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.

Finally submitted (two days late) a manuscript for the BMC Bioinformatics Special Issue on Biodiversity Informatics organised by Neil Sarkar and sponsored by EOL and CBOL. The manuscript, entitled "bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics" describes my bioGUID project. If you are interested made pre-print available at Nature Precedings (hdl:10101/npre.2009.3079.1).

OK, really must stop avoiding what I'm supposed to be doing (writing a paper, already missed the deadline), but continuing the theme of LSIDs and short URLs, it occurs to me that LSIDs can be seen as a disaster (don't work in webrowsers, nobody else uses them, hard to implement, etc.) or an opportunity.

Short URLs have been a topic of discussion recently, perhaps sparked by the article URL Shorteners: Which Shortening Service Should You Use?. Many will have encountered short URLs in Twitter tweets. Leigh Dodds (@ldodds) asked I guess Leigh's talking about the need for short URLs in tweets, but I wonder about the more general question of why we need URL shorteners at all.

The LSID discussion rumbles on (see my earlier post). One issue that has re-emerged is the use of HTTP proxies in RDF documents.

The LSID discussion has flared up (again) on the TDWG mailing lists. This discussion keeps coming around (I've touched on it here and here), this time it was sparked by the LSID SourceForge site being broken (the part where you get the code is OK). Some of the issues being raised include: Nobody uses LSIDs except the biodiversity informatics crowd, have we missed something?

The e-Biosphere online forum has a topic entitled Why open source code?

The e-Biosphere meeting in London June 1-3 has announced a The e-Biosphere 09 Informatics Challenge: The "real time" aspect of the challenge seems a bit forced.