Difference between revisions of "Semantics of phenotype annotations"

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(Class generalization)
(Class generalization)
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(''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'''))
  
Very strong statement - says that all Siluriformes have a bifurcated caudal fin, no exceptions. This allows no observation of polymorphism or evolutionary reversal. But it does allow you to make one statement and then return any catfish species in a query for species with members having bifurcated caudal fins.
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Very strong statement - says that all Siluriformes have a bifurcated caudal fin, no exceptions. This allows no observation of polymorphism or evolutionary reversal. But it does allow you to make one statement and then return any catfish species in a query for species with members having bifurcated caudal fins. This is the logic of annotations in the existing Phenoscape Knowledgebase.
  
 
===Observation annotation===
 
===Observation annotation===

Revision as of 01:20, 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))

Very strong statement - says that all Siluriformes have a bifurcated caudal fin, no exceptions. This allows no observation of polymorphism or evolutionary reversal. But it does allow you to make one statement and then return any catfish species in a query for species with members having bifurcated caudal fins. This is the logic of annotations in the existing Phenoscape Knowledgebase.

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)))