Forge Tools reactome_pathways

reactome_pathways read

scidex.forge.reactome_pathways

Look up Reactome biological pathways for a gene symbol or gene set. Returns Reactome stable IDs (R-HSA-*), names, species, top-level pathway categories, matched input genes, and Reactome URLs. Uses the Reactome ContentService REST API with no API key.

HTTP: POST /api/scidex/forge/reactome_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.reactome_pathways``.",
  "properties": {
    "gene_symbol": {
      "anyOf": [
        {
          "maxLength": 30,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Single HGNC gene symbol, e.g. ``BRCA1`` or ``TP53``. Mutually exclusive with ``gene_symbols``.",
      "title": "Gene Symbol"
    },
    "gene_symbols": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "maxItems": 20,
          "minItems": 1,
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "HGNC gene symbols, 1-20 per call. When more than one gene is supplied, only shared Reactome pathways/categories are returned.",
      "title": "Gene Symbols"
    },
    "species": {
      "default": "Homo sapiens",
      "description": "Species name or common taxon shorthand. Defaults to ``Homo sapiens``.",
      "maxLength": 80,
      "minLength": 1,
      "title": "Species",
      "type": "string"
    },
    "include_lower_level": {
      "default": false,
      "description": "When false, collapse matched pathways to their Reactome top-level pathway categories. When true, return lower-level pathway records with ``top_level_pathway`` populated.",
      "title": "Include Lower Level",
      "type": "boolean"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of pathway records to return.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeReactomeIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ReactomePathway": {
      "description": "One Reactome pathway record.",
      "properties": {
        "pathway_id": {
          "description": "Reactome stable ID, e.g. ``R-HSA-5685942``.",
          "title": "Pathway Id",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Reactome pathway display name.",
          "title": "Name",
          "type": "string"
        },
        "species": {
          "default": "",
          "description": "Species for the pathway.",
          "title": "Species",
          "type": "string"
        },
        "top_level_pathway": {
          "default": "",
          "description": "Top-level Reactome pathway category, e.g. ``DNA Repair``.",
          "title": "Top Level Pathway",
          "type": "string"
        },
        "gene_count": {
          "default": 0,
          "description": "Number of requested genes matched to this pathway record.",
          "title": "Gene Count",
          "type": "integer"
        },
        "matched_genes": {
          "description": "Subset of input genes found in this pathway.",
          "items": {
            "type": "string"
          },
          "title": "Matched Genes",
          "type": "array"
        },
        "reactome_url": {
          "default": "",
          "description": "Canonical Reactome pathway URL.",
          "title": "Reactome Url",
          "type": "string"
        },
        "evidence_type": {
          "default": "reactome_direct_mapping",
          "description": "How the pathway was produced: direct mapping, search fallback, or top-level rollup.",
          "title": "Evidence Type",
          "type": "string"
        }
      },
      "required": [
        "pathway_id"
      ],
      "title": "ReactomePathway",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.reactome_pathways``.",
  "properties": {
    "pathways": {
      "items": {
        "$ref": "#/$defs/ReactomePathway"
      },
      "title": "Pathways",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total pathways/categories found after multi-gene filtering before limit.",
      "title": "Total Found",
      "type": "integer"
    },
    "total_pathways_found": {
      "default": 0,
      "description": "Compatibility alias for ``total_found``.",
      "title": "Total Pathways Found",
      "type": "integer"
    },
    "matched_genes": {
      "description": "Distinct input genes with at least one returned pathway match.",
      "items": {
        "type": "string"
      },
      "title": "Matched Genes",
      "type": "array"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for upstream lookups.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "title": "ForgeReactomeOut",
  "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/reactome_pathways' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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