Forge Tools oncokb

oncokb read

scidex.forge.oncokb

Query OncoKB (Memorial Sloan Kettering) for clinical significance of a cancer mutation. Returns oncogenicity classification (Oncogenic/Likely Oncogenic/Neutral/Unknown), mutation effect on protein function, the highest OncoKB evidence level (1=FDA-recognized, 2=standard care, 3A/3B=compelling clinical, 4=biological, R1/R2=resistance), and all therapeutic implications with drug names, evidence levels, and FDA-approval status. Complements CIViC variants (community evidence) with OncoKB's structured FDA-tier biomarker programme. API: https://www.oncokb.org/api/v1/ — free academic use; set ONCOKB_API_TOKEN for authenticated bulk access.

HTTP: POST /api/scidex/forge/oncokb

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.oncokb``.",
  "properties": {
    "hugo_symbol": {
      "description": "HGNC Hugo gene symbol (e.g. ``'BRAF'``, ``'TP53'``, ``'EGFR'``). Case-insensitive; OncoKB normalises internally.",
      "maxLength": 64,
      "title": "Hugo Symbol",
      "type": "string"
    },
    "alteration": {
      "description": "Protein change in standard notation (e.g. ``'V600E'``, ``'R175H'``). Prefix ``p.`` is accepted but not required.",
      "maxLength": 128,
      "title": "Alteration",
      "type": "string"
    },
    "tumor_type": {
      "anyOf": [
        {
          "maxLength": 128,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional OncoKB tumor type code or name (e.g. ``'BRCA'`` for Breast Invasive Carcinoma, ``'LUAD'`` for Lung Adenocarcinoma). When omitted OncoKB returns pan-cancer implications. See https://www.oncokb.org/cancerTypes for codes.",
      "title": "Tumor Type"
    }
  },
  "required": [
    "hugo_symbol",
    "alteration"
  ],
  "title": "ForgeOncoKBIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "OncoKBTreatment": {
      "description": "One therapeutic implication from OncoKB.",
      "properties": {
        "drugs": {
          "description": "Drug names included in this treatment regimen.",
          "items": {
            "type": "string"
          },
          "title": "Drugs",
          "type": "array"
        },
        "level": {
          "default": "",
          "description": "OncoKB evidence level: 1 (FDA-recognized), 2 (standard care), 3A (compelling clinical), 3B (standard care other indication), 4 (biological), R1/R2 (resistance).",
          "title": "Level",
          "type": "string"
        },
        "level_description": {
          "default": "",
          "description": "Human-readable description of the evidence level.",
          "title": "Level Description",
          "type": "string"
        },
        "indication": {
          "default": "",
          "description": "Cancer type or tumor type indication for this treatment.",
          "title": "Indication",
          "type": "string"
        },
        "fda_approved": {
          "default": false,
          "description": "True when level is 1 (FDA-recognized biomarker).",
          "title": "Fda Approved",
          "type": "boolean"
        },
        "pmids": {
          "description": "PubMed IDs supporting this therapeutic implication.",
          "items": {
            "type": "string"
          },
          "title": "Pmids",
          "type": "array"
        }
      },
      "title": "OncoKBTreatment",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.oncokb``.",
  "properties": {
    "hugo_symbol": {
      "description": "The Hugo gene symbol that was queried.",
      "title": "Hugo Symbol",
      "type": "string"
    },
    "alteration": {
      "description": "The protein alteration that was queried.",
      "title": "Alteration",
      "type": "string"
    },
    "oncogenicity": {
      "default": "",
      "description": "OncoKB oncogenicity classification: Oncogenic, Likely Oncogenic, Neutral, Likely Neutral, Inconclusive, or Unknown.",
      "title": "Oncogenicity",
      "type": "string"
    },
    "mutation_effect": {
      "default": "",
      "description": "Mutation effect on protein function: Gain-of-function, Loss-of-function, Switch-of-function, Neutral, Inconclusive, or Unknown.",
      "title": "Mutation Effect",
      "type": "string"
    },
    "highest_sensitive_level": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Highest OncoKB sensitive level (1, 2, 3A, 3B, 4) for this mutation. None when no sensitivity evidence exists.",
      "title": "Highest Sensitive Level"
    },
    "highest_resistance_level": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Highest OncoKB resistance level (R1, R2) for this mutation. None when no resistance evidence exists.",
      "title": "Highest Resistance Level"
    },
    "treatments": {
      "description": "Therapeutic implications with drug, level, and indication.",
      "items": {
        "$ref": "#/$defs/OncoKBTreatment"
      },
      "title": "Treatments",
      "type": "array"
    },
    "tumor_type_summary": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Tumor-type-specific clinical summary from OncoKB, or None.",
      "title": "Tumor Type Summary"
    },
    "gene_summary": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Brief gene-level summary from OncoKB, or None.",
      "title": "Gene Summary"
    },
    "not_found": {
      "default": false,
      "description": "True when OncoKB returned no annotation for this mutation (unknown gene, unrecognised alteration, or no data).",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "OncoKB (oncokb.org)",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "hugo_symbol",
    "alteration",
    "took_ms"
  ],
  "title": "ForgeOncoKBOut",
  "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/oncokb' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "hugo_symbol": "",
  "alteration": ""
}'

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