obophenotype / obophenotype/uberon

Add DPs for mereological sums of structures (muscles, musculature; vessels, vasculature)

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@aleixpuigb is already working on this.

Since Aug 11, 2023.

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Description

Uberon has historically followed FMA in drawing a distinction between Xs and Xature.

Xs form an is-a hierarchy, inferred automatically for "X P = X and R some P" e.g.

  • blood vessel
    • [i] hindlimb blood vessel
      • [i] foot blood vessel

Xature shadows the partonomy

  • blood vasculature
    • [p] hindlimb blood vasculature
      • [p] foot blood vasculature

This is harder to infer, a known issue with OWL

same for muscles, musculature, and other structures

Maintaining the two hierarchies also makes combining with other ontologies harder as they will often use vessel vs vasculature interchangeably

We have two choices

  1. Retain current structure, but fully document, make DPs, and create procedures to avoid ragged hierarchies
  2. Collapse distinction, use vessel is-a hierarchy, add vasculature as synonyms, and if an application needs to refer to the merelogical sum of Xs and X-segments that are part of a P, then they do that using the base X concept and the complex axiomatization happens in that application

If we go with 1 then we need to be very clear about what X vasculature/musculature means. Is it all muscles part-of X? or part of and overlapping? or muscles and muscle parts that are in X? Is it the maximal mereological sum or any mereological sum?

This is actually a really hard thing to get right, and a harder thing to explain to people and to mentally reason over

For this reason, I am tending towards 2. However, this should not be done lightly. We need to look at implications for phenotype axiomatization some of which may depend on X vs Xature (specifically use of part-of vs is-a in uberon) to get desired inferences, cc @dosumis @matentzn

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