Wikipathways Ext Tools#

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

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

Available Tools#

WikiPathways_find_pathways_by_gene (Type: WikiPathwaysExtTool)#

Find WikiPathways pathways containing an exact gene label. Results use stable limit/offset pagina…

WikiPathways_find_pathways_by_gene tool specification

Tool Information:

  • Name: WikiPathways_find_pathways_by_gene

  • Type: WikiPathwaysExtTool

  • Description: Find WikiPathways pathways containing an exact gene label. Results use stable limit/offset pagination and an exact SPARQL count: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. data.total_pathways is the exact total, not the current-page length. Human AKT1 currently matches more than 100 pathways, so complete retrieval requires multiple pages.

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’.

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

WikiPathways_get_pathway_genes (Type: WikiPathwaysExtTool)#

Get the genes involved in a WikiPathways pathway. gene_count counts distinct gene products; `ge…

WikiPathways_get_pathway_genes tool specification

Tool Information:

  • Name: WikiPathways_get_pathway_genes

  • Type: WikiPathwaysExtTool

  • Description: Get the genes involved in a WikiPathways pathway. gene_count counts distinct gene products; genes lists every symbol label WikiPathways records for them, which is larger because one gene product carries several aliases (AKT, AKT1, Akt1 are one node) and occasionally an unrelated symbol – use gene_products for node-level identifiers and their exact labels. By default every gene product is returned regardless of which database annotated it; set code only when you need genes cross-referenced to one identifier system, and note most pathways are annotated from Entrez Gene or Ensembl rather than HGNC. Useful for extracting gene sets from curated pathways for enrichment analysis or network building. Example: WP254 (Apoptosis) has 87 gene products (139 labels) including AKT1, APAF1, BAD, BAK1, BAX, BCL2, BCL2L1, BID, CASP3, CASP8, CASP9, CFLAR, CYCS, DIABLO, FADD, FAS, NFKB1, TP53, TRAF1, XIAP.

Parameters:

  • pathway_id ([‘string’, ‘null’]) (optional) WikiPathways pathway identifier. Examples: ‘WP254’ (Apoptosis, 87 gene products), ‘WP179’ (Cell cycle), ‘WP4216’ (Chromosomal and microsatellite instability), ‘WP1584’ (Type II diabetes mellitus). Required unless wpid is given instead.

  • wpid ([‘string’, ‘null’]) (optional) Alias for pathway_id, matching the parameter name used by the sibling WikiPathways_get_pathway tool. Provide either pathway_id or wpid.

  • code ([‘string’, ‘null’]) (optional) Optional filter restricting results to gene products annotated from one identifier system: ‘H’ (HGNC), ‘En’ (Ensembl), ‘S’ (UniProt), ‘L’ (Entrez Gene), ‘Ce’ (ChEBI, metabolites). Omit to return every gene product in the pathway. Most pathways are annotated from Entrez Gene or Ensembl and carry no HGNC-sourced entries, so filtering can legitimately return 0.

Example Usage:

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

WikiPathways_get_pathway_metabolites (Type: WikiPathwaysExtTool)#

Get the metabolite/compound participants (wp:Metabolite nodes) of a WikiPathways pathway. Unlike …

WikiPathways_get_pathway_metabolites tool specification

Tool Information:

  • Name: WikiPathways_get_pathway_metabolites

  • Type: WikiPathwaysExtTool

  • Description: Get the metabolite/compound participants (wp:Metabolite nodes) of a WikiPathways pathway. Unlike WikiPathways_get_pathway_genes (which returns gene products only), this returns the small-molecule metabolites that are the central entities of a metabolic pathway, each with its canonical cross-reference identifier (HMDB, ChEBI, KEGG, ChemSpider, etc.), the dc:source datasource, and a representative label. Example: WP534 (Glycolysis & Gluconeogenesis, human) returns metabolites including D-Glucose (https://identifiers.org/hmdb/HMDB0000122), Aspartate (HMDB0000191), and D-Glyceraldehyde 3-phosphate (HMDB0001112). Use for metabolic-network reconstruction, metabolite-set enrichment, and mapping measured metabolites onto curated pathways.

Parameters:

  • pathway_id ([‘string’, ‘null’]) (optional) WikiPathways pathway identifier. Examples: ‘WP534’ (Glycolysis & Gluconeogenesis), ‘WP78’ (TCA cycle), ‘WP143’ (Fatty acid beta-oxidation), ‘WP550’ (Biogenic amine synthesis). Required unless wpid is given instead.

  • wpid ([‘string’, ‘null’]) (optional) Alias for pathway_id, matching the parameter name used by the sibling WikiPathways_get_pathway tool. Provide either pathway_id or wpid.

Example Usage:

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