Bioregistry in GigaDB

[cthoyt]

Chris Hunter presented at Biocuration 2023 that GigaDB is annotating datasets using controlled vocabularies (mostly ontologies). It would be great to use the Bioregistry in this in a few places:

1. Give context to what kind of reference a thing is for. E.g., if you see PATO:0000001, the Bioregistry's API can tell you a bit about what PATO is such as the full name, a description, keywords, links to the issue tracker, the responsible person, etc.
2. Bioregistry can be used to generate a link based on the CURIE in a few ways:
   • the CURIE can be formatted into a URL like in https://bioregistry.io/PATO:0000001
   • if it's done on the backend, the Python package can be used to turn a CURIE into a URL, either by formatting into the Bioregistry resolver or directly generating the appropriate link
   • we're thinking about making a javascript package that can be used to do this fully on the front end
3. The Bioregistry can be used to standardize and validate the integrity of these annotations:
   • make sure standard prefixes are used so they can be readily integrated with other data sources
   • make sure the identifiers match the regular expression in the Bioregistry database, so you don't get nonsense like PATO:ABCDEFG

I will look into https://github.com/gigascience/gigadb-website to see there's a possibility to demonstrate this in a lightweight way.

See also:

• https://github.com/gigascience/gigadb-website/issues/905
• https://github.com/gigascience/gigadb-website/issues/824
• https://github.com/gigascience/gigadb-website/issues/424

[cthoyt]

@only1chunts I will reach out to you about this next week! I hope you had a safe trip home.

[only1chunts]

Thanks Charlie, I just got back to UK, hope you're travel also goes smoothly. I know we have a GitHub ticket for something like this already, but I can't log in on my phone to check the number and link it, I'll try to remember to do that when I get back to my desk.

On Thu, 27 Apr 2023, 16:25 Charles Tapley Hoyt, @.***> wrote:

@only1chunts https://github.com/only1chunts I will reach out to you about this next week! I hope you had a safe trip home.

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[cthoyt]

@only1chunts I have found some relevant issues and linked them in the original description. I guess we should also keep @rija in the loop