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Semantic Biochemical Journal delivers a lifeline to researchers
For researchers drowning in a sea of data, help is at hand. New and powerful publishing software that will help life scientists work more efficiently is launched today by Portland Press Limited, publisher for the Biochemical Society.
The latest edition of its flagship journal, the Biochemical Journal, uses the new software, called Utopia, to enable readers to interact with and manipulate the information in the journal’s scientific papers more effectively.
“Semantic publishing software is not new,” said Rhonda Oliver, the Managing Director of Portland Press Limited, “but the Utopia document management system used by Portland Press is different for several reasons. First, the editorial staff carry out all text mark-up – this removes the need for authors to have to do this and ensures rigour and consistency. Secondly, the Utopia system ‘overlays' the additional, semantic data on to existing text, rather than embedding it into the text initially where it cannot be subsequently altered. This means that Utopia’s features can be used with any document – even one that has laid on a laptop, unread, for many years”.
The new semantic Biochemical Journal will turn static images, tables and text into objects that can be linked, annotated, visualized and analysed interactively. Terms and phrases in the paper are linked to external websites, ontologies and databases, including Portland Press Limited’s own glossary of around 3000 defined terms in biochemistry and the life sciences. Extra data such as images and videos can be embedded into the text and there are links to interactive tools for sequence alignment and 3-D molecular visualization.
These external services are accessed via plug-ins that are filtered through a “semantic core”. Because they are web-based it makes it easier to customize the Utopia software for other subject areas. Initially, the developers at Manchester have concentrated on providing access to protein sequencing and structural analysis, but they plan to extend the scope to systems and chemical biology, and to the medical and health sciences as the necessary information sets and databases in these areas are already in place and accessible.
Future developments of the system will include a document management system, and a feature to let the reader add notes and comments to an article – perhaps just for their own use or to share with other readers or reviewers.
Professor Peter Shepherd, Professor of Cellular Signalling at the University of Auckland, New Zealand and the Chair of the Editorial Board of the Biochemical Journal, is unequivocal in his support of this new approach to scientific publishing: “By enabling researchers to link up their knowledge and to get more out of the literature, the semantic Biochemical Journal will prevent scientists wasting countless hours either repeating experiments that they didn’t know had been performed before, or worse, trying to verify facts that they didn’t know had been shown to be false”.
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