From 997fe5070ca4fea7699e3761aaedf491e546c8bc Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Tue, 26 Nov 2024 23:13:38 -0500 Subject: [PATCH] update to refcurie (#233) * update to refcurie * process refCuries on containers --- .requirements.txt | 2 +- ...frequency-study-result-profile-source.yaml | 9 +- .../va-spec/base/domain-entities-source.yaml | 13 ++- ...al-impact-study-result-profile-source.yaml | 8 +- schema/va-spec/base/json/Contribution | 12 +-- schema/va-spec/base/json/DataSet | 12 +-- schema/va-spec/base/json/Document | 4 +- schema/va-spec/base/json/EvidenceLine | 8 +- ...rimentalVariantFunctionalImpactStudyResult | 2 +- schema/va-spec/base/json/Method | 4 +- schema/va-spec/base/json/Statement | 4 +- schema/va-spec/base/json/TherapyGroup | 4 +- .../base/json/VariantPathogenicityProposition | 8 +- schema/va-spec/base/va-core-source.yaml | 99 ++++++++++--------- 14 files changed, 103 insertions(+), 86 deletions(-) diff --git a/.requirements.txt b/.requirements.txt index 5effd771..4d4ac9b2 100644 --- a/.requirements.txt +++ b/.requirements.txt @@ -2,7 +2,7 @@ pytest sphinx ~= 7.2 sphinx-rtd-theme ~= 1.3 pyyaml -ga4gh.gks.metaschema==0.3.0b17 +ga4gh.gks.metaschema==0.3.1 jsonschema referencing jupyterlab diff --git a/schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml b/schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml index e3effea6..37ea2acf 100644 --- a/schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml +++ b/schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml @@ -8,6 +8,11 @@ imports: vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml +namespaces: + gks.core: /ga4gh/schema/gks-core/1.x/json/ + vrs: /ga4gh/schema/vrs/2.x/json/ + cat-vrs: /ga4gh/schema/cat-vrs/1.x/json/ + $defs: CohortAlleleFrequencyStudyResult: inherits: va-core:StudyResult @@ -28,8 +33,8 @@ $defs: extends: focus description: The Allele for which frequency results are reported. oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Allele" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: vrs:Allele + - $refCurie: gks.core:iriReference focusAlleleCount: type: integer description: The number of occurrences of the focusAllele in the cohort. diff --git a/schema/va-spec/base/domain-entities-source.yaml b/schema/va-spec/base/domain-entities-source.yaml index 8fcb7c82..5598d92e 100644 --- a/schema/va-spec/base/domain-entities-source.yaml +++ b/schema/va-spec/base/domain-entities-source.yaml @@ -6,6 +6,9 @@ strict: true imports: gks-core: ../../gks-core/gks-core-source.yaml +namespaces: + gks.core: /ga4gh/schema/gks-core/1.x/json/ + $defs: # Condition data structure for consolidating the different forms of conditions, individual vs co-occurring traits Condition: @@ -14,7 +17,7 @@ $defs: A set of traits (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement. oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + - $refCurie: gks.core:MappableConcept - $ref: "#/$defs/TraitSet" # TraitSet data structure to provide support for co-occuring traits (i.e. diseases, phenotypes, etc.) @@ -29,7 +32,7 @@ $defs: type: array ordered: false items: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- A list of conditions (diseases, phenotypes, traits) that are co-occurring. minItems: 2 @@ -40,7 +43,7 @@ $defs: description: >- A group of therapies (TherapyGroup) or a single therapy (drug, procedure, behavioral intervention, etc.). oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + - $refCurie: gks.core:MappableConcept - $ref: "#/$defs/TherapyGroup" # TherapyGroup data structure to provide support for combination therapies (i.e. drug treatment, etc.) @@ -52,13 +55,13 @@ $defs: A group of therapies that are applied together to treat a condition. properties: groupType: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: The type of the therapy group. therapies: type: array ordered: false items: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- A list of therapies that are applied together to treat a condition. minItems: 2 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 315da96d..a9f0650b 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 @@ -8,6 +8,10 @@ imports: vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml +namespaces: + gks.core: /ga4gh/schema/gks-core/1.x/json/ + vrs: /ga4gh/schema/vrs/2.x/json/ + $defs: ExperimentalVariantFunctionalImpactStudyResult: inherits: va-core:StudyResult @@ -24,8 +28,8 @@ $defs: focusVariant: extends: focus oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/MolecularVariation" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: vrs:MolecularVariation + - $refCurie: gks.core:iriReference description: The genetic variant for which a functional impact score is generated. functionalImpactScore: type: number diff --git a/schema/va-spec/base/json/Contribution b/schema/va-spec/base/json/Contribution index 4bd7a5e6..774e5dcf 100644 --- a/schema/va-spec/base/json/Contribution +++ b/schema/va-spec/base/json/Contribution @@ -37,14 +37,14 @@ "$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." }, "subtype": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", "description": "A specific type of activity the Activity instance represents.", - "$comment": "This attribute can be used to report a specific type for the Activity in cases where a model does not define Activity subclasses for this purpose. Implementers can define their own set of data set type codes/terms, to match the needs of the domain or application." + "$comment": "This attribute can be used to report a specific type for the Activity in cases where a model does not define Activity subclasses for this purpose. Implementers can define their own set of data set type codes/terms, to match the needs of the domain or application.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, "date": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/date", "description": "The date that the Activity was completed.", - "$comment": "By convention, populate this attribute with the date the activity was completed (e.g. in cases where the activity spans multiple days). The date MUST be formatted as a date string in ISO8601 format \"YYYY-MM-DD\"." + "$comment": "By convention, populate this attribute with the date the activity was completed (e.g. in cases where the activity spans multiple days). The date MUST be formatted as a date string in ISO8601 format \"YYYY-MM-DD\".", + "$ref": "/ga4gh/schema/gks-core/1.x/json/date" }, "specifiedBy": { "type": "array", @@ -73,8 +73,8 @@ "$comment": "Note that this MUST be a single agent (which can be a Person, or an Organization). If multiple Agents contributed to an entity, a separate Contribution instances MUST be created to describe each." }, "activityType": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "The specific type of activity performed or role played by an agent in making the contribution (e.g. for a publication, agents may contribute as a primary author, editor, figure designer, data generator, etc.). Values of this property may be framed as activities, or as contribution roles (e.g. using terms from the Contribution Role Ontology (CRO))." + "description": "The specific type of activity performed or role played by an agent in making the contribution (e.g. for a publication, agents may contribute as a primary author, editor, figure designer, data generator, etc.). Values of this property may be framed as activities, or as contribution roles (e.g. using terms from the Contribution Role Ontology (CRO)).", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" } }, "required": [ diff --git a/schema/va-spec/base/json/DataSet b/schema/va-spec/base/json/DataSet index e346f803..3cc12f2c 100644 --- a/schema/va-spec/base/json/DataSet +++ b/schema/va-spec/base/json/DataSet @@ -47,8 +47,8 @@ "subtype": { "maturity": "draft", "$comment": "This attribute can be used to report a specific type for the DataSet, in cases where a model does not define DataSet subclasses for this purpose. Implementers can define their own set of data set type codes/terms, to match the needs of the domain or application.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A specific type of data set the DataSet instance represents (e.g. a 'clinical data set', a 'sequencing data set', a 'gene expression data set', a 'genome annotation data set')" + "description": "A specific type of data set the DataSet instance represents (e.g. a 'clinical data set', a 'sequencing data set', a 'gene expression data set', a 'genome annotation data set')", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, "reportedIn": { "oneOf": [ @@ -62,9 +62,9 @@ "description": "A document in which the the Method is reported." }, "releaseDate": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/date", "description": "Indicates the date a version of a DataSet was formally released.", - "$comment": "This attribute may apply to version and distribution-level DataSet representations. It refers to when the data set was released, which may be different than the data set was generated." + "$comment": "This attribute may apply to version and distribution-level DataSet representations. It refers to when the data set was released, which may be different than the data set was generated.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/date" }, "version": { "type": "string", @@ -72,9 +72,9 @@ "$comment": "This property can capture version information for resources such as data sets and documents that get published and released as a unit for community use. These may go through rounds of revisions that add or modify content, but don\u2019t change the identity of the resource. Use this attribute in cases where version is not reflected in an identifier associated with the data set." }, "license": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", "description": "A specific license that dictates legal permissions for how a data set can be used (by whom, where, for what purposes, with what additional requirements, etc.)", - "$comment": "Where possible, provide a URL pointing to the license or a description of it (e.g. \"https://creativecommons.org/licenses/by/4.0/\"). Otherwise, provide a free-text name or description of the license (e.g. \"CC-BY\")." + "$comment": "Where possible, provide a URL pointing to the license or a description of it (e.g. \"https://creativecommons.org/licenses/by/4.0/\"). Otherwise, provide a free-text name or description of the license (e.g. \"CC-BY\").", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" } }, "required": [ diff --git a/schema/va-spec/base/json/Document b/schema/va-spec/base/json/Document index bbdbbeba..3addcae5 100644 --- a/schema/va-spec/base/json/Document +++ b/schema/va-spec/base/json/Document @@ -47,8 +47,8 @@ "subtype": { "maturity": "draft", "$comment": "This attribute can be used to report a specific type for the Document, in cases where a model does not define Document subclasses for this purpose. Implementers can define their own set of document type codes/terms, to match the needs of their application.", - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A specific type of document that a Document instance represents (e.g. 'publication', 'patent', 'pathology report')" + "description": "A specific type of document that a Document instance represents (e.g. 'publication', 'patent', 'pathology report')", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, "title": { "type": "string", diff --git a/schema/va-spec/base/json/EvidenceLine b/schema/va-spec/base/json/EvidenceLine index 44af3f2f..3eb8104d 100644 --- a/schema/va-spec/base/json/EvidenceLine +++ b/schema/va-spec/base/json/EvidenceLine @@ -135,17 +135,17 @@ "description": "The direction of support that the Evidence Line is determined to provide toward its target Proposition (supports, disputes, neutral)" }, "strengthOfEvidenceProvided": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", "description": "The strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value.", - "$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." + "$comment": "Values of this attribute can be defined by for a given profile based on domain/application needs, but should be framed in qualitative terms (e.g. 'strong', 'moderate', 'weak'). The 'scoreOfEvidenceProvided' attribute can be used to report quantitative assessments of evidence provided.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, "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." }, "evidenceOutcome": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "A term summarizing the overall outcome of the evidence assessment represented by the Evidence Line, in terms of the direction and strength of support it provides for or against the target Proposition." + "description": "A term summarizing the overall outcome of the evidence assessment represented by the Evidence Line, in terms of the direction and strength of support it provides for or against the target Proposition.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" } }, "required": [ diff --git a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult index 82c2cb07..a980b271 100644 --- a/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult +++ b/schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult @@ -93,7 +93,7 @@ } ], "description": "The assay that was performed to generate the reported functional impact score.", - "$comment": "Examples - a specific experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification. Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')." + "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (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": { "$ref": "/ga4gh/schema/va-spec/1.x/base/json/DataSet", diff --git a/schema/va-spec/base/json/Method b/schema/va-spec/base/json/Method index 92ecd11f..254239ef 100644 --- a/schema/va-spec/base/json/Method +++ b/schema/va-spec/base/json/Method @@ -45,9 +45,9 @@ "default": "Method" }, "subtype": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", "description": "A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol').", - "$comment": "This attribute can be used to report a specific type for the Method, in cases where a model does not define Method subclasses for this purpose. Implementers can define their own set of method type codes/terms, to match the needs of their application." + "$comment": "This attribute can be used to report a specific type for the Method, in cases where a model does not define Method subclasses for this purpose. Implementers can define their own set of method type codes/terms, to match the needs of their application.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, "reportedIn": { "oneOf": [ diff --git a/schema/va-spec/base/json/Statement b/schema/va-spec/base/json/Statement index 5e439f4b..a55d493d 100644 --- a/schema/va-spec/base/json/Statement +++ b/schema/va-spec/base/json/Statement @@ -126,9 +126,9 @@ "description": "A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. Instructions for how to interpret the menaing of a given score may be gleaned from the method or document referenced in 'specifiedBy' attribute. " }, "classification": { - "$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.", - "$comment": "Permissible values for this attribute are typically selected to be succinct and familiar in the target community of practice - and can be provided to report of a statement's conclusion in user-friendly terms. For example, in a Statement assessing the proposition that \"BRCA2 c.8023A>G is pathogenic for Breast Cancer\", and reporting a direction of 'supports' and strength of 'likely', the term 'likely pathogenic' from the ACMG Variant Interpretation Guidelines would be used as a subject classification." + "$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.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, "hasEvidenceLines": { "type": "array", diff --git a/schema/va-spec/base/json/TherapyGroup b/schema/va-spec/base/json/TherapyGroup index 672658af..5a41e68e 100644 --- a/schema/va-spec/base/json/TherapyGroup +++ b/schema/va-spec/base/json/TherapyGroup @@ -20,8 +20,8 @@ "$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": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "The type of the therapy group." + "description": "The type of the therapy group.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, "therapies": { "type": "array", diff --git a/schema/va-spec/base/json/VariantPathogenicityProposition b/schema/va-spec/base/json/VariantPathogenicityProposition index bf9a0d78..49bbfe40 100644 --- a/schema/va-spec/base/json/VariantPathogenicityProposition +++ b/schema/va-spec/base/json/VariantPathogenicityProposition @@ -99,12 +99,12 @@ "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject. When the subject is a genetic variation, the object is often a disease, phenotype, therapeutic intervention, or gene." }, "penetranceQualifier": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "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. " + "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. ", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" }, "modeOfInheritanceQualifier": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept", - "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) are recommended to specify." + "description": "Reports a pattern of inheritance expected for the pathogenic effect of the variant. HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) are recommended to specify.", + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" } }, "required": [ diff --git a/schema/va-spec/base/va-core-source.yaml b/schema/va-spec/base/va-core-source.yaml index e43230e8..92580abe 100644 --- a/schema/va-spec/base/va-core-source.yaml +++ b/schema/va-spec/base/va-core-source.yaml @@ -9,6 +9,11 @@ imports: vrs: ../../vrs/vrs-source.yaml gks-core: ../../gks-core/gks-core-source.yaml +namespaces: + gks.core: /ga4gh/schema/gks-core/1.x/json/ + vrs: /ga4gh/schema/vrs/2.x/json/ + cat-vrs: /ga4gh/schema/cat-vrs/1.x/json/ + $defs: # abstract core classes section -- InformationEntity, Activity, StudyResult, Proposition InformationEntity: @@ -26,7 +31,7 @@ $defs: specifiedBy: oneOf: - $ref: "#/$defs/Method" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:iriReference description: >- A specification that describes all or part of the process that led to creation of the Information Entity @@ -55,10 +60,10 @@ $defs: items: oneOf: - $ref: "#/$defs/Document" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:iriReference description: A document in which the the Information Entity is reported. # dateAuthored: - # $ref: "/ga4gh/schema/gks-core/1.x/json/datetime" + # $refCurie: gks.core: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 @@ -91,7 +96,7 @@ $defs: Activities may use, generate, modify, move, or destroy one or more entities. heritableProperties: subtype: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- A specific type of activity the Activity instance represents. $comment: >- @@ -99,7 +104,7 @@ $defs: a model does not define Activity subclasses for this purpose. Implementers can define their own set of data set type codes/terms, to match the needs of the domain or application. date: - $ref: "/ga4gh/schema/gks-core/1.x/json/date" + $refCurie: gks.core:date description: >- The date that the Activity was completed. $comment: >- @@ -145,9 +150,9 @@ $defs: heritableProperties: focus: oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/Entity" - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:Entity + - $refCurie: gks.core:MappableConcept + - $refCurie: gks.core:iriReference description: >- The specific participant, subject or experimental unit in a Study that data included in the StudyResult object is about - e.g. a particular variant in a population allele frequency @@ -255,9 +260,9 @@ $defs: 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" + - $refCurie: vrs:MolecularVariation + - $refCurie: cat-vrs:CategoricalVariant + - $refCurie: gks.core:iriReference description: A variant that is the subject of the Proposition. @@ -278,7 +283,7 @@ $defs: default: Method description: MUST be "Method". subtype: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol'). @@ -289,7 +294,7 @@ $defs: reportedIn: oneOf: - $ref: "#/$defs/Document" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:iriReference description: A document in which the the Method is reported. # license: # type: string @@ -325,7 +330,7 @@ $defs: If multiple Agents contributed to an entity, a separate Contribution instances MUST be created to describe each. activityType: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- The specific type of activity performed or role played by an agent in making the contribution (e.g. for a publication, agents may contribute as a primary author, editor, figure designer, @@ -354,7 +359,7 @@ $defs: $comment: >- The need for subtype is not yet clear, though the content that could be added to this leaving this field in draft is obvious. Leaving in draft until this sees regular use. - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- A specific type of document that a Document instance represents (e.g. 'publication', 'patent', 'pathology report') @@ -492,7 +497,7 @@ $defs: 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" + $refCurie: gks.core:MappableConcept score: type: number maturity: draft @@ -507,7 +512,7 @@ $defs: The 'score' attribute serves the same purpose as 'strength', but allows for a quantitative assessment based on a numerical score. classification: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core: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 @@ -525,7 +530,7 @@ $defs: items: anyOf: - $ref: "#/$defs/EvidenceLine" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:iriReference 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 @@ -594,7 +599,7 @@ $defs: - $ref: "#/$defs/StudyResult" - $ref: "#/$defs/Statement" - $ref: "#/$defs/EvidenceLine" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:iriReference description: >- An individual piece of information that was evaluated as evidence in building the argument represented by an Evidence Line. @@ -615,7 +620,7 @@ $defs: The direction of support that the Evidence Line is determined to provide toward its target Proposition (supports, disputes, neutral) strengthOfEvidenceProvided: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- 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. @@ -630,7 +635,7 @@ $defs: against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value. evidenceOutcome: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- A term summarizing the overall outcome of the evidence assessment represented by the Evidence Line, in terms of the direction and strength of support it provides for or against the target Proposition. @@ -659,7 +664,7 @@ $defs: subtype: maturity: draft $comment: the need for a DataSet subtype is not yet clear. Leaving in draft until then. - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- A specific type of data set the DataSet instance represents (e.g. a 'clinical data set', a 'sequencing data set', a 'gene expression data set', @@ -672,10 +677,10 @@ $defs: reportedIn: oneOf: - $ref: "#/$defs/Document" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:iriReference description: A document in which the the Method is reported. releaseDate: - $ref: "/ga4gh/schema/gks-core/1.x/json/date" + $refCurie: gks.core:date description: Indicates the date a version of a DataSet was formally released. $comment: >- This attribute may apply to version and distribution-level DataSet representations. @@ -690,7 +695,7 @@ $defs: revisions that add or modify content, but don’t change the identity of the resource. Use this attribute in cases where version is not reflected in an identifier associated with the data set. license: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- A specific license that dictates legal permissions for how a data set can be used (by whom, where, for what purposes, with what additional requirements, etc.) @@ -725,7 +730,7 @@ $defs: characteristics: type: array items: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept ordered: false description: >- A feature or role shared by all members of the StudyGroup, representing a criterion for @@ -744,15 +749,15 @@ $defs: Reports a gene impacted by the variant, which may contribute to the association described in the Proposition. oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:MappableConcept + - $refCurie: gks.core:iriReference alleleOriginQualifier: description: >- Reports whether the Proposition should be interpreted in the context of an inherited (germline) variant, an acquired (somatic) mutation, or another more nuanced concept. oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:MappableConcept + - $refCurie: gks.core:iriReference # Variant Functional Impact Proposition ExperimentalVariantFunctionalImpactProposition: @@ -777,8 +782,8 @@ $defs: objectSequenceFeature: extends: object oneOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" - - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + - $refCurie: gks.core:iriReference + - $refCurie: gks.core:MappableConcept description: >- The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is reported. @@ -787,7 +792,7 @@ $defs: An assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold. anyOf: - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $refCurie: gks.core:iriReference - $ref: "#/$defs/Document" - type: object additionalProperties: true @@ -820,8 +825,8 @@ $defs: objectCondition: extends: object oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: Condition + - $refCurie: gks.core:iriReference description: The disease that is evaluated for diagnosis. required: - predicate @@ -846,8 +851,8 @@ $defs: objectTumorType: extends: object oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: Condition + - $refCurie: gks.core:iriReference description: >- The tumor type for which the variant impact is evaluated. required: @@ -873,17 +878,17 @@ $defs: objectCondition: extends: object oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: Condition + - $refCurie: gks.core:iriReference description: The :ref:`Condition` for which the variant impact is stated. penetranceQualifier: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept 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: - $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + $refCurie: gks.core:MappableConcept description: >- Reports a pattern of inheritance expected for the pathogenic effect of the variant. HPO terms within the hierarchy of 'HP:0000005' (mode of inheritance) are recommended @@ -913,8 +918,8 @@ $defs: objectCondition: extends: object oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: Condition + - $refCurie: gks.core:iriReference description: The disease that is evaluated for outcome. required: - predicate @@ -944,12 +949,12 @@ $defs: 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" + - $ref: Therapeutic + - $refCurie: gks.core:iriReference conditionQualifier: oneOf: - - $ref: "/ga4gh/schema/va-spec/1.x/base/json/Condition" - - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference" + - $ref: Condition + - $refCurie: gks.core: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