Sadly I won't be at TDWG 2009, at least not in person. However, there is a session on wikis, which may contain this brief screencast of my iTaxon experiments. The screencast was made in haste, but tries to convey some of the ideas behind these experiments, especially the idea that by linking data together we can generate more interesting and rich views of objects such as scientific publications.

One of the more glaring limitations of my BHL viewer described in the previous post is that it can take a while to load all the page thumbnails (there can be hundreds). Given that one of the original motivations for this project was a faster viewer, this kinda sucks.

In between the chaos that is term-time I've been playing with ways to view Biodiversity Heritage Library content. The viewer is crude, and likely to go off-line at any moment while I fuss with it, the you can view an example here.

Continuing with my exploration of the Biodiversity Heritage Library one obstacle to linking BHL content with nomenclature databases is the lack of a consistent way to refer to the same bibliographic item (e.g., book or journal). For example, the Amphibia Species of the World (ASW) page for Gastrotheca aureomaculata gives the first reference for this name as: Gastrotheca aureomaculata Cochran and Goin, 1970, Bull. U.S. Natl.

Thinking about ways to improve the performance of some of my web servers I've begun to toy with Memcached.

After some fussing and hair pulling I've constructed a demo of linking a journal to the Biodiversity Heritage Library and displaying the results in Zotero (see my earlier post for rationale).After some searching I managed to retrieve metadata for several hundred article from the Bulletin of Zoological Nomenclature . Using a local copy of the BHL metadata, I wrote a script that looked up each article in BHL and found the URL of the first

One thing I find myself doing (probably more often than I should) is adding a reference to my Zotero library for an item in the Biodiversity Heritage Library (BHL). BHL doesn't have article-level metadata (see But where are the articles?), so when I discover a page of interest (e.g., one that contains the original description of a taxon) I store metadata for the article containing that page in my Zotero library.

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.

Time for a quick and dirty Friday afternoon hack. Based on responses to the BHL timeline I released two days ago, I've created a version that can compare the history of two names using sparklines (created using Google's Chart API). I use sparklines to give a quick summary of hits over time (grouped by decade).The demo is here. It's crude (minimal error checking, no progress bars while it talks to BHL), but it's home time.

Stumbled across this cool visualisation project by Petra Isenberg at Calgary University. Collaborative tree comparison uses a tabletop system to enable two (or more) people to interact when comparing (in this case) phylogenies.