Closed dhimmel closed 2 years ago
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 NCBIGene:10533
(for gene/protein) and NCBITaxon:10095
(for species) instead of EntrezGene:10533
and NCBI:txid10095
?
Do you mean that it is more standardized to use
NCBIGene:10533
(for gene/protein) andNCBITaxon:10095
(for species) instead ofEntrezGene:10533
andNCBI:txid10095
?
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:
EntrezGene
as an alternative prefix for NCBIGene
.I just added in EntrezGene
to https://bioregistry.io/registry/ncbigene, but I don't really see a standardized way to reconcile things that look like NCBI:txid10095 since it doesn't follow the spirit of CURIEs. You could always do some text-based preprocessing if you get stuff like this.
@dhimmel @cthoyt
Thank you for your suggestions! We will consider replacing current prefixes with the prefixes in BioRegistry.
Hi @cthoyt,
I was checking BioRegistry and noticed something that I'd like to clarify. While Entrez Gene ID has the preferred prefix NCBIGene
, MESH ID does not and instead uses the prefix mesh
in its CURIE. My first question is why some CURIEs use preferred prefixes while others use prefixes. My second question is whether it is common in CURIE to use lowercased prefixes such as mesh:C063233
rather than MESH:C063233
as BERN2 does.
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.