uPheno OBO Purls forward to http://ontologies.berkeleybop.org/

[kshefchek]

Some uPheno OBO purls resolve to http://ontologies.berkeleybop.org/, for example http://purl.obolibrary.org/obo/GO_0022008PHENOTYPE

Should these be resolving elsewhere, or is Monarch effectively the source for these IRIs?

See https://github.com/monarch-initiative/dipper/issues/741

[matentzn]

These URIs will disappear eventually, but not soon. I will keep an eye on it. I dont think they need to redirect anywhere (since they will be obsoleted), but if @cmungall believes they should, we need to make some hacky redirect I think on the GO repo, but I dont think we should bother.

[monicacecilia]

Dear @matentzn If we do end up choosing to not bother with the hack, is there an alternative that can help us informing users when they come across broken links such as the one Kent shared? --> http://purl.obolibrary.org/obo/GO_0022008PHENOTYPE

We should either do something about it now, or let users know.

I see that @kshefchek is trying to remove the OBO PURLs in https://github.com/monarch-initiative/monarch-ui/issues/171 - but it is not planned to happen before we release monarch-ui v1.0.

I'm just basically here thinking our loudly on how to avoid releasing with this error... 😞

[matentzn]

So there are three possible solutions:

1. monarch ui implements a custom redirect for a set of known namespaces (that currently dont go anywhere)
2. we create a special PURL redirect rule for these IRIs on OBO foundry level
3. we replace them by uPheno terms

Monarch UI:

• Pro: easy enough if-else logic somewhere in the code; covers other namespaces such as ICD9 etc that currently don't go anywhere
• Contra: we don't like modelling exceptions in code (creates another burden of maintenance)

OBO purl redirect

• Pro: easy to do
• Contra: there is nothing really perfect to redirect to; does not cover non-"PHENOTYPE" terms; requires a bit of hacking with OBO foundry config files.

I think this can be done; but I need to know where the link SHOULD redirect.. We could try and redirect simply to the GO term? So clicking on this:

http://purl.obolibrary.org/obo/GO_0022008PHENOTYPE

will bring you here:

http://purl.obolibrary.org/obo/GO_0022008

? Or can we just link this back to some Monarch.org page perhaps? redirecting to:

https://monarchinitiative.org/phenotype/GO:0022008PHENOTYPE

Maybe that is the best idea for now?

uPheno solution.

• Pro: Proper handling of all the IRIs ending in "PHENOTYPE", redirecting to upheno pages; preferred solution.
• Contra: Currently no resources to do this; will not be before January. Also, does not cover any of the other IRIs that currently not resolve (ICD9, etc).

Let me know of your decision (solution 1 or 2)