Forge Tools cancer_hotspots

cancer_hotspots read

scidex.forge.cancer_hotspots

Query MSKCC Cancer Hotspots (cancerhotspots.org) for recurrent mutation hotspots in a gene. Returns statistically significant residues with tumour counts, q-values, amino acid variant composition, and tumour type breakdown. Complements COSMIC (curated somatic catalog) with statistical hotspot detection across tumour types.

HTTP: POST /api/scidex/forge/cancer_hotspots

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.cancer_hotspots``.",
  "properties": {
    "gene_symbol": {
      "description": "HGNC/Hugo gene symbol to query (e.g. ``BRAF``, ``TP53``).",
      "maxLength": 64,
      "minLength": 1,
      "title": "Gene Symbol",
      "type": "string"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeCancerHotspotsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "HotspotMutation": {
      "description": "One recurrent mutation hotspot from Cancer Hotspots.",
      "properties": {
        "residue": {
          "description": "Residue identifier (e.g. ``V600`` or range ``592-604`` for indels).",
          "title": "Residue",
          "type": "string"
        },
        "tumor_count": {
          "default": 0,
          "description": "Total tumour samples harbouring this hotspot.",
          "minimum": 0,
          "title": "Tumor Count",
          "type": "integer"
        },
        "q_value": {
          "default": "",
          "description": "Q-value (statistical significance of the hotspot).",
          "title": "Q Value",
          "type": "string"
        },
        "hotspot_type": {
          "default": "",
          "description": "Hotspot type: ``single residue`` or ``in-frame indel``.",
          "title": "Hotspot Type",
          "type": "string"
        },
        "transcript_id": {
          "default": "",
          "description": "Ensembl transcript ID.",
          "title": "Transcript Id",
          "type": "string"
        },
        "amino_acid_position": {
          "additionalProperties": {
            "type": "integer"
          },
          "description": "Position range ``{start, end}``.",
          "title": "Amino Acid Position",
          "type": "object"
        },
        "variant_amino_acid": {
          "additionalProperties": {
            "type": "integer"
          },
          "description": "Map of mutant amino acid letter to tumour count (e.g. ``{E: 833}``).",
          "title": "Variant Amino Acid",
          "type": "object"
        },
        "tumor_type_composition": {
          "additionalProperties": {
            "type": "integer"
          },
          "description": "Map of tissue type name to tumour count.",
          "title": "Tumor Type Composition",
          "type": "object"
        }
      },
      "required": [
        "residue"
      ],
      "title": "HotspotMutation",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.cancer_hotspots``.",
  "properties": {
    "gene_symbol": {
      "description": "Gene symbol queried.",
      "title": "Gene Symbol",
      "type": "string"
    },
    "hotspots": {
      "description": "Recurrent mutation hotspots for the gene.",
      "items": {
        "$ref": "#/$defs/HotspotMutation"
      },
      "title": "Hotspots",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the gene was not found in the Cancer Hotspots database.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "cancer_hotspots",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeCancerHotspotsOut",
  "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/cancer_hotspots' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

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