omnilab / uniprot

1.x-dev 2026-10-15 01:38 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

• sequence
• science
• biology
• uniprot
• protein
• omnilab
• uniprotkb

Published on Packagist.org on 2026-10-15 01:50 UTC

README

UniProtKB for glitchr/omnilab: a protein by its accession or its entry name; its names, gene, organism, function, length, mass and sequence, where it sits in the cell, its cofactors and the ligands of its binding sites, its keywords; its genes in NCBI Gene and Ensembl as cross-references for the Collector to follow, and its organism, its PDB structures and its ligands as related things; UniProt's search, page after page. Through the UniProt REST API, no key.

$uniprot = (new UniProtSourceFactory($http))->create(['mailto' => '[e-mail]']);
$hbb = $uniprot->entity('P68871');
$hbb->label;                                     // Hemoglobin subunit beta
$hbb->value('gene');                             // HBB
$hbb->property('mass');                          // 15998 Da
$hbb->property('sequence_length');               // 147 aa
$hbb->identifier(Scheme::NCBI_GENE);             // 3043
$hbb->related('organism')->value(Scheme::NCBI_TAXON); // 9606
$hbb->related('ligand')->keys();                 // chebi:58248, chebi:60344 (2,3-bisphosphoglycerate, heme b)
$uniprot->entity('HBB_HUMAN');                   // the same, by its entry name; 'A4GX73', merged into it, too
$uniprot->search(new Query('gene:HBB AND organism_id:9606', limit: 10));

omnilab:
    sources:
        uniprot:
            factory: uniprot
            options:
                mailto: '[e-mail]'   # in the User-Agent: whom UniProt writes to before it blocks a caller
                sequence: 2000                 # the longest sequence given as a property, in residues; 0: none
                structures: 20                 # how many PDB structures to keep among the related things; 0: none

With NCBI and Wikidata configured too, the Collector follows a protein to its gene and its item: $collector->collect('uniprot', 'P68871') reaches NCBI Gene by GeneID 3043 and Wikidata by the UniProt accession its item carries (P352).

Terms of use

UniProt's data is under CC BY 4.0: cite UniProt where you show it. No key, no account; no rate is published for the REST API (only the stream endpoint, not used here, answers 429 when too many run at once). The source asks each entry for the fields it reads - one call, a few dozen kilobytes instead of hundreds - and makes its calls in series: cache what it answers.

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

License: MIT.