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

Propagation

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".

Put another way, the definition makes clear that the phenotype is actually possessed by some organism or organisms which are members of the annotated taxon. The organism is also a member of every parent taxon of that taxon, so those taxa also exhibit the phenotype.

Some vs. All

The exhibits relation has "some of" semantics. As described above, an exhibits annotation tells us that some organism or organisms in that taxon possess the phenotype. This works well for describing characteristics of evolving entities such as taxa. We can only state what we have seen. Since membership in a taxon is, ontologically, decided only by genealogy and not by any defining characteristic, it is always possible that a new or undiscovered member of a taxon may exhibit some quality. Diagnostic characters may epistemologically suggest membership in a taxon, but such characters are not the cause of membership: genus-differentia definitions of taxa cannot be constructed.

These semantics are consistent whether we create annotations on leaf taxa (species) or on higher taxa. Annotations to higher taxa are exactly the same as those that might be inferred by a reasoner from annotations to its member taxa. An annotation to a higher taxon tells us only that some member of that taxon possesses the phenotype, but does not provide knowledge that any particular member taxon possesses the phenotype. For example, an annotation entered such as:

  • Cyprinidae exhibits "notched caudal fin"

does not tell us whether its member taxon Danio rerio has a "notched caudal fin". It might.

Annotating ancestral or default conditions

It might be expected that one could annotate a phenotype for an order (or any taxon), and thus "apply" that phenotype to all species within that order. However, as explained above:

  1. Such an annotation does not generate any more knowledge than we put in. We know that some member(s) of the order exhibit the phenotype, but not which species or which families (member taxa of the order).
  2. Furthermore, we do not know whether this phenotype was the ancestral condition for members of that order, or evolved in only one specialized member lineage.

There are ways in which we can address these two situations. If we are entering a phenotype which applies to every member of some higher taxon (like an order), we should generate annotations at the level of specificity which we desire. Concretely, if we "know" that every species in some order has phenotype X, we should create exhibits annotations for every species in the taxonomy belonging to that order for phenotype X, attaching the appropriate evidence code (e.g. "evidence based on everybody says so"). In this way we explicitly capture the facts we want to rely on, with the weight of evidence (perhaps weak) we want to provide. This does not preclude a convenient interface for "expanding" a single taxonomic annotation to generate annotations for all its member taxa when this is desired.

We cannot rely on logical inferences from ontological reasoning to know the phenotype of the most recent common ancestor for a particular clade. This requires evolutionary inferences from phylogenetic analysis. However, we may want to add inferred annotations from such analyses to our datastore. One possibility is to use a different annotation. Instead of exhibits, one could also create statements such as "Taxon X ancestrally_exhibits Phenotype Y". Such annotations could have evidence codes related to the type of evolutionary analysis supporting them. Like exhibits annotations, ancestrally_exhibits annotations would unfortunately not provide information about current phenotypic states of descendant taxa.

Shortcomings and questions

  • What are the criteria for which phenotypes are possessed by an organism? I.e. a missing fin could have been severed by a biologist. Can phenotypes which are the product of an organism's "developmental system" be distinguished from less interesting phenotypes such as severed fins? [This is distinguishable for being unique to individual specimens and a phenotype for which no statement of homology can possibly be made --Tjvision 22:06, 9 February 2009 (EST)]
  • Considering only taxonomic exhibits statements, we don't know which phenotypes co-occur (or don't) within one individual organism. [Unless multiple annotations are made to a single specimen --Tjvision 22:06, 9 February 2009 (EST)]
  • What are use-cases for the ancestrally_exhibits annotations?