Forge Tools kegg_compound

kegg_compound read

scidex.forge.kegg_compound

Look up KEGG COMPOUND small molecule records by compound ID (e.g. C00031) or by name (e.g. 'atp', 'glucose'). Returns molecular formula, exact mass, molecular weight, associated KEGG pathways, enzyme EC numbers, and reaction IDs. Distinct from forge_hmdb_metabolites (human metabolome focus) and forge_chebi_compound (ontology classification) — KEGG COMPOUND is the canonical cross-species metabolic network reference.

HTTP: POST /api/scidex/forge/kegg_compound

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_compound``.",
  "properties": {
    "compound_id": {
      "default": "",
      "description": "KEGG compound ID (e.g. ``C00031`` for D-Glucose, ``C00002`` for ATP). Takes priority over ``name`` when both are supplied.",
      "title": "Compound Id",
      "type": "string"
    },
    "name": {
      "default": "",
      "description": "Compound name to search (e.g. ``atp``, ``glucose``, ``acetyl-CoA``). Case-insensitive. Used only when ``compound_id`` is empty.",
      "title": "Name",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of compounds to return (name-search mode only). Default 10.",
      "maximum": 50,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeKeggCompoundIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "KeggCompound": {
      "description": "One KEGG compound record in the response.",
      "properties": {
        "compound_id": {
          "description": "KEGG compound ID (e.g. ``C00031``).",
          "title": "Compound Id",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Preferred compound name.",
          "title": "Name",
          "type": "string"
        },
        "formula": {
          "default": "",
          "description": "Molecular formula (e.g. ``C6H12O6``).",
          "title": "Formula",
          "type": "string"
        },
        "exact_mass": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Exact monoisotopic mass (Da).",
          "title": "Exact Mass"
        },
        "mol_weight": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Average molecular weight (Da).",
          "title": "Mol Weight"
        },
        "pathways": {
          "description": "Associated KEGG pathway entries.",
          "items": {
            "type": "string"
          },
          "title": "Pathways",
          "type": "array"
        },
        "enzymes": {
          "description": "EC numbers of enzymes acting on this compound.",
          "items": {
            "type": "string"
          },
          "title": "Enzymes",
          "type": "array"
        },
        "reactions": {
          "description": "KEGG reaction IDs involving this compound.",
          "items": {
            "type": "string"
          },
          "title": "Reactions",
          "type": "array"
        }
      },
      "required": [
        "compound_id"
      ],
      "title": "KeggCompound",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.kegg_compound``.",
  "properties": {
    "query": {
      "description": "The compound_id or name that was queried.",
      "title": "Query",
      "type": "string"
    },
    "compounds": {
      "description": "Matching KEGG compound records.",
      "items": {
        "$ref": "#/$defs/KeggCompound"
      },
      "title": "Compounds",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no compound matched the query.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeKeggCompoundOut",
  "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_compound' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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