Some serious displacement activity. I'm toying with adding phylogenies to iSpecies, probably sourced from the PhyLoTA browser. This raises the issue of how to display trees on a web page. PhyLoTA itself uses bitmap images, such as this one:but I'd like to avoid bitmaps. I toyed with using SVG, but that has it's own series of issues (it basically has to be served as a separate file). So, I've spent a couple of hours playing with the element.

I've just spent a frustrating few minutes trying to find a reference in BioStor. The reference in question isand comes from the Reptile Database page for the gecko Phyllodactylus gilberti HELLER, 1903. This is primary database for reptile taxonomy, and supplies the Catalogue of Life, which repeats this reference verbatim.Thing is, this reference doesn't exist! Page 39 of Proc. Biol. Soc.

I'm in the midst of rebuilding iSpecies (my mash-up of Wikipedia, NCBI, GBIF, Yahoo, and Google search results) with the aim of outputting the results in RDF. The goal is to convert iSpecies from a pretty crude "on-the-fly" mash-up to a triple store where results are cached and can be queried in interesting ways. Why?

Thinking about next steps for my BioStor project, one thing I keep coming back to is the problem of how to dramatically scale up the task of finding taxonomic literature online.

To much fanfare (e.g., Nature News , "Linnaeus meets the Internet" doi:10.1038/news.2010.221), on May 5th PLoS ONE published Sandy Knapp's "Four New Vining Species of Solanum (Dulcamaroid Clade) from Montane Habitats in Tropical America" doi:10.1371/journal.pone.0010502.

Mendeley have called for proposals to use their forthcoming API. The API will publicly available soon, but in a clever move Mendeley will provide early access to developers with cool ideas.Image by Mendeley.com Given that the major limitation of the Biodiversity Heritage Library (from my perspective) is the lack of article-level metadata, and Mendeley has potentially lots of such data, I wonder whether this is something that could be explored.

The BBC web site has an article entitled Giant deep sea jellyfish filmed in Gulf of Mexico which has footage of Stygiomedusa gigantea , and mentions an associated fish, Thalassobathia pelagica .One thing that frustrates me beyond belief is how hard it is to get more information about these organisms. Put another way, the biodiversity informatics community is missing a huge opportunity here.

Random half-formed idea time. Thinking about marking up an article (e.g., from PLoS) with a phylogeny (such as the image below, see doi:10.1371/journal.pone.0001109.g001), I keep hitting the fact that existing web-based tree viewers are, in general, crap.Given that a PLoS article is an XML document, it would be great if the tree diagram was itself XML, in particular SVG.

At long last the peer-reviewed version of the paper "Enhanced display of scientific articles using extended metadata" (doi:10.1016/j.websem.2010.03.004), in which I describe my entry in the Elsevier Grand Challenge, has finally appeared in the journal Web Semantics: Science, Services and Agents on the World Wide Web . The pre-print version of this paper has been online (hdl:10101/npre.2009.3173.1) for a year prior to appearance of the

The context for this post is the PLos markup meeting held at the California Academy of Sciences over the weekend (many thanks to Brian Fisher for the invitation). PLoS are launching a "biodiversity hub" and were looking for ideas on how to implement this.

The ability to create PDFs for the articles BioStor extracts from the Biodiversity Heritage Library has been the single most requested feature for BioStor. I've taken a while to get around to this -- for a bunch of reasons -- but I've finally added it today.