omnilab / chebi

1.x-dev 2026-10-17 10:25 UTC

Requires

• php: >=8.2
• omniscient/omnilab: ^1.0@dev
• symfony/http-client: ^6.4|^7.0|^8.0

Requires (Dev)

• phpunit/phpunit: ^11.0

MIT

• Marco Meyer

• science
• ontology
• chemistry
• ebi
• inchikey
• omnilab
• chebi

Published on Packagist.org on 2026-10-17 12:17 UTC

README

ChEBI for omniscient/omnilab: a chemical entity of biological interest by its ChEBI id, an InChIKey, a CAS number, a KEGG id or a name; its definition, formula, masses, charge, structure (SMILES, InChI, InChIKey, an SVG depiction), its place in ChEBI's ontology - what it is a kind of, its roles, its functional parents, its conjugates - and its identifiers in other bases for the Collector to follow; a search. Through the REST API of ChEBI 2.0, no key.

$chebi = (new ChebiSourceFactory($http))->create(['mailto' => '[e-mail]']);
$caffeine = $chebi->entity('CHEBI:27732');
$caffeine->description;                          // A trimethylxanthine in which the three methyl groups are located at positions 1, 3, and 7. ...
$caffeine->property('molecular_weight');         // 194.194 g/mol
$caffeine->properties('is_a');                   // purine alkaloid, trimethylxanthine
$caffeine->properties('has_role');               // immunosuppressive agent, mutagen, ... central nervous system stimulant ... (34)
$caffeine->identifier(Scheme::CAS);              // 58-08-2
$caffeine->image;                                // https://www.ebi.ac.uk/chebi/backend/api/public/compound/27732/structure/ (SVG)
$chebi->entity('RYYVLZVUVIJVGH-UHFFFAOYSA-N');   // the same, by its InChIKey; or '58-08-2', 'C07481', 'theine'
$chebi->search(new Query('caffeine', limit: 10));

omnilab:
    sources:
        chebi:
            factory: chebi
            options:
                mailto: '[e-mail]'   # in the User-Agent: whom the EBI writes to before it blocks a caller
                synonyms: 20                   # how many to keep; 0: none

With PubChem and Wikidata configured too, the Collector follows a compound from one to the others: $collector->collect('pubchem', 'caffeine') reaches ChEBI by caffeine's InChIKey.

Terms of use

ChEBI is run by EMBL-EBI, free and without a key. Its data is under CC BY 4.0 - cite ChEBI where you show it - and governed by EMBL-EBI's terms of use, which reserve the right to block a client that loads the services unreasonably. No rate is published for ChEBI's API: the source makes its calls in series, one per entity by ChEBI id, two otherwise; cache what it answers.

See docs/ for what is read, how it maps, and what ChEBI does not give here.

Responsibility

This package is an independent, unofficial client: it is not affiliated with, endorsed by or sponsored by EMBL-EBI (ChEBI). 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: MIT.