Difference between revisions of "Absence Phenotypes in OWL"
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Phenotypes describing the absence of a type of structure require particular consideration for both semantic modeling and reasoning. | Phenotypes describing the absence of a type of structure require particular consideration for both semantic modeling and reasoning. | ||
| − | ==EQ modeling== | + | ==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: | 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''') | ''has_part'' some ('''dorsal fin''' and ''bearer_of'' some '''serrated''') | ||
| − | or describe this class of phenotypes (from the quality | + | or describe this class of phenotypes (from the perspective of the quality): |
'''serrated''' and ''inheres_in'' some '''dorsal fin''' | '''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'''. | ||
Revision as of 18:15, 22 July 2013
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.
