Absence Phenotypes in OWL

Phenotypes describing the absence of a type of structure require particular consideration for both semantic modeling and reasoning.

Basic EQ modeling

We generally represent phenotypes as classes describing relationships between an entity and a quality. The entity is usually an anatomical structure, such as a dorsal fin, which is the bearer_of some quality, such as an instance of serrated. The inverse of bearer_of is inheres_in, so we can either describe the set of organisms with this phenotype:

has_part some (dorsal fin and bearer_of some serrated)

or describe this class of phenotypes (from the perspective of the quality):

serrated and inheres_in some dorsal fin

These expressions are not equivalent but describe different aspects of the same data model.

"Absent" quality

The PATO ontology of phenotypic qualities includes a commonly used quality absent. However, using this term in the above EQ model is problematic. For the entity dorsal fin and the quality absent, we would end up with an expression such as has_part some (dorsal fin and bearer_of some absent). The obvious problem is that this asserts the existence of a dorsal fin, needed to bear the instance of absent.

Using OWL class complements or cardinality

Instead of representing absence with a quality, we can describe it in OWL using a class complement (logical negation):

not (has_part some dorsal fin)

"Lacks all parts of type" quality

The solution provided by PATO for the above problem is the "relational" quality lacks all parts of type. Relational qualities in PATO are further specified by a relation to another class, for example sensitivity toward ultraviolet light. So instead of describing an entity dorsal fin which bears an absent quality, we should instead describe the entity body which bears a quality lacks all parts of type toward dorsal fin.