Semantics of phenotype annotations

From phenoscape

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

Formatting key: OWL individual, OWL class, OWL property

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 generally 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)))

This type of annotation simply says that some member of the given taxon has been observed with the phenotype. This works very well with polymorphic conditions and has no problem with evolutionary reversals. This form is pretty weak as an annotation to a broad taxon like Siluriformes (an order), but would be the most appropriate choice for species-level data.

Ancestral state annotation

Siluriformes Type (has_progenitor some (has_part some (caudal_fin and bearer_of some bifurcated)))

This annotation describes the ancestral state for the given taxon - the phenotype possessed by the nearest common ancestor of all the members of the taxon. This is like the "class generalization" but will not produce logical inconsistencies when previously unknown reversals are discovered.