uberon

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Subset report report update

2

Changed ordering of the flow and the version of docker-practice/actions-setup-docker is set to 1.0.8

ubyndr

I realize there may be smaller issues for this but I think we should tackle this as a whole We want all metazoan ssAOs plus bridge axioms plus Uberon to...

cmungall

Add a document on how to use uberon for microbiome samples

2

Describe how to use Uberon with MIxS

cmungall

Proper use of 'derives from' in referencing UBERON anatomical parts for FoodOn

5

In FoodOn we need to reference plant and animal parts and products derived from them without necessarily implying they are connected to the anatomy of whole organisms. Currently our pattern...

ddooley

Add spatial disjointness axioms between major organs

7

example problem: penicillar artery is inferred to be part of both spleen and aorta. These kinds of errors creep in due to confusion about branching-part-of vs connecting-part-of: https://github.com/obophenotype/uberon/wiki/Branching-structures-Design-Pattern Local decisions...

cmungall

Add anti-slims for various taxonomic groupings

10

Add antislims that can be applied that should be excluded from specific releases E.g. * exclude_from_mammal_release * exclude_from_vertebrate_release These are formally weaker than never-in-taxon. In particular, they are safe for...

cmungall

Bodily fluid label is inncorrect given modelling, need real bodily fluid class, PATO needs a property of a fluid class?

4

**Uberon term** bodily ~~fluid~~ liquid http://purl.obolibrary.org/obo/UBERON_0006314 bodily gas http://purl.obolibrary.org/obo/UBERON_0034873 **Bug description** Uberon is missing a bodily fluid class that is a superclass of bodily gas and bodily liquid. The underlying...

tgbugs

Ensure definitions of vessels precisely define boundaries

1

Consider the relationship of the lingual artery (L) to the external carotid (EC):  According to the scheme here, we have two (equally valid IMO) ways to model this mereologically...

cmungall

Documentation request: How to review an Uberon pull request

1

We need to break our reliance on @cmungall and @dosumis for reviewing Uberon pull requests. Can we develop a definite recipe that we can follow that allow us to spread...

matentzn

Two 'anatomical entity' in Uberon

9

**Uberon term** Two term in UBERON, UBERON_0001062 and CARO_0000000 with same label 'anatomical entity' **Bug description** Are these terms same? If same, why do they have different super classes? If...

zhengj2007