Utopia Documents brings a fresh new perspective to reading scientific literature

They say that knowledge is power…. but what about when it’s inaccessible, locked away in journals and databases? Research carried out at The University of Manchester has led to the creation of Utopia Documents, a PDF reader that unlocks this information, highlighting and visualising relevant data from multiple sources.

Utopia Documents is a PDF reader that links biomedical data-sets with scientific literature, allowing researchers to better analyse and interpret their data. This software has been adopted by international publishing houses, allowing them to explore new business models, and by pharmaceutical companies, providing new opportunities to explore more efficient, cost-effective methods for exploiting and sharing in-house data and knowledge.

Led by Professor Teresa Attwood and Dr Steve Pettifer at The University of Manchester, the team from the School of Computer Science began by developing easy-to-use software tools to facilitate protein sequences analysis. Specifically, they demonstrated the feasibility of using Web services for semantic integration of disparate bioinformatics tools and databases by creating the Utopia sequence analysis suite. Their subsequent innovation was to use these semantic technologies to allow for two-way links between research data and scientific literature.  

A publishing first

In 2007, Utopia came to the attention of the managing director of Portland Press Limited, who needed to add value to their static online content. With support from Portland Press, the team demonstrated that Utopia’s interactive tools could be integrated directly with PDF articles. Utopia Documents was born.

This collaborative project resulted in the launch of the semantic Biochemical Journal in 2009, a digital, semantically enriched version of the leading bioscience journal. The Head of Portland Press’ Editorial Department says that Utopia Documents ‘enables our readers to have a richer and more interactive experience when engaging with our flagship publication.’

“Utopia Documents provides a key missing link between the content of published papers and many distinct scientific databases, a first for scholarly publishing.” Chief Executive of the Association of Learned and Professional Society Publishers

Offering a way of enriching their vast, inert PDF back-catalogues and driving users towards their online content, Utopia Documents has been picked up, and further developed, by other publishers. For example, the Royal Society of Chemistry integrated ChemSpider – a free chemical structure database – with Utopia Documents, rolling this new functionality out across their entire publishing platform.

Drug development

Top pharmaceutical companies have noted that a significant number – possibly as many as 25% - of late-stage failures could be eliminated years earlier by making all internal information in documents more widely available. Utopia Documents enables pharmaceutical companies to more easily recover and exploit in-house knowledge that is otherwise lost during the drug-discovery process.

Utopia Documents “is potentially saving researchers, in academic as well as the (pharmaceutical) industry, considerable time and effort to find the right reagents to replicate or set up experiments.” CEO of AQnowledge

AstraZeneca’s Informatics Director explains, “keeping track of biomedical research… is of paramount importance in our work of developing new medicines. Combined with R&D pressure it can be difficult for our research staff to keep on top of these articles. Utopia fills an important gap for AZ scientists and allows them to more effectively work with scientific PDF articles through a variety of different ways.” He continues, “Foremost is the ability to turn a static article into an interactive experience that links not only external data but also internal AZ data to enhance the PDF which enables our researchers to more rapidly analyse an article, exposes related links/data that may have been missed and also exposes our investment in key internal resources more widely.”

Collaboration with Bio-Prodict, a Dutch computational biotech company, has already seen the release of bespoke, pharmaceutically-relevant database-plugins for Utopia Documents.

Spin out

In 2012 the Utopia intellectual property was transferred into a spin out company, Lost Island Labs, to manage the interface between Utopia and its industrial partners, to create a more sustainable environment for its development, and to share revenues with The University of Manchester. Visit the Utopia Documents website.

Background

The original aim of the research was to develop easy-to-use software tools to facilitate protein sequence analysis. From this work, a series of innovations followed. 

The key steps were:

  1. From 2002, the researchers showed how semantic approaches could be used to integrate conventional bioinformatics tools. The first prototype, combing the functionality of a multiple protein sequence alignment editor with a 3D molecular viewer, was realised in the public release of the Utopia sequence analysis suite.
  2. The research team went on to demonstrate the feasibility of using Web services for semantic integration of disparate tools and data-sets within the Utopia framework.
  3. In 2007, Utopia came to the attention of the managing director of Portland Press Limited, who needed to add value to their static online content. With support from Portland Press, the researchers demonstrated the feasibility of integrating Utopia’s interactive tools directly with PDF articles, thereby creating Utopia Documents.
  4. The researchers went on to demonstrate the feasibility of deploying the Utopia Suite behind security –controlled company firewalls.
  5. A subsequent collaboration with BioProdict, a Dutch computational biotech company, saw the release of bespoke, pharmaceutically-relevant database-plugins for Utopia Documents.

The work remains highly productive, with numerous on-going collaborations with the publishing and pharmaceutical industries. 

Lead Academics

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