Forge Tools genecards

genecards read

scidex.forge.genecards

Query GeneCards (genecards.org) for comprehensive synthesized gene summaries aggregated from 150+ databases including UniProt, NCBI Gene, Ensembl, OMIM, GO, GTEx, HPO, and DrugBank. GeneCards is the most widely cited human gene portal. Returns: synthesized summary, gene aliases, chromosomal location, tissue expression profile, disease associations, drug interaction count, and Gene Ontology terms. Distinct from forge_ncbi_gene (Entrez primary records) and forge_mygene_info (MyGene.info JSON index). Requires GENECARDS_API_KEY env var (free key: genecards.org/Guide/Api). Input: gene symbol (e.g. 'TP53'), optional sections list ∈ {'summaries','expression','diseases','drugs','go'}. API: GET https://api.genecards.org/v1/genes/<SYMBOL>.

HTTP: POST /api/scidex/forge/genecards

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.genecards``.",
  "properties": {
    "gene": {
      "description": "HGNC gene symbol to look up (e.g. ``'TP53'``, ``'BRCA1'``, ``'APOE'``). Case-insensitive; the verb normalises to uppercase.",
      "maxLength": 64,
      "title": "Gene",
      "type": "string"
    },
    "sections": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional list of GeneCards sections to include in the response. Valid values: ``'summaries'``, ``'expression'``, ``'diseases'``, ``'drugs'``, ``'go'``. Pass ``None`` (default) to request all sections.",
      "title": "Sections"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeGeneCardsIn",
  "type": "object"
}
Output schema 
{
  "description": "Response shape for ``scidex.forge.genecards``.",
  "properties": {
    "gene_symbol": {
      "description": "Official gene symbol returned by GeneCards (normalised to uppercase).",
      "title": "Gene Symbol",
      "type": "string"
    },
    "summary": {
      "default": "",
      "description": "Synthesized narrative gene summary aggregated from 150+ databases (up to 2000 chars).",
      "title": "Summary",
      "type": "string"
    },
    "aliases": {
      "description": "Gene synonyms and alternate names from GeneCards.",
      "items": {
        "type": "string"
      },
      "title": "Aliases",
      "type": "array"
    },
    "chromosomal_location": {
      "default": "",
      "description": "Cytogenetic chromosomal location (e.g. ``'17p13.1'``).",
      "title": "Chromosomal Location",
      "type": "string"
    },
    "expression_profile": {
      "additionalProperties": true,
      "description": "Tissue/cell-type expression levels from GeneCards expression data (keys: tissue name; values: expression level or score).",
      "title": "Expression Profile",
      "type": "object"
    },
    "disease_associations": {
      "description": "Disease names associated with this gene in GeneCards.",
      "items": {
        "type": "string"
      },
      "title": "Disease Associations",
      "type": "array"
    },
    "drug_count": {
      "default": 0,
      "description": "Number of drugs known to interact with this gene.",
      "title": "Drug Count",
      "type": "integer"
    },
    "go_terms": {
      "description": "Gene Ontology term names annotated to this gene.",
      "items": {
        "type": "string"
      },
      "title": "Go Terms",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when GeneCards has no record for the queried gene symbol.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "GeneCards (genecards.org) — 150+ database aggregator",
      "description": "Data source attribution.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "ForgeGeneCardsOut",
  "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/genecards' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

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