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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Bourne imagines reading a description of a molecule's active site, being instantly able to access its atomic co-ordinates, and thence to explore the interactions described in the paperIn this 2009 BJ paper, Vandermarliere et al. [64] describe the catalytic site of Bacillus subtilis arabinoxylan arabinofuranohydrolase. The catalytic domain is shown in blue and the carbohydrate-binding module in green. For readers viewing this article using UD, explore further by clicking on the UD logo.
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Figure 10: Bourne imagines reading a description of a molecule's active site, being instantly able to access its atomic co-ordinates, and thence to explore the interactions described in the paperIn this 2009 BJ paper, Vandermarliere et al. [64] describe the catalytic site of Bacillus subtilis arabinoxylan arabinofuranohydrolase. The catalytic domain is shown in blue and the carbohydrate-binding module in green. For readers viewing this article using UD, explore further by clicking on the UD logo.

Mentions: In a similar state of reverie, Bourne has a vision in which journals provide software for visualizing and interpreting their published content, obviating the need for specialized knowledge in handling esoteric tools; he envisages such software ultimately allowing various forms of basic analysis (simple statistical tests, principal-component analysis, and so on), making new levels of comprehension possible [36,63]. More specifically, he asks us to imagine reading a description of a molecule's active site in a paper, being instantly able to access its atomic co-ordinates, and thence to explore the interactions described in the paper, perhaps something like the scenario illustrated in Figure 10?


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)

Bourne imagines reading a description of a molecule's active site, being instantly able to access its atomic co-ordinates, and thence to explore the interactions described in the paperIn this 2009 BJ paper, Vandermarliere et al. [64] describe the catalytic site of Bacillus subtilis arabinoxylan arabinofuranohydrolase. The catalytic domain is shown in blue and the carbohydrate-binding module in green. For readers viewing this article using UD, explore further by clicking on the UD logo.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 10: Bourne imagines reading a description of a molecule's active site, being instantly able to access its atomic co-ordinates, and thence to explore the interactions described in the paperIn this 2009 BJ paper, Vandermarliere et al. [64] describe the catalytic site of Bacillus subtilis arabinoxylan arabinofuranohydrolase. The catalytic domain is shown in blue and the carbohydrate-binding module in green. For readers viewing this article using UD, explore further by clicking on the UD logo.
Mentions: In a similar state of reverie, Bourne has a vision in which journals provide software for visualizing and interpreting their published content, obviating the need for specialized knowledge in handling esoteric tools; he envisages such software ultimately allowing various forms of basic analysis (simple statistical tests, principal-component analysis, and so on), making new levels of comprehension possible [36,63]. More specifically, he asks us to imagine reading a description of a molecule's active site in a paper, being instantly able to access its atomic co-ordinates, and thence to explore the interactions described in the paper, perhaps something like the scenario illustrated in Figure 10?

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