Wednesday, May 09, 2018

iSpecies meets Lifemap

It's been a little quiet on this blog as I've been teaching, and spending a lot of time data wrangling and trying to get my head around "data lakes" and "triple stores". So there are a few things to catch up on, and a few side projects to report on.

I continue to play with iSpecies, which is a simple mashup off biodiversity data sources. When I last blogged about iSpecies I'd added TreeBASE as a source (iSpecies meets TreeBASE). iSpecies also queries Open Tree of Life, and I've always wanted a better way of displaying the phylogenetic context of a species or genus. TreeBASE is great for a detailed, data-driven view, but doesn't put the taxon in a larger context, nor does the simple visualisation I developed for Open Tree of Life.

A nice large-scale tree visualisation is Lifemap (see De Vienne, D. M. (2016). Lifemap: Exploring the Entire Tree of Life. PLOS Biology, 14(12), e2001624. doi:10.1371/journal.pbio.2001624), and it dawned on me that since Lifemap uses the same toolkit (leaflet.js) that I use to display a map of GBIF records, I could easily add it to iSpecies. After looking at the Lifemap HTML I figured out the API call I need to pan the map to given taxon using Open Tree of Life taxon identifiers, and violà, I now have a global tree of life that shows where the query taxon fits in that tree.

Here's a screenshot of a search for Podocarpus showing the first 300 records from GBIF, and the position of Podocarpus in the tree of life. The tree is interactive so you can zoom and pan just like the GBIF map.

Screenshot 2018 05 09 16 58 00

Here's another one for the genus Timonius:

Screenshot 2018 05 09 17 58 32

Very much still at the "quick and dirty" stage, but I continue to marvel at how much information can be assembled "on the fly" from a few sources, and how much richer this seems than what biodiversity informatics projects offer. There's a huge amount of information that is simpy being missed or under-utilised in this area.