Forge Tools intogen_drivers

intogen_drivers read

scidex.forge.intogen_drivers

Query IntOGen (intogen.org) for cancer driver gene evidence. IntOGen identifies driver genes by analysing mutational patterns across thousands of tumour genomes, using dN/dS ratios, spatial clustering, and positional hotspot methods to detect selection. Returns per-cancer-type driver entries with q-values (FDR-corrected significance), detection methods, mutation counts, and sample sizes. Input: gene symbol (e.g. 'TP53'), optional cancer_type substring filter. API: GET https://www.intogen.org/search — free, no key required.

HTTP: POST /api/scidex/forge/intogen_drivers

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.intogen_drivers``.",
  "properties": {
    "gene_symbol": {
      "description": "HGNC Hugo gene symbol to look up (e.g. ``'TP53'``, ``'KRAS'``, ``'BRCA1'``). Case-insensitive; the verb normalises to uppercase.",
      "maxLength": 64,
      "title": "Gene Symbol",
      "type": "string"
    },
    "cancer_type": {
      "anyOf": [
        {
          "maxLength": 200,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional cancer type filter. When provided, only entries whose ``cancer_type`` contains this string (case-insensitive) are returned. Pass ``None`` (default) to return all cancer types.",
      "title": "Cancer Type"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeIntOGenDriversIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "DriverMethod": {
      "description": "One detection method evidence for a driver gene.",
      "properties": {
        "method": {
          "description": "Method used to detect the gene as a driver: ``'dnds'`` (dN/dS ratio), ``'clustering'`` (spatial mutation clustering), ``'hotspots'`` (recurrent positional hotspots), or ``'significance'`` (overall significance).",
          "title": "Method",
          "type": "string"
        },
        "q_value": {
          "description": "q-value (FDR-corrected p-value) for this method. Lower = more significant driver evidence. Range: 0.0–1.0.",
          "title": "Q Value",
          "type": "number"
        },
        "cancer_type": {
          "default": "",
          "description": "Cancer type where this method detected driver role.",
          "title": "Cancer Type",
          "type": "string"
        }
      },
      "required": [
        "method",
        "q_value"
      ],
      "title": "DriverMethod",
      "type": "object"
    },
    "IntogenDriver": {
      "description": "One gene–cancer type driver entry from IntOGen.",
      "properties": {
        "cancer_type": {
          "default": "",
          "description": "Cancer type for which this gene is a validated driver.",
          "title": "Cancer Type",
          "type": "string"
        },
        "q_value": {
          "default": 0,
          "description": "Overall q-value (FDR-corrected significance) for the gene as a driver in this cancer type. Lower = more significant.",
          "title": "Q Value",
          "type": "number"
        },
        "methods": {
          "description": "Detection methods supporting the driver classification.",
          "items": {
            "$ref": "#/$defs/DriverMethod"
          },
          "title": "Methods",
          "type": "array"
        },
        "mutation_count": {
          "default": 0,
          "description": "Number of mutations observed in the gene across the cohort.",
          "title": "Mutation Count",
          "type": "integer"
        },
        "sample_count": {
          "default": 0,
          "description": "Number of samples analysed in this cancer type.",
          "title": "Sample Count",
          "type": "integer"
        }
      },
      "title": "IntogenDriver",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.intogen_drivers``.",
  "properties": {
    "gene_symbol": {
      "description": "The gene symbol that was queried (normalised to uppercase).",
      "title": "Gene Symbol",
      "type": "string"
    },
    "drivers": {
      "description": "Driver entries from IntOGen for this gene, one per cancer type where the gene is a statistically significant driver.",
      "items": {
        "$ref": "#/$defs/IntogenDriver"
      },
      "title": "Drivers",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when IntOGen has no driver gene evidence for this gene (or after filtering, no entries remain).",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "IntOGen (intogen.org)",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeIntOGenDriversOut",
  "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/intogen_drivers' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

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