Wednesday, November 28, 2012

ZooBank data model

I'm trying to get my head around the data model used by ZooBank to store taxonomic names. To do this, I've built a graph for the species Belonoperca pylei described by Baldwin & Smith described in:
Baldwin, C. C., & Smith, W. L. (1998). Belonoperca pylei, a new species of seabass (Teleostei: Serranidae: Epinephelinae: Diploprionini) from the cook islands with comments on relationships among diploprionins. Ichthyological Research, 45(4), 325–339. doi:10.1007/BF02725185

After extracting some data from ZooBank API I created a DOT file connecting the various "taxon name usages" associated with Belonoperca pylei and constructed a graph using GraphViz:
You can grab the DOT file here, and a bigger version of the image is on Flickr. I've labelled taxon names and references with plain text as well as the UUIDs that serve as identifiers in ZooBank. (Update: the original diagram had Belonoperca pylei Baldwin & Smith, 1998 sensu Eschmeyer [9F53EF10-30EE-4445-A071-6112D998B09B] in the wrong place, which I've now fixed.)

This is a fairly simple case of a single species, but it's already starting to look a tad complicated. We have Belonoperca pylei Baldwin & Smith, 1998 linked to its original description (doi:10.1007/BF02725185) and to the genus Belonoperca Fowler & Bean, 1930 (linked to its original publication as interpreted by ("sensu") Baldwin & Smith, 1998. Belonoperca Fowler & Bean 1930 sensu Baldwin & Smith 1998 is linked to the original use of that genus (i.e., Belonoperca Fowler & Bean, 1930). Then we have the species Belonoperca pylei Baldwin & Smith, 1998 as understood in Eschmeyer's 2004 checklist.

Notice that each usage of a taxon name gets linked back to a previous usage, and names are linked to higher names in a taxonomic hierarchy. When the species Belonoperca pylei was described it was placed in the genus Belonoperca, when Belonoperca was described it was placed in the family Serranidae, and so on.