This guest post by Tony Rees explores some of the themes from his recent talk 10 years of Global Biodiversity Databases: Are We There Yet?. 10 years of global biodiversity databases: are we there yet? from Tony Rees A couple of months ago I received an invitation to address the upcoming 2015 meeting of the Malacological Society of Australasia (Australian and New Zealand mollusc persons for the uninitiated) on
Following on from Testing the GBIF taxonomy with the graph database Neo4J I've added a more complex test that relies on linking taxa to names. In this case I've picked some legume genera ( Coursetia and Poissonia ) where there have been frequent changes of name.
I've been playing with the graph database Neo4J to investigate aspects of the classification of taxa in GBIF's backbone classification. Neo4J is a graph database, and a number of people in biodiversity informatics have been playing with it. Nicky Nicolson at Kew has a nice presentation using graph databases to handle names Building a names backbone, and the Open Tree of Life project use it in their tree machine.
Quick notes on modelling taxonomic names in databases, as part of an ongoing discussion elsewhere about this topic. Simple model One model that is widely used (e.g., ITIS, WoRMS) and which is explicit in Darwin Core Archive is something like this: We have a table for taxa and we don't distinguish between taxa and their names. the taxonomic hierarchy is represented by the parentID field, which points to your parent.
Browsing JSTOR's Global Plants database I was struck by the number of comments people have made on individual plant specimens. For example, for the Holotype of Scorodoxylum hartwegianum Nees (K000534285) there is a comment from Håkan Wittzell that the "Collection number should read 1269 according to Plantae Hartwegianae". In JSTOR the collection number is 1209. Now, many (if not all) of these specimens will also be in GBIF.
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.
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.
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.