Pathwaycommons Tools

Configuration File: pathwaycommons_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the pathwaycommons_tools.json configuration file.

Available Tools

PathwayCommons_get_neighborhood (Type: PathwayCommonsTool)

Get the interaction neighborhood for a gene from Pathway Commons. Returns all known interactions …

PathwayCommons_get_neighborhood tool specification

Tool Information:

  • Name: PathwayCommons_get_neighborhood

  • Type: PathwayCommonsTool

  • Description: Get the interaction neighborhood for a gene from Pathway Commons. Returns all known interactions (protein-protein, regulatory, catalytic, complex membership) for the query gene from 22 integrated databases. Each interaction includes the partner gene, interaction type (interacts-with, controls-state-change-of, controls-expression-of, in-complex-with, etc.), data source, and PubMed references. Useful for building gene interaction networks and finding functional partners.

Parameters:

  • gene (string) (required) Gene symbol (e.g., BRCA1, TP53, EGFR)

  • limit ([‘integer’, ‘null’]) (optional) Graph search depth (1 = direct neighbors, 2 = neighbors of neighbors). Default 1. Higher values return much more data.

  • datasource ([‘string’, ‘null’]) (optional) Filter by data source: reactome, kegg, biogrid, intact, hprd, pid, corum, ctd, drugbank

  • max_results ([‘integer’, ‘null’]) (optional) Maximum number of interactions to return (default: 100)

Example Usage:

query = {
    "name": "PathwayCommons_get_neighborhood",
    "arguments": {
        "gene": "example_value"
    }
}
result = tu.run(query)

PathwayCommons_get_pathway (Type: PathwayCommonsTool)

Get detailed pathway information from Pathway Commons by URI. Returns the pathway name, participa…

PathwayCommons_get_pathway tool specification

Tool Information:

  • Name: PathwayCommons_get_pathway

  • Type: PathwayCommonsTool

  • Description: Get detailed pathway information from Pathway Commons by URI. Returns the pathway name, participants (proteins, small molecules, complexes), and processes (interactions, catalysis, controls). Use URIs from PathwayCommons_search results. Covers Reactome, KEGG, WikiPathways, PID, and other sources. Response is parsed from BioPAX/JSON-LD format.

Parameters:

Example Usage:

query = {
    "name": "PathwayCommons_get_pathway",
    "arguments": {
        "uri": "example_value"
    }
}
result = tu.run(query)

PathwayCommons_search (Type: PathwayCommonsTool)

Search Pathway Commons for pathways, interactions, and molecular entities across 22 integrated da…

PathwayCommons_search tool specification

Tool Information:

  • Name: PathwayCommons_search

  • Type: PathwayCommonsTool

  • Description: 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.

Parameters:

  • query (string) (required) Search query: gene symbol (BRCA1, TP53), protein name, pathway name, or keyword

  • type ([‘string’, ‘null’]) (optional) BioPAX entity type filter (default: all types)

  • datasource ([‘string’, ‘null’]) (optional) Data source filter: reactome, kegg, wikipathways, pid, biogrid, intact, hprd, panther, netpath, corum, ctd, drugbank, msigdb, mirtarbase

  • organism ([‘string’, ‘null’]) (optional) Organism filter: taxonomy ID (9606 for human, 10090 for mouse) or organism name

  • page ([‘integer’, ‘null’]) (optional) Page number for pagination (0-based, 100 results per page)

Example Usage:

query = {
    "name": "PathwayCommons_search",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)