Forge Tools pathway_commons

pathway_commons read

scidex.forge.pathway_commons

Query Pathway Commons (pathwaycommons.org) for biological pathway context. Pathway Commons aggregates curated data from Reactome, KEGG, WikiPathways, PANTHER, HumanCyc, PhosphoSitePlus, and 20+ other databases into a unified network. Input: a gene symbol (e.g. 'BRCA1') to return containing pathways, or a pathway name to return participant genes. Output: pathway_name, datasource, participant_genes (list), interaction_type, url, evidence_pmids. Capped to top 10 pathways. API: GET https://www.pathwaycommons.org/pc2/search — free, no auth required.

HTTP: POST /api/scidex/forge/pathway_commons

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.pathway_commons``.",
  "properties": {
    "query": {
      "description": "Either a gene symbol (e.g. ``'BRCA1'``) to find containing pathways, or a pathway name to look up its participant genes. Pathway Commons resolves ambiguous inputs across 20+ databases.",
      "title": "Query",
      "type": "string"
    },
    "search_type": {
      "default": "gene",
      "description": "What kind of entity ``query`` represents. One of: ``'gene'`` (query is a gene symbol; return containing pathways) or ``'pathway'`` (query is a pathway name; return participant genes). Default ``'gene'``.",
      "title": "Search Type",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of pathways to return (default 10, max 10).",
      "maximum": 10,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgePathwayCommonsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "PathwayCommonsPathway": {
      "description": "One pathway record from Pathway Commons.",
      "properties": {
        "pathway_name": {
          "description": "Human-readable pathway name.",
          "title": "Pathway Name",
          "type": "string"
        },
        "datasource": {
          "default": "",
          "description": "Originating database (e.g. Reactome, KEGG, WikiPathways).",
          "title": "Datasource",
          "type": "string"
        },
        "participant_genes": {
          "description": "Gene symbols participating in this pathway.",
          "items": {
            "type": "string"
          },
          "title": "Participant Genes",
          "type": "array"
        },
        "interaction_type": {
          "default": "",
          "description": "Type of interaction represented by the pathway (e.g. 'pathway', 'interaction', 'biochemical', or empty).",
          "title": "Interaction Type",
          "type": "string"
        },
        "url": {
          "default": "",
          "description": "Pathway URL on the originating database.",
          "title": "Url",
          "type": "string"
        },
        "evidence_pmids": {
          "description": "PubMed IDs providing evidence for this pathway.",
          "items": {
            "type": "string"
          },
          "title": "Evidence Pmids",
          "type": "array"
        }
      },
      "required": [
        "pathway_name"
      ],
      "title": "PathwayCommonsPathway",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.pathway_commons``.",
  "properties": {
    "pathways": {
      "description": "Pathway records from Pathway Commons matching the query.",
      "items": {
        "$ref": "#/$defs/PathwayCommonsPathway"
      },
      "title": "Pathways",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total number of matching pathways before limit was applied.",
      "title": "Total Found",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True when the query had no matches in Pathway Commons.",
      "title": "Not Found",
      "type": "boolean"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for upstream API calls in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "title": "ForgePathwayCommonsOut",
  "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/pathway_commons' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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