sssom.yaml has oddly specific prefixes

[cmungall]

https://github.com/mapping-commons/sssom-py/blob/master/schema/sssom.yaml#L6-L14

I think the following can be removed:

• neuronames
• orphanet/ordo

[matentzn]

The reason I added them is because they are different then the defaults (supplied by bioregistry, @cthoyt).

Basically when transforming an ontology like uberon, I added prefixes there if a) I didn't like the prefix assigned by bioregisrty or b) the prefix URL didn't exist in bioregisrty.

How should this be managed?

[cthoyt]

Interestingly when I was reading through the OpenTargets stuff, I realized the Bioregistry's Orphanet/ordo URI made no sense and actually updated it a few days ago in https://github.com/biopragmatics/bioregistry/commit/21906c3.

I see you're using neuroname but I neuronames is already available in the Bioregistry http://bioregistry.io/registry/neuronames. We could add a synonym annotation to neuronames, but I don't ever recall seeing it written that way before.

If something's missing from the Bioregistry I would highly suggest you make a new prefix request 🚀

For the rest where you want to override what is happening in the Bioregistry, I think this makes total sense. Yesterday I had a short discussion with Chris and implemented https://github.com/biopragmatics/bioregistry/pull/169, so we can explicitly annotate the mixed case prefix for oboInOwl in the new preferred_prefix field there.

[matentzn]

Some bioregistry tickets:

• https://github.com/biopragmatics/bioregistry/issues/183
• https://github.com/biopragmatics/bioregistry/issues/182
• https://github.com/biopragmatics/bioregistry/issues/187

[cthoyt]

I think the bioregistry updates in the bioregistry tickets should have made these two annotations from the original issue obsolete