README

Not tested live. KEGG's API at rest.kegg.jp is "made available only for academic use by academic users"; non-academic use of KEGG needs a commercial licence from Pathway Solutions. This package was not exercised against the service: the answers' format was checked on a handful of calls on 2026-10-15 while it was written (the test fixtures are trimmed excerpts of them), and no live check is kept. Whoever runs it must be an academic user or hold a licence: that is theirs to obtain (see Responsibility). Details in docs/index.md.

KEGG, the Kyoto Encyclopedia of Genes and Genomes, for omniscient/omnilab: a compound (C07481, caffeine), a drug (D00528), a reaction (R00200), a pathway map (map00010, hsa00010) or an enzyme (2.7.1.40) by its KEGG identifier - names, formula and masses, a reaction's equation, a pathway's class and description, an enzyme's class and systematic name; the same thing in CAS, ChEBI, ChEMBL and Rhea as identifiers; the reactions, pathways, enzymes, compounds and GO terms it is tied to as related things -; a compound by its ChEBI id; a search. No key.

$kegg = (new KeggSourceFactory($http))->create(['mailto' => 'support@glitchr.io']);
$caffeine = $kegg->entity('C07481');            // or 'cpd:C07481', 'CHEBI:27732' (KEGG's conv), its page
$caffeine->value('molecular_weight');           // 194.19 g/mol
$caffeine->identifiers->keys();                 // cas:58-08-2, chebi:27732, kegg:D00528
$caffeine->related('pathway')->keys();          // kegg.pathway:map00232 (Caffeine metabolism), ...
$caffeine->value('pubchem_sid');                // 9684: KEGG links PubChem substances, not compounds
$reaction = $kegg->entity('R00200');            // ATP:pyruvate 2-O-phosphotransferase
$reaction->identifiers->keys();                 // rhea:18160: the Collector follows it into omnilab/rhea
$reaction->related('compound')->keys();         // kegg:C00002, kegg:C00022, kegg:C00008, kegg:C00074
$kegg->entity('EC 2.7.1.40')->label;            // pyruvate kinase
$kegg->entity('map00010')->related('go')->keys();   // go:0006096, go:0006094
$kegg->search(new Query('caffeine'));           // C07481 Caffeine, C13403 Sodium caffeine benzoate

omnilab:
    sources:
        kegg:
            factory: kegg
            options:
                mailto: 'support@glitchr.io'   # in the User-Agent
                databases: ['compound']        # what search() searches: compound, drug, reaction, pathway, enzyme
                throttle: 0.34                 # KEGG blocks a caller above three calls a second

Terms of use

KEGG is "an original database product, copyright Kanehisa Laboratories", and "not a public database" (kegg.jp/kegg/legal.html). Its API "is made available only for academic use by academic users"; non-academic users follow KEGG's "Non-academic use of KEGG" and need a licence from Pathway Solutions, which operates KEGG's FTP sites. Academic users who use KEGG to provide a service need an academic service provider licence. At most three calls a second, or the caller is blocked. Cite KEGG: Kanehisa, M. and Goto, S., KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res. 28, 27-30 (2000), and the latest paper kegg.jp lists.

Responsibility

This package is an independent, unofficial client: it is not affiliated with, endorsed by or sponsored by Kanehisa Laboratories and Pathway Solutions (KEGG). It reaches their service on behalf of whoever runs it, and it does not redistribute their data beyond the short excerpts recorded as test fixtures. Its MIT licence covers this package's code only and grants no right to the service or to its data.

Whoever installs and runs this package is responsible for complying with the terms above, for obtaining whatever they require (an account, a key, a licence or subscription, an attribution or a citation, a rate limit to respect), and for any use made of what it returns. The authors publish it free of charge, make no commercial use of it, and accept no liability for how it is used (see LICENSE).

License (of this package's code): MIT.

omnilab / kegg

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