Ensure definitions of vessels precisely define boundaries

[cmungall]

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

https://github.com/obophenotype/uberon/wiki/Branching-structures-Design-Pattern

1. L connecting-branch-of EC:
   • The segment of the EC that is shown above is morphologically a tube
   • L is also a tube
   • L is not part of EC
   • more specifically, L and EC share no parts
   • L and EC are adjacent, and more specifically they connect and allow the flow of blood from the EC to the L
2. L branching-part-of EC:
   • The segment of the EC that is shown above is morphologically a tree
   • L is a part of EC.
   • more specifically, L is a branching part of EC
   • There is an implicit (unnamed) structure that is the "stem" of the EC (corresponding to the concept of EC in 1 above).

In pragmatic terms, if we have a enthothelial cell in L, then if we follow 1, that cell would not be returned in a query for all cells in the EC. If we follow 2, the cell would be returned in this query.

Currently in the ontology many of the text definitions don't make it clear which of the above models are followed. In some cases, logical axioms may force an interpretation, but this is not super-clear to people using uberon who are not experts in OWL and RO

We should go through the ontology and make it very clear what our boundary commitments are. This is difficult as I think some of the concepts are inherently fuzzy. This task should also be done in concert with a strategy for checking the entailments.

One possibility is that we follow FMA and make two concepts and have two hierarchies for tubes and trees. This may make the ontology harder for general use, but easier for precise use.

[shawntanzk]

I see a merged PR with this - is this fixed?

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This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.