Wikipathways Tools

Configuration File: wikipathways_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

WikiPathways_get_pathway (Type: WikiPathwaysGetTool)

Fetch pathway content by WPID (JSON/GPML). Use to programmatically access pathway nodes/edges/met…

WikiPathways_get_pathway tool specification

Tool Information:

  • Name: WikiPathways_get_pathway

  • Type: WikiPathwaysGetTool

  • Description: Fetch pathway content by WPID (JSON/GPML). Use to programmatically access pathway nodes/edges/metadata for enrichment reporting or network visualization.

Parameters:

  • wpid (string) (required) WikiPathways identifier (e.g., ‘WP254’).

  • format (string) (optional) Response format: ‘json’ for structured, ‘gpml’ for GPML XML.

Example Usage:

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

WikiPathways_search (Type: WikiPathwaysSearchTool)

Text search across community-curated pathways (disease, metabolic, signaling). Use to discover re…

WikiPathways_search tool specification

Tool Information:

  • Name: WikiPathways_search

  • Type: WikiPathwaysSearchTool

  • Description: Text search across community-curated pathways (disease, metabolic, signaling). Use to discover relevant pathways for a topic/gene set and obtain WPIDs for retrieval/visualization.

Parameters:

  • query (string) (required) Free-text query (keywords, gene symbols, processes), e.g., ‘p53’, ‘glycolysis’.

  • organism (string) (optional) Organism filter (scientific name), e.g., ‘Homo sapiens’.

Example Usage:

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