I'm revisiting the idea of building a wiki of phylogenies using Semantic Mediawiki. One problem with a project like this is that it can rapidly explode.

I've written up some thoughts on Wikipedia for a short invited review to appear (pending review) in Organisms, Environment, and Diversity (ISSN 1439-6092). The manuscript, entitled "Wikipedia as an encyclopaedia of life" is available as a preprint from Nature Precedings (hdl:10101/npre.2010.4242.1). The opening paragraph is: The content will be familiar to readers of this blog, although the essay is perhaps a slightly more sober

Continuing the theme of taxonomic classification in Wikipedia, I'm perversely delighted that Wikipedia demonstrates Gregg's paradox so nicely. The late John R. Gregg wrote several papers and a book exploring the logical structure of taxonomy.

Wikipedia is wonderful, but parts of it are horribly broken. Take, for example, taxonomic classifications. A classification is a rooted tree, which means that each node in the tree has a single parent. We can store trees in databases in a variety of ways. For example, for each node we could store a list of its children, or we could store the single unique parent of each node. Ideally we'd choose to store one or other, but not both.

Stumbled across Alex Wild's post Pyramica vs Strumigenys : why does it matter?, which takes as it's starting point a minor edit war on the Wikipedia page for Pyramica . Alex gives the background to the argument about whether Pyramica is a synonym of Strumigenys , and investigates the issue using the surprisingly small about of data available in GenBank.

Andrew Su has posted an analysis of Gene Wiki, a project to provide Wikipedia pages on every human gene: This result is interesting in that an existing resource (Gene Cards) beats Wikipedia, but only just.

Quick post (really should be doing something else). Reading Jeff Atwood's post Mixing Oil and Water: Authorship in a Wiki World lead me to IBM's wonderful history flow tool to visualise the edit history of a Wikipedia page. There's a nice paper describing history flow (doi:10.1145/985692.985765, free PDF here). Inspired by this I decided to try and implement history flow in PHP and SVG.

Given that one response to my post on Fungi in Wikipedia was to say that fungi are also charismatic, so maybe I should try [insert unsexy taxon name here]. So, I've now looked at all the species I extracted from Wikipedia (nearly 72,000), ran the Google searches, and here are the results: Site How many times is it the top hit?

One response to the analysis I did of the Google rank of mammal pages in Wikipedia is to suggest that Wikipedia does well for mammals because these are charismatic. It's been suggested that for other groups of taxa Wikipedia might not be so prominent in the search results. As a quick test I extracted the 1552 fungal species I could find in Wikipedia and repeated the analysis.

Playing a bit more with the Wikipedia mammal data, there are some interesting patterns to note.