Limits...
Calling International Rescue: knowledge lost in literature and data landslide!

Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer SR, Thorne D - Biochem. J. (2009)

Bottom Line: With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist?We ask you, please, to read the instructions carefully.The time has come: you may turn over your papers...

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK. teresa.k.attwood@manchester.ac.uk

ABSTRACT
We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard - too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here - a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers...

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Lynch imagines being able to toggle between a published table of numerical values and their graphical representationFor readers viewing this article using UD, from this typical table of data from the European Journal of Pharmaceutical Sciences [62], explore the result of clicking on the UD logo. Reproduced from Corti, G., Maestrelli, F., Cirri, M., Zerrouk, N. and Mura, P. (2006) Development and evaluation of an in vitro method for prediction of human drug absorption II. Demonstration of the method suitability. European Journal of Pharmaceutical Science 27, 354–362, Copyright (2006) with permission from Elsevier.
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Figure 9: Lynch imagines being able to toggle between a published table of numerical values and their graphical representationFor readers viewing this article using UD, from this typical table of data from the European Journal of Pharmaceutical Sciences [62], explore the result of clicking on the UD logo. Reproduced from Corti, G., Maestrelli, F., Cirri, M., Zerrouk, N. and Mura, P. (2006) Development and evaluation of an in vitro method for prediction of human drug absorption II. Demonstration of the method suitability. European Journal of Pharmaceutical Science 27, 354–362, Copyright (2006) with permission from Elsevier.

Mentions: Although the initiatives outlined above may differ slightly in their specific aims, they are nevertheless reflections of the same overall aspiration – to make the data and knowledge sequestered in the literature more readily accessible and re-usable. The results, to date, are encouraging, and it is interesting to see the common themes that have emerged: most are HTML- or XML-based, providing hyperlinks to external websites and term definitions from relevant ontologies via colour-coded textual highlights. But these are only first steps towards much more far-reaching possibilities, and new ideas and new tools are clearly still needed. Lynch, for example, imagines a future in which there exists a wide range of specialized visualization tools for various forms of structured data [37]. It would be useful, he suggests, to be able to toggle between a rendered image and its underlying data-set, or between a published table of numerical values and their graphical representation, perhaps like the scenario shown in Figure 9?


Calling International Rescue: knowledge lost in literature and data landslide!

Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer SR, Thorne D - Biochem. J. (2009)

Lynch imagines being able to toggle between a published table of numerical values and their graphical representationFor readers viewing this article using UD, from this typical table of data from the European Journal of Pharmaceutical Sciences [62], explore the result of clicking on the UD logo. Reproduced from Corti, G., Maestrelli, F., Cirri, M., Zerrouk, N. and Mura, P. (2006) Development and evaluation of an in vitro method for prediction of human drug absorption II. Demonstration of the method suitability. European Journal of Pharmaceutical Science 27, 354–362, Copyright (2006) with permission from Elsevier.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2805925&req=5

Figure 9: Lynch imagines being able to toggle between a published table of numerical values and their graphical representationFor readers viewing this article using UD, from this typical table of data from the European Journal of Pharmaceutical Sciences [62], explore the result of clicking on the UD logo. Reproduced from Corti, G., Maestrelli, F., Cirri, M., Zerrouk, N. and Mura, P. (2006) Development and evaluation of an in vitro method for prediction of human drug absorption II. Demonstration of the method suitability. European Journal of Pharmaceutical Science 27, 354–362, Copyright (2006) with permission from Elsevier.
Mentions: Although the initiatives outlined above may differ slightly in their specific aims, they are nevertheless reflections of the same overall aspiration – to make the data and knowledge sequestered in the literature more readily accessible and re-usable. The results, to date, are encouraging, and it is interesting to see the common themes that have emerged: most are HTML- or XML-based, providing hyperlinks to external websites and term definitions from relevant ontologies via colour-coded textual highlights. But these are only first steps towards much more far-reaching possibilities, and new ideas and new tools are clearly still needed. Lynch, for example, imagines a future in which there exists a wide range of specialized visualization tools for various forms of structured data [37]. It would be useful, he suggests, to be able to toggle between a rendered image and its underlying data-set, or between a published table of numerical values and their graphical representation, perhaps like the scenario shown in Figure 9?

Bottom Line: With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist?We ask you, please, to read the instructions carefully.The time has come: you may turn over your papers...

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK. teresa.k.attwood@manchester.ac.uk

ABSTRACT
We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard - too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here - a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers...

Show MeSH
Related in: MedlinePlus