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.
Holly Bik (@hollybik) has an opinion piece in PLoS Biology entitled "Let’s rise up to unite taxonomy and technology" https://doi.org/10.1371/journal.pbio.2002231 (thanks to @sjurdur for bringing this to my attention). It's a passionate plea for integrating taxonomic knowledge and "omics" data.
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.
A decade ago (OMG, that can't be right, an actual decade ago) I created "iSpecies", a simple little tool to mashup a variety of data from GBIF, NCBI, Yahoo, Wikipedia, and Google Scholar to create a search engine for species.
I'm in the midst of rebuilding iSpecies (my mash-up of Wikipedia, NCBI, GBIF, Yahoo, and Google search results) with the aim of outputting the results in RDF. The goal is to convert iSpecies from a pretty crude "on-the-fly" mash-up to a triple store where results are cached and can be queried in interesting ways. Why?
What follows are some random thoughts as I try and sort out what things I want to focus on in the coming days/weeks. If you don't want to see some wallowing and general procrastination, look away now.I see four main strands in what I've been up to in the last year or so:servicesmashupswikisphyloinformaticsLet's take these in turns. Services Not glamourous, but necessary.
The latest post on the EOL blog (Biodiversity in a rapidly changing world) really, really annoys me. It claims thatNope, I suggest it demonstrates just how limited EOL is. If I view the page for the red lionfish I get an out of date map from GBIF that shows a very limited distribution, and doesn't show the introductions in Florida and the Bahamas (I have to wade through text to find reference to the Florida introduction, and the page doesn't
Given that the clones are hot on my heels, I feel the need to add more bells and whistles to iSpecies. The first new feature is automated tagging, and uses Yahoo's Term Extraction API.
Mauro Cavalcanti has released e-Species, "a taxonomically intelligent biodiversity search engine" written in Python that mimics much of the functionality of iSpecies. The project is open source, with a SourceForge page, although no files seem to be available yet.
Resurrecting iSpecies after moving it to a new folder on one of my servers, and browsing popular searches, I keep coming across clearly erroneous distributions. FishBase seems a major culprit. For example, the common pandora Pagellus erythrinus is a marine fish, yet GBIF displays numerous occurrences in mainland Africa (dots with black centre on map below).What gives?