Decide on action for FMA entry in OBO

[cmungall]

Currently hardcoded to be the ancient obo format version I made. Should be made the complete ontology now it is in OWL. obo-basic can be a subproduct

[cmungall]

cc @trapperkeeper

Now FMA natively produces OWL (not valid OWL2 but will be soon) do we just point directly to it? Do we create a distinct OBO-compatible version? (e.g. OBO PURLs, standard annotation properties and object properties)?

[trapperkeeper]

Of course my vote, speaking for the FMA team, would be to use the FMA directly. It is confusing having multiple differing versions in play.

[cmungall]

From @trapperkeeper

URL: http://sig.biostr.washington.edu/share/downloads/fma/release/latest/fma.owl
tracker: https://bitbucket.org/uwsig/fma/issues

[cmungall]

What should the status of the OBO purls be? Both class purls and ontology purls?

1. Keep these active, and have them direct to an 'OBO translation' of FMA
2. Obsolete them
3. FMA obsoletes its existing purls and joins the OBO system

We are effectively doing 1 right now. With the new FMA being natively OWL we can update the translation to be a minimal one of rewriting IRIs, thus the OBO shadow will be semantically equivalent

2 may well break lots of things

3 is up to @trapperkeeper but I suspect the answer is no

See also OBOFoundry/purl.obolibrary.org#63 (comment)

[trapperkeeper]

Sorry for the late response. I brought this issue up with the FMA team but, as suspected, we are not prepared to obsolete our existing purls. First, some of our purls are already in use, as data annotations, referenced from other sources like UMLS, etc. Second, there are multiple community ontology efforts out there, and sometimes professional tension between them. The FMA, in an attempt to remain neutral, has adopted a purl that is not aligned with any specific effort (just trying to remain Switzerland here).

Of course, there are factors that may affect FMA purls. The future of purl.org being one that we are watching.

Regarding choices 1 or 2, from our perspective if would, of course, be nice if there were only one set of purls. But, for legacy reasons and to maintain exiting references I can certainly understand that some mapping or translation method may be necessary.

[cmungall]

Thanks

Just to point out one thing: purl.obolibrary.org is now completely
independent of purl.org. You should not use purl.org for anything as the
future is, as you hinted, in doubt. purl.org could vanish tomorrow and
the obolibrary ontologies would not be affected

On 14 Dec 2015, at 13:16, trapperkeeper wrote:

Sorry for the late response. I brought this issue up with the FMA team
but, as suspected, we are not prepared to obsolete our existing purls.
First, some of our purls are already in use, as data annotations,
referenced from other sources like UMLS, etc. Second, there are
multiple community ontology efforts out there, and sometimes
professional tension between them. The FMA, in an attempt to remain
neutral, has adopted a purl that is not aligned with any specific
effort (just trying to remain Switzerland here).

Of course, there are factors that may affect FMA purls. The future of
purl.org being one that we are watching.

Regarding choices 1 or 2, from our perspective if would, of course, be
nice if there were only one set of purls. But, for legacy reasons and
to maintain exiting references I can certainly understand that some
mapping or translation method may be necessary.

---

Reply to this email directly or view it on GitHub:
#21 (comment)

[trapperkeeper]

Any purl scheme is a tie to a purl provider, be it purl.org or purl.obolibrary.org. We chose purl.org some time ago because we thought, at the time, that it would be the most universal and neutral provider. We expected the purl user community to embrace the unbranded purl and therefore expected it to be a stable resource. They are now on the ropes, as you say. However, we are already using them. Those FMA purls are already out there in the world. So, until we know its fate for sure, we are holding out to see what happens to purl.org. There is some talk of it being picked up and maintained by w3id.org:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1511&L=DC-ARCHITECTURE&F=&S=&P=3711
https://groups.google.com/forum/#!topic/persistenturls/Zpd4BHQxxIM

[cmungall]

any more thoughts on this? http://purl.org/sig/ont/fma.owl still doesn't resolve

[trapperkeeper]

I can make it resolve to a web accessible copy of the OWL file itself, but it does not specify a version of the ontology. OK, I have modified the PURL to resolve to the latest version (i.e. http://sig.biostr.washington.edu/share/downloads/fma/release/latest/fma.owl ). I'm not sure of the context in which this arose, does this fit the bill?

…

-Todd From: Chris Mungall <notifications@github.com> Reply-To: "OBOFoundry/OBOFoundry.github.io" <reply@reply.github.com> Date: Thursday, November 30, 2017 at 8:18 AM To: "OBOFoundry/OBOFoundry.github.io" <OBOFoundry.github.io@noreply.github.com> Cc: trapperkeeper <det@uw.edu>, Mention <mention@noreply.github.com> Subject: Re: [OBOFoundry/OBOFoundry.github.io] FMA (#21) any more thoughts on this? http://purl.org/sig/ont/fma.owl still doesn't resolve — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[cstoeckert]

Tested link and its resolving