Entities with taxonomic context
Our phenotype annotations currently employ linking a phenotype composition to a taxon via an exhibits relation. However this model has not provided an obvious way to employ taxon-specific homology annotations to the anatomical entities being annotated. This page describes an alternative representation of phenotype annotations which seems to provide a solution for employing homology annotations as well as anatomical relations which are taxon-specific.
Phenotype annotations
Our current phenotype annotation model has the form "a particular taxon has some phenotype, consisting of some quality inhering in some anatomical entity":
Danio rerio exhibits sigmoid^inheres_in(vertebra 1)
The phenotype is a post-composition with the following properties:
sigmoid^inheres_in(vertebra 1) is_a sigmoid sigmoid^inheres_in(vertebra 1) inheres_in vertebra 1
This annotation can be stated differently as "some anatomical entity, in a particular taxon, has some quality":
vertebra 1^in_taxon(Danio rerio) has_quality sigmoid
The entity is a post-composition with the following properties:
vertebra 1^in_taxon(Danio rerio) is_a vertebra 1 vertebra 1^in_taxon(Danio rerio) in_taxon Danio rerio
Taking into account the contents of the TAO and TTO ontologies, we can infer useful statements such as:
vertebra 1^in_taxon(Danio rerio) is_a vertebra 1^in_taxon(Cyprinidae) vertebra 1^in_taxon(Danio rerio) is_a bone
Taxonomically variable ontology relationships
Using these entity post-compositions, we can assert taxon-specific anatomical relationships such as:
vertebra 1^in_taxon(Cyprinidae) part_of Weberian apparatus
Now if we search for phenotype annotations in which the subject entity is part_of the Weberian apparatus, we will find the one about vertebra 1 of Danio rerio:
vertebra 1^in_taxon(Danio rerio) has_quality sigmoid
However, we would correctly not find an annotation about vertebra 1 in Chanos chanos, which is not in Cyprinidae:
vertebra 1^in_taxon(Chanos chanos) has_quality serrated
