Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

NTR "has life cycle stage" relation #742

Closed
wants to merge 12 commits into from
Closed

NTR "has life cycle stage" relation #742

wants to merge 12 commits into from

Conversation

ddooley
Copy link
Contributor

@ddooley ddooley commented Aug 10, 2023

And "collected during life cycle stage" relation. See #598

@ddooley
new "has life cycle stage" relation
2cd3d1f 
And "collected during life cycle stage" relation.
@ddooley ddooley requested a review from anitacaron as a code owner August 10, 2023 08:10
@anitacaron anitacaron requested a review from wdduncan August 11, 2023 10:53
@anitacaron anitacaron linked an issue Aug 11, 2023 that may be closed by this pull request
NTR:relationship for specifying stage of an individual #598
Closed
anitacaron
anitacaron requested changes Aug 16, 2023
View reviewed changes
Copy link
Collaborator

@anitacaron anitacaron left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Please add an example of usage for both. (making Charles' review official)

cthoyt
cthoyt reviewed Oct 2, 2023
View reviewed changes
src/ontology/ro-edit.owl Outdated Show resolved Hide resolved
cthoyt
cthoyt suggested changes Oct 2, 2023
View reviewed changes
Copy link
Collaborator

@cthoyt cthoyt left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

My original feedback for adding an example has been satisfied, but there is still an issue where there is some spurious diff in the ro-edit.owl for "DLSafeRule" elements

@github-actions GitHub Actions
Copy link
Contributor

github-actions bot commented Jan 1, 2024

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.

@github-actions github-actions bot added the stale label Jan 1, 2024
anitacaron
anitacaron previously approved these changes Jan 22, 2024
View reviewed changes
Copy link
Collaborator

@anitacaron anitacaron left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Technically approved. Still needs ontology review.

anitacaron
anitacaron previously approved these changes Jan 22, 2024
View reviewed changes
Copy link
Collaborator

@anitacaron anitacaron left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Technically approved. Still needs ontology review.

@github-actions github-actions bot removed the stale label Jan 23, 2024
@wdduncan
Copy link
Collaborator

has life cycle stage is a subproperty of participates in, and the range of participates in is occurrent. However, the range of has life cycle stage is life cycle stage and life cycle stage is not a subclass of occurrent.

cmungall
cmungall reviewed Apr 22, 2024
View reviewed changes
src/ontology/ro-edit.owl Outdated Show resolved Hide resolved
cmungall
cmungall requested changes Apr 22, 2024
View reviewed changes
Copy link
Contributor

@cmungall cmungall left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Only assert on one direction

anitacaron
anitacaron requested changes May 8, 2024
View reviewed changes
src/ontology/ro-edit.owl Outdated Show resolved Hide resolved
anitacaron
anitacaron approved these changes Jul 15, 2024
View reviewed changes
Copy link
Collaborator

@anitacaron anitacaron left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Technically, I approve. Still need ontology review.

@anitacaron anitacaron requested a review from cmungall July 15, 2024 09:15
@wdduncan
Copy link
Collaborator

The domain/range issue mentioned above still needs to be resolved.

@cmungall cmungall changed the title NTR "has life cycle stage" relation NTR "specimen from organism" (formerly "has life cycle stage") relation Aug 12, 2024
@cmungall cmungall changed the title NTR "specimen from organism" (formerly "has life cycle stage") relation NTR "has life cycle stage" relation Aug 12, 2024
@cmungall
Copy link
Contributor

has life cycle stage is a subproperty of participates in, and the range of participates in is occurrent. However, the range of has life cycle stage is life cycle stage and life cycle stage is not a subclass of occurrent

It should be, but this is a general issue with RO imports and will be addressed by COB. As it's not pertinent to this PR, I suggest making a new issue, since the D/R declarations are correct in this PR.

@ddooley
Copy link
Contributor Author

ddooley commented Aug 12, 2024

It turns out "in taxon" allows for assignment (at instance and class level) of both organisms and processes/life stages to taxa, so we can express that "pupal stage in taxon Rhopalocera". So there is no need for "has life cycle stage/life cycle stage of".

Discussion on Aug 12 recommended that "life cycle stage of" be a narrow synonym of "in taxon".

A side issue is that "in taxon" doesn't have a reverse relation, so there's no relation to put opposite relation narrow synonym on.

@ddooley ddooley closed this Aug 12, 2024
ddooley added a commit that referenced this pull request Aug 12, 2024
@ddooley
Narrow synonym arising from pull 742 discussion
3d3a4f6 
#742
@ddooley ddooley mentioned this pull request Aug 12, 2024
Merged
anitacaron pushed a commit that referenced this pull request Nov 5, 2024
@ddooley
Narrow synonym arising from pull 742 discussion (#805)
6e81993 
#742
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@cthoyt cthoyt cthoyt approved these changes

@anitacaron anitacaron anitacaron approved these changes

@wdduncan wdduncan Awaiting requested review from wdduncan

@cmungall cmungall Awaiting requested review from cmungall

Assignees

@ddooley ddooley

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

NTR:relationship for specifying stage of an individual
5 participants
@ddooley @wdduncan @cmungall @anitacaron @cthoyt