Viewing scientific articles on the iPad: the PLoS Reader

Continuing on from my previous post Viewing scientific articles on the iPad: towards a universal article reader, here are some brief notes on the PLoS iPad app that I've previously been critical of.

There are two key things to note about this app. The first is that it uses the page turning metaphor. The article is displayed as a PDF, a page at a time, and the user swipes the page to turn it over. Hence, the app is simulating paper on the iPad screen.

But perhaps more interesting is that, unlike the Nature app discussed earlier, the PLoS app doesn't use a custom API to retrieve articles. Instead the app uses RSS feeds from the PLoS site. PLoS provides journal-specific RSS feeds, as well as subject-specific feeds within journals (see, for example, the PLoS ONE home page). The PLoS Reader app takes these feeds and uses them to create a list of articles the reader can choose from.

A nice feature of the PLoS ATOM feeds is the provision of links to alternative formats for the article (unlike many journal RSS feeds, which provide just a DOI or a URL). For example, the feed item for the article "Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing" doi:10.1371/journal.pone.0012303 contains links to the PDF and XML versions of the article:

<link rel="related" 
   type="application/pdf" 
   href="http://www.plosone.org/article/fetchObjectAttachment.action?uri=info:doi/10.1371/journal.pone.0012303&representation=PDF" 
   title="(PDF) Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing" />
<link rel="related" 
   type="text/xml" 
   href="http://www.plosone.org/article/fetchObjectAttachment.action?uri=info:doi/10.1371/journal.pone.0012303&representation=XML" 
   title="(XML) Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing" />

This makes the task of an article reader much easier. Rather than attempt to screen scrape the article web page, or rely on a rule for constructing the link to the desired file, the feed provides an explicit URL to the different available formats.

I've not seen this feature in other journal RSS feeds, although article web pages sometimes provide this information. BMC journals, for example, provide <link rel="alternate"> tags in the web page for each article, from which we can extract links to the XML and PDF versions, and some journals (BMC included) provide the Google Scholar metadata data tag <meta name="citation_pdf_url"> to link to the PDF. Hence, a generic article reader will need to be able to extract metadata tags from article web pages as it seeks formats suitable to display.

Show me the trees! Playing with the TreeBASE API

Being in an unusually constructive mood, I've spent the last couple of days playing with the TreeBASE II API, in an effort to find out how hard it would be to replace TreeBASE's frankly ghastly interface.

After some hair pulling and bad language I've got something to work. It's very crude, but gives a glimpse at what can be done. If you visit http://iphylo.org/~rpage/mytreebase/ and enter a taxon name, my code paddles off and queries TreeBASE to see if it has any phylogenies for that taxon. Gears grind, RSS feeds are crunched, a triple store is populated, NEXUS files are grabbed and Newick trees extracted, small creatures are needlessly harmed, and at last some phylogeny thumbnails are rendered in SVG (based on code I mentioned earlier), grouped by study. Functionality is limited (you can't click on the trees to make them bigger, for example), and the bibliographic information TreeBASE stores for studies is a bit ropey, but you get the idea.



What I'm looking for at this stage is a very simple interface that answers the question "show me the trees", which I think is the most basic question you can ask of TreeBASE (and one its own web interface makes unnecessarily hard). I've also gained some inspiration from the BioText search engine.

If you want to give it a try, here are some examples. These examples should be fairly responsive as the data is cached, but if you try searching for other taxa you may have a bit of a wait while my code talks to TreeBASE.

• Engystomops (Túngara Frog)
• Apteryx (kiwi)
• Coursetia
• Viburnum
• Physeter (sperm whale)