PhD week 8: Structuring taxonomic descriptions

Biological taxonomy is the science of categorising the plants and animals that share this world with us. A critical part of this characterisation is the writing of a description detailing the features which (done well) allows others to identify members of the species in question. Traditionally, this is a piece of prose that is very technical and very dry to read. There is, however, a move towards standardising and atomizing descriptive information, to enable it to be more readily re-used for a variety of applications.

The first attempt at this was the DELTA format, which was drafted as early as 1975. This format is becoming somewhat dated, and efforts are being made to produce an XML-based standard, known as Structured Descriptive Data (SDD).

Computer programs that can be used to produce these structured datasets include LUCID, xper2 and Open DELTA. Somewhat more complex is the taxonomy editor produced by the European Distributed Insitute of Taxonomy, that appears to be the tool for populating their scratchpads.

For some fairly detailed commentary regarding the promises and challenges offered by this revolution in taxonomic data management, ZooKeys published a special issue on e-Infrastructures for data publishing in biodiversity science.

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Read:
   Wallis GP, Trewick SA. 2009. New Zealand phylogeography: evolution on a small continent. Molecular Ecology 18: 3548–3580
    Grant PR, Grant BR. 2008. How and Why Species Multiply. The Radiation of Darwin's Finches. Princeton: Princeton University Press
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 44–47

Websites:
New Zealand's Geological Timescale
Importing DICOM images into Blender
3D slicer
ImageJ wiki

Watched:
Game of Thrones Season One