Difference between revisions of "Semantics of phenotype annotations"

From phenoscape
Jump to: navigation, search
(Class generalization)
Line 1: Line 1:
In Phenoscape data annotation, we typically model a phenotype as a class expression describing a set of organisms, for example <nowiki>'</nowiki>''has_part'' some ('''caudal fin''' and ''bearer_of'' some '''bifurcated''')<nowiki>'</nowiki>. How precisely this phenotype class is related to a taxon has important consequences for the resulting inferences and thus queries for phenotypes across the taxonomy. This is most important when making annotations to higher-level taxa. How should these annotations propagate to sub-taxa?
+
In Phenoscape data annotation, we typically model a phenotype as a class expression describing a set of organisms, for example <nowiki>'</nowiki>''has_part'' some ('''caudal_fin''' and ''bearer_of'' some '''bifurcated''')<nowiki>'</nowiki>. How precisely this phenotype class is related to a taxon has important consequences for the resulting inferences and thus queries for phenotypes across the taxonomy. This is most important when making annotations to higher-level taxa. How should these annotations propagate to sub-taxa?
  
 
This page assumes that taxa are represented as OWL individuals, and the taxonomy is a tree of ''subclade_of''/''contains_clade'' relationships. For example:
 
This page assumes that taxa are represented as OWL individuals, and the taxonomy is a tree of ''subclade_of''/''contains_clade'' relationships. For example:

Revision as of 01:00, 29 August 2011

In Phenoscape data annotation, we typically model a phenotype as a class expression describing a set of organisms, for example 'has_part some (caudal_fin and bearer_of some bifurcated)'. How precisely this phenotype class is related to a taxon has important consequences for the resulting inferences and thus queries for phenotypes across the taxonomy. This is most important when making annotations to higher-level taxa. How should these annotations propagate to sub-taxa?

This page assumes that taxa are represented as OWL individuals, and the taxonomy is a tree of subclade_of/contains_clade relationships. For example:

Ictalurus_punctatus subclade_of Ictalurus subclade_of Ictaluridae subclade_of Siluriformes

These are transitive, so that Ictalurus is a subclade_of Siluriformes. Individual organisms are related to taxa via member_of/has_member. A member_of a taxon X which is a subclade_of taxon Y is also a member_of taxon Y.

Types of phenotype annotations

Class generalization

(member_of value Siluriformes) subClassOf (has_part some (caudal_fin and bearer_of some bifurcated))

Ancestral state annotation

Observation annotation