Forge Tools kegg_pathways

kegg_pathways read

scidex.forge.kegg_pathways

Find KEGG biological pathways for one or more gene symbols. Returns pathways ranked by how many input genes they contain, with pathway name, description, annotated gene count, and a direct KEGG URL. Essential for metabolic and signalling context in gene-function and hypothesis-grounding workflows.

HTTP: POST /api/scidex/forge/kegg_pathways

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.kegg_pathways``.",
  "properties": {
    "genes": {
      "description": "NCBI gene symbols or KEGG gene IDs (e.g. ``BRCA1``, ``TP53``). 1–20 genes per call. Symbols are case-insensitive in KEGG but canonical HGNC capitalisation is recommended.",
      "items": {
        "type": "string"
      },
      "maxItems": 20,
      "minItems": 1,
      "title": "Genes",
      "type": "array"
    },
    "organism": {
      "default": "hsa",
      "description": "KEGG organism code. Defaults to ``hsa`` (Homo sapiens). Common alternates: ``mmu`` (mouse), ``rno`` (rat), ``dme`` (fly).",
      "maxLength": 5,
      "minLength": 2,
      "title": "Organism",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of pathways to return. Pathways are ranked by how many of the input genes matched them (descending). Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "genes"
  ],
  "title": "ForgeKEGGPathwaysIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "KEGGPathway": {
      "description": "One KEGG pathway in the response.",
      "properties": {
        "pathway_id": {
          "description": "KEGG pathway ID (e.g. ``hsa05200``).",
          "title": "Pathway Id",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Pathway name.",
          "title": "Name",
          "type": "string"
        },
        "description": {
          "default": "",
          "description": "Pathway description (may be empty).",
          "title": "Description",
          "type": "string"
        },
        "gene_count": {
          "default": 0,
          "description": "Total genes annotated in this pathway.",
          "title": "Gene Count",
          "type": "integer"
        },
        "matched_genes": {
          "description": "Subset of input genes found in this pathway.",
          "items": {
            "type": "string"
          },
          "title": "Matched Genes",
          "type": "array"
        },
        "kegg_url": {
          "default": "",
          "description": "Canonical KEGG pathway URL.",
          "title": "Kegg Url",
          "type": "string"
        }
      },
      "required": [
        "pathway_id"
      ],
      "title": "KEGGPathway",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.kegg_pathways``.",
  "properties": {
    "pathways": {
      "items": {
        "$ref": "#/$defs/KEGGPathway"
      },
      "title": "Pathways",
      "type": "array"
    },
    "total_pathways_checked": {
      "default": 0,
      "description": "Total unique pathways found across all input genes before limit.",
      "title": "Total Pathways Checked",
      "type": "integer"
    }
  },
  "title": "ForgeKEGGPathwaysOut",
  "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/kegg_pathways' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "genes": []
}'

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