Difference between revisions of "Semantics of phenotype annotations"

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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.
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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 ''member_of''/''has_member'' relationships. For example:
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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 ''member_of''  Ictalurus ''member_of'' Ictaluridae ''member_of'' Siluriformes
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Ictalurus_punctatus ''subclade_of''  Ictalurus ''subclade_of'' Ictaluridae ''subclade_of'' Siluriformes
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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.
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==Types of phenotype annotations==
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===Class generalization===
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===Ancestral state annotation===
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===Observation annotation===

Revision as of 00:57, 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

Ancestral state annotation

Observation annotation