Wikipathways Ext Tools

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

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

Available Tools

WikiPathways_find_pathways_by_gene (Type: WikiPathwaysExtTool)

Find all WikiPathways pathways containing a specific gene. Takes a gene identifier (HGNC symbol, …

WikiPathways_find_pathways_by_gene tool specification

Tool Information:

  • Name: WikiPathways_find_pathways_by_gene

  • Type: WikiPathwaysExtTool

  • Description: Find all WikiPathways pathways containing a specific gene. Takes a gene identifier (HGNC symbol, Entrez ID, or Ensembl ID) and returns all pathways in which that gene appears. Useful for understanding the biological context of a gene across curated pathway databases. Example: searching for ‘TP53’ returns multiple pathways including WP254 (Apoptosis), WP179 (Cell Cycle), and others. Supports multiple species.

Parameters:

  • gene (string) (required) Gene identifier to search. Examples: ‘TP53’, ‘BRCA1’, ‘EGFR’, ‘7157’ (Entrez), ‘ENSG00000141510’ (Ensembl).

  • species (string) (optional) Species to filter results. Default: ‘Homo sapiens’. Other options: ‘Mus musculus’, ‘Rattus norvegicus’, ‘Danio rerio’.

Example Usage:

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

WikiPathways_get_pathway_genes (Type: WikiPathwaysExtTool)

Get all genes (as gene symbols) involved in a WikiPathways pathway. Returns the list of HGNC gene…

WikiPathways_get_pathway_genes tool specification

Tool Information:

  • Name: WikiPathways_get_pathway_genes

  • Type: WikiPathwaysExtTool

  • Description: Get all genes (as gene symbols) involved in a WikiPathways pathway. Returns the list of HGNC gene symbols for human pathways, or equivalent organism-specific gene identifiers. Useful for extracting gene sets from curated pathways for enrichment analysis or network building. Example: WP254 (Apoptosis) returns 88 genes including AKT1, APAF1, BAD, BAK1, BAX, BCL2, BCL2L1, BID, CASP3, CASP8, CASP9, CFLAR, CYCS, DIABLO, FADD, FAS, NFKB1, TP53, TRAF1, XIAP, and more.

Parameters:

  • pathway_id (string) (required) WikiPathways pathway identifier. Examples: ‘WP254’ (Apoptosis, 88 genes), ‘WP179’ (Cell cycle, 100+ genes), ‘WP4216’ (Chromosomal and microsatellite instability), ‘WP1584’ (Type II diabetes mellitus).

  • code (string) (optional) Identifier system code for returned genes. Options: ‘H’ (HGNC symbols, default), ‘En’ (Ensembl), ‘S’ (UniProt), ‘L’ (Entrez Gene), ‘Ce’ (ChEBI for metabolites).

Example Usage:

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