diff --git a/gdcdictionary/schemas/somatic_mutation.yaml b/gdcdictionary/schemas/somatic_mutation.yaml new file mode 100755 index 0000000..8a9f58d --- /dev/null +++ b/gdcdictionary/schemas/somatic_mutation.yaml @@ -0,0 +1,134 @@ +$schema: "http://json-schema.org/draft-04/schema#" + +id: "somatic_mutation" +title: Somatic Mutations +type: object +namespace: https://vpodc.org/ +category: clinical +program: '*' +project: '*' +description: > + Mutations extracted from a patient's sequencing results. +additionalProperties: false +submittable: true +validators: null + +systemProperties: + - id + - project_id + - state + - created_datetime + - updated_datetime + +links: + - name: cases + backref: somatic_mutations + label: associated_with + target_type: case + multiplicity: many_to_one + required: true + +uniqueKeys: + - [id] + - [project_id, submitter_id] + +required: + - cases + - submitter_id + - type + +properties: + $ref: "_definitions.yaml#/ubiquitous_properties" + + ActiveClinicalTrials: + description: > + ActiveClinicalTrials + type: string + + BxMorphology: + description: > + BxMorphology + type: string + + BxType: + description: > + BxType + type: string + + ClinicallyActionable: + description: > + ClinicallyActionable + type: number + + Consequence: + description: > + Consequence + type: string + + DaysFromAnchorDateToBxDate: + description: > + DaysFromAnchorDateToBxDate + type: integer + + DaysFromAnchorDateToBxResultsDate: + description: > + DaysFromAnchorDateToBxResultsDate + type: integer + + DrugsAssociatedWithResistance_IndicatedTumorTypes: + description: > + DrugsAssociatedWithResistance_IndicatedTumorTypes + type: string + + DrugsAssociatedWithSensitivity_IndicatedTumorTypes: + description: > + DrugsAssociatedWithSensitivity_IndicatedTumorTypes + type: string + + DrugsAssociatedWithSensitivity_OtherTumorTypes: + description: > + DrugsAssociatedWithSensitivity_OtherTumorTypes + type: string + + Exon_PGDonly: + description: > + Exon_PGDonly + type: number + + Fold: + description: > + Fold + type: number + + Gene: + description: > + Gene + type: string + + Lab: + description: > + Lab + type: string + + MutantFraction: + description: > + MutantFraction + type: number + + Mutation: + description: > + Mutation + type: string + + TotalNumberMutations: + description: > + TotalNumberMutations + type: integer + + TrialPhase: + description: > + TrialPhase + type: number + + cases: + $ref: "_definitions.yaml#/to_one" diff --git a/gdcdictionary/schemas/actionable_mutation.yaml b/gdcdictionary/schemas/unused/actionable_mutation.yaml similarity index 100% rename from gdcdictionary/schemas/actionable_mutation.yaml rename to gdcdictionary/schemas/unused/actionable_mutation.yaml diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..c49a4ef --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,16 @@ +[tool.poetry] +name = "gdcdictionary" +version = "0.0.0" +description = "Data Dictionary for VPODC" +authors = ["Center for Translational Data Science at the University of Chicago "] +license = "Apache-2.0" +readme = "README.md" + + +[tool.poetry.dependencies] +python = "^3.9" + + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api"