Difference between revisions of "Semantics of phenotype annotations"
Jim Balhoff (talk | contribs) (→Types of phenotype annotations) |
Jim Balhoff (talk | contribs) (→Types of phenotype annotations) |
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===Class generalization=== | ===Class generalization=== | ||
(''member_of'' value '''''Siluriformes''''') SubClassOf (''has_part'' some ('''caudal_fin''' and ''bearer_of'' some '''bifurcated''')) | (''member_of'' value '''''Siluriformes''''') SubClassOf (''has_part'' some ('''caudal_fin''' and ''bearer_of'' some '''bifurcated''')) | ||
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+ | ===Observation annotation=== | ||
+ | '''''Siluriformes''''' Type (''has_member'' some (''has_part'' some ('''caudal_fin''' and ''bearer_of'' some '''bifurcated'''))) | ||
===Ancestral state annotation=== | ===Ancestral state annotation=== | ||
'''''Siluriformes''''' Type (''has_progenitor'' some (''has_part'' some ('''caudal_fin''' and ''bearer_of'' some '''bifurcated'''))) | '''''Siluriformes''''' Type (''has_progenitor'' some (''has_part'' some ('''caudal_fin''' and ''bearer_of'' some '''bifurcated'''))) | ||
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Revision as of 01:08, 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))
Observation annotation
Siluriformes Type (has_member some (has_part some (caudal_fin and bearer_of some bifurcated)))
Ancestral state annotation
Siluriformes Type (has_progenitor some (has_part some (caudal_fin and bearer_of some bifurcated)))