omnilab / chebi

1.x-dev 2026-10-15 00:47 UTC

Requires

• php: >=8.2
• glitchr/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 2026-10-15 00:59 UTC

README

ChEBI for glitchr/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.

License: MIT.