Forge Tools wikip_pathways

wikip_pathways read

scidex.forge.wikip_pathways

Find WikiPathways community-curated biological pathways for one or more gene symbols. Returns pathways ranked by how many input genes they contain, with pathway name, species, WikiPathways URL, and description. Covers 3,000+ pathways across species; complements KEGG and Reactome lookups.

HTTP: POST /api/scidex/forge/wikip_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.wikip_pathways``.",
  "properties": {
    "gene_symbols": {
      "description": "HGNC gene symbols (e.g. ``BRCA1``, ``TP53``). 1–20 genes per call.",
      "items": {
        "type": "string"
      },
      "maxItems": 20,
      "minItems": 1,
      "title": "Gene Symbols",
      "type": "array"
    },
    "species": {
      "default": "Homo sapiens",
      "description": "Species to filter pathways by. Defaults to ``Homo sapiens``. Common alternatives: ``Mus musculus``, ``Rattus norvegicus``.",
      "title": "Species",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of pathways to return. Pathways are ranked by how many of the input genes matched (descending). Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeWikiPathwaysIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "WikiPathwayEntry": {
      "description": "One WikiPathways pathway in the response.",
      "properties": {
        "pathway_id": {
          "description": "WikiPathways ID (WP### format).",
          "title": "Pathway Id",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Pathway name.",
          "title": "Name",
          "type": "string"
        },
        "species": {
          "default": "",
          "description": "Species this pathway applies to.",
          "title": "Species",
          "type": "string"
        },
        "url": {
          "default": "",
          "description": "Canonical WikiPathways URL.",
          "title": "Url",
          "type": "string"
        },
        "gene_count": {
          "default": 0,
          "description": "Total data nodes in this pathway.",
          "title": "Gene Count",
          "type": "integer"
        },
        "data_nodes": {
          "description": "Data node labels (gene symbols) from the pathway.",
          "items": {
            "type": "string"
          },
          "title": "Data Nodes",
          "type": "array"
        },
        "description": {
          "default": "",
          "description": "Pathway description (may be empty).",
          "title": "Description",
          "type": "string"
        },
        "matched_genes": {
          "description": "Subset of input genes found in this pathway.",
          "items": {
            "type": "string"
          },
          "title": "Matched Genes",
          "type": "array"
        }
      },
      "required": [
        "pathway_id"
      ],
      "title": "WikiPathwayEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.wikip_pathways``.",
  "properties": {
    "pathways": {
      "items": {
        "$ref": "#/$defs/WikiPathwayEntry"
      },
      "title": "Pathways",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total unique pathways found across all input genes before limit.",
      "title": "Total Found",
      "type": "integer"
    },
    "matched_genes": {
      "description": "Distinct input genes that matched at least one pathway.",
      "items": {
        "type": "string"
      },
      "title": "Matched Genes",
      "type": "array"
    }
  },
  "title": "ForgeWikiPathwaysOut",
  "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/wikip_pathways' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.