omnilab / hgnc

1.x-dev 2026-11-10 11:24 UTC

Requires

• php: >=8.2
• omnisense/omnilab: ^1.0@dev
• symfony/http-client: ^6.4|^7.0|^8.0

Requires (Dev)

• phpunit/phpunit: ^11.0

MIT

• Marco Meyer

• science
• biology
• omnilab
• hgnc
• genes
• gene nomenclature
• human genome
• omim

Published on Packagist.org on 2026-11-10 12:33 UTC

README

HGNC for omnisense/omnilab: a human gene of the HUGO Gene Nomenclature Committee by its HGNC id (HGNC:4827), its approved symbol (HBB), a previous symbol or an alias that one gene alone bears (FAM46C is TENT5C), or an id HGNC records for it (NCBI Gene, Ensembl, UniProt, OMIM) - with its approved name, locus group and type, chromosomal location, previous symbols and names, aliases, gene groups, status and dates, MANE Select transcripts, RefSeq and CCDS ids; its NCBI Gene, Ensembl, UniProt and OMIM ids as cross-references; a search over every field. Through HGNC's REST service, no key.

$hgnc = (new HgncSourceFactory($http))->create(['mailto' => '[e-mail]']);
$gene = $hgnc->entity('HBB');                // or 'HGNC:4827', 'ENSG00000244734', 'omim:141900'
$gene->id->display();                         // HGNC:4827
$gene->description;                           // hemoglobin subunit beta
$gene->value('map_location');                 // 11p15.4
$gene->identifiers()->keys();                 // hgnc:4827, ncbi.gene:3043, ensembl:ENSG00000244734, uniprot:P68871, omim:141900
$hgnc->entity('FAM46C')->label;               // TENT5C
$hgnc->search(new Query('hemoglobin', limit: 5));   // 15 genes

omnilab:
    sources:
        hgnc:
            factory: hgnc
            options:
                mailto: '[e-mail]'   # in the User-Agent

A gene is named in the core's hgnc scheme (hgnc:4827, displayed HGNC:4827). The Collector walks from HGNC into NCBI Gene, Ensembl, UniProt ($collector->collect('hgnc', 'HBB')), and into HGNC from any of them.

Terms of use

HGNC releases all its data under CC0 (genenames.org/about/license) and recommends attribution: Seal R. L. et al., "Genenames.org: the HGNC resources in 2023", Nucleic Acids Res. 2023, 10.1093/nar/gkac888. HGNC asks for 10 calls a second at most: the source waits 0.1 s between two calls.

Usage policy

Declared as data in policy.json (read at https://www.genenames.org/help/rest/ on 2026-11-10), and honoured on every request by the core: a limit reached waits when its window ends within max_wait seconds, else the request is not sent (Usage policies).

• Limits: 10 a second.
• Licence: CC0-1.0; commercial use: allowed.
• Credit: not required: Genenames.org: the HGNC and PGNC resources in 2026, Nucleic Acids Res. (HGNC, RRID:SCR_002827) (https://www.genenames.org/about/license/).
• Needs: nothing.

Responsibility

This package is an independent, unofficial client: it is not affiliated with, endorsed by or sponsored by the HUGO Gene Nomenclature Committee. 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.