Difference between revisions of "Semantics of phenotype annotations"
Jim Balhoff (talk | contribs) |
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 ('''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. | + | 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 '' | + | 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 '' | + | 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=== |
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.