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Use preferred bioregistry prefixes for normalized entity identifiers #3
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I’d be happy to help. I’d like to try running bern2 myself locally and I’m sure doing this would make it easier to evaluate if the results are useful |
Hi @dhimmel Thank you for your suggestions for improving BERN2. Do you mean that it is more standardized to use |
Exactly. I see a benefit if all entities tagged are represented as Bioregistry supported CURIEs to make integration with other datasets the most straightforward as possible. Additional notes:
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I just added in |
Hi @cthoyt, I was checking BioRegistry and noticed something that I'd like to clarify. While Entrez Gene ID has the preferred prefix |
Related to the discussion in dmis-lab#3, the Bioregistry has the logic for generating URLs given CURIEs
Great to see that BERN2 normalizes entities to compact identifiers in
resource:identifier
format. I noticed that there is an opportunity to standardize the prefixes used with Bioregistry:NCBITaxon
prefix as per http://bioregistry.io/registry/ncbitaxonNCBIGene
prefix as per http://bioregistry.io/registry/ncbigeneFYI I didn't check all the entity types BERN2 is capable of tagging for whether they use the preferred prefix.
@cthoyt might also be helpful here.
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