omnilab / quickgo

1.x-dev 2026-10-17 10:27 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

• annotations
• science
• go
• biology
• uniprot
• omnilab
• gene ontology
• quickgo

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

README

The Gene Ontology for omniscient/omnilab, through QuickGO, the EBI's browser of GO terms and annotations: a GO term (GO:0005829, cytosol) with its name, definition, aspect, synonyms, comment, whether it is obsolete, its direct parents by relation (is_a, part_of, regulates...) and its children; a UniProt protein (P68871) with the terms it is annotated to, by aspect, as properties (with their evidence codes) and related things; the annotations themselves, with their evidence, reference and curator; a search of terms by text. No key.

$quickgo = (new QuickGoSourceFactory($http))->create(['mailto' => '[e-mail]']);
$term = $quickgo->entity('GO:0005829');
$term->kind;                                   // cellular component
$term->related('part_of')->keys();             // go:0005737 (cytoplasm)
$term->related('is_a')->keys();                // go:0110165 (cellular anatomical structure)
$protein = $quickgo->entity('uniprot:P68871');
$protein->related('process')->keys();          // go:0006954, go:0015670, go:0015671... (11)
$protein->properties('biological_process');    // oxygen transport (GO:0015671; IBA, IEA, IDA, NAS, TAS, IMP)...
$quickgo->annotations('P68871');               // 93 Annotation objects (outside the contract)
$quickgo->search(new Query('apoptosis', limit: 3));   // 352 terms

omnilab:
    sources:
        quickgo:
            factory: quickgo
            options:
                mailto: '[e-mail]'   # in the User-Agent
                annotation_pages: 5            # pages of 200 annotations a protein's reading takes at most

A term is named in the core's go scheme (go:0005829, displayed GO:0005829). The Collector reaches QuickGO from any source that gives a UniProt accession ($collector->collect('uniprot', 'P68871')): the protein's GO terms join it as related things.

Terms of use

The Gene Ontology and its annotations are under CC BY 4.0 (geneontology.org/docs/go-citation-policy); QuickGO is a service of the EMBL-EBI (terms of use). Cite The Gene Ontology Consortium, "The Gene Ontology knowledgebase in 2023", Genetics 2023, 10.1093/genetics/iyad031, and Binns D. et al., "QuickGO: a web-based tool for Gene Ontology searching", Bioinformatics 2009, 10.1093/bioinformatics/btp536. No rate is published.

Responsibility

This package is an independent, unofficial client: it is not affiliated with, endorsed by or sponsored by EMBL-EBI (QuickGO) and the Gene Ontology 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.