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 cap on the number of returned candidate compounds.

Example Usage:

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

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_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)

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