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oborel / obo-relations

RO is an ontology of relations for use with biological ontologies
http://oborel.github.io/
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rename "exposure event or process" to "exposure of organism" (issue 599) #606

Closed wdduncan closed 7 months ago

wdduncan commented 2 years ago
wdduncan commented 2 years ago

Fixes #599

@matentzn @diatomsRcool @laurenechan @cmungall The goal of this PR is to fix the confusion created by having both exposure event and exposure event or process classes in ECTO.

It also relates to COB issue https://github.com/OBOFoundry/COB/issues/192.
If COB mints a new IRI for exposure event, we may need to obsolete this class.

wdduncan commented 2 years ago

COB has added the class exposure of organism (PR).
The class has not been added to a COB release (i.e., it is only in cob-edit.owl). I've submitted an issue concerning when COB will create a release.

wdduncan commented 1 year ago

@cmungall This is being held up b/c we are waiting on new release of COB. Are you the only one who release COB? Can you assign some else?

github-actions[bot] commented 1 year ago

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 commented 1 year ago

Update: The COB class needed is ready. I just need to find the time to circle back to this.

github-actions[bot] commented 1 year ago

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 commented 1 year ago

@anitacaron I've been holding of on this until the COB is ready so that I can use the COB class.

anitacaron commented 1 year ago

@wdduncan, Do you need help fixing the conflicts in the ro-edit.owl?

wdduncan commented 1 year ago

@anitacaron I don't think there will be any conflicts (I hope).
Now that exposure of organism is in COB, I think I just need to change the IRI for exposure event or process (and label) to match the COB class (which currently not in RO).

anitacaron commented 1 year ago

There's already a conflict in this branch, but I'll wait for you to add the COB term. Do you need help importing COB?

wdduncan commented 1 year ago

Just an update:
Waiting on #717 to complete before continuing on this. That PR has a COB import file that I will used to add the necessary class.

anitacaron commented 1 year ago

COB is already ready to use. It was merged in PR #736. I can fix the conflict in the edit file.

wdduncan commented 1 year ago

COB is already ready to use. It was merged in PR https://github.com/oborel/obo-relations/pull/736. I can fix the conflict in the edit file.

@anitacaron Your help would be greatly appreciated! :)

github-actions[bot] commented 10 months ago

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 commented 10 months ago

This has been open for quite a while. I need to review to see what needs to be done in order to finish.

wdduncan commented 10 months ago

Still working on this.

wdduncan commented 10 months ago

We recommend the ECTO group mint an ID for exposure event for now, with the understanding it may be deprecated and replaced by a COB class eventually

We will then replace the usage of the current RO class in domains and ranges with the ECTO URI (and later with the COB URI)

@anitacaron @cmungall The IRI has been changed to COB_0001000 (from COB). Can we move forward now.

github-actions[bot] commented 7 months ago

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.