Forge Tools hgnc_gene_lookup

hgnc_gene_lookup read

scidex.forge.hgnc_gene_lookup

Look up authoritative gene nomenclature from HGNC (HUGO Gene Nomenclature Committee). Returns HGNC ID, approved symbol, approved name, locus type, locus group, chromosomal location, previous symbols, alias symbols, UniProt IDs, OMIM IDs, Ensembl gene ID, and RefSeq accession. When search_aliases=True (default), also resolves alias and previous symbols so inputs like HER2 or ERBB1 map to their canonical HGNC entry. Complements forge_ncbi_gene with multi-database cross-reference resolution. No API key required.

HTTP: POST /api/scidex/forge/hgnc_gene_lookup

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.hgnc_gene_lookup``.",
  "properties": {
    "gene_symbol": {
      "description": "Gene symbol to look up (e.g. ``'BRCA1'``). Matched first against approved symbols; when no match is found and ``search_aliases=True``, also searched in previous and alias symbols.",
      "title": "Gene Symbol",
      "type": "string"
    },
    "search_aliases": {
      "default": true,
      "description": "When True (default), also query previous-symbol and alias-symbol endpoints if the primary symbol fetch returns no results.",
      "title": "Search Aliases",
      "type": "boolean"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeHGNCIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "HGNCEntry": {
      "description": "One HGNC gene record.",
      "properties": {
        "hgnc_id": {
          "description": "HGNC stable identifier (e.g. 'HGNC:1097').",
          "title": "Hgnc Id",
          "type": "string"
        },
        "approved_symbol": {
          "default": "",
          "description": "Current approved gene symbol.",
          "title": "Approved Symbol",
          "type": "string"
        },
        "approved_name": {
          "default": "",
          "description": "Full approved gene name.",
          "title": "Approved Name",
          "type": "string"
        },
        "locus_type": {
          "default": "",
          "description": "Gene product type (e.g. 'gene with protein product').",
          "title": "Locus Type",
          "type": "string"
        },
        "locus_group": {
          "default": "",
          "description": "Broader locus grouping (e.g. 'protein-coding gene').",
          "title": "Locus Group",
          "type": "string"
        },
        "chromosomal_location": {
          "default": "",
          "description": "Cytogenetic band location (e.g. '17q21.31').",
          "title": "Chromosomal Location",
          "type": "string"
        },
        "previous_symbols": {
          "description": "Formerly approved gene symbols.",
          "items": {
            "type": "string"
          },
          "title": "Previous Symbols",
          "type": "array"
        },
        "alias_symbols": {
          "description": "Alternative/alias gene symbols.",
          "items": {
            "type": "string"
          },
          "title": "Alias Symbols",
          "type": "array"
        },
        "uniprot_ids": {
          "description": "UniProt accessions for the gene product.",
          "items": {
            "type": "string"
          },
          "title": "Uniprot Ids",
          "type": "array"
        },
        "omim_ids": {
          "description": "OMIM MIM IDs for the gene.",
          "items": {
            "type": "string"
          },
          "title": "Omim Ids",
          "type": "array"
        },
        "ensembl_gene_id": {
          "default": "",
          "description": "Ensembl stable gene ID (e.g. 'ENSG00000012048').",
          "title": "Ensembl Gene Id",
          "type": "string"
        },
        "refseq_accession": {
          "default": "",
          "description": "First RefSeq mRNA accession (e.g. 'NM_007294').",
          "title": "Refseq Accession",
          "type": "string"
        },
        "status": {
          "default": "",
          "description": "HGNC approval status (e.g. 'Approved').",
          "title": "Status",
          "type": "string"
        }
      },
      "required": [
        "hgnc_id"
      ],
      "title": "HGNCEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.hgnc_gene_lookup``.",
  "properties": {
    "query_symbol": {
      "description": "The symbol that was queried.",
      "title": "Query Symbol",
      "type": "string"
    },
    "hgnc_entries": {
      "description": "HGNC gene records matching the query.",
      "items": {
        "$ref": "#/$defs/HGNCEntry"
      },
      "title": "Hgnc Entries",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total number of matching HGNC records.",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream API calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query_symbol",
    "took_ms"
  ],
  "title": "ForgeHGNCOut",
  "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/hgnc_gene_lookup' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

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