Forge Tools rhea_reactions

rhea_reactions read

scidex.forge.rhea_reactions

Query the Rhea biochemical reaction database (rhea-db.org) for expert-curated stoichiometric reaction equations. Accepts a Rhea ID (RHEA:10596) for direct lookup or free text (compound name, gene name) for full-text search. Returns reaction equations with ChEBI compound IDs for all substrates and products, UniProt annotation count, EC number, and transport/balance flags. Rhea is the primary reaction annotation database for UniProt, covering 14,000+ curated reactions linked to ChEBI and 250,000+ UniProt enzyme entries. API: GET https://www.rhea-db.org/rhea — free, no authentication required.

HTTP: POST /api/scidex/forge/rhea_reactions

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.rhea_reactions``.",
  "properties": {
    "query": {
      "description": "Free-text search term (compound name, gene/protein name, etc.) or a Rhea reaction identifier (``RHEA:10596``).  Rhea ID queries fetch the specific reaction directly; free-text searches the full Rhea database.",
      "maxLength": 500,
      "title": "Query",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of reactions to return (default 10, max 100).",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeRheaIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "RheaReaction": {
      "description": "One Rhea biochemical reaction record.",
      "properties": {
        "rhea_id": {
          "description": "Rhea reaction identifier (e.g. RHEA:10596).",
          "title": "Rhea Id",
          "type": "string"
        },
        "equation": {
          "description": "Human-readable stoichiometric equation string.",
          "title": "Equation",
          "type": "string"
        },
        "chebi_ids": {
          "description": "ChEBI IDs of all substrates and products in the reaction.",
          "items": {
            "type": "string"
          },
          "title": "Chebi Ids",
          "type": "array"
        },
        "uniprot_count": {
          "default": 0,
          "description": "Number of UniProt entries annotated with this reaction.",
          "title": "Uniprot Count",
          "type": "integer"
        },
        "ec_number": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "EC number of the catalysing enzyme class (e.g. 3.6.1.3) when available.",
          "title": "Ec Number"
        },
        "is_transport": {
          "default": false,
          "description": "True when the reaction represents a transport event.",
          "title": "Is Transport",
          "type": "boolean"
        },
        "is_balanced": {
          "default": true,
          "description": "True when the stoichiometric equation is charge- and mass-balanced.",
          "title": "Is Balanced",
          "type": "boolean"
        }
      },
      "required": [
        "rhea_id",
        "equation"
      ],
      "title": "RheaReaction",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.rhea_reactions``.",
  "properties": {
    "query": {
      "description": "The input query string, echoed back.",
      "title": "Query",
      "type": "string"
    },
    "reactions": {
      "description": "Matching Rhea reaction records.",
      "items": {
        "$ref": "#/$defs/RheaReaction"
      },
      "title": "Reactions",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the query returned no reactions.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeRheaOut",
  "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/rhea_reactions' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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