Kegg Ext Tools

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

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

Available Tools

KEGG_get_compound (Type: KEGGExtTool)

Get KEGG compound/metabolite details including names, formula, molecular weight, associated pathw…

KEGG_get_compound tool specification

Tool Information:

  • Name: KEGG_get_compound

  • Type: KEGGExtTool

  • Description: Get KEGG compound/metabolite details including names, formula, molecular weight, associated pathways, enzymes, and database cross-references. Example: C00002 (ATP) has formula C10H16N5O13P3, molecular weight 507.18, and is involved in hundreds of metabolic reactions and pathways. Covers metabolites, cofactors, drugs, and other small molecules in the KEGG COMPOUND database.

Parameters:

  • compound_id (string) (required) KEGG compound ID (e.g., ‘C00002’ for ATP, ‘C00031’ for D-Glucose, ‘C00033’ for Acetate, ‘C00186’ for Ethanol). Always starts with ‘C’ followed by 5 digits.

Example Usage:

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

KEGG_get_gene_pathways (Type: KEGGExtTool)

Get all KEGG pathways that a gene participates in. Returns pathway IDs and names for a given KEGG…

KEGG_get_gene_pathways tool specification

Tool Information:

  • Name: KEGG_get_gene_pathways

  • Type: KEGGExtTool

  • Description: Get all KEGG pathways that a gene participates in. Returns pathway IDs and names for a given KEGG gene identifier. Example: hsa:7157 (human TP53) participates in 51 pathways including p53 signaling pathway (hsa04115), apoptosis (hsa04210), cell cycle (hsa04110), and 48 disease pathways (various cancers, viral infections). Requires KEGG organism:id format.

Parameters:

  • gene_id (string) (required) KEGG gene identifier in organism:id format. Examples: ‘hsa:7157’ (human TP53), ‘hsa:672’ (human BRCA1), ‘mmu:22059’ (mouse Trp53). Use organism prefix: hsa=human, mmu=mouse, rno=rat, dme=fly, sce=yeast.

Example Usage:

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

KEGG_get_pathway_genes (Type: KEGGExtTool)

Get all genes in a KEGG pathway. Returns gene IDs for all member genes of a specific pathway. Exa…

KEGG_get_pathway_genes tool specification

Tool Information:

  • Name: KEGG_get_pathway_genes

  • Type: KEGGExtTool

  • Description: Get all genes in a KEGG pathway. Returns gene IDs for all member genes of a specific pathway. Example: hsa04115 (p53 signaling pathway) contains genes including CDK2 (hsa:1017), CDK4 (hsa:1019), CDK6 (hsa:1021), CDKN1A (hsa:1026), CDKN2A (hsa:1029), and many more involved in p53-mediated cell cycle arrest, apoptosis, and senescence.

Parameters:

  • pathway_id (string) (required) KEGG pathway identifier (e.g., ‘hsa04115’ for p53 signaling pathway, ‘hsa04110’ for cell cycle, ‘hsa04210’ for apoptosis). Use organism prefix: hsa=human, mmu=mouse.

Example Usage:

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