core.owl edit: add process to domain to range of concretizes

[wdduncan]

• add process (BFO_0000015) to domain of concretizes
• update definition of concretizes to include process
• add process (BFO_0000015) to range of is concretized as
• update definition of is concretized as to include process

Fixes #650

I added process to domains and ranges in the core.owl file. Let me know if I was supposed to update ro-edit.owl instead.

[shawntanzk]

I added process to domains and ranges in the core.owl file. Let me know if I was supposed to update ro-edit.owl instead.

I might not be the right person to review this as I do not know where the components/core.owl derives from (I see that it is a custom component but has no makepoint in ro.makefile) but I do realise that those terms are not in ro-edit.owl (as in they are pulled in my importing component). I guess one can add those triples in edit as just dangling triples, but that would be a bit ugly in the edit owl file, so I would like you assume adding it to core is right, but again, cant figure out where core.owl came from.

PS is there a reason for all the other additions/changes in components/core.owl? (eg addition of all the BFO terms, and rdf:description to owl:class)

[wdduncan]

@anitacaron I still need two reviews to approve.

[github-actions]

This PR has not seen any activity in 90 days and has been marked as stale. If it is no longer needed, please close the PR. Otherwise, please update the PR with a status update.

[jhpoelen]

fyi @cmungall @shawntanzk please consider reviewing @wdduncan 's pull request related to "add process to domain to range of concretizes"

[shawntanzk]

@jhpoelen sorry this slipped out of my radar when I changed job. As with my previous comment, I am not sure I am qualified enough to review this PR. Would need replies to my questions above before I can make a call. Thanks

Would probably need a bit more indepth look into why QC is failing too, but I think that should come after understanding the PR better

[jhpoelen]

@shawntanzk thanks for taking the time to respond and for sharing your notes.

@wdduncan can you please review the failed QC for this pull request? Also, please nominate other reviewers as hinted in @shawntanzk earlier comment.

[wdduncan]

@shawntanzk thanks for taking the time to respond and for sharing your notes.

@wdduncan can you please review the failed QC for this pull request? Also, please nominate other reviewers as hinted in @shawntanzk earlier comment.

@jhpoelen There is some issue going on with components/core.owl. When I tried to open the file locally, I got the error:

org.xml.sax.SAXParseException; systemId: file:/Users/duncanw/repos/OBO/obo-relations/src/ontology/components/core.owl; lineNumber: 14; columnNumber: 45; Attribute "xmlns:terms" was already specified for element "rdf:RDF".

I copied the core.owl from the master branch, and now core.owl opens w/o any issues. git diff did not return any changes. So, I will push core.owl, although I don't know what changed.

[wdduncan]

I pinged @balhoff and @ddooley as reviewers.

[shawntanzk]

Looks like theres no diff now lol - pulling this in would make no difference >.<
@wdduncan I think the changes you made were in core.owl so when you brought it over from master, it removed all the changes. I see that in the branch now, there isn't the domain and ranges that you added, and the definition is back to the old one.
I have pushed a reverted version of core.owl - please do check that it is the changes you want. Thanks

PS reverted it back to where @anitacaron pushed master into this branch before @jhpoelen commented. Might need updating >.<

[wdduncan]

Thanks @shawntanzk !
There was duplicate xmlns:terms="http://purl.org/dc/terms/" in the rdfs/xml file for some reason. I've deleted it.

[github-actions]

This PR has not seen any activity in 90 days and has been marked as stale. If it is no longer needed, please close the PR. Otherwise, please update the PR with a status update.

[wdduncan]

@balhoff @ddooley @bpeters42 @cmungall Can one you review this? I believe we've agreed to do this. The PR needs to be approved.

[cmungall]

See comments here:

#650 (comment)

[cmungall]

I have re-reviewed this in light of the original issue. I see it is just making axioms logically consistent with bfo2020-core, which seems reasonable as it shares the label.

As an aside, I attempted to crystalize the policy here:

• Document policy for implicitly mirrored relations with the same label #807

[anitacaron]

The dc:license annotation is just defined and not being used. I'll go through all the files and remove them in another PR.