J. Allen Baron
J. Allen Baron
@sbello what might the Alliance need to make this change? @lschriml, the only thing I can think of that we need to change, beyond the data in the ontology, is...
@fschiettecatte does capitalization matter? Any preference for MIM vs mim?
Do we want to change all references from OMIM to MIM? I'm wondering about the name of some files, e.g. [DOreports/OMIMinDO.tsv](https://github.com/DiseaseOntology/HumanDiseaseOntology/blob/main/DOreports/OMIMinDO.tsv), and references to OMIM in [src/ontology/README_DO_Files](https://github.com/DiseaseOntology/HumanDiseaseOntology/blob/main/src/ontology/README_DO_Files).
> -- I would keep the file names OMIM I agree that it's probably best to change only the prefixes. >-- make test/make release Nothing needs to be done for...
We've decided to push this change back one additional month to the April release to provide more time for the many resources using DO to prepare for this change.
A test release, equivalent to official release `v2024-02-28`, with "OMIM:" prefixes replaced as "MIM:" has been created on the `mim_test_release` branch. Test files are available at https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/mim_test_release/src/ontology Please distribute this...
Yes, acronym ([OMO:0003012](http://www.ebi.ac.uk/ols4/ontologies/omo/properties/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOMO_0003012?lang=en)) is a new synonym type that would also be an exception. Honestly, the query at UBERON linked by @anitacaron (with minor modification) is probably the best bet...
I decided to look more closely at execution time differences using doid-edit.owl and uberon.owl (because I had it on hand, not the edit file). Just switching to the subquery approach...
As an alternative to creating an exclusion for abbreviations and acronyms, could we introduce a new synonym predicate, something like `skos:closeMatch` for synonyms `oboInOwl:hasCloseSynonym`? I guess a new synonym predicate...
All tests passed but it doesn't look like there's one specifically for the output of the `duplicate_exact_synonym` query. After checking that ROBOT built correctly with this PR, I ran some...