Pathwaycommons Tools#

Configuration File: pathwaycommons_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

PathwayCommons_get_neighborhood (Type: PathwayCommonsTool)#

Get an interaction neighborhood from Pathway Commons. The API’s extended TXT response contains bo…

PathwayCommons_get_neighborhood tool specification

Tool Information:

  • Name: PathwayCommons_get_neighborhood

  • Type: PathwayCommonsTool

  • Description: Get an interaction neighborhood from Pathway Commons. The API’s extended TXT response contains both an interaction table and a separate participant-attribute table; only genuine interaction rows are returned. Large graphs are recoverably paginated: max_results is page size; start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. metadata.total_interactions is the complete interaction-table size and metadata.complete_graph_retrieved confirms that local pagination uses the full upstream graph.

Parameters:

  • gene (string) (required) Pathway Commons source identifier. A full BioPAX URI from PathwayCommons_search is precise; a bare gene symbol or other identifier is exploratory because the API performs search and ID mapping and may start from multiple entities. metadata.source_resolution records the mode.

  • 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

  • organism ([‘string’, ‘null’]) (optional) Optional organism filter, preferably an NCBI taxonomy ID such as 9606.

  • direction ([‘string’, ‘null’]) (optional) Graph traversal direction; default is undirected.

  • pattern ([‘array’, ‘null’]) (optional) Optional SIF interaction-type filters.

  • subpw ([‘boolean’, ‘null’]) (optional) Whether graph traversal may enter sub-pathways. Omit to use the upstream default.

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

  • offset (integer) (optional) Zero-based interaction offset. Continue with metadata.next_offset.

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_paths_between (Type: PathwayCommonsTool)#

Find mechanistic paths connecting genes in Pathway Commons. Edge results are recoverably paginate…

PathwayCommons_paths_between tool specification

Tool Information:

  • Name: PathwayCommons_paths_between

  • Type: PathwayCommonsTool

  • Description: Find mechanistic paths connecting genes in Pathway Commons. Edge results are recoverably paginated: max_results is page size; start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. Uncached graph queries can be slow.

Parameters:

  • genes ([‘array’, ‘string’]) (required) Two or more source identifiers, e.g. [“BRCA1”, “BRCA2”, “TP53”], or a comma-separated string. Full BioPAX URIs are precise; bare identifiers invoke exploratory search and ID mapping.

  • limit ([‘integer’, ‘null’]) (optional) Path length limit (graph search distance). Default 1 (direct mechanistic links). Higher values include longer indirect paths and 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 edges to return (default: 200)

  • organism ([‘string’, ‘null’]) (optional) Optional organism filter, preferably an NCBI taxonomy ID such as 9606.

  • pattern ([‘array’, ‘null’]) (optional) Optional SIF interaction-type filters.

  • subpw ([‘boolean’, ‘null’]) (optional) Whether graph traversal may enter sub-pathways. Omit to use the upstream default.

  • offset (integer) (optional) Zero-based edge offset. Continue with metadata.next_offset.

Example Usage:

query = {
    "name": "PathwayCommons_paths_between",
    "arguments": {
        "genes": "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.). Results use the upstream fixed page size of 100: start with page=0 and continue with metadata.next_page while metadata.has_more is true. metadata.total_hits is exact. Optionally filter by BioPAX entity type and data source. Use PathwayCommons_get_pathway with a 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) Zero-based page number. Pathway Commons fixes the page size at 100; use metadata.next_page to retrieve all results.

Example Usage:

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