README

STRING for omnisense/omnilab: a protein by its STRING id (9606.ENSP00000269305, TP53), a UniProt accession, an Ensembl protein or a name in a species, with its preferred name, protein name, annotation and species, its Ensembl protein as a cross-reference, and its interaction partners as related things - each partner's combined score a property; the network among several proteins, and their functional enrichment (GO, KEGG, Reactome, Pfam, InterPro, diseases, tissues...). Through STRING's API, no key.

$string = (new StringSourceFactory($http))->create(['mailto' => 'support@glitchr.io']);
$protein = $string->entity(Identifier::of(Scheme::UNIPROT, 'P68871'));   // or '9606.ENSP00000494175', 'HBB'
$protein->label;                              // HBB
$protein->value('protein_name');              // Hemoglobin subunit beta
$protein->identifiers()->keys();              // string:9606.ENSP00000494175, ensembl:ENSP00000494175, uniprot:P68871
$protein->related('interactor')->keys();      // string:9606.ENSP00000251595 (HBA2), ... (10)
$protein->property('interaction');            // Interaction with HBA2: 0.999
$string->partners('9606.ENSP00000494175', 5); // Interaction objects: names, score, evidence channels
$string->network(['HBB', 'HBA1', 'HBA2']);    // the three interactions among them
$string->enrichment(['HBB', 'HBA1', 'HBA2', 'HBD', 'HBZ', 'ALAS2']);   // 185 terms, FDR < 5 %

omnilab:
    sources:
        string:
            factory: string
            options:
                mailto: 'support@glitchr.io'   # in the User-Agent
                caller_identity: 'omnilab'     # sent with every call, as STRING asks
                species: '9606'                # the NCBI taxon a name or an accession is looked up in
                partners: 10                   # entity()'s partners (0: none, one call)
                required_score: 400            # 400 medium, 700 high, 900 highest confidence

A protein is named in the core's string scheme. The Collector reaches STRING from any source that gives a UniProt accession or an Ensembl protein ($collector->collect('uniprot', 'P68871')).

Terms of use

STRING's data are under CC BY 4.0 (string-db.org/cgi/access); cite Szklarczyk D. et al., "The STRING database in 2025: protein networks with directionality of regulation", Nucleic Acids Res. 2025, 10.1093/nar/gkae1113. STRING asks for one call a second at most and for the caller's identity: the source waits 1 s between two calls and sends caller_identity.

Responsibility

This package is an independent, unofficial client: it is not affiliated with, endorsed by or sponsored by the STRING consortium. 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.