Re-enable OWL generation

[cthoyt]

This pull request re-enables generating owl in the make gen-project command.

It's not documented, but I assume the reason that OWL was excluded was there were upstream bugs in the LinkML implementation that were causing it to fail. I reported this as a bug in linkml/linkml#3358 and sent a pull request that fixes it in linkml/linkml#3359.

This PR includes the output of the OWL generation after applying the patch to LinkML

Note: the upstream PR was merged promptly, but tests in this PR won't pass until the upstream linkml repository gets released to PyPI containing that fix

[matentzn]

@cthoyt I need to do this - this is a little more complex. I will try to handle it next week.

[cthoyt]

@matentzn this is super low priority, it's just something I noticed was weird that wasn't changing during the re-generation

[matentzn]

Sorry I thought this was something else. Why do we need a OWL rendering of the SSSOM schema?

[cthoyt]

🤷 it seems to be something built into LinkML output. One could also ask "why do we need protobuf"

either way, there is something that's already been output before, and it's awfully out of date. so we should either update it, or delete it.

[matentzn]

either way, there is something that's already been output before, and it's awfully out of date. so we should either update it, or delete it.

I would prefer if we get rid of the OWL representation of the schema for now.

[cthoyt]

@matentzn okay, deleted this file in #539 as an alternative