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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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pattern for using multiple PATO terms? #251

Closed sbello closed 6 years ago

sbello commented 6 years ago

Is there a way to use more than one PATO term in a logical definition? For example we have the MP term 'plush coat' defined as 'coat has a thick, velvet-like appearance' I think I could define this using both the PATO term 'increased thickness' and the term 'soft' but I'm unsure how or if this would work in the standard patterns. All the other terms have a single PATO term preceding the entity being described. Thanks, Sue

cmungall commented 6 years ago

In this case I think plush is a perfectly lovely PATO term. PATO could have axioms that state that this quality is composed of a softness aspect and an increased thickness (using has-part). This has some pragmatic advantages in that if we want to compare with a cat or otter ontology we don't have to rely on picking the same pair of PATO terms.

If we did was to post coordinate I'd just taken an expression like

has-part some (Q and inheres-in some E)

and replace the Q with (quality and has-part some Q1 and has-part some Q2)

possibly adding more sub-qualities.

obviously you have to watch your parentheses and make sure the nesting is happening at the right level - another reason to pre-coordinate.

All this is consistent with the BFO guide, where quality partonomies are encouraged.

sbello commented 6 years ago

Thanks! I'll submit a request to PATO for a new term.

sbello commented 6 years ago

PATO ticket https://github.com/pato-ontology/pato/issues/142

matentzn commented 6 years ago

@sbello Can this be closed?

sbello commented 6 years ago

Sure