Thursday, March 03, 2016

iSpecies meets TreeBASE

I'm continuing to play with the new version of iSpecies, seeing just how far one can get by simply grabbing JSON from various sources and mashing them up. Since the Open Tree of Life is pretty unresolved ("OMG it's full of stars") I've started to grab trees from TreeBASE and add those. Sadly TreeBASE is showing it's age and doesn't have a JSON API, so I had to break my rule of only using HTML and Javascript in iSpecies and I had to write some PHP wrappers to talk to TreeBASE. Now, when you search for a genus or species you may see a list of studies from TreeBASE, and a popup menu where you can select a tree to view.

Below is a example (searching for the plant genus Fitzalania). Ispecies treebase

This example shows one reason phylogenies are useful. Although GBIF (which supplies the data for the map) recognises Fitzalania, a recent study in TreeBASE shows that this renders Meiogyne paraphyletic, and so moves the Fitzalania to Meiogyne. Hence GBIF's taxonomy is somewhat behind the current state of knowledge about these plants.

The paper merging these two genra (doi:10.1600/036364414x680825) also shows up in the CrossRef results. Unfortunately TreeBASE doesn't have the DOI for the paper, so linking these two results (the TreeBASE study and the corresponding paper) will require some work. This is another reason why I'm playing with iSpecies: I want to see how many identifiers we can uncover to connect results from different sources, and how many cross links we need to add before it all comes together in a nice linked graph of data.