the subject Variant and object Sequence Feature whose function it may alter.", - "$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" - }, - "objectSequenceFeature": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is assessed.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "studyContextQualifier": { - "description": "The assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.", - "$comment": "The attribute is required in order to explicitly specify an assay or study context in which the reported impact was observed. It's value can be a Document object, or an IRI pointing to a document that describes the assay/study. This may be a publication, a database record, or a bespoke document.", - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "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).", - "$comment": "Implementers may use a set of terms to use here that reflect the specific types of functional impact(s) measured by the assay(s) employed. It is recommended that terms are drawn from established terminologies where possible.", - "type": "string", - "enum": [ - "increased activity/function", - "decreased activity/function", - "novel activity/function", - "dominant negative activity/function" - ] - } - }, - "required": [ - "objectSequenceFeature", - "predicate", - "studyContextQualifier", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyResult b/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyResult deleted file mode 100644 index 39ac885..0000000 --- a/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyResult +++ /dev/null @@ -1,149 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XExperimentalVariantFunctionalImpactStudyResult", - "title": "XExperimentalVariantFunctionalImpactStudyResult", - "maturity": "draft", - "type": "object", - "description": "A StudyResult that reports a functional impact score from a variant functional assay or study.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "componentResult": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyResult" - }, - "description": "Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population) .", - "$comment": "This attribute allows data creators to break down a StudyResult into finer-grained StudyResult instances with a narrower scope. For example, a StudyResult about the frequency of an allele in a global population of individuals can be broken down into separate 'component' Results about distinct subpopulations of individuals in the source data (e.g. frequency of the allele in asian vs african subpopulations, or male vs female subgroups)." - }, - "studyGroup": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/StudyGroup", - "description": "A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult.", - "$comment": "For example, in a StudyResult holding allele frequency data, this attribute points to a StudyGroup object that describes characteristics of the population that the frequency data was generated from (e.g. 'East Asian', 'Female')." - }, - "ancillaryResults": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true - }, - "qualityMeasures": { - "maturity": "draft", - "$comment": "This field is different from most GKS objects by allowing any content to be added, and so is independently versioned.", - "type": "object", - "additionalProperties": true - }, - "type": { - "type": "string", - "const": "ExperimentalVariantFunctionalImpactStudyResult", - "default": "ExperimentalVariantFunctionalImpactStudyResult", - "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyResult\"." - }, - "focusVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/MolecularVariation" - } - ], - "description": "The genetic variant for which a functional impact score is generated.", - "$comment": "The 'focus' of a StudyResult is the what anchors selection of all data items and provenance information that it contains. This focus may be a single participant or subject of a study (e.g. one patient in a clinical study, or one allele in a population frequency analysis). It may be a study group defined as an experimental unit in the study (e.g. a specific treatment arm of a clinical study). Or it may be a variable defined as a unit of analysis in the study (e.g. 'exposure to nicotine' in an analysis correlating this variable with clinical outcomes)." - }, - "functionalImpactScore": { - "type": "number", - "description": "The score of the variant impact measured in the assay or study." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "The assay that was performed to generate the reported functional impact score.", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "sourceDataSet": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/DataSet" - }, - "description": "The full data set that provided the reported the functional impact score. ", - "maximum": 1, - "$comment": "In most cases, a StudyResult will be generated using data from one source dataset - but it is possible multiple datasets related to a single study contain data about a particular focus that get collected into a single StudyResult instance." - } - }, - "required": [ - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyStatement b/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyStatement deleted file mode 100644 index e369207..0000000 --- a/schema/va-spec/base/json/XExperimentalVariantFunctionalImpactStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XExperimentalVariantFunctionalImpactStudyStatement", - "title": "XExperimentalVariantFunctionalImpactStudyStatement", - "maturity": "draft", - "type": "object", - "description": "A statement reporting a conclusion from a single assay or study about the functional impact of a variant on a sequence feature (typically a gene or gene product).", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "ExperimentalVariantFunctionalImpactStudyStatement", - "default": "ExperimentalVariantFunctionalImpactStudyStatement", - "description": "MUST be \"ExperimentalVariantFunctionalImpactStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XExperimentalVariantFunctionalImpactStudyProposition", - "description": "The proposition for which the study provides evidence - that the subject variant impacts the function of the object sequence feature.", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantDiagnosticStudyProposition b/schema/va-spec/base/json/XVariantDiagnosticStudyProposition deleted file mode 100644 index 56a00f5..0000000 --- a/schema/va-spec/base/json/XVariantDiagnosticStudyProposition +++ /dev/null @@ -1,115 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantDiagnosticStudyProposition", - "title": "XVariantDiagnosticStudyProposition", - "type": "object", - "maturity": "draft", - "description": "A Proposition reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantDiagnosticStudyProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantDiagnosticStudyProposition", - "default": "VariantDiagnosticStudyProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Proposition.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "isDiagnosticInclusionCriterionFor", - "isDiagnosticExclusionCriterionFor" - ] - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The disease that is evaluated for diagnosis.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "type": "string", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", - "type": "string", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the diagnostic association in the Proposition.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "objectCondition", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantDiagnosticStudyStatement b/schema/va-spec/base/json/XVariantDiagnosticStudyStatement deleted file mode 100644 index e96b791..0000000 --- a/schema/va-spec/base/json/XVariantDiagnosticStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantDiagnosticStudyStatement", - "title": "XVariantDiagnosticStudyStatement", - "type": "object", - "maturity": "draft", - "description": "A Statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantDiagnosticStudyStatement", - "default": "VariantDiagnosticStudyStatement", - "description": "MUST be \"VariantDiagnosticStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantDiagnosticStudyProposition", - "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object disease. ", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantOncogenicityStudyProposition b/schema/va-spec/base/json/XVariantOncogenicityStudyProposition deleted file mode 100644 index ea93602..0000000 --- a/schema/va-spec/base/json/XVariantOncogenicityStudyProposition +++ /dev/null @@ -1,116 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantOncogenicityStudyProposition", - "title": "XVariantOncogenicityStudyProposition", - "maturity": "draft", - "type": "object", - "description": "A Proposition reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantOncogenicityStudyProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantOncogenicityStudyProposition", - "default": "VariantOncogenicityStudyProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Proposition.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "isOncogenicFor", - "isProtectiveFor", - "isPredisposingFor" - ] - }, - "objectTumorType": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The tumor type for which the variant impact is evaluated.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the oncogenic role in the Proposition.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "objectTumorType", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantOncogenicityStudyStatement b/schema/va-spec/base/json/XVariantOncogenicityStudyStatement deleted file mode 100644 index 7cbfebf..0000000 --- a/schema/va-spec/base/json/XVariantOncogenicityStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantOncogenicityStudyStatement", - "title": "XVariantOncogenicityStudyStatement", - "maturity": "draft", - "type": "object", - "description": "A Statement reporting a conclusion from a single study that supports or refutes a variant's effect on oncogenesis for a specific tumor type - based on interpretation of the study's results.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantOncogenicityStudyStatement", - "default": "VariantOncogenicityStudyStatement", - "description": "MUST be \"VariantOncogenicityStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantOncogenicityStudyProposition", - "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object tumor type.", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPathogenicityEvidenceLine b/schema/va-spec/base/json/XVariantPathogenicityEvidenceLine deleted file mode 100644 index 92a178d..0000000 --- a/schema/va-spec/base/json/XVariantPathogenicityEvidenceLine +++ /dev/null @@ -1,139 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityEvidenceLine", - "title": "XVariantPathogenicityEvidenceLine", - "maturity": "draft", - "type": "object", - "description": "An Evidence Line that describes the strength and direction of support provided by one or more evidence items for or against the pathogenicity of a variant for a particular disease. ", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "scoreOfEvidenceProvided": { - "type": "number", - "description": "A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value." - }, - "type": { - "type": "string", - "const": "VariantPathogenicityEvidenceLine", - "default": "VariantPathogenicityEvidenceLine", - "description": "MUST be \"VariantPathogenicityEvidenceLine\"." - }, - "hasEvidenceItems": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "An Information Entity that was assessed as evidence in determining the possible pathogenicity of a variant (e.g. a Functional Impact Study Statement or Study Result).", - "$comment": "A given Evidence Line may be supported by one or many individual evidence items. What matters is that all evidence items in a given Evidence Line get collectively assessed and assigned direction and strength as a single argument for or against a target proposition.\nDifferent types and scales of information entity can serve as evidence (experimental measurements or observations, data tables or figures, images, prior assertions, etc.) Only when assessed as evidence do we consider the information to be an 'Evidence Item'. For example, a piece of population frequency data about BRCA2 c.8023A>G becomes an Evidence Item when it is assessed for the support it may offer for a target proposition (e.g. the prospect of the variant\u2019s pathogenicity)." - }, - "directionOfEvidenceProvided": { - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ], - "description": "The direction of support that the Evidence Line is determined to provide for its target Variant Pathogenicity Proposition, based on assessment of its evidence items (i.e. does the evidence line support or dispute the possible pathogenicity of the subject variant, or remain neutral)" - }, - "strengthOfEvidenceProvided": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "The strength of support that an Evidence Line is determined to provide for or against the pathogenicity of the assessed variant. Strength is evaluated relative to the direction indicated by the directionOfEvidenceProvided attribute.", - "$comment": "Values of this attribute can be defined by for a given profile based on domain/application needs, but should be framed in qualitative terms (e.g. 'strong', 'moderate', 'weak'). The 'scoreOfEvidenceProvided' attribute can be used to report quantitative assessments of evidence provided.", - "type": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "targetProposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityProposition", - "description": "The possible fact toward which the strength and direction of evidence provided by functional assay data was evaluated (here, a proposition that the assessed variant may be pathogenic for a particular disease). " - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A method that specifies how evidence items used in the Evidence Line are to be evaluated and weighed as evidence for or against the pathogenicity of the assessed variant.", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - } - }, - "required": [ - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPathogenicityProposition b/schema/va-spec/base/json/XVariantPathogenicityProposition deleted file mode 100644 index 58658c5..0000000 --- a/schema/va-spec/base/json/XVariantPathogenicityProposition +++ /dev/null @@ -1,119 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityProposition", - "title": "XVariantPathogenicityProposition", - "maturity": "draft", - "type": "object", - "description": "A proposition describing the role of a variant in causing an inherited condition.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "Must be \"VariantPathogenicityProposition\"", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantPathogenicityProposition", - "default": "VariantPathogenicityProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "const": "isCausalFor" - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The Condition for which the variant impact is stated.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "penetranceQualifier": { - "type": "string", - "enum": [ - "high", - "low", - "risk allele" - ], - "description": "Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. " - }, - "modeOfInheritanceQualifier": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding" - }, - "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. Use HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) to specify." - }, - "geneContextQualifier": { - "description": "Reports the gene through which the pathogenic effect asserted for the variant is mediated (i.e. it is the variant's impact on this gene that is responsible for causing the condition).", - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - } - }, - "required": [ - "objectCondition", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPathogenicityStatement b/schema/va-spec/base/json/XVariantPathogenicityStatement deleted file mode 100644 index 63cc4c9..0000000 --- a/schema/va-spec/base/json/XVariantPathogenicityStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityStatement", - "title": "XVariantPathogenicityStatement", - "type": "object", - "maturity": "draft", - "description": "A Statement describing the role of a variant in causing an inherited condition.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantPathogenicityStatement", - "default": "VariantPathogenicityStatement", - "description": "MUST be \"VariantPathogenicityStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantPathogenicityProposition", - "description": "The proposition that the subject variant is associated with the object disease.", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPrognosticStudyProposition b/schema/va-spec/base/json/XVariantPrognosticStudyProposition deleted file mode 100644 index dfd0497..0000000 --- a/schema/va-spec/base/json/XVariantPrognosticStudyProposition +++ /dev/null @@ -1,115 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPrognosticStudyProposition", - "title": "XVariantPrognosticStudyProposition", - "type": "object", - "maturity": "draft", - "description": "A Proposition reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "type": { - "type": "string", - "description": "MUST be \"VariantPrognosticStudyProposition\".", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "VariantPrognosticStudyProposition", - "default": "VariantPrognosticStudyProposition" - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Proposition.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "associatedWithBetterOutcomeFor", - "associatedWithWorseOutcomeFor" - ] - }, - "objectCondition": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "The disease that is evaluated for outcome.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the proposition should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the prognostic association in the Proposition.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "objectCondition", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantPrognosticStudyStatement b/schema/va-spec/base/json/XVariantPrognosticStudyStatement deleted file mode 100644 index f4cb933..0000000 --- a/schema/va-spec/base/json/XVariantPrognosticStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantPrognosticStudyStatement", - "title": "XVariantPrognosticStudyStatement", - "type": "object", - "maturity": "draft", - "description": "A Statement reporting a conclusion from a single study about whether a variant is associated with an improved or worse outcome for a disease - based on interpretation of the study's results.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantPrognosticStudyStatement", - "default": "VariantPrognosticStudyStatement", - "description": "MUST be \"VariantPrognosticStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantPrognosticStudyProposition", - "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object disease outcome.", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantTherapeuticResponseStudyProposition b/schema/va-spec/base/json/XVariantTherapeuticResponseStudyProposition deleted file mode 100644 index 8b1b74d..0000000 --- a/schema/va-spec/base/json/XVariantTherapeuticResponseStudyProposition +++ /dev/null @@ -1,127 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantTherapeuticResponseStudyProposition", - "title": "XVariantTherapeuticResponseStudyProposition", - "maturity": "draft", - "type": "object", - "description": "A Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results.", - "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.", - "$comment": "Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to re-use an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/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.", - "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." - }, - "type": { - "type": "string", - "description": "Must be \"Proposition\"", - "$comment": "MUST be the label of a concrete class from the data model.", - "const": "Proposition", - "default": "Proposition" - }, - "propositionText": { - "type": "string", - "description": "A natural-language expression of the Proposition's meaning. e.g. \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\"." - }, - "subjectVariant": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" - } - ], - "description": "A variant that is the subject of the Statement.", - "$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)." - }, - "predicate": { - "type": "string", - "description": "The relationship declared to hold between the subject and the object of the Statement.", - "$comment": "When applied to represent a particular type of Proposition (via 'Profiling'), implementers can define a value set of predicates for the relationships relevant in the domain.", - "enum": [ - "predictsSensitivityTo", - "predictsResistanceTo" - ] - }, - "objectTherapeutic": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Therapeutic" - } - ], - "description": "A drug administration or other therapeutic procedure that the neoplasm is intended to respond to.", - "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject, e.g. for Genetic Variation subjects the object is often a disease, drug, gene, molecular consequence, functional impact on gene or protein." - }, - "conditionQualifier": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - }, - { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Condition" - } - ], - "description": "Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response statements." - }, - "alleleOriginQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or both (combined).", - "enum": [ - "germline", - "somatic", - "combined" - ] - }, - "allelePrevalenceQualifier": { - "type": "string", - "description": "Reports whether the statement should be interpreted in the context of the variant being rare or common.", - "enum": [ - "rare", - "common" - ] - }, - "geneContextQualifier": { - "description": "Reports a gene impacted by the variant, which may contribute to the therapeutic sensitivity or resistance reported in the Statement. ", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - } - }, - "required": [ - "conditionQualifier", - "objectTherapeutic", - "predicate", - "subjectVariant", - "type" - ], - "additionalProperties": false -} \ No newline at end of file diff --git a/schema/va-spec/base/json/XVariantTherapeuticResponseStudyStatement b/schema/va-spec/base/json/XVariantTherapeuticResponseStudyStatement deleted file mode 100644 index 2c627d1..0000000 --- a/schema/va-spec/base/json/XVariantTherapeuticResponseStudyStatement +++ /dev/null @@ -1,150 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/XVariantTherapeuticResponseStudyStatement", - "title": "XVariantTherapeuticResponseStudyStatement", - "maturity": "draft", - "type": "object", - "description": "A Statement reporting a conclusion from a single study about the role of a variant in modulating the response of a neoplasm to drug administration or other therapeutic procedures - based on interpretation of the study's results.", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the Entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.", - "$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." - }, - "label": { - "type": "string", - "description": "A primary name for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the Entity." - }, - "alternativeLabels": { - "type": "array", - "ordered": false, - "items": { - "type": "string" - }, - "description": "Alternative name(s) for the Entity." - }, - "extensions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" - }, - "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", - "$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." - }, - "specifiedBy": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Method" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ], - "description": "A specification that describes all or part of the process that led to creation of the Information Entity", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." - }, - "contributions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Contribution" - }, - "description": "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.", - "$comment": "This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent." - }, - "reportedIn": { - "type": "array", - "ordered": false, - "items": { - "oneOf": [ - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/Document" - }, - { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" - } - ] - }, - "description": "A document in which the the Information Entity is reported." - }, - "dateAuthored": { - "type": "string", - "format": "datetime", - "description": "Indicates when the information content expressed in the Information Entity was generated.", - "$comment": "The term 'authored' is used in the model to refer to the generation of abstract 'information content', as opposed to creation of a concrete encoding of this information in a specific language, format, or physical artifact. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent, and metadata about when a particular concrete encoding of this information was created (e.g. a row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity)." - }, - "derivedFrom": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/InformationEntity" - }, - "description": "Another Information Entity from which this Information Entity is derived, in whole or in part." - }, - "recordMetadata": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/RecordMetadata", - "description": "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).", - "$comment": "This attribute holds a structured RecordMetadata object, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status." - }, - "direction": { - "description": "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'direction' attribute is used to indicate whether the Statement's Proposition is *supported* by the agent's assessment (when evidence favors its validity), is *disputed* by the agent's assessment (when evidence argues against its validity), or remains *neutral* (when conflicting or insufficient evidence exists to assert one direction or the other). (Enumerated values = 'supports', 'disputes', 'neutral').", - "type": "string", - "enum": [ - "supports", - "neutral", - "disputes" - ] - }, - "strength": { - "description": "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject,' 'predicate', 'object', and optional 'qualifier' attributes. An assessment of the Proposition's validity can be captured using 'direction', 'strength', and 'score' attributes. The 'strength' attribute is used to report the strength of this assessment in the direction indicated. Strength can be framed as a *level of confidence* that the Proposition is true or false, or as a *level of evidence* that supports or disputes it. Data creators can define the permissible values for the 'strength' attribute to indicate which of these facets is being assessed (e.g. 'high confidence' vs 'low confidence', or 'strong evidence' vs 'weak evidence') - or they can choose values that don't commit to one or the other if they don't want to make the distinction (e.g. 'high' vs 'medium' vs 'low').", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - }, - "score": { - "type": "number", - "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it.", - "$comment": "Statements put forth a Proposition that expresses some possible fact about the world, and may provide an assessment of this proposition's validity (i.e. how likely it is to be true or false based on evaluated evidence). The semantics of the Proposition are captured in the 'subject', 'predicate', 'object', and optional 'qualifier' attributes. The assessment of the Proposition's validity are captured in 'direction', 'strength', and 'score' attributes. The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score." - }, - "statementText": { - "type": "string", - "description": "A natural-language expression of what a Statement asserts to be true.", - "$comment": "This attribute captures what a Statement says as human readable free text. e.g. that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", or that \"there is moderate evidence supporting the pathogenicity of BRCA2 c.8023A>G for Breast Cancer\". This optional attribute can be used instead of, or as a complement to, a structured representation of Statement semantics that uses the subject-predicate-object-qualifier pattern." - }, - "classification": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." - }, - "hasEvidenceLines": { - "type": "array", - "ordered": false, - "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/EvidenceLine" - }, - "description": "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items).", - "$comment": "Evidence Lines result from the interpretation of one or more pieces of information to build an argument for or against a particular Proposition. These arguments have direction (supporting / disputing) and strength (e.g. strong, moderate, weak) relative to the Proposition they are evaluated against. For example, ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant in different populations may be collectively assessed to provide an argument of 'moderate' strength in 'support of ' a proposition that the variant is pathogenicity for breast cancer. Evidence Lines are useful in cases where a data provider wants to describe in detail how information was assessed as evidence to generate and score different arguments for or against a Statement's proposition. Evidence Lines can be omitted if such information is not available or needed." - }, - "type": { - "type": "string", - "const": "VariantTherapeuticResponseStudyStatement", - "default": "VariantTherapeuticResponseStudyStatement", - "description": "MUST be \"VariantTherapeuticResponseStudyStatement\"." - }, - "proposition": { - "$ref": "/ga4gh/schema/va-spec/1.x/base/json/XVariantTherapeuticResponseStudyProposition", - "description": "Reports the conclusion of the study, which is that the subject variant is associated with therapeutic sensitivity or resistance to the object therapeutic. ", - "$comment": "This attribute supports an alternate modeling pattern, which encapsulates the structured semantics of the possible fact asserted or evaluated by a Statement in a separate 'Proposition' object - instead of using the 'subject', 'predicate', 'object', and 'qualifier' properties defined in the Statement object itself. " - } - }, - "required": [ - "proposition", - "type" - ], - "additionalProperties": false -} \ No newline at end of file