Difference between revisions of "Semantics of phenotype annotations"
Jim Balhoff (talk | contribs) (→Class generalization) |
Jim Balhoff (talk | contribs) |
||
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 (''' | + | 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.
Contents
Types of phenotype annotations
Class generalization
(member_of value Siluriformes) subClassOf (has_part some (caudal_fin and bearer_of some bifurcated))