Forge Tools clingen_gene_validity

clingen_gene_validity read

scidex.forge.clingen_gene_validity

Query ClinGen for expert-panel gene-disease validity classifications. Returns ClinGen classifications (Definitive/Strong/Moderate/Limited/Disputed/Refuted/No Known Disease Relationship) with expert panel, SOP version, supporting PubMed IDs, and disease identifiers (MONDO/OMIM). Complements ClinVar (variant significance) and DisGeNET (curated associations) with authoritative expert-panel clinical validity scores. REST API: https://search.clinicalgenome.org/kb/gene-validity — free, no auth.

HTTP: POST /api/scidex/forge/clingen_gene_validity

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.clingen_gene_validity``.",
  "properties": {
    "gene_symbol": {
      "description": "HGNC gene symbol to query (e.g. ``'BRCA1'``, ``'SCN1A'``). ClinGen returns all expert-panel curations for this gene.",
      "maxLength": 64,
      "title": "Gene Symbol",
      "type": "string"
    },
    "disease_term": {
      "default": "",
      "description": "Optional disease name filter (case-insensitive substring match on disease_name). Empty string returns all classifications for the gene.",
      "maxLength": 256,
      "title": "Disease Term",
      "type": "string"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeClinGenIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ClinGenClassification": {
      "description": "One ClinGen expert-panel gene-disease validity classification.",
      "properties": {
        "gene_symbol": {
          "description": "HGNC gene symbol.",
          "title": "Gene Symbol",
          "type": "string"
        },
        "disease_name": {
          "description": "Disease name from ClinGen.",
          "title": "Disease Name",
          "type": "string"
        },
        "disease_id": {
          "description": "Disease identifier (MONDO or OMIM curie, e.g. 'MONDO:0011450').",
          "title": "Disease Id",
          "type": "string"
        },
        "classification": {
          "description": "ClinGen validity classification: Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Known Disease Relationship.",
          "title": "Classification",
          "type": "string"
        },
        "sop": {
          "default": "",
          "description": "SOP version used for curation (e.g. 'SOP8').",
          "title": "Sop",
          "type": "string"
        },
        "expert_panel": {
          "default": "",
          "description": "Name of the ClinGen expert panel that performed the curation.",
          "title": "Expert Panel",
          "type": "string"
        },
        "pmids": {
          "description": "PubMed IDs supporting this classification.",
          "items": {
            "type": "string"
          },
          "title": "Pmids",
          "type": "array"
        },
        "last_updated": {
          "default": "",
          "description": "Date of last curation update (YYYY-MM-DD or ISO 8601).",
          "title": "Last Updated",
          "type": "string"
        }
      },
      "required": [
        "gene_symbol",
        "disease_name",
        "disease_id",
        "classification"
      ],
      "title": "ClinGenClassification",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.clingen_gene_validity``.",
  "properties": {
    "gene_symbol": {
      "description": "The gene symbol that was queried.",
      "title": "Gene Symbol",
      "type": "string"
    },
    "classifications": {
      "description": "ClinGen expert-panel gene-disease validity classifications. Filtered by disease_term when provided.",
      "items": {
        "$ref": "#/$defs/ClinGenClassification"
      },
      "title": "Classifications",
      "type": "array"
    },
    "total_found": {
      "description": "Total classifications matching the gene (before disease_term filter). Equals len(classifications) when no filter is applied.",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol",
    "total_found",
    "took_ms"
  ],
  "title": "ForgeClinGenOut",
  "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/clingen_gene_validity' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

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