Forge Tools civic_variants

civic_variants read

scidex.forge.civic_variants

Query CIViC (Clinical Interpretation of Variants in Cancer) for clinical actionability of genomic variants. Returns cancer-specific evidence: drug sensitivity/resistance (Predictive), survival outcome (Prognostic), germline cancer risk (Predisposing), and cancer type diagnosis (Diagnostic). Complements clinvar_variant with oncology clinical interpretation. Evidence levels A (FDA validated) to E (inferential); CIViC score 0-100.

HTTP: POST /api/scidex/forge/civic_variants

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.civic_variants``.",
  "properties": {
    "gene_symbols": {
      "description": "HGNC gene symbols to query (e.g. ``['BRAF', 'EGFR']``). At least one symbol is required.",
      "items": {
        "type": "string"
      },
      "minItems": 1,
      "title": "Gene Symbols",
      "type": "array"
    },
    "variant_filter": {
      "default": "",
      "description": "Optional substring filter on variant name (e.g. ``V600E``). Case-insensitive.",
      "maxLength": 128,
      "title": "Variant Filter",
      "type": "string"
    },
    "evidence_types": {
      "description": "Optional list of evidence types to include. Valid values: ``Predictive``, ``Prognostic``, ``Predisposing``, ``Diagnostic``. Empty list means all types are returned.",
      "items": {
        "type": "string"
      },
      "title": "Evidence Types",
      "type": "array"
    },
    "significance_filter": {
      "default": "",
      "description": "Optional substring filter on evidence significance (e.g. ``Sensitizes``, ``Resistance``). Case-insensitive.",
      "maxLength": 128,
      "title": "Significance Filter",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of variants to return (default 20, max 200).",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeCIViCIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "CIViCEvidenceItemOut": {
      "description": "One clinical evidence item in the response.",
      "properties": {
        "evidence_id": {
          "description": "CIViC evidence item ID.",
          "title": "Evidence Id",
          "type": "string"
        },
        "evidence_type": {
          "description": "Evidence type: Predictive, Prognostic, Predisposing, or Diagnostic.",
          "title": "Evidence Type",
          "type": "string"
        },
        "disease": {
          "default": "",
          "description": "Disease name.",
          "title": "Disease",
          "type": "string"
        },
        "drugs": {
          "description": "Associated drug names (relevant for Predictive evidence).",
          "items": {
            "type": "string"
          },
          "title": "Drugs",
          "type": "array"
        },
        "significance": {
          "default": "",
          "description": "Clinical significance (e.g. Sensitizes, Resistance, Better OS).",
          "title": "Significance",
          "type": "string"
        },
        "evidence_level": {
          "default": "",
          "description": "Evidence level A-E: A=Validated (FDA approved), B=Clinical (published trial), C=Case study, D=Preclinical, E=Inferential.",
          "title": "Evidence Level",
          "type": "string"
        },
        "citation_pmid": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PubMed ID for the supporting publication, or None.",
          "title": "Citation Pmid"
        }
      },
      "required": [
        "evidence_id",
        "evidence_type"
      ],
      "title": "CIViCEvidenceItemOut",
      "type": "object"
    },
    "CIViCVariantOut": {
      "description": "One CIViC variant with clinical evidence in the response.",
      "properties": {
        "variant_id": {
          "description": "CIViC variant ID.",
          "title": "Variant Id",
          "type": "string"
        },
        "gene": {
          "description": "Gene symbol (e.g. ``BRAF``).",
          "title": "Gene",
          "type": "string"
        },
        "variant_name": {
          "description": "Variant name (e.g. ``V600E``).",
          "title": "Variant Name",
          "type": "string"
        },
        "civic_score": {
          "default": 0,
          "description": "CIViC evidence score (0–100). Higher = more/stronger clinical evidence.",
          "title": "Civic Score",
          "type": "number"
        },
        "evidence_count": {
          "default": 0,
          "description": "Total number of evidence items for this variant.",
          "title": "Evidence Count",
          "type": "integer"
        },
        "top_evidence": {
          "description": "Up to 5 top evidence items (highest evidence level first).",
          "items": {
            "$ref": "#/$defs/CIViCEvidenceItemOut"
          },
          "title": "Top Evidence",
          "type": "array"
        },
        "civic_url": {
          "default": "",
          "description": "Direct link to this variant's CIViC page.",
          "title": "Civic Url",
          "type": "string"
        }
      },
      "required": [
        "variant_id",
        "gene",
        "variant_name"
      ],
      "title": "CIViCVariantOut",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.civic_variants``.",
  "properties": {
    "variants": {
      "description": "Matching CIViC variants with clinical evidence.",
      "items": {
        "$ref": "#/$defs/CIViCVariantOut"
      },
      "title": "Variants",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total variants found across all queried genes before the ``limit`` was applied. May exceed ``len(variants)``.",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeCIViCOut",
  "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/civic_variants' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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