omnilab / reactome

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

• science
• reactions
• biology
• uniprot
• omnilab
• chebi
• reactome
• pathways

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

README

Reactome for omniscient/omnilab: a pathway or a reaction by its stable identifier - R-HSA-70171, glycolysis; R-HSA-70420, a reaction of it - with its names, species, summary, compartments, GO biological process, Rhea reaction, inputs, outputs and catalyst, review status, release dates, DOI and diagram; its participants as related things (the UniProt proteins and the ChEBI small molecules it involves), its organism, its sub-events and its orthologous events in other species; a search by text; and the pathways or reactions of a protein or a small molecule. Through Reactome's Content Service, no key.

$reactome = (new ReactomeSourceFactory($http))->create(['mailto' => '[e-mail]']);
$pathway = $reactome->entity('R-HSA-70171');
$pathway->label;                          // Glycolysis
$pathway->value('compartment');           // cytosol (GO:0005829)
$pathway->value('go_biological_process'); // canonical glycolysis (GO:0061621)
$pathway->related('protein')->keys();     // uniprot:P30153, ... (79)
$pathway->related('molecule')->keys();    // chebi:15377, ... (32)
$pathway->related('event')->keys();       // reactome:R-HSA-170822, reactome:R-HSA-70420, ... (16)
$reactome->search(new Query('glycolysis', limit: 3));   // Glycolysis, Regulation of glycolysis by..., Glucose metabolism (76 matches)
$reactome->pathways('P68871');            // hemoglobin beta's ten pathways (outside the contract)

omnilab:
    sources:
        reactome:
            factory: reactome
            options:
                mailto: '[e-mail]'   # in the User-Agent
                species: 'Homo sapiens'        # what a search and pathways() keep; 'all': every species
                participants: true             # entity() asks for the participants (a second call)

A pathway is named in the core's reactome scheme. With Wikidata configured too, the Collector follows a pathway from Wikidata's Reactome ID (P3937) into Reactome ($collector->collect('wikidata', 'Q45317172'), glycolysis); a protein's pathways come from pathways().

Terms of use

Reactome's data are under CC0, its other content (text, illustrations) under CC BY 4.0 (reactome.org/license); attribution is encouraged: cite the current paper (The Reactome Knowledgebase 2026, Nucleic Acids Res. 2025, 10.1093/nar/gkaf1223). No rate is published.

Responsibility

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