Steve Baskauf has concluded a thoughtful series of blog posts on RDF and biodiversity informatics with http://baskauf.blogspot.co.uk/2015/07/confessions-of-rdf-agnostic-part-7.html. In this post he discussed the "Rod Page Challenge", which was a series of grumpy posts I wrote (starting with this one) where I claimed RDF basically sucked, and to illustrate this I issued a challenge for people to do something interesting with some RDF I provided.
Two ongoing challenges in biodiversity informatics are getting data into a form that is usable, and linking that data across different projects platforms. A recent and interesting approach to this problem are "data journals" as exemplified by the Biodiversity Data Journal. I've been exploring some data from this journal that has been aggregated by GBIf and EOL, and have come across a few issues.
I spent last Friday and Saturday at ( Research in the 21st Century: Data, Analytics and Impact , hashtag #ReCon_15) in Edinburgh. Friday 19th was conference day, followed by a hackday at CodeBase. There's a Storify archive of the tweets so you can get a sense of the meeting. Sitting in the audience a few things struck me. No identifier wars, DOIs have won and are everywhere.
I've published a short note on my work on geophylogenies and GeoJSON in PLoS Currents Tree of Life : At the time of writing the DOI hasn't registered, so the direct link is here. There is a GitHub repository for the manuscript and code. I chose PLoS Currents Tree of Life because it is (supposedly) quick and cheap.
This post is a response to Ross Mounce's post Text mining for museum specimen identifiers. As Ross notes in that post, mining literature for specimen codes is something I've been interested in for a while (search for specimen codes on iPhylo), and @Aime Rankin (formerly an undergraduate student at Glasgow) did some work on this as well. It's great to see progress in this area.
This a quick writeup of an analysis I did to make the case that the list of names held by the Index of Organism Names (ION) (part of Thomson Reuters) would be very useful for GBIF. I must declare a bias, in that I've spent a good chunk of the last 3-4 years exploring the ION database and investigating ways to link the taxonomic names it contains to the primary taxonomic literature, culminating in building BioNames.
I've put off writing this post about the Bouchout Declaration for a number of reasons. I attended the meeting that launched the declaration last year, and from my perspective that was a frustrating meeting.
Playing with the my "material examined" tool I've been working on, I wondered whether I could make use of it in, say, a spreadsheet. Imagine that I have a spreadsheet of museum codes and want to look those up in GBIF. I could create a service for Open Refine but Open Refine is a bit big and clunky, you have to fire up a Java application and point your browser at it, and Open Refine isn't as intuitive or as flexible as a spreadsheet.
The six finalists for the GBIF Ebbe Nielsen Challenge have been announced by GBIF: The finalists all receive a €1,000 prize, and now have the possibility to refine their work and compete for the grand prize of €20,000 (€5000 for second place). As the rather cheesy quote above suggests, I think the challenge has been a success in terms of the interest generated, and the quality of the entrants.
I've put together a working demo of some code I've been working on to discover GBIF records that correspond to museum specimen codes. The live demo is at http://bionames.org/~rpage/material-examined/ and code is on GitHub. To use the demo, simply paste in a specimen code (e.g., "MCZ 24351") and click Find and it will do it's best to parse the code, then go off to GBIF and see what it can find.