Viewing scientific articles on the iPad: browsing articles

In previous articles I've looked at how various apps display scientific articles. The apps I looked at were:

• PLoS Reader
• Nature
• Papers
• Mendeley

So, where next? As Ian Mulvany noted in a comment on an earlier post, I haven't attempted to summarise the best user interface metaphors for navigation. Rather than try and do that in the abstract, I'd like to create some prototypes to play with various ideas. The Sencha Touch framework looks a good place to start. It's web-based, so things can be prototyped rapidly (I'm not going to learn Objective C anytime soon). There's a moderately steep learning curve, unless you've written a lot of Javascript (I've dond some, but not a lot), but it seems to offer a lot of functionality. Another advantage of developing a web app is that it keeps the focus on making the content accessible across devices, and using the web as the means to display and interact with content.

Then there is also the issue (in addition to displaying an individual article) of how to browse and find articles to view. Here are some possibilities.

Publisher's stream
Apps such as the Nature app and the PLos Reader provide you with a stream of articles from a single publisher. This is obviously a bit limiting for the reader, but might have some advantages if the publisher has specifically enhanced their content for devices such as the iPad.

Personal library
Apps such as Mendeley and Papers provide articles from your personal library. These are papers you care about, and one you may make active use of.

Social
Social readers such as Flipboard show the power of bringing together in one place content derived from social streams, such as Twitter and Facebook, as well as curated sources and publisher streams. Mendeley and other social bookmarking services (e.g., CiteULike, Connotea) could be used to provide social similar streams of papers for an article viewer. Here the goal is probably to find out what papers people you know find interesting.

Spatial
In an earlier post I used a map to explore papers in my BioStor archive. This would be an obvious thing to add to an iPad app, especially as the iPad knows where you are. Hence, you could imagine browsing papers about areas that are near you, or perhaps by authors near you. This would be useful if, say, you wanted to know about ecological or health studies of the area you live in. If the geographic search was for people rather than papers, you could easily discovering what kind of research is published by universities or other research bodies that are near your current location.

Of course, Earth is not the only thing we can explore spatially. Google maps can display other bodies in the solar system, (e.g., Mars), as well as the night sky. Imagine being interested in astronomy and being able to browse papers about specific planetary or stellar objects. Likewise, genomes can be browsed using Google maps-inspired browsers (e.g., jBrowse), so we could have an app where you could easily retrieve articles about a particular gene or other region of a genome.

Categories
Another way to browse content is by topic. Classifying knowledge into categories is somewhat fraught, but there are some obvious wasy this could be useful. A biologist might want to navigate content by taxonomic group, particularly if they want to browse through the 1000's of articles published in a journal such as Zootaxa (hence my experiments on browsing EOL). Of course, a tree is not the only way to navigate hierarchical content. Treemaps are another example, and I've played with various versions in the past (see here and here).



I have a love-hate relationship with treemaps, but some of the most interesting work I've seen on treemaps has been motivated by displaying information on small screens, e.g. "Using treemaps to visualize threaded discussion forums on PDAs" (doi:10.1145/1056808.1056915).

Summary
These notes list some of the more obvious ways to browse a collection of articles. It would be fun to explore these (and other approaches) in parallel with thinking about how to display the actual articles. These two issues are related, in the sense that the more metadata we can extract from the articles (such as keywords, taxonomic names and other named entities, geographic localities, etc.) the richer the possibilities for finding our way through those articles.

ReaderMeter: what's in a name?

Dario Taraborelli has released ReaderMeter, an elegant app built on top of the Mendeley API. You enter an author's name and it summarises that authorship's readership in Mendeley. The app provides some summary statistics (mine are shown below), and if you click on the horizontal bar corresponding to a paper, you can see a visualisation of who is reading your paper, including a nice map.

As ever with author names, there are issues of people's name having more than one spelling. In Mendeley I'm known as Roderic D. M. Page, R. D. M. Page, Rod Page, Roderic Page, Roderic D. M. Page, and doubtless some others. Searching ReaderMeter using different spellings of my name gives different results. There are various approaches to tackling this problem, I've touched on one approach earlier.

However, there's a different way to tackle this problem in the context of apps like ReaderMeter, because if you're a Mendeley user you can assert that you are the author of a paper (these papers live in your "My Publications" collection). Using Mendeley's API, an app could retrieve this list of publications (providing the user gave it access), and we could compute readership statistics from the set of articles "known" to be authored (leaving aside the issue of people gaming the system by spuriously claiming authorship). In this way the app relies on the default behaviour of Mendeley users - uploading and self-identifying the articles they've written.

Implementing a feature like this posses two problems. The first is access to a user's data. Mendeley's API supports OAuth, so it could be done in such a way that only the account's user could authorise the app to access this list. The app could store the fact that the user has verified that the list of publications. Think of it as a bit like Amazon's Real Name™ feature.

The other obstacle is Mendeley's API, which returns readership statistics for public documents (i.e., those in the central aggregation). At present, using the API there is no way to link the global id for a Mendeley reference (e.g., ae7dd6a0-6d09-11df-936c-0026b95e484c) with the local id (e.g., 3582682802) that reference has in a user's collection, unless we resort to trying to match articles by searching by identifiers or article titles. If the API exposed these links, apps like ReaderMeter could become even more powerful (and personalised).

Viewing scientific articles on the iPad: iBooks

Apple's iBooks app is an ePub and PDF reader, and one could write a lengthy article about its interface. However, in the context of these posts on visualising the scientific article there's one feature that has particularly struck me. When reading a book that cited other literature the citations are hyper-links: click on one and iBooks forwards you (via the page turning effect) to the reference in the book's bibliography. This can be a little jarring (one minute you're reading the page, next you're in the bibliography), but to help maintain context the reference is preceded by the snippet of text in which it is cited:

To make this concrete, here's an example from Clarky Shirky's "Cognitive Surplus."

In the body of the text (left) the text "notes in his book The Success of Open Source" (which I've highlighted in blue) is a hyper-link. Click on it, and we see the source of the citation (right), together with the text that formed the hyper-link. This context helps remind you why you wanted to follow up the citation, and also provides the way back to the text: click on the context snippet and you're taken back to the original page.

Providing context for a citation is a nice feature, and there are various ways to do this. For example, the Elsevier Life Sciences Challenge entry by Wan et al. ("Supporting browsing-specific information needs: Introducing the Citation-Sensitive In-Browser Summariser", doi:10.1016/j.websem.2010.03.002, see also an earlier version on CiteSeer) takes a different approach. Rather than provide local context for a citation in an article (a la iBooks), Wan et al. provide context-sensitive summaries of the reference cited to help the the reader judge whether it's worth her time to fetch the reference and read it.

Both of these approaches suggest that we could be a lot more creative about how we display and interact with citations when viewing an article.

Viewing scientific articles on the iPad: Mendeley

Previously I've looked at the Nature, PLoS, and Papers apps, now it's the turn of the Mendeley iPad app. As before, this isn't a review of the app as such, I'm more interested in documenting how the app interface works, with a view to discovering if there are consistent metaphors we can use for navigating bibliographic databases.

Perhaps the key difference between Mendeley and the other apps is that Mendeley is cloud-based, in that the bibliography exists on Mendeley's servers, as well as locally on your desktop, iPad, or iPhone. Hence, whereas the Nature and PLoS apps consume a web stream of documents, and Papers enables you to sync collections between desktop and iOS devices, Mendeley syncs to central web server. At present this appears to be done over HTTPS. Mendeley recently released an API, which I've discussed at length. Mendeley's app doesn't use this API, which is a pity because if it did I suspect the API would be getting the love it needs from Mendeley's developers.

Like Papers, the Mendley app uses a split view, where the left-hand panel is used for navigation.

You can drill down to lists of references, and display basic details about an article.

PDF
The Mendeley app is a PDF viewer, but whereas the PLoS app has page turning, and the Papers app scrolls pages from left to right, the Mendeley app displays PDF pages vertically (which is probably the more natural way to scroll through content on the iPad):

Summary
It's clearly early days for the Mendeley app, but it's worth noting two of its most obvious limitations. Firstly, it depends entirely on the user's existing Mendeley bibliography - you can't add to this using the app, it's simply a viewer. Compare this to Papers which can access a suite of search engines from which you can download new papers (albeit with some limitations, for example the Papers iPad app doesn't seem to support extracting metadata via XMP, unlike the desktop version). Secondly, despite Mendeley having as one of its goals being a

research network that allows you to keep track of your colleagues' publications, conference participations, awards etc., and helps you discover people with research interests similar to yours

the Mendeley app lacks any social features, apart from sharing by email(!). I think designing social interactions in bibliographic apps will be a challenge. For an example of what social reading can look like, check out Flipboard.

Viewing scientific articles on the iPad: Papers

Continuing the series of posts about reading scientific articles on the iPad, here are some quick notes on perhaps the most polished app I've seen, Papers for iPad. As with earlier posts on the Nature and PLoS apps, I'm not writing an in-depth review - rather I'm interested in the basic interface design.

Papers is available for the Mac, as well as the iPhone and iPad. Unlike social bibliographic apps such as Zotero and Mendeley, Papers lacks a web client. Instead, all your PDFs are held on your Mac, which can be wirelessly synced with Papers on the iPad or iPhone.

Navigation popover

Papers makes extensive of use of the split view, in which the screen is split into two panes, the left-hand split becoming a popover when you hold the iPad in porrtait orientation. Almost all of the functionality of the iPhone version is crammed into the left-hand split. The popover displays the main interface categories (library, help, collections that you've put PDFs into), collections of documents, metadata for individual papers (which you can edit), as well as search results from a wide range of databases:

Some of these features you encounter as you drill down, say from library to list of papers, to details about a document, others you can access by clicking on the tab bar at the bottom.

PDF display
Like the PLoS app, Papers displays PDFs. It doesn't use a page-turning effect, rather you swipe through the pages from left to right, with the current page indicated below in a page control (what Sencha Touch describe as a carousel control).

Given that the document being displayed is a PDF there is no interaction with the images or citations, but you can add highlights and annotations.

Summary
Papers is the first of the iPad apps I've discussed that isn't limited to a single publisher. If and article is online, or in your copy of Papers for the Mac, then you can view it in Papers for iPad. It is the app that I use on a day to day basis, although the PDF viewer can feel a little clunky. I think anyone designing an application reader should play with Papers for a while, if only to see the level of functionality that can be embedded in the basic iPad split view.