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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
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Fix capitalisation typo in increased ccc count pattern #950

Open matentzn opened 6 days ago

matentzn commented 6 days ago

As we face out the use of CARO, we need to update the corresponding patterns from CARO: cellular organism to the UBERON: multicellular organism for "whole organism" patterns.

Clare72 commented 6 days ago

The CARO term is not specifically multicellular:

A general term for organism that is agnostic about single cell vs multi-cellular

Using the UBERON term would change these patterns so that they become unsuitable for unicellular organisms, so I think you need to get some unicellular organism people to sign off on this.

sbello commented 6 days ago

@matentzn This CARO to UBERON change, restricts this pattern to multicellular organisms. Was this intended? As the patterns are all related to resistance/sensitivity of an organism to a chemical I would have thought we would want this to apply to both single cell and multicellular organisms.

matentzn commented 6 days ago

Which other class should I be using though? since we align all anatomy on Uberon, I need some kind of Uberon class here..

My goal here is only to get rid of the CARO class (it is the only remaining CARO dependency in uPheno which I am completely redoing now) - I am fine with whatever alternative you suggest..

Clare72 commented 6 days ago

If you really need to use UBERON right now, you probably need to go up to 'anatomical structure'. Though it would be better to get a uni/multi-cellular-agnostic 'whole organism' term made. (Is there a reason UBERON doesn't have this already?)

sbello commented 6 days ago

I agree with @Clare72 I think we should go up to http://purl.obolibrary.org/obo/UBERON_0000061 'anatomical structure' this is an ancestor of 'multicellular organism' and looking at the tree in OLS this should cover things like CL - cell and GO - cellular anatomical entity. It should cover all that we need.

cmungall commented 6 days ago

COB?

matentzn commented 6 days ago

I am fine with using COB, but COB is still using the CARO class: https://www.ebi.ac.uk/ols4/ontologies/cob/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCARO_0001010

Maybe we can remove that mapping in COB, and use the COB class?