Forge Tools gdc_genomics

gdc_genomics read

scidex.forge.gdc_genomics

Query the NCI Genomic Data Commons (GDC) for cancer genomics data files. Returns file records with UUIDs, data types, project codes, file sizes, and download URLs across all GDC programs (TCGA, CGCI, FM-AD, and more). Complements scidex.forge.tcga_genomics (mutation statistics) and scidex.forge.cbioportal_mutations (clinical annotations) by providing file-level access for downstream analysis. API: https://api.gdc.cancer.gov/ — public, open-access files require no token.

HTTP: POST /api/scidex/forge/gdc_genomics

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.gdc_genomics``.",
  "properties": {
    "gene_symbol": {
      "anyOf": [
        {
          "maxLength": 30,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Gene symbol to filter files by (e.g. ``TP53``, ``KRAS``). Returns files associated with cases carrying mutations in this gene. At least one of ``gene_symbol`` or ``project_id`` is required.",
      "title": "Gene Symbol"
    },
    "project_id": {
      "anyOf": [
        {
          "maxLength": 64,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "GDC project ID (e.g. ``TCGA-BRCA``, ``CGCI-BLGSP``). Narrows results to files from a specific GDC cancer project. At least one of ``gene_symbol`` or ``project_id`` is required.",
      "title": "Project Id"
    },
    "data_category": {
      "default": "all",
      "description": "Data category filter: ``'Sequencing Reads'``, ``'Transcriptome Profiling'``, ``'Simple Nucleotide Variation'``, ``'Copy Number Variation'``, ``'DNA Methylation'``, ``'all'``. Default: ``'all'``.",
      "title": "Data Category",
      "type": "string"
    },
    "access": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Access tier filter: ``'open'`` (public data) or ``'controlled'`` (requires GDC_TOKEN). When None, returns files from both tiers.",
      "title": "Access"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of file records to return. Default 20.",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeGDCIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "GDCFileRecord": {
      "description": "One GDC data file record.",
      "properties": {
        "file_id": {
          "description": "GDC file UUID (used for download).",
          "title": "File Id",
          "type": "string"
        },
        "file_name": {
          "default": "",
          "description": "Data file name.",
          "title": "File Name",
          "type": "string"
        },
        "data_type": {
          "default": "",
          "description": "Genomic data type (e.g. ``Gene Expression Quantification``).",
          "title": "Data Type",
          "type": "string"
        },
        "data_category": {
          "default": "",
          "description": "Data category (e.g. ``Transcriptome Profiling``).",
          "title": "Data Category",
          "type": "string"
        },
        "data_format": {
          "default": "",
          "description": "File format (e.g. ``TSV``, ``VCF``, ``BAM``).",
          "title": "Data Format",
          "type": "string"
        },
        "file_size": {
          "default": 0,
          "description": "File size in bytes.",
          "title": "File Size",
          "type": "integer"
        },
        "project_id": {
          "default": "",
          "description": "GDC project code (e.g. ``TCGA-BRCA``).",
          "title": "Project Id",
          "type": "string"
        },
        "case_count": {
          "default": 0,
          "description": "Number of cases (patients) associated with this file.",
          "title": "Case Count",
          "type": "integer"
        },
        "access": {
          "default": "",
          "description": "Access tier: ``open`` or ``controlled``.",
          "title": "Access",
          "type": "string"
        },
        "download_url": {
          "default": "",
          "description": "GDC download endpoint URL. Open-access files are publicly downloadable; controlled-access files require a GDC data access token.",
          "title": "Download Url",
          "type": "string"
        }
      },
      "required": [
        "file_id"
      ],
      "title": "GDCFileRecord",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.gdc_genomics``.",
  "properties": {
    "files": {
      "description": "GDC data file records, capped at ``limit``.",
      "items": {
        "$ref": "#/$defs/GDCFileRecord"
      },
      "title": "Files",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total files matching the query (may exceed ``len(files)``).",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "title": "ForgeGDCOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/gdc_genomics' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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