README

ClinVar for omniscient/omnilab, through the NCBI's E-utilities: a variation by its VariationID (15333) or VCV accession (VCV000015333) with its name, type, germline classification, review status and date, the conditions it was classified for, its genes, protein change, molecular consequence, location, SPDI, allele frequencies, aliases and number of submissions; its dbSNP id as a cross-reference, its genes (NCBI Gene) and its conditions (Mondo, OMIM, Orphanet, HPO) as related things; a search in ClinVar's query language. No key needed.

$clinvar = (new ClinVarSourceFactory($http))->create(['mailto' => 'support@glitchr.io']);
$hbs = $clinvar->entity('VCV000015333');
$hbs->label;                              // NM_000518.5(HBB):c.20A>T (p.Glu7Val)
$hbs->value('classification');            // Pathogenic
$hbs->value('review_status');             // criteria provided, multiple submitters, no conflicts
$hbs->synonyms;                           // E6V, HbS
$hbs->identifiers()->keys();              // clinvar:15333, dbsnp:rs334
$hbs->related('condition')->keys();       // mondo:0020989, omim:141749, ..., mondo:0011382, ...
$clinvar->search(new Query('HBB[gene] AND pathogenic[clinsig]', limit: 5));   // 634 variations

omnilab:
    sources:
        clinvar:
            factory: clinvar
            options:
                mailto: 'support@glitchr.io'   # E-utilities' email, as NCBI asks, and the User-Agent
                api_key: '%env(NCBI_API_KEY)%' # optional: ten calls a second instead of three

A variation is named in the core's clinvar scheme (clinvar:15333, displayed VCV000015333). The Collector walks from ClinVar into the GWAS Catalog by its rs id ($collector->collect('clinvar', '15333', 1, ['gwas'])).

Terms of use

ClinVar asks whoever distributes or copies its data to attribute ClinVar as a data source and to cite one of its publications (its usage page): Landrum M. J. et al., "ClinVar: updates to support classifications of both germline and somatic variants", Nucleic Acids Res. 2025, 10.1093/nar/gkae1090. The E-utilities ask for the tool's name and an email address with every call, and three calls a second at most without an API key (ten with one): the source sends both and waits 0.34 s (0.1 s) between two calls. The key is an option, never written in the package.

Responsibility

This package is an independent, unofficial client: it is not affiliated with, endorsed by or sponsored by NCBI (ClinVar). 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.

omnilab / clinvar

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