Entities with taxonomic context

From phenoscape
Revision as of 02:38, 4 March 2009 by Jpb15 (talk | contribs) (Phenotype annotations)

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 can be stated differently as "some anatomical entity, in a particular taxon, has some quality":

vertebra 1^in_taxon(Danio rerio) has_quality sigmoid

Taxonomically variable ontology relationships

Homology annotations