e-Biosphere '09 kicks off next week, and features the challenge: Originally I planned to enter the wiki project I've been working on for a while, but time was running out and the deadline was too ambitious. Hence, I switched to thinking about RSS feeds. The idea was to first create a set of RSS feeds for sources that lack them, which I've been doing over at http://bioguid.info/rss, then integrate these feeds in a useful way.

For the last two days I've been participating in a NESCent meeting on Dryad, a "repository of data underlying scientific publications, with an initial focus on evolutionary biology and related fields". The aim of Dryad is to provide a durable home for the kinds of data that don't get captured by existing databases such as GenBank and TreeBASE (for example, the Excel spreadsheets, Word files, and tarballs of data that, if they are lucky, make it

Continuing with RSS feeds, I've now added wrappers around IPNI that will return for each plant family a list of names added to the IPNI database in the last 30 days. You can see the list at here. One thing which is a constant source of frustration for me is the disconnect between nomenclators (lists of published names for species) and scientific publishing.

Although I'd been thinking of getting the wiki project ready for e-Biosphere '09 as a challenge entry, lately I've been playing with RSS has a complementary, but quicker way to achieve some simple integration. I've been playing with RSS on and off for a while, but what reignited my interest was the swine flu timemap I made last week. The neatest thing about the timemap was how easy it was to make.

Tweets from @ attilacsordas and @stew alerted me to the Google Map of the H1N1 Swine Flu outbreak by niman. Ryan Schenk commented: "It'd be a million times more useful if that map was hooked into a timeline so you could see the spread.", which inspired me to knock together a timemap of swine flu. The timemap takes the RSS feed from niman's map and generates a timemap using Nick Rabinowitz's Timemap library.

Thinking about the GUID mess in biodiversity informatics, stumbling across some documents about the PILIN (Persistent Identifier Linking INfrastructure) project, and still smarting from problems getting hold of specimen data, I thought I'd try and articulate one solution. Firstly, I think biodiversity informatics has made the same mistake as digital librarians in thinking that people care where the get information from.

CrossRef has been having some issues with it's OpenURL resolver over the weekend, which means that attempts to retrieve metadata from a DOI, or to find a DOI from metadata, have been thwarted. While annoying (see The dangers of the ‘free’ cloud: The Case of CrossRef), in one sense it's reassuring that it's not just biodiversity data providers that are having problems with service availability.

For fun I quickly programmed a little tool for bioGUID that makes use of Connotea's web api. When an article is displayed, the page loads a Javascript script that makes a call to a simple web service that looks up a reference in Connotea and displays a tag cloud if the reference is found.

OK, second rant of the day. One of my favourite online specimen databases is AntWeb. For a while the ability to harvest data from this database using the venerable DiGIR protocol hasn't been possible, due to various issues at the California Academy of Sciences.

PLoS Computational Biolgy has recently published "Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article" (doi:10.1371/journal.pcbi.1000361) by David Shotton and colleagues. As a proof of concept, they took Reis et al. (doi:10.1371/journal.pntd.0000228) and "semantically enhanced" it: The enhanced article is here: doi:10.1371/journal.pntd.0000228.x001.