Difference between revisions of "Entities with taxonomic context"
(→Taxonomically variable ontology relationships) |
(→Phenotype annotations) |
||
| Line 3: | Line 3: | ||
==Phenotype annotations== | ==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": | Our current phenotype annotation model has the form "a particular taxon has some phenotype, consisting of some quality inhering in some anatomical entity": | ||
| + | '''Old form''' | ||
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: | The phenotype is a post-composition with the following properties: | ||
| Line 8: | Line 9: | ||
sigmoid^''inheres_in''(vertebra 1) ''inheres_in'' vertebra 1 | 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": | This annotation can be stated differently as "some anatomical entity, in a particular taxon, has some quality": | ||
| + | '''New form''' | ||
vertebra 1^''in_taxon''(Danio rerio) ''has_quality'' sigmoid | vertebra 1^''in_taxon''(Danio rerio) ''has_quality'' sigmoid | ||
The entity is a post-composition with the following properties: | The entity is a post-composition with the following properties: | ||
Revision as of 03:07, 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":
Old form 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":
New form 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
Searching for phenotype annotations in which the subject entity is vertebra 1 would return both statements.
