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.

The GBIF Ebbe Nielsen Challenge has closed and we have 23 submissions for the jury to evaluate. There's quite a range of project types (and media, including sound and physical objects), and it's going to be fascinating to evaluate all the entries (some of which are shown below). This is the first time GBIF has run this challenge, so it's gratifying to see so much creativity in response to the challenge.

Quick notes on another example of data duplication in GBIF. I'm in the process of building a tool to map specimen codes to GBIF records, and came across the following example.

Below I sketch what I believe is a straightforward way GBIF could tackle the issue of annotating and cleaning its data. It continues a series of posts Annotating GBIF: some thoughts, Rethinking annotating biodiversity data, and More on annotating biodiversity data: beyond sticky notes and wikis on this topic. Let's simplify things a little and state that GBIF at present is essentially an aggregation of Darwin Core Archive files.

Each year about this time, as I ponder what to devote my time on in the coming year, I get exasperated and frustrated that each year will be like the previous one, and biodiversity informatics will seem no closer to getting its act together. Sure, we are putting more and more data online, but we are no closer to linking this stuff together, or building things that people can use to do cool science with.

The GBIF Ebbe Nielsen Challenge is open! From the official announcement First prize is €20,000, full details on prizes and entry requirements are on the Challenge web site.

Following on from the discussion of the African chameleon data, I've started to explore Angelique Hjarding's data in more detail. The data is available from figshare (doi:10.6084/m9.figshare.1141858), so I've grabbed a copy and put it in github. Several things are immediately apparent. There is a lot of ungeoreferenced data. With a little work this could be geotagged and hence placed on a map.

Just back from GB21, the GBIF Governing Board meeting (the first such meeting I've attended). It was in New Delhi, and this was also my first time in india, which is an amazing place.

This is guest post by Angelique Hjarding in response to discussion on this blog about the paper below. Thank you for highlighting our recent publication and for the very interesting comments. We wanted to take the opportunity to address some of the issues brought up in both your review and from reader comments. One of the most important issues that has been raised is the sharing of cleaned and vetted datasets.

If we view biodiversity data as part of the "biodiversity knowledge graph" then specimens are a fairly central feature of that graph. I'm looking at ways to link specimens to sequences, taxa, publications, etc., and doing this across multiple data providers. Here are some rough notes on trying to model this in a simple way.