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hubmapconsortium / ccf-validation-tools

HRA ASCT+B Validation Reports
https://hubmapconsortium.github.io/ccf-validation-tools/
Apache License 2.0
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Bogus present_in_taxon assertion on UBERON:8440041 #293

Closed gouttegd closed 9 months ago

gouttegd commented 10 months ago

The file UB_ASCTB_subset.owl asserts that tuberal nucleus (sensu Rodentia) is present in taxon some Homo sapiens.

As the label of the Uberon term implies, tuberal nucleus (sensu Rodentia) is rodent-specific and is not the same thing as the lateral tuberal nucleus of primates.

anitacaron commented 10 months ago

It's in the Brain table, @emquardokus. Do we still have time to fix it?

aleixpuigb commented 10 months ago

In the Allen brain, line 111, AS5. We can propose to authors if tuber cinereum is more appropriate since it is a related synonym of tuberal region (SME label) and it is part of the hypothalamus (AS4).

emquardokus commented 9 months ago

@anitacaron I've removed this and contacted Jeremy Miller for next revision. I had not recommended this and in fact had written "no grouping term for regions within region" when looking through Uberon for hypothalamas to map the remaining regions of the brain that were in his table. I was specifically looking to see whether there were "exact synonyms" or conservative close synonyms which just had words mixed differently but not the absolute exact syntax as what was in his table. Anything questionable or with no exact or close to exact synonym, I did not recommend. This must have come from some sort of automated mapping he did. I will discuss with him. The suggestion by @aleixpuigb does look to be the correct match tuber cinereum so I will mention to him.

anitacaron commented 9 months ago

Thank you, @emquardokus! I double-checked in the new release from today that the term tuberal nucleus (sensu Rodentia) is not in the subset file.