Relating taxa to phenotypes

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In Phenoscape, we are annotating the phenotypes of species as described in systematic literature. Because we are working within an ontological framework, we require a well-defined relation to link a taxon to a phenotype. This page describes the properties of, and issues related to, our proposed relation, exhibits.

Defining exhibits

Proposed definition

A taxon X exhibits phenotype Y if phenotype Y has been observed in some organism which is a member of taxon X.

Discussion

In an ideal world, all phenotype annotations would be directly to some organism specimen where the phenotype was observed. However, for various reasons direct specimen annotation is not feasible in practice. So, we create phenotype annotations for "leaf" taxa, species. As the given definition suggests, exhibits statements do not preclude polymorphism within the taxon. Some member organsims of that taxon may have one phenotype while others may have another. For example:

  • Species X exhibits "round dorsal fin"

is not in conflict with another annotation:

  • Species X exhibits "pointed dorsal fin"

Both have been observed within members of this species. Furthermore, phenotypic qualities within PATO cannot really be considered to be alternatives to one another. For example:

  • Species X exhibits "yellow dorsal fin"

would not be supposed an alternative to either of the previous two phenotypes. The situation is no different between "round" and "pointed" themselves.

Implications

If a taxon X exhibits a phenotype, this should hold implications for related taxa. Specifically, the parent taxon of X should be inferred to also exhibit that phenotype. This is more easily understood when it is recognized that member taxa do not stand in a subtype or subclass relation to their parent taxa. It is instead purely a genealogical relation. So when one asks, "What phenotypes does the genus Danio exhibit?", the answer is "All the phenotypes exhibited by its member species".

To be incorporated: logical inferences from ontological reasoning vs. evolutionary inferences from phylogenetic analysis