Wednesday, June 19, 2013

A new way to view taxonomic publications

One of goals of BioNames is to be more than simply another taxonomic database. In particular, I'm interested in the idea of having a platform for viewing taxonomic publications. One way to think about this is to consider the experience of viewing Wikipedia. For any given page in Wikipedia there will be links to other, related content in Wikipedia. Reading an article about a city, you can go and read about the country the city occurs in. Reading about a battle, you can discover more about the generals who fought it. The ability to discover all this interconnected information in one place is compelling.

I'd like something similar for taxonomy. Given that a taxonomic database is in essence a collection of taxonomic names and publications, and a taxonomic publication is in essence a collection of names and citations of taxonomic publications, why not embed the publication within the database and have the names and citations link to the corresponding entries in the database?

Based on some earlier efforts (e.g., Towards an interactive taxonomic article: displaying an article from ZooKeys) and inspired by the eLife Lens project, I've created a live demo of a way to view articles from the journal ZooKeys. Below is a screencast:

If you want to try this out, here are some live examples:

Note the pattern in the URL, just append the DOI for an article to

Everything is a bit rough, but it's working well enough for you to get the basic idea. Code is in github Essentially the viewer grabs the ZooKeys HTML, extracts the URL for the XML file, fetches that, then uses some XSLT style sheets to convert the XML into something viewable. There's a sprinkling of Javascript to call the BioNames API. Much of the code could be tweaked to accepted other NLM XML-based articles, such as content from PLoS and the BMC journals.

One direction this could go in is to make a viewer like this the default viewer in BioNames for ZooKeys articles, so that instead of being restricted to a PDF you can interactively navigate between the article and the cited literature. Indeed, the very action of locating cited references in BioNames builds citation links. We could imagine extending the approach to content that isn't in NLM XML, such as Zootaxa PDFs, or content from BHL. Eventually I'd like to have the taxonomic literature fully embedded in the database, not as PDF or image silos, but as documents linked to names and literature. The journal becomes a database.