Forge Tools disgenet

disgenet read

scidex.forge.disgenet

Query DisGeNET for curated gene-disease associations. Returns associations with GDA scores (0-1), UMLS disease identifiers, evidence source databases (OMIM, ClinVar, UniProt, …), and PubMed citation counts. Supports multiple genes, min-score filtering, and MeSH disease-class filtering. Critical for dark-genome hypothesis generation and drug-repurposing candidate evaluation.

HTTP: POST /api/scidex/forge/disgenet

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.disgenet``.",
  "properties": {
    "gene_symbols": {
      "description": "HGNC gene symbols to query (e.g. ``['BRCA1', 'TP53']``). DisGeNET is queried once per gene; results are aggregated and de-duplicated by (gene, disease) pair. 1–10 genes per call.",
      "items": {
        "type": "string"
      },
      "maxItems": 10,
      "minItems": 1,
      "title": "Gene Symbols",
      "type": "array"
    },
    "min_score": {
      "default": 0,
      "description": "Minimum GDA score (0.0–1.0) to include in results. The GDA score reflects evidence breadth and strength across integrated sources; higher = more confident association. Default 0.0 returns all curated associations.",
      "maximum": 1,
      "minimum": 0,
      "title": "Min Score",
      "type": "number"
    },
    "disease_class": {
      "anyOf": [
        {
          "maxLength": 10,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional MeSH disease class filter (e.g. ``'C04'`` for neoplasms, ``'F03'`` for mental disorders). Passed to the DisGeNET API as a server-side filter. See DisGeNET docs for the full class hierarchy.",
      "title": "Disease Class"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of gene-disease associations to return, sorted by score descending (across all input genes). Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeDisGeNETIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "GeneDisease": {
      "description": "One gene-disease association in the DisGeNET response.",
      "properties": {
        "gene_symbol": {
          "description": "HGNC gene symbol.",
          "title": "Gene Symbol",
          "type": "string"
        },
        "disease_name": {
          "description": "Disease name (DisGeNET canonical).",
          "title": "Disease Name",
          "type": "string"
        },
        "disease_id": {
          "description": "UMLS Concept Unique Identifier (CUI), e.g. ``'C0006826'``.",
          "title": "Disease Id",
          "type": "string"
        },
        "score": {
          "description": "GDA score in [0.0, 1.0]. Composites genetic, somatic, drug, and literature evidence; higher = stronger.",
          "title": "Score",
          "type": "number"
        },
        "evidence_sources": {
          "description": "Source databases contributing to this association (e.g. ``['OMIM', 'ClinVar', 'UniProt']``).",
          "items": {
            "type": "string"
          },
          "title": "Evidence Sources",
          "type": "array"
        },
        "pmid_count": {
          "default": 0,
          "description": "Total PubMed citations supporting the association.",
          "title": "Pmid Count",
          "type": "integer"
        }
      },
      "required": [
        "gene_symbol",
        "disease_name",
        "disease_id",
        "score"
      ],
      "title": "GeneDisease",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.disgenet``.",
  "properties": {
    "associations": {
      "description": "Gene-disease associations sorted by score descending. De-duplicated by (gene_symbol, disease_id) across all input genes.",
      "items": {
        "$ref": "#/$defs/GeneDisease"
      },
      "title": "Associations",
      "type": "array"
    },
    "returned": {
      "description": "Length of ``associations``.",
      "title": "Returned",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for all upstream API calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "returned",
    "took_ms"
  ],
  "title": "ForgeDisGeNETOut",
  "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/disgenet' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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