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EBIvariation / trait-curation

A web application for manual curation of trait-to-ontology mappings, including provenance and integration with EBI SPOT stack.
Apache License 2.0
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Log/track all terms which have “Obsolete” in their name, but are not marked as obsolete in OLS responses #65

Open tskir opened 4 years ago

tskir commented 4 years ago

Originally I though we should make a whole new page to dedicate to that; but now I think that would be an overkill. So it would be sufficient to simply log all such occurrences during OLS queries (in a way which would be easily greppable from the logs).

The situation when the term has "Obsolete" in its name, but not the is_obsolete flag, must not be automatically considered obsolete by the app.

tskir commented 4 years ago

Reported the one term which we know of so far in https://github.com/EBISPOT/OLS/issues/391.

jamesamcl commented 4 years ago

This would assign semantic meaning to something that should not be considered meaningful (the label), and would be problematic for terms that literally describe something that is obsolete, but the term itself is not obsolete. For example:

https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C63553

https://www.ebi.ac.uk/ols/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_0004312

I personally think it would be cleaner if the ontologies use the owl:deprecated property or similar if they want to deprecate a term, as it should not be up to OLS to look for substrings in labels to decide this.

@henrietteharmse what do you think?

henrietteharmse commented 4 years ago

@udp I think your assessment is spot on. If a term in an ontology is obsolete is should indicate so by using owl:deprecated.

tskir commented 4 years ago

@udp @henrietteharmse Thank you for your comments and clarifications! They do make a lot of sense. I will change the scope of this ticket so that the word “obsolete” in any term's name will not automatically cause it to become obsolete. Rather, such cases will be logged and examined manually, to see whether the problems like the one in https://github.com/EBISPOT/OLS/issues/391 recur in the future.