More than just PDFs

by Vijay Shankar Balakrishnan, Labtimes 04/2013

Cloud reading isn’t exactly a new idea: two putti sitting on a cloud reading, painted by Valerio Castello in the 17th century.

Do you print the research articles to read them? If so, how many do you print every day? If you say, “A lot!” then it’s time to bring the numbers down – not to read, but to print!

Obviously, reading a chosen article leads to reading further, from the citations therein. But printing calls upon several known problems, from storage space to the use of energy and resources. Not only that. Do you want to annotate vital points, while reading on your PC; or read a few articles in parallel; or while reading, to interact with other researchers who are involved in the study? Then printed articles are simply too old-fashioned for such a ‘cloud reading’. But which document format would you choose? The traditional PDF? If you nod ‘yes’ for this too, then it is still not an interactive reading. Thanks to new software tools, you can go beyond the conventional PDFs. Now that’s good news, isn’t it?! But what is wrong with the ceremonious PDFs?

Yes, they are self-contained and optimised for eyes, both on computer and paper! But you know that you cannot interact with the figures or tables, let alone the interaction with other human readers online. You might have tried interacting with images on an article’s parent website using a browser, in either its XML or HTML or XHTML­ format. These formats support semantic annotation, i.e., tagging of the objects (data and images) to the text; thus they are better than the good old PDFs (Pettifer et. al. Learned Publishing. 2011; 24:207-220).

Different formats

However, each format has its own pros and cons. But wouldn’t it be good if a PDF could be this interactive? I am sure you know about the interactive PDFs and the DOI (Digital Object Identifier) for articles. But have you ever wondered about the right tools to make use of these two?

Well, now there is Utopia Documents created by Steve Pettifer and colleagues at the University of Manchester, to bridge the gap between the article formats (Attwod et. al. Bioinformatics. 2010; 26:568-74; Velterop and Michael, Lab Times. 2012; 04:44-45). ReadCube is another such tool developed by Siniša Hrvatin and Robert McGrath of Labtiva Inc, Cambridge, Massachusetts. Qiqqa, from Quantisle Ltd., Cambridge (UK), is another application devoted, not only for reading, annotating and interacting but also for reference management. There are more such reference-managing applications, available both online and offline, such as Zotero, iCite, Mendeley, Papers, PaperPile, RefMan, EndNote, etc.

Rent an article

Utopia Documents, ReadCube and Qiqqa, however, are unique in their own respects for reading research articles as interactive PDFs. For example, ReadCube has its Web-reader format, which is used by Nature, Frontiers, and Wiley group of journals ( Using ReadCube online, you can rent or buy articles, unless there is a relevant subscription to them. All the same, if you want to experience these readers as browser-free applications, all you have to do is to download and install them on your computer!

Briefly, there are certain common features in these readers. Firstly, either you can read articles from your local library, or search and download from the source journal, or query PubMed or Google Scholar, using the built-in browser. They make use of identifiers of the article, like DOI, and save the procured articles as interactive (or enhanced) PDFs, by retrieving metadata from the databases.

Secondly, aside from the enhanced PDFs, you can also see the embedded and linked list of references from the article. In addition, for instance, in Utopia Documents and Qiqqa, a tab also tags more articles by the authors and similar other articles. Achieving such features is the uniqueness of these readers, which otherwise, you could only have used in any of the browser-friendly formats in the respective website.

Thirdly, it is possible to do OCR (Optical Character Recognition) of images (figures and tables) in the PDFs. This allows you to interact with, for instance, the molecular structures published in the article, in 3D, or to analyse the supplementary information. There are also features, like linking articles to other stand-alone reference and document managers, such as EndNote, LaTeX or BibTeX. Using PubMed’s PubReader, you may also find these connections between the data and the text of an article.

Alternative metric

ReadCube and Utopia Documents also have features that show article level metrics, which are recently believed to be as reliable as citation numbers ( These alternative metric systems help readers to explore the outreach of a particular study through, for example, public networking sites or blogs or journalists. In addition, being registered on such readers, this feature encourages you to ‘network’ with other users online.

Last Changed: 04.07.2013