Embryonic development-related phenotype terms should be grouped together - UPHENO:0050108, UPHENO:3000001

[rays22]

The logical definitions of Xenopus phenotype terms (XPO) are well aligned with uPheno patterns and thus they would be expected to be grouped together with related phenotype terms from other taxa. This is not the case for developmental biology phenotypes, because of the:

• lack of logical axiom alignment of the relevant term definitions in other model organism phenotype ontologies, and/or
• non-process based modelling of developmental phenotypes in logical definitions.

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Examples

• UPHENO:0050108 developmental process phenotype
  • XPO:0133403 abnormal developmental process
    http://purl.obolibrary.org/obo/UPHENO_0050108
    • Does XPO:0133403 have a uPheno-aligned EQ axiom? YES
    • Can we group this term computationally with phenotype terms from other model organism ontologies that also have matching uPheno-aligned EQ axioms? YES

What about the seemingly related HP and MP terms that are manually asserted to be 'embryonic development/birth phenotypes'?

• UPHENO:3000001 embryonic development/birth phenotype
  • HP:0001197 Abnormality of prenatal development or birth
    • Does HP:0001197 have a uPheno-aligned EQ axiom? YES, but despite some process related references like "prenatal development" or "birth" in the term label, HP:0001197 is NOT defined logically as an abnormality of a biological process. The EQ follows the abnormal anatomical entity uPheno pattern. In this particular case the anatomical entity is an organism at some stage in a developmental process it participates in.
    • Can we group this term computationally with phenotype terms from other model organism ontologies that also have matching uPheno-aligned EQ axioms? YES, but not with terms like XPO:0133403 that is defined in terms of abnormal developmental processes.
  • MP:0005380 embryo phenotype
    • Does MP:0005380 have a uPheno-aligned EQ axiom? NO
    • Can we group this term computationally with phenotype terms from other model organism ontologies that also have matching uPheno-aligned EQ axiom? NO