*Apologies for cross posting*
Bringing life science to life with semantic publishing - a new direction for
the Biochemical Journal
“Pdfs paralyse the proper and efficient use of scientific knowledge. By
burying information in static, unconnected journal articles and by placing
fragments of that knowledge in disparate, hard to access databases,
scientists waste 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.” says Professor Terri Attwood,
whose Manchester University team, with the help of funding from Portland
Press Limited, have developed new and powerful publishing software that will
help life scientists work more efficiently.
Launched by Portland Press Limited (www.portlandpress.com), this software,
called Utopia Documents, has been used to transform the latest edition of
their flagship journal, the Biochemical Journal, (www.biochemj.org) by
dynamically linking documents to research data, enabling 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 (www.biochemj.org) 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, glossaries and databases. Extra data such as
images and videos can be embedded into the text and there are links to
interactive tools to manipulate protein sequences and to see molecular
structures in 3-D.
The Utopia software accesses and adds in these external services via the
Web. This makes it easier to customize the software for other subject areas.
Initially, the developers have concentrated on providing access to protein
sequencing and structural analysis, but they plan to extend the scope to
other areas of biology, and to the medical and health sciences as the
necessary information sets and databases in these subjects are already in
place and accessible.
Future developments of the system include 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, reviewers and editorial staff.
Further information available from Kerry Cole
Kerry Cole
Head of Marketing and Sales
Portland Press Ltd
Commerce Way
Colchester
Essex CO2 8HP
United Kingdom
T: 01206 796351
F: 01206 798650
E: [log in to unmask]
W:www.portlandpress.com
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