Add bioregistry as IRI candidate discovery source

[JJ-Author]

see e.g. https://bioregistry.io/registry/ero
offer json output including download links and uri scheme as starting point for Archivo

[cthoyt]

Hi @JJ-Author, I am one of the maintainers of the Bioregistry. I am happy to answer any questions you have about it, discuss potential new features, content, exports, etc.

[JJ-Author]

Hey, @cthoyt thanks for your message. Indeed i found that you also provide RDF here https://bioregistry.io/download
but this option is not shown here https://bioregistry.io/registry/ when clicking the download button. Is there a reason for that? (live export vs. snashot releases?)

[cthoyt]

Yes, it's the case that the RDF dump is generated on the nightly build and isn't part of the live website. You can expect that it's up-to-date though, since everything is automated!

Direct download link: https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/rdf/schema.ttl https://github.com/biopragmatics/bioregistry/blob/main/exports/rdf/bioregistry.ttl

[RiddhiMenroy]

Is this thread still active?
I'm very new to github, could you please guide me on what's going on in here

[JJ-Author]

Hey @RiddhiMenroy, with the issues tagged as "enhancements" we keep record of our wishlist. We might tackle these once we have free resources or a student that is interested in doing it.
But feel free to comment what you are looking for.

[cthoyt]

hi @JJ-Author and @RiddhiMenroy, is there anything I can do from the Bioregistry side to help this out?

[RiddhiMenroy]

Nothing yet, thanks!

…

On Fri, 17 Mar 2023 at 04:51, Charles Tapley Hoyt ***@***.***> wrote: hi @JJ-Author <https://github.com/JJ-Author> and @RiddhiMenroy <https://github.com/RiddhiMenroy>, is there anything I can do from the Bioregistry side to help this out? — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A2HCURXMNFAXHY6BWUXUWQLW4ON7XANCNFSM6AAAAAAR7ULOB4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[yum-yab]

Bioregistry is now part of the discovery process.

I used the registry available at https://bioregistry.io/api/registry?format=json, and the download_rdf and the download_owl fields since all archivo needs are the RDF files.
Unfortunately many ontologies do not have that field, is there a better way to access turtle/rdfxml files of the bioregistry ontologies @cthoyt?

[cthoyt]

Many of the resources in the Bioregistry neither have an RDF nor OWL artifact associated with them, so this isn't a surprise. If I had to guess, maybe <5% of the resources for which an RDF or OWL actually exists do not have it already annotated in the Bioregistry (i.e., low false negative rate)

FYI, some of them might have download_obo which you can convert to OWL using robot.

[yum-yab]

Ok, but the parsing of obo files (and generally more supported formats) is an issue of its own. I'll close this one in favor of this one