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

GAZ is inconsistent #35

Open
matentzn opened this issue Dec 26, 2020 · 6 comments
Open

GAZ is inconsistent #35

matentzn opened this issue Dec 26, 2020 · 6 comments

Comments

@matentzn
Copy link

In an attempt to set up a uniform set of quality control checks across OBO ontologies, we noticed that GAZ is currently inconsistent. Due to its size, its a bit hard to determine run the reasoner in protege, so here the explanation for the inconsistency:

Thing SubClassOf Nothing

Reason for inconsistency:

grassland area is ultimately classified as an immaterial entity:

undersea feature is ultimately classified as a material entity

Nothing can be both material and immaterial

Tualatin Mountains are instances of both of the above.

Which seems to come from a bad interaction between ENVO and GAZ. This may not solve the deeper modelling issue, but at least could drastically reduce the error severity: removing the type assertions on Tualatin Mountains.
@cmungall
Copy link
Member

cmungall commented Dec 27, 2020 via email

@cmungall
Copy link
Member

cmungall commented Dec 27, 2020 via email

@matentzn
Copy link
Author

Ouuf sorry you are right; I was a bit premature only looking at 1 explanation..

The results using 3 explanations look like more individuals can be the cause of the inconsistencies:

Tualatin Mountains

Municipality of Heinola (1)

Municipality of Heinola (2)

Axiom Impact

Axioms used 3 times

Axioms used 2 times

Axioms used 1 times

Ontologies used:

Who are the main stakeholders of GAZ to at least contemplate the migration of the useful parts in GAZ to Wikidata, and then maybe replace it with a "OBO wikidata module" or something like that?

@matentzn matentzn mentioned this issue Mar 5, 2021
Closed
@cmungall cmungall mentioned this issue Mar 9, 2021
Closed
@cmungall
Copy link
Member

cmungall commented Mar 9, 2021

I think obsoletion is too strong. GAZ is mentioned in standards like MIxS. If we obsolete it, it will be unavailable in some browsers, confusing people. (although behavior is not consistent across browsers here)

I think that MIxS6 should recommend wikidata over GAZ. I made a ticket: GenomicsStandardsConsortium/mixs#116

I don't think we should obsolete before MIxS ceases to recommend. More generally I think we need a policy analogous to term obsoletion that is user-focused. An ontology SHOULD not be obsoleted IF there exists a non-obsolete standard S that references O. Maybe fairsharing can help?

However, GAZ should absolutely be marked inactive in OBO. It currently says it is active which is definitely not true!

One day I hope to merge enrich wikidata with GAZ https://github.com/cmungall/environments2wikidata... but meanwhile we should still recommend wikidata over GAZ

@matentzn
Copy link
Author

matentzn commented Mar 9, 2021

Ok! Sounds good! Happy with inactive as a compromise for now, but I would like to make it explicit somewhere that active ontologies in the OBO foundry should be logically consistent. Its just so annoying that I cant process it.. Would you at the very least agree if I made a PR to get rid of all the disjointness constraints?

@lschriml
Copy link
Collaborator

lschriml commented Mar 9, 2021 via email

@cmungall cmungall mentioned this issue Feb 6, 2023
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@cmungall @lschriml @matentzn