Following on from my previous post about visualising the mammalian classification in Wikipedia, I've extracted the largest component from the graph for all mammal taxa in Wikipedia, and it is a tree. This wasn't apparent in the previous diagram, where the component appeared as a big ball due to the layout algorithm used.

As part of my on-going experiments with Wikipedia as a repository of taxonomic information, I've extracted mammal pages from Wikipedia.

While thinking about measuring the quality of Wikipedia articles by counting the number of times they cite external literature, and conversely measuring the impact of papers by how many times they're cited in Wikipedia, I discovered, as usual, that somebody has already done it. I came across this nice paper by Finn Årup Nielsen (arXiv:0705.2106v1) (originally published in First Monday as a HTML document, I've embedded the PDF from arXiv

What follows are some random thoughts as I try and sort out what things I want to focus on in the coming days/weeks. If you don't want to see some wallowing and general procrastination, look away now.I see four main strands in what I've been up to in the last year or so:servicesmashupswikisphyloinformaticsLet's take these in turns. Services Not glamourous, but necessary.

Sometimes it's just amazing/frightening how long a piece of software remains useful. I wrote Nexus Data Editor (NDE) in the late 1990's, mainly to keep my then PhD student Vince Smith happy.

At the end of day two of the GBIF LSID-GUID Task Group I put together this crude diagram to summarise some of the possible links between biodiversity data and the larger linked data cloud, which I, among others, have argued is where biodiversity informatics should be heading. Here's my hastily put together diagram (created using the wonderful OmniGraffle):I've put GBIF at the centre since we're at GBIF, and it's them we are trying to convince.

Following on from my previous post about Wikispecies (which generated some discussion on TAXACOM) I've played some more with Wikispecies. AS a first step I've added a Wikispecies RSS feed to my list of RSS feeds. This feed takes the original Wikispecies RSS feed for new pages (generated by the page Special:NewPages ) and tries to extract some details before reformatting it as an ATOM feed.

This post was prompted by Stephen Thorpe's post on TAXACOM about Wikispecies in which he wrote (in a thread discussing Roger Hyam's recent blog post) thatI beg to differ. Wikispecies runs on a database (the Mediawiki software uses a database to store the wiki), and Mediawiki can be thought of as a database of semi-structured text, but it lacks a lot of the functionality database users would expect.

I've added Index Fungorum to the list of RSS feeds that I generate at bioguid.info/rss.

Lately I've become more and more interested in moving data off my machine(s) and into the cloud.

This morning I posted this tweet: My grumpiness (on this occasion, seems lots of things seem to make me grumpy lately) is that often journal RSS feeds leave a lot to be desired. As RSS feeds are a major source of biodiversity information (for a great example of their use see uBio's RSS, described in doi:10.1093/bioinformatics/btm109) it would be helpful if publishers did a few basic things.