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
vertebra^in_taxon(Cyprinidae) has_quality sigmoid
bone^in_taxon(Cyprinidae) has_quality shape