Tuesday, April 1, 2014

Holotype, Quirotype, Pseudogenotype, Pliogenotype - TaxonWorks will support them all!

The Species File Group has always sought to provide robust nomenclatural "auditing" in our software. We include many tests to ensure that nomenclatural metadata conforms to the applicable governing rules. In an effort to further formalize aspects of these tests we recently released the NOMEN ontology, a resource that we hope evolves into a community-based standard. Today, we're very happy to announce a second, similar initiative focused on supporting the types of types used in the Linnean systems of nomenclature.

Taxonomists are very familiar with the concept of types. The usage of some types of types are governed according to a code of nomenclature, for example there are special rules regarding holotypes (the name bearing specimen for a species name) in the ICZN. The usage of other types of types are not governed, they are merely useful to taxonomists who are managing a lot of different data. For example an author may reference an allotype, the opposite sex specimen of a primary type, but this reference has no "legal" or "binding" consequences according to the zoological code. As it turns out, within botany and zoology, the number of different types of types found in the literature is surprisingly large. In 1933 these were cataloged by Donald Frizzell who enumerated a whopping 233 meta-type references.

Our announcement today means that TaxonWorks has committed to supporting the use of all 233 different meta-types identified by Frizzel. Sure, this is a daunting task whose utility may be marginal, but if you want to record that your phototype is of a nepionotype, you should be able to! If you are tracking onomatypes for distribution mapping purposes, TaxonWorks has you covered. Things can get complicated, Frizzel himself notes:
... a specimen which any working systematist would regard as a paratype might very well be at the same time an adelfotype, an alloparatype, an androtype, lipotype, a mimotype and a paraedoeotype.
Amazing! Frizzel's work is now over 80 years old, we can be assured that potentially hundreds of new types of types exist, floating around in the literature. We are committed to finding these renegade types, and plan to spend months deciphering what they mean and how they will be useful in the age of cybertaxonomy. The existence of so many different types of types reflects the complexities inherent in doing biology, among (many) others they reflect concepts of location, life stage, sex, season collected, age, or anatomy. In other words, to model these type concepts in a semantic way we're going to have to build and then use ontologies that formalize all of life as we know it! This is a minor problem that we expect to resolve in a month or two.

Stay tuned here for updates, for now you can check out our current progress.