Bench philosophy: PDF-Viewer Utopia Documents

Reading the Whole Story
byJan Velterop and John Michael, Labtimes 04/2012

The Utopia Documents PDF-viewer has redefined the reading of scientific literature, giving it a fresh perspective by combining the convenience and reliability of the PDF with the flexibility and power of the Web.

Apart from forming the ‘minutes of science’, creating a stable record of ideas and discoveries, the scientific literature is the ‘connective tissue’ of scientific knowledge. This connective tissue, quite literally, gives research findings context. No idea exists in isolation. There is no article that stands on its own, without citations or references to other articles. The scientific article has also been described as a ‘story that persuades with data’. Just because something has been published doesn’t mean that the story is over. Giving coherence to the story, to scientific know­ledge – or at least attempting to do so – has always been the function of academic literature, and the way this is done, to this day, is via citations and references.

The article’s metadata and references appear in a clickable form. Click image to enlarge

Good reasons for PDFs

In the last decade and a half, with the emergence of the Web, the connectivity of the literature has been enhanced by the possibility of hyperlinks, potentially linking a vast number of information sources with the simple click of a mouse. In Web (HTML) versions of articles, that is. Not in PDF versions. However, the majority of scientific articles are still ‘consumed’ in the form of PDFs. There are many good reasons for that. For instance, PDFs are eminently portable, they can therefore reside on your own computer and are accessible, even if you are not online. They cannot be sneakily changed by the publisher (not that a publisher would ever dream of doing that, of course) and they have ‘edges’, as self-contained entities. While the occasional ‘hard-wired’ hyperlink can be found in modern PDFs, the format doesn’t have the connectivity potential of HTML. Or rather, it didn’t, for that has now changed.

Utopia Documents, a PDF-viewer developed under the leadership of Steve Pettifer by computer scientists and life scientists at the University of Manchester, is bridging the connectivity gap between Web formats and PDFs (Attwood et al., Bioinformatics, 2010, 26, 568-574). Reading the research literature with Utopia Documents enables you to connect PDFs’ static content to the dynamic world of online content.

Utopia Documents reconnects PDFs with the ongoing discussion, with the story, if you wish. It not only provides links to related and relevant articles but to the blogosphere, to online data sources and to social media sites. This way you can see what other researchers have been saying about the article you’re reading and about its subject matter too. Utopia Documents’ Figure Browser makes it easy to have a quick look at the illustrations in an article, providing a graphical overview of a paper’s content, and an easy way to navigate from figure to figure.

The new PDF-reader makes it easy to explore an article’s content and claims, and also to investigate other recent articles that discuss the same or similar topics. With a look-and-feel that blends real-time updates with the typographic elegance of published articles, the PDF-viewer brings up-to-date information directly to your desktop. And up-to-date has to be taken quite literally, as it is not unusual to come across a link to a related article that’s been added to PubMed only a few minutes before. Utopia Documents also automatically shows article metrics, such as the number of times the article is mentioned in blogs, on Twitter, or in the news and it is certainly not a rare occasion to see the metrics change between two views.

A bubble menu emerges if a term is highlighted in the text. Click image to enlarge

Convenient use

A key feature of Utopia Documents for researchers is the convenience it offers. Are you looking for clarification of a given term, or more information about it? You can do just that, with integrated semantic search. Or do you want to interact directly with datasets belonging to the article, or with curated database entries, play with molecular structures, edit sequence and alignment data, even plot and export tabular data? A few clicks in the PDF or the readers sidebar will enable you to do that. No need for copying and pasting or error-prone re-typing in browsers or other applications.

For the life science researcher a number of highly relevant databases are incorporated, including a highly practical database of laboratory supplies and materials and their manufacturers (‘for the lab’), but the integrated search ensures that databases not (yet) incorporated are also easily located and accessed. If you want to cite the article in question in an article of your own, Utopia Documents gives you seven common reference-formatting standards to choose from. A simple copy and paste suffices to get the reference in the required format, again without having to do any error-prone re-typing.

The left screenshot at the bottom of the previous page shows a typical Utopia Documents title page from a scientific article. In the main panel it looks as it would do in any other PDF reader but, in the sidebar to the right, the article’s metadata and references appear in ‘clickable’ form. This makes it easy to follow up the cited material via search engines and digital libraries. If one highlights a term or phrase in the text (right screenshot), a ‘bubble menu’ appears. Clicking on ‘explore’ retrieves and shows in a new sidebar definitions and auxiliary data, fetched in real time from the configured databases, each of which is expandable to show details that can be clicked to go to the information’s source (the arrows show which element has been expanded). The screenshot at the top of this page shows the floating comments pane, which appears if one chooses the comments option from the ‘bubble menu’.

A floating comments pane appears after choosing the comment option in the bubble menu. Click image to enlarge

Adding private notes

And because “the story doesn’t stop with the published article”, you can make private notes for yourself, annotate a document for others to see, or take part in an online discussion directly from the PDF you’re reading. If you are being asked to peer-review a paper for a journal, you might in some cases even want to suggest to the Editor or publisher that you use Utopia Documents for that, removing, as it does, the need for sending reviewer reports or annotated documents back to the publisher.

With Utopia Documents, publishers and libraries can offer enriched scientific articles just by encouraging the scientists and students they serve to use the free Utopia Documents PDF-reader, and so make more of the scientific literature at hand. Utopia Documents is truly free – registration is only needed if one uses the comments function (for reasons of maintaining the integrity of scientific discourse, Utopia Documents does not allow anonymous comments). Although registration is encouraged, it is not necessary to use any of the other features of Utopia Documents.

Flexible system

Utopia Documents is currently optimised for the life science-biomedical-biochemical scientific discipline spectrum but can be used in any domain. It does not itself provide any domain-specific functionality for processing or analysing data but relies on external services; these are accessed via plug-ins whose appearance in the software interface is mediated by a ‘semantic core’ (the core can in principle be customised to any subject area by incorporating the relevant discipline-specific ontologies). Reliance on external Web services is one of the strengths of the system because it allows great flexibility for customising the functionality of the software (obviating the need for the developers to second-guess all current and future potential user needs).

Some journals, such as the Biochemical Journal published by Portland Press and those published by the Royal Society of Chemistry, provide extra tags in their PDFs that enable Utopia Documents to extend its functionality even further. Embedded mark-ups enable Utopia Documents to provide the appropriate links to interactive tools for sequence alignment, for instance, and molecular visualisation, rendering pictures of protein structures into dynamic, rotatable, manipulable 3D formats. Publishers who wish to do the same or introduce similar features are encouraged to take up contact with us at

Last Changed: 10.11.2012