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. format=’json’ (default) returns structured metadata (uri, title, o…

WikiPathways_get_pathway tool specification

Tool Information:

  • Name: WikiPathways_get_pathway

  • Type: WikiPathwaysGetTool

  • Description: Fetch pathway content by WPID. format=’json’ (default) returns structured metadata (uri, title, organism) plus a recoverably paginated gene-participant table (id, label, datasource) via WikiPathways’ SPARQL endpoint, for enrichment reporting or network visualization; data.gene_count and metadata.total_gene_rows are exact row totals, data.gene_product_count is the exact distinct node count, and later pages continue with gene_offset=metadata.next_gene_offset. format=’gpml’ returns the pathway’s complete raw GPML XML (nodes, edges, coordinates, exact upstream layout) from the official static asset URL instead – use this when you need the full pathway diagram/model, not just its gene list. Errors clearly if the WPID has no GPML file or isn’t in the SPARQL endpoint.

Parameters:

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

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

  • gene_limit (integer) (optional) Gene-participant rows per page when format=json.

  • gene_offset (integer) (optional) Zero-based gene-participant row offset; continue with metadata.next_gene_offset.

Example Usage:

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

WikiPathways_search (Type: WikiPathwaysSearchTool)#

Search pathway titles in the current WikiPathways SPARQL dataset. Results are recoverably paginat…

WikiPathways_search tool specification

Tool Information:

  • Name: WikiPathways_search

  • Type: WikiPathwaysSearchTool

  • Description: Search pathway titles in the current WikiPathways SPARQL dataset. Results are recoverably paginated: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. The endpoint does not expose a cheap exact count, so metadata.total_hits is null and metadata.total_hits_is_known is false.

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’.

  • limit (integer) (optional) Number of pathways per page.

  • offset (integer) (optional) Zero-based result offset; continue with metadata.next_offset.

Example Usage:

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