[Typo/Error] Synonym appears as both exact AND broad or related for the same term

[ghost]

Uberon term Multiple terms. For example, https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0013528 (and other Brodmann area terms).

Bug description There are several instances where the same synonym is used as both an exact synonym and a broad synonym for the same term. There are also instances where a synonym is annotated as both an exact and related synonym. For example, see UBERON_0013528 Brodmann (1909) area 11:

In this case, the repeated synonyms probably should only be related to the term with the has_exact_synonym relationship.

These examples were discovered by spot checking and may represent a global issue of duplicate synonyms.

[shawntanzk]

Suggestion: whenever there is exact and something else - prefer something else? eg broad preferred When people come by any terms that they don't think is right, they should make a ticket

[shawntanzk]

https://github.com/monarch-initiative/mondo/tree/master/src/sparql/update <- can use SPARQL query from here and modify. Discuss in next CL/UBERON call and make decision on this

[ghost]

whenever there is exact and something else - prefer something else? eg broad preferred

In the example that prompted this ticket, the exact duplicate synonyms should be retained and the broad and related synonyms removed.

[paolaroncaglia]

Also see https://github.com/obophenotype/uberon/issues/2053

[shawntanzk]

Action: change all to exact and create a PR for review

[ghost]

Checking in on the status of this... not sure what "Icebox" is. Will the synonyms in question have to be fixed manually?

[shawntanzk]

@bvarner-ebi - its in icebox as it depends on discussions here https://github.com/obophenotype/uberon/issues/2363 will put it in the agenda for cl/uberon call

good job past Shawn, apparently already added it to agenda heh

[github-actions[bot]]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

[anitacaron]

Blocked by:

• [ ] https://github.com/obophenotype/uberon/issues/2363

[github-actions[bot]]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

[ghost]

Blocked by:

• [ ] Should synonym scopes be contextual? #2363

@anitacaron, since the issue noted above is closed I removed the "blocked" label from this issue. Is there anything else that is required before getting this issue fixed?

[ghost]

No action plan described. @anitacaron, please consider reassigning as appropriate.