Utopia Documents and The Semantic Biochemical Journal experiment

Teresa K Attwood


Recent technological advances have led to the accumulation of data on an unprecedented scale. Adding to this information overload is the advent of desk-top sequencing, with machines capable of delivering terabytes of data per hour. The problem is, the rush to increase the amounts of  information we collect does not in itself bestow a miraculous increase in knowledge. For information to be usable, it needs to be stored and organised in ways that allow us to access it, to analyse it, to annotate it and to relate it to other information. Unfortunately, to date, we have failed to store and organise much of the rapidly accumulating information (whether in databases or documents) in rigorous, principled ways, so that finding what we want and understanding what’s already known become increasingly exhausting, frustrating and costly experiences. In this Letter, we briefly outline a new development with Portland Press Ltd., the so-called Semantic Biochemical Journal experiment [6]. Behind this ‘experiment’ is a new software tool, Utopia Documents, which builds on the Utopia suite described in previous EMBnet.news articles, and elsewhere [e.g., 7-9]. Here, we provide a sketch of these new developments, in order to provide a taster of what can be achieved through academic-journal-publisher collaboration.


semantic annotation; semantic mark-up; interactive PDF


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