Kegg Ext Tools#

Configuration File: kegg_ext_tools.json Tool Type: Local Tools Count: 7

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

Available Tools#

KEGG_find_compound (Type: KEGGExtTool)#

Search the KEGG COMPOUND database for candidate metabolites by exact (monoisotopic) mass, average…

KEGG_find_compound tool specification

Tool Information:

  • Name: KEGG_find_compound

  • Type: KEGGExtTool

  • Description: Search the KEGG COMPOUND database for candidate metabolites by exact (monoisotopic) mass, average molecular weight, molecular formula, or name keyword. This is the inverse of KEGG_get_compound: given an MS peak mass or a molecular formula, it returns the candidate KEGG compound IDs to identify. Provide exactly one of: exact_mass, mol_weight, formula, or name (they are mutually exclusive). exact_mass and mol_weight accept a single value (e.g. 174.05) or a range ‘low-high’ (e.g. ‘300-310’). Examples: exact_mass 174.05 -> C00493, C04236, C16588, C17696, C18307, C18312, C21281; formula ‘C6H12O6’ -> C00031 (glucose), C00095 (fructose), C00124 (galactose), …; name ‘caffeine’ -> C07481.

Parameters:

  • exact_mass ([‘string’, ‘number’, ‘null’]) (optional) Monoisotopic / exact mass to search by. Single value (e.g. 174.05) or a range as ‘low-high’ (e.g. ‘174-175’). Mutually exclusive with mol_weight, formula, name.

  • mol_weight ([‘string’, ‘number’, ‘null’]) (optional) Average molecular weight to search by. Single value or a range as ‘low-high’ (e.g. ‘300-310’). Mutually exclusive with exact_mass, formula, name.

  • formula ([‘string’, ‘null’]) (optional) Molecular formula to search by, e.g. ‘C6H12O6’. Mutually exclusive with exact_mass, mol_weight, name.

  • name ([‘string’, ‘null’]) (optional) Compound name or keyword to search by, e.g. ‘caffeine’, ‘glucose’. Mutually exclusive with exact_mass, mol_weight, formula.

  • query ([‘string’, ‘null’]) (optional) Alias for ‘name’: compound name or keyword to search by.

  • max_results ([‘integer’, ‘null’]) (optional) Optional page size for candidate compounds. The complete upstream total is always reported.

  • offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use next_offset to continue.

Example Usage:

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

KEGG_get_compound (Type: KEGGExtTool)#

Get complete KEGG compound/metabolite details. In addition to names, formula, mass, pathways, enz…

KEGG_get_compound tool specification

Tool Information:

  • Name: KEGG_get_compound

  • Type: KEGGExtTool

  • Description: Get complete KEGG compound/metabolite details. In addition to names, formula, mass, pathways, enzymes, and cross-references, preserves REACTION, MODULE, NETWORK, BRITE, ATOM, BOND, every other KEGG flat-file field, and the raw record so uncommon sections are never silently omitted.

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_enzyme (Type: KEGGExtTool)#

Retrieve a KEGG ENZYME entry by EC number. Returns all NAMEs (accepted name plus synonyms), the C…

KEGG_get_enzyme tool specification

Tool Information:

  • Name: KEGG_get_enzyme

  • Type: KEGGExtTool

  • Description: Retrieve a KEGG ENZYME entry by EC number. Returns all NAMEs (accepted name plus synonyms), the CLASS hierarchy (the 3-level EC enzyme tree, e.g. Transferases -> Transferring phosphorus-containing groups -> Phosphotransferases with an alcohol group as acceptor), the SYSNAME (systematic name), the catalyzed REACTION, SUBSTRATEs and PRODUCTs, and the gene ORTHOLOGY (KO) entries. Use for enzyme annotation, EC-to-reaction mapping, and pathway gene-function lookup. Example: 2.7.1.1 -> NAME ‘hexokinase’ (+6 synonyms), CLASS ‘Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor’, SYSNAME ‘ATP:D-hexose 6-phosphotransferase’.

Parameters:

  • ec_number (string) (optional) Enzyme Commission (EC) number, e.g. ‘2.7.1.1’ (hexokinase), ‘1.1.1.1’ (alcohol dehydrogenase), ‘2.7.1.11’ (phosphofructokinase). The ‘ec:’ / ‘EC ‘ prefix is stripped automatically.

  • enzyme_id (string) (optional) Alias for ec_number.

  • id (string) (optional) Alias for ec_number.

Example Usage:

query = {
    "name": "KEGG_get_enzyme",
    "arguments": {
    }
}
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) (optional) 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.

  • gene_symbol (string) (optional) Alias for gene_id: human gene symbol (e.g. ‘TP53’, ‘BRCA1’). Auto-resolved to KEGG gene ID using organism=’hsa’.

  • gene (string) (optional) Alias for gene_id: human gene symbol (e.g. ‘TP53’, ‘EGFR’).

  • organism (string) (optional) KEGG organism code for gene symbol resolution (default: ‘hsa’ for human). Used only when gene_symbol is provided instead of gene_id.

Example Usage:

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

KEGG_get_module (Type: KEGGExtTool)#

Retrieve a KEGG MODULE entry: a functional reaction-unit (a defined set of reaction steps) that i…

KEGG_get_module tool specification

Tool Information:

  • Name: KEGG_get_module

  • Type: KEGGExtTool

  • Description: Retrieve a KEGG MODULE entry: a functional reaction-unit (a defined set of reaction steps) that is a building block of metabolism. Returns the NAME, the DEFINITION (the K-number boolean expression of ordered reaction steps), the CLASS hierarchy, the member REACTIONs, the participating COMPOUNDs, the ORTHOLOGY (KO/EC mappings), and the parent PATHWAYs. KEGG modules are central to metabolic reconstruction and completeness analysis. Example: M00001 = ‘Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate’, DEFINITION ‘(K00844,K12407,K00845,…) (K01810,…) …’, CLASS ‘Pathway modules; Carbohydrate metabolism; Central carbohydrate metabolism’.

Parameters:

  • module_id (string) (optional) KEGG module identifier, e.g. ‘M00001’ (glycolysis EM pathway), ‘M00002’ (glycolysis core, 3-carbon), ‘M00003’ (gluconeogenesis), ‘M00009’ (citrate cycle, TCA). ‘M’ prefix is added automatically if omitted.

  • id (string) (optional) Alias for module_id.

Example Usage:

query = {
    "name": "KEGG_get_module",
    "arguments": {
    }
}
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)

KEGG_get_reaction (Type: KEGGExtTool)#

Retrieve a KEGG REACTION entry by R-number. Returns the reaction NAME, the human-readable DEFINIT…

KEGG_get_reaction tool specification

Tool Information:

  • Name: KEGG_get_reaction

  • Type: KEGGExtTool

  • Description: Retrieve a KEGG REACTION entry by R-number. Returns the reaction NAME, the human-readable DEFINITION, the balanced EQUATION using KEGG C-number compound stoichiometry, the catalyzing ENZYME EC number(s), the RCLASS (reaction class) codes, and the parent PATHWAYs and MODULEs. Use for getting reaction stoichiometry and EC mapping in metabolic-network and flux modeling. Example: R00200 -> NAME ‘ATP:pyruvate 2-O-phosphotransferase’, EQUATION ‘C00002 + C00022 <=> C00008 + C00074’, ENZYME 2.7.1.40, RCLASS RC00002/RC00015, PATHWAY rn00010 (glycolysis).

Parameters:

  • reaction_id (string) (optional) KEGG reaction identifier (R-number), e.g. ‘R00200’ (pyruvate kinase), ‘R01786’ (glucokinase/hexokinase), ‘R00756’ (phosphofructokinase). The ‘rn:’ prefix and ‘R’ are normalized automatically.

  • id (string) (optional) Alias for reaction_id.

Example Usage:

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