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Add GeneCards as a gene datasource - #56

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Add GeneCards as a gene datasource#56
builder-lifemap wants to merge 1 commit into
bridgedb:mainfrom
builder-lifemap:add/genecards

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Adds GeneCards as a gene datasource.

I'm from the GeneCards team at the Weizmann Institute of Science. GeneCards is a human gene compendium, freely available for academic use since 1997, that aggregates 193 sources per gene. It is keyed on the HGNC-approved gene symbol, so it maps directly from the existing HGNC symbol datasource with no new identifier mapping required.

Column Value
datasource_name GeneCards
system_code Gc — checked against the current file, unused (taken codes beginning with G are G, Ge, Gg, Gl, Gp, Gpl, Gpt, Gw)
website_url https://www.genecards.org/
linkout_pattern https://www.genecards.org/card/$id
example_identifier BRCA1
entity_identified gene
single_species Homo sapiens
identifier_type 0 — secondary identifier. HGNC remains the symbol authority; GeneCards is an aggregating resource, which matches the header file's "useful as secondary linkouts" definition.
uri urn:miriam:genecards — identifiers.org namespace genecards, MIR:00000323, not deprecated
regex ^[A-Za-z-0-9_]+(\@)?$ — the pattern registered at identifiers.org, kept identical for consistency
official_name GeneCards
wikidata_property (empty — see note below)
bioregistry genecards.gene — see note below
category gene

Ran the local integrity checks before submitting: column count matches datasources_headers.tsv (14), and BRCA1 matches the supplied regex. genecards is present in the MIRIAM registry.

Two notes on the deliberately-caveated columns:

  1. wikidata_property is empty because no GeneCards property currently exists on Wikidata (verified via property search, SPARQL, and a full entity dump). We are proposing one, and I'll follow up here if it is accepted so the column can be filled.

  2. bioregistry is genecards.gene, which is the canonical prefix today (genecards is registered as its synonym). That record is currently flagged deprecated: true, which we believe is inherited from a stale Integbio sub-record rather than an assessment of the resource — GeneCards is actively maintained and shipped v6 this year. We've raised that with the Bioregistry maintainers (genecards.gene is marked deprecated but is actively maintained; uri_format and homepage also outdated biopragmatics/bioregistry#2019). If test_valid_bioregistry objects to the deprecated prefix, I'm happy to leave column 13 empty until that is resolved — just say which you'd prefer.

Happy to adjust identifier_type, the regex, or the naming to suit your conventions.

GeneCards (Weizmann Institute of Science) is keyed on the HGNC-approved gene
symbol, so it maps directly from the existing HGNC symbol datasource without
new identifier mapping.

System code Gc was checked against the current file and is unused.
@egonw egonw self-assigned this Aug 4, 2026
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