Paper: "Unifying the identification of biomedical entities with the Bioregistry"

Figure 2 from the article, showing Bioregistry
website screenshots. CC-BY.

Identifiers are central to FAIR. Our BiGCaT research group (see also this Scholia page) studies how to answer biological questions and identifiers are then essential to integrate experimental data (e.g. omics data) with existing knowledge (e.g. biological pathway databases). BridgeDb is our go to tool here, of course.

BridgeDb has since Open PHACTS (doi:10.1016/j.drudis.2012.05.016) support for identifiers.org (doi:10.1093/bioinformatics/btaa864). This support is also used in the WikiPathways RDF at this moment (doi:10.1371/journal.pcbi.1004989).

Bioregistry was recently started as complementary to identifiers.org. Fully open source, GitHub-hosted, automated, modern support for CURIEs making it integrate with RDF better, etc. And run like a open science project, and not just an open source project. Oh, and it integrates ontology support. We already used it for the European Registry of Materials identifier (see this post, doi:10.1186/s13321-022-00614-7).

Because identifers.org and Bioregistry work slightly differently, Helena and I added complementary support for Bioregistry to BridgeDb, which we are already using on the new WikiPathways website. The ball actually got rolling because Charles actually submitted a patch to add Bioregistry prefixes. This means that you can convert CURIEs to full IRIs, to identifiers.org URLs, etc. You can even use this from Bacting (doi:10.21105/joss.02558) and pybacting.

Anyway, the Bioregistry project published a paper and I am happy to have been part of it: Unifying the identification of biomedical entities with the Bioregistry (doi:10.1038/s41597-022-01807-3).