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mgijax / mammalian-phenotype-ontology

Standard terms for annotating mammalian phenotypic data
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obsolete podocyte foot process (UBERON term) #2624

Open sbello opened 6 years ago

sbello commented 6 years ago

For some reason the UBERON term 'podocyte foot process' UBERON:0004355 is showing as 'obsolete podocyte foot process' when displayed in OLS see https://www.ebi.ac.uk/ols/ontologies/mp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0004355 Checking the MP-edit.owl file and the UBERON file in OLS (https://www.ebi.ac.uk/ols/ontologies/doid/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0004355) this doesn't appear to be an obsolete term so I'm not sure what is happening here. This UBERON term is used in 3 MP terms (MP:0008059, MP:0008139, MP:0008138)

cmungall commented 6 years ago

It is indeed obsolete in uberon, replaced by GO:0098846 ! podocyte foot

The reason it doesn't show in MP is probably because the import module needs to be refreshed. @drseb @balhoff we should meet sometime and discuss the best strategy for keeping this synchronized.

btw, there is a new command in robot, once the import module is refreshed you can do

robot repair -i mp-edit.owl -o mp-edit-repaired.owl

this will use replaced by (but not consider) to update. I'd be careful with this at first as it's a new command and hasn't been used much in the wild yet!

drseb commented 6 years ago

Can you suggest a Skype in January?

sbello commented 6 years ago

Sounds good to me. I was also wondering if there was a way to move a term into an import file if it was accidentally saved saved in the MP file? I've noticed a few of these and would like to move them into the correct place and was wondering if there was a way to do this other than deleting and re-adding the term.

sbello commented 6 years ago

Given that this involves only 3 MP terms I just fixed the definitions to use the GO term