Difference between revisions of "Entities with taxonomic context"
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Our current phenotype annotation model has the form "a particular taxon has some phenotype, consisting of some quality inhering in some anatomical entity": | 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) | 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": | 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 | vertebra 1^''in_taxon''(Danio rerio) ''has_quality'' sigmoid | ||
Revision as of 02:38, 4 March 2009
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
