feat: adding expression input schemas

pydantic_models/expression_input.py

@@ -0,0 +1,151 @@
+#!/usr/bin/env python
+"""Generating json schema for expression data via pydantic models."""
+
+from __future__ import annotations
+
+from enum import Enum
+import json
+from typing import List, Optional
+
+from pydantic import BaseModel, Extra, Field
+
+class ExpressionAggregated(BaseModel):
+    """Expression object for aggregated data."""
+    assayGroupId: str = Field(
+        description="Identifier for the assay group.",
+    )
+    min: float = Field(
+        description='Minimum value in the assay group.',
+    )
+    q1: float = Field(
+        description='First quantile of values in the assay group.',
+    )
+    q2: float = Field(
+        description='Median of values in the assay group.',
+    )
+    q3: float = Field(
+        description='third quantile of values in the assay group.',
+    )
+    max: float = Field(
+        description='Maximum expression value in the assay group.',
+    )
+
+    class Config:
+        extra = Extra.forbid
+        anystr_strip_whitespace = True
+
+class ExpressionAggregatedSchema(BaseModel):
+    """Schema for aggregated expression data."""
+    geneProductId: str = Field(
+        description="Identifier of measured gene product, protein or transcript.",
+        examples=['ENSG00000157764', 'Q9HC10'],
+    )
+    unit: str = Field(
+        description='Unit of the expression value.',
+        examples=['tpms'],
+    )
+    expression: List[ExpressionAggregated]
+
+    class Config:
+        title = 'OpenTargets-gene-expression-aggregated'
+        extra = Extra.forbid
+        anystr_strip_whitespace = True
+
+class ExperimentalDesign(BaseModel):
+    """Experimental design object."""
+    assayGroupId: str = Field(
+        description="Identifier for the assay group.",
+    )
+    assayId: str = Field(
+        description="Identifier for the assay.",
+    )
+    assayGroup: str = Field(
+        description='Group of the assay.',
+    )
+    age: str = Field(
+        description='Age of the organism.',
+    )
+    cultivar: str = Field(
+        description='Cultivar name.',
+    )
+    genotype: str = Field(
+        description='Genotype of the organism.',
+    )
+    organismPart: str = Field(
+        description='Part of the organism.',
+    )
+
+    class Config:
+        extra = Extra.forbid
+        anystr_strip_whitespace = True
+
+class ExpressionUnAggregated(BaseModel):
+    """Expression object for unaggregated data."""
+    assayId: str = Field(
+        description="Identifier for the assay.",
+    )
+    value: float = Field(
+        description='Expression value in the assay.',
+    )
+
+    class Config:
+        extra = Extra.forbid
+        anystr_strip_whitespace = True
+
+class ExpressionUnaggregatedSchema(BaseModel):
+    """Schema for unaggregated expression data."""
+    geneProductId: str = Field(
+        description="Identifier of measured gene product, protein or transcript.",
+        examples=['ENSG00000157764', 'Q9HC10'],
+    )
+    unit: str = Field(
+        description='Unit of the expression value.',
+        examples=['tpms'],
+    )
+    expression: List[ExpressionUnAggregated]
+
+    class Config:
+        title = 'OpenTargets-gene-expression-unaggregated'
+        extra = Extra.forbid
+        anystr_strip_whitespace = True
+
+
+class StudyMetadataSchema(BaseModel):
+    """Schema for expression metadata."""
+    experimentId: str = Field(
+        description="Identifier for the experiment.",
+    )
+    experimentType: str = Field(
+        description='Type of the experiment.',
+    )
+    species: str = Field(
+        description='Species name.',
+        examples=['Sorghum bicolor'],
+    )
+    speciesOntURI: str = Field(
+        description='Species ontology URI.',
+        examples=['http://purl.obolibrary.org/obo/NCBITaxon_4558'],
+    )
+    pubmedIds: List[str] = Field(
+        description='List of pubmed identifiers.',
+        examples=['28186631'],
+    )
+    provider: str = Field(
+        description='Provider of the data.',
+    )
+    experimentalDesigns: List[ExperimentalDesign]
+
+def main():
+    with open('expression_aggregated.json', 'wt') as f:
+        f.write(ExpressionAggregatedSchema.schema_json(indent=2))
+
+    with open('expression_unaggregated.json', 'wt') as f:
+        f.write(ExpressionUnaggregatedSchema.schema_json(indent=2))
+
+    with open('expression_study_metadata.json', 'wt') as f:
+        f.write(StudyMetadataSchema.schema_json(indent=2))
+
+
+
+if __name__ == '__main__':
+    main()

schemas/expression_aggregated.json

@@ -0,0 +1,85 @@
+{
+  "title": "OpenTargets-gene-expression-aggregated",
+  "description": "Schema for aggregated expression data.",
+  "type": "object",
+  "properties": {
+    "geneProductId": {
+      "title": "Geneproductid",
+      "description": "Identifier of measured gene product, protein or transcript.",
+      "examples": [
+        "ENSG00000157764",
+        "Q9HC10"
+      ],
+      "type": "string"
+    },
+    "unit": {
+      "title": "Unit",
+      "description": "Unit of the expression value.",
+      "examples": [
+        "tpms"
+      ],
+      "type": "string"
+    },
+    "expression": {
+      "title": "Expression",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/ExpressionAggregated"
+      }
+    }
+  },
+  "required": [
+    "geneProductId",
+    "unit",
+    "expression"
+  ],
+  "additionalProperties": false,
+  "definitions": {
+    "ExpressionAggregated": {
+      "title": "ExpressionAggregated",
+      "description": "Expression object for aggregated data.",
+      "type": "object",
+      "properties": {
+        "assayGroupId": {
+          "title": "Assaygroupid",
+          "description": "Identifier for the assay group.",
+          "type": "string"
+        },
+        "min": {
+          "title": "Min",
+          "description": "Minimum value in the assay group.",
+          "type": "number"
+        },
+        "q1": {
+          "title": "Q1",
+          "description": "First quantile of values in the assay group.",
+          "type": "number"
+        },
+        "q2": {
+          "title": "Q2",
+          "description": "Median of values in the assay group.",
+          "type": "number"
+        },
+        "q3": {
+          "title": "Q3",
+          "description": "third quantile of values in the assay group.",
+          "type": "number"
+        },
+        "max": {
+          "title": "Max",
+          "description": "Maximum expression value in the assay group.",
+          "type": "number"
+        }
+      },
+      "required": [
+        "assayGroupId",
+        "min",
+        "q1",
+        "q2",
+        "q3",
+        "max"
+      ],
+      "additionalProperties": false
+    }
+  }
+}

schemas/expression_study_metadata.json

@@ -0,0 +1,119 @@
+{
+  "title": "StudyMetadataSchema",
+  "description": "Schema for expression metadata.",
+  "type": "object",
+  "properties": {
+    "experimentId": {
+      "title": "Experimentid",
+      "description": "Identifier for the experiment.",
+      "type": "string"
+    },
+    "experimentType": {
+      "title": "Experimenttype",
+      "description": "Type of the experiment.",
+      "type": "string"
+    },
+    "species": {
+      "title": "Species",
+      "description": "Species name.",
+      "examples": [
+        "Sorghum bicolor"
+      ],
+      "type": "string"
+    },
+    "speciesOntURI": {
+      "title": "Speciesonturi",
+      "description": "Species ontology URI.",
+      "examples": [
+        "http://purl.obolibrary.org/obo/NCBITaxon_4558"
+      ],
+      "type": "string"
+    },
+    "pubmedIds": {
+      "title": "Pubmedids",
+      "description": "List of pubmed identifiers.",
+      "examples": [
+        "28186631"
+      ],
+      "type": "array",
+      "items": {
+        "type": "string"
+      }
+    },
+    "provider": {
+      "title": "Provider",
+      "description": "Provider of the data.",
+      "type": "string"
+    },
+    "experimentalDesigns": {
+      "title": "Experimentaldesigns",
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/ExperimentalDesign"
+      }
+    }
+  },
+  "required": [
+    "experimentId",
+    "experimentType",
+    "species",
+    "speciesOntURI",
+    "pubmedIds",
+    "provider",
+    "experimentalDesigns"
+  ],
+  "definitions": {
+    "ExperimentalDesign": {
+      "title": "ExperimentalDesign",
+      "description": "Experimental design object.",
+      "type": "object",
+      "properties": {
+        "assayGroupId": {
+          "title": "Assaygroupid",
+          "description": "Identifier for the assay group.",
+          "type": "string"
+        },
+        "assayId": {
+          "title": "Assayid",
+          "description": "Identifier for the assay.",
+          "type": "string"
+        },
+        "assayGroup": {
+          "title": "Assaygroup",
+          "description": "Group of the assay.",
+          "type": "string"
+        },
+        "age": {
+          "title": "Age",
+          "description": "Age of the organism.",
+          "type": "string"
+        },
+        "cultivar": {
+          "title": "Cultivar",
+          "description": "Cultivar name.",
+          "type": "string"
+        },
+        "genotype": {
+          "title": "Genotype",
+          "description": "Genotype of the organism.",
+          "type": "string"
+        },
+        "organismPart": {
+          "title": "Organismpart",
+          "description": "Part of the organism.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "assayGroupId",
+        "assayId",
+        "assayGroup",
+        "age",
+        "cultivar",
+        "genotype",
+        "organismPart"
+      ],
+      "additionalProperties": false
+    }
+  }
+}