search

information-artifact-ontology / ontology-metadata

OBO Metadata Ontology
Creative Commons Zero v1.0 Universal
19 stars 8 forks source link

add individual: out of scope #75

Closed nicolevasilevsky closed 2 years ago

nicolevasilevsky commented 3 years ago

close https://github.com/information-artifact-ontology/ontology-metadata/issues/77

matentzn commented 3 years ago

@cmungall @zhengj2007

Should we be using OMO namespace

zhengj2007 commented 3 years ago

It sounds good to me to use OMO prefix.

Is any issue tracker associated with this pull request?

Besides, for adding 'out of scope' as one of 'obsolescence reason specification' options, it also needs to update 'obsolescence reason specification' equivalent axiom.

nicolevasilevsky commented 3 years ago

I did not create a ticket @zhengj2007, would you like me to?

We need this for Mondo.

zhengj2007 commented 3 years ago

@nicolevasilevsky Would be nice to have an issue tracker associated with the changes and using 'ontology term requester' and 'term tracker item' annotations with the term to indicate who request the term and details about it. So, we can trace back if anyone have questions. Thanks!

nicolevasilevsky commented 3 years ago

@zhengj2007 done!

zhengj2007 commented 3 years ago

@nicolevasilevsky Would you like to update the annotations associated with the new individual and add it to 'obsolescence reason specification' equivalent axiom in the OWL file?

alanruttenberg commented 3 years ago

It doesn't seem that 'out of scope' would be a reason for obsolescence on its own unless the class was duplicated in another ontology, in which case the duplication would be the reason for obsoleting. Otherwise an out-of-scope term would migrate to the appropriate ontology, no?

On Tue, Nov 2, 2021 at 4:30 PM jie zheng @.***> wrote:

@nicolevasilevsky https://github.com/nicolevasilevsky Would you like to update the annotations associated with the new individual and add it to 'obsolescence reason specification' equivalent axiom in the OWL file?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/information-artifact-ontology/ontology-metadata/pull/75#issuecomment-958143332, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAB3CDTBRZ3CBO6T75KPBUTUKBJ7NANCNFSM5HERLJUA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

nicolevasilevsky commented 3 years ago

@alanruttenberg this is for the Mondo Disease Ontology, where we bring in terms from other sources but sometimes they are considered out of scope for Mondo but they still exist in another source ontology.

alanruttenberg commented 3 years ago

Is the term brought in with the original URL?

On Tue, Nov 2, 2021 at 4:54 PM Nicole Vasilevsky @.***> wrote:

@alanruttenberg https://github.com/alanruttenberg this is for the Mondo Disease Ontology, where we bring in terms from other sources but sometimes they are considered out of scope for Mondo but they still exist in another source ontology.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/information-artifact-ontology/ontology-metadata/pull/75#issuecomment-958158584, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAB3CDQN3X7MHAETPHIWAWDUKBMZTANCNFSM5HERLJUA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

nicolevasilevsky commented 3 years ago

All the terms in Mondo have a Mondo ID and we add database cross references to the source terms. So the term that is being obsoleted is a Mondo term.

alanruttenberg commented 3 years ago

I see. I don't think I want to know why MONDO would mint a new IRI for an existing term...

nicolevasilevsky commented 3 years ago

@zhengj2007 i made your requested changes

matentzn commented 2 years ago

I just lost my vote @alanruttenberg against numeric IDs but this PR is a good illustration of why we had the debate in #82

I need to literally google 3 (!) APs now just to see whether @nicolevasilevsky used the correct APs for the term.

image

Anyways. I know. Better diff tools will solve it. That was not the point though!