omnilab / pubchem

1.x-dev 2026-10-14 23:29 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

• cas
• science
• pubchem
• chemistry
• compounds
• inchikey
• omnilab

Published on Packagist.org on 2026-10-15 00:26 UTC

README

PubChem for glitchr/omnilab: a compound by its CID, a name, an InChIKey, an InChI, a CAS number, a SMILES, or an identifier of another base PubChem keeps among its synonyms (ChEBI, ChEMBL, Wikidata, UNII, DSSTox); its computed properties with their units, its synonyms, its description, the image of its 2D structure, and its identifiers in other bases for the Collector to follow; a search by name. No key.

$pubchem = (new PubChemSourceFactory($http))->create(['mailto' => '[e-mail]']);
$caffeine = $pubchem->entity('caffeine');
$caffeine->property('molecular_weight');        // 194.19 g/mol
$caffeine->value('tpsa');                       // Quantity: 58.4 Ų
$caffeine->identifier(Scheme::CHEBI);           // 27732
$caffeine->image;                               // https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2519/PNG
$pubchem->entity('CN1C=NC2=C1C(=O)N(C(=O)N2C)C'); // the same, by its SMILES
$pubchem->search(new Query('caffeine', limit: 10));

omnilab:
    sources:
        pubchem:
            factory: pubchem
            options:
                mailto: '[e-mail]'   # in the User-Agent: whom NCBI writes to before it blocks a caller
                synonyms: 20                   # how many to keep; 0: none, one call less per compound
                description: true              # false: one call less per compound
                throttle: 0.2                  # PubChem allows five calls a second: never lower

Terms of use

PubChem is run by the NCBI (U.S. National Library of Medicine), free and without a key. Its usage policy asks for at most five calls a second, 400 a minute and 300 seconds of running time a minute; a caller over it is blocked for a while. The source leaves 0.2 s between two calls and a compound costs up to four: cache what it answers. PubChem's records are free to use; some depositors attach terms to what they deposited (each source's page on PubChem says), and NCBI's policies apply.

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

License: MIT.