Cortexa research tool·chemistry·pathwaycommons

PathwayCommons Search

Search Pathway Commons for pathways, interactions, and molecular entities across 22 integrated databases (Reactome, KEGG, WikiPathways, PID, BioGRID, IntAct, HPRD, etc.). Search by gene symbol, protein name, or keyword. Optionally filter by BioPAX entity type (Pathway, Protein, SmallMolecule, Complex) and data source. Returns pathway URIs, names, data sources, and participant/process counts. Use PathwayCommons_get_pathway with returned URI for full pathway details.

Livelast probed 2026-04-30 23:07Z· 110msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 110ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "datasource": {
      "description": "Data source filter: reactome, kegg, wikipathways, pid, biogrid, intact, hprd, panther, netpath, corum, ctd, drugbank, msigdb, mirtarbase",
      "type": [
        "string",
        "null"
      ]
    },
    "organism": {
      "description": "Organism filter: taxonomy ID (9606 for human, 10090 for mouse) or organism name",
      "type": [
        "string",
        "null"
      ]
    },
    "page": {
      "description": "Page number for pagination (0-based, 100 results per page)",
      "minimum": 0,
      "type": [
        "integer",
        "null"
      ]
    },
    "query": {
      "description": "Search query: gene symbol (BRCA1, TP53), protein name, pathway name, or keyword",
      "type": "string"
    },
    "type": {
      "description": "BioPAX entity type filter (default: all types)",
      "enum": [
        "Pathway",
        "Protein",
        "SmallMolecule",
        "Complex",
        "ProteinReference",
        "SmallMoleculeReference",
        "PhysicalEntity",
        "Interaction",
        null
      ],
      "type": [
        "string",
        "null"
      ]
    }
  },
  "required": [
    "query"
  ],
  "type": "object"
}

Examples (1)

Default PathwayCommons Search call

public-safeinput

{
  "query": "BRCA1"
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_PathwayCommons_search
Tool name: PathwayCommons_search
Added: 2026-04-30 22:47Z
Tags: tooluniverse

PathwayCommons Search

Livelast probed 2026-04-30 23:07Z· 110msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "datasource": { "description": "Data source filter: reactome, kegg, wikipathways, pid, biogrid, intact, hprd, panther, netpath, corum, ctd, drugbank, msigdb, mirtarbase", "type": [ "string", "null" ] }, "organism": { "description": "Organism filter: taxonomy ID (9606 for human, 10090 for mouse) or organism name", "type": [ "string", "null" ] }, "page": { "description": "Page number for pagination (0-based, 100 results per page)", "minimum": 0, "type": [ "integer", "null" ] }, "query": { "description": "Search query: gene symbol (BRCA1, TP53), protein name, pathway name, or keyword", "type": "string" }, "type": { "description": "BioPAX entity type filter (default: all types)", "enum": [ "Pathway", "Protein", "SmallMolecule", "Complex", "ProteinReference", "SmallMoleculeReference", "PhysicalEntity", "Interaction", null ], "type": [ "string", "null" ] } }, "required": [ "query" ], "type": "object" }