Forge Tools metacyc_pathways

metacyc_pathways read

scidex.forge.metacyc_pathways

Query MetaCyc for comprehensive metabolic pathway data. Returns pathways containing a gene of interest or matching a pathway name keyword. Covers >3,000 pathways from >15,000 organisms — broader than KEGG or Reactome. Each result includes the MetaCyc pathway ID, name, enzymatic reactions, metabolites, and gene products. Complements scidex.forge.kegg_pathways and scidex.forge.wikip_pathways. API: https://websvc.biocyc.org/ — public, no API key required.

HTTP: POST /api/scidex/forge/metacyc_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.metacyc_pathways``.",
  "properties": {
    "gene_symbol": {
      "anyOf": [
        {
          "maxLength": 30,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "HGNC gene symbol (e.g. ``TP53``, ``BRCA1``). Returns MetaCyc pathways in which this gene's enzyme product participates. At least one of ``gene_symbol`` or ``pathway_name`` is required.",
      "title": "Gene Symbol"
    },
    "pathway_name": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Pathway name or keyword to search (e.g. ``glycolysis``, ``citric acid cycle``). Matched against MetaCyc pathway names. At least one of ``gene_symbol`` or ``pathway_name`` is required.",
      "title": "Pathway Name"
    },
    "organism": {
      "default": "human",
      "description": "Organism to prioritise when querying by gene symbol (e.g. ``human``, ``mouse``, ``rat``, ``yeast``, ``ecoli``). Default: ``human``.",
      "maxLength": 50,
      "title": "Organism",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of pathways to return (1–100). Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeMetaCycIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "MetaCycPathway": {
      "description": "One MetaCyc pathway record.",
      "properties": {
        "pathway_id": {
          "description": "MetaCyc pathway frame ID (e.g. ``PWY-5026``).",
          "title": "Pathway Id",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Common pathway name.",
          "title": "Name",
          "type": "string"
        },
        "organism": {
          "default": "",
          "description": "Taxonomic range or primary organism.",
          "title": "Organism",
          "type": "string"
        },
        "url": {
          "default": "",
          "description": "Canonical MetaCyc URL.",
          "title": "Url",
          "type": "string"
        },
        "reaction_count": {
          "default": 0,
          "description": "Number of enzymatic reactions.",
          "title": "Reaction Count",
          "type": "integer"
        },
        "reactions": {
          "description": "Up to 10 reaction frame IDs (e.g. ``PGLUCISOM-RXN``).",
          "items": {
            "type": "string"
          },
          "title": "Reactions",
          "type": "array"
        },
        "metabolites": {
          "description": "Key metabolite frame IDs from the pathway.",
          "items": {
            "type": "string"
          },
          "title": "Metabolites",
          "type": "array"
        },
        "gene_products": {
          "description": "Gene/enzyme product frame IDs in this pathway.",
          "items": {
            "type": "string"
          },
          "title": "Gene Products",
          "type": "array"
        },
        "pathway_class": {
          "default": "",
          "description": "Pathway superclass (e.g. ``Generation of Precursor Metabolites and Energy``).",
          "title": "Pathway Class",
          "type": "string"
        }
      },
      "required": [
        "pathway_id"
      ],
      "title": "MetaCycPathway",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.metacyc_pathways``.",
  "properties": {
    "pathways": {
      "description": "MetaCyc pathway records, capped at ``limit``.",
      "items": {
        "$ref": "#/$defs/MetaCycPathway"
      },
      "title": "Pathways",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total pathways found before applying ``limit``.",
      "title": "Total Found",
      "type": "integer"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "title": "ForgeMetaCycOut",
  "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/metacyc_pathways' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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