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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Related in: MedlinePlus

Comparison of a page from a ‘naked’ 2003 BJ article [59] (a) with a semantically enriched counterpart (b), annotated using more than 100 different ontologiesThe colour overlay denotes the number of semantic relationships for particular areas (green areas having the least and red the most), illustrating the extent of the opportunities for mark-up that exist on a single page, and hence the need to balance both appropriate mark-up tools and appropriate levels of manual intervention to make this information usefully accessible to readers: mark-up too much information, and the reader is overwhelmed; mark-up too little, and the reader is denied access to the full semantic richness of the article. For readers viewing this article using UD, click on the UD logo.
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Figure 12: Comparison of a page from a ‘naked’ 2003 BJ article [59] (a) with a semantically enriched counterpart (b), annotated using more than 100 different ontologiesThe colour overlay denotes the number of semantic relationships for particular areas (green areas having the least and red the most), illustrating the extent of the opportunities for mark-up that exist on a single page, and hence the need to balance both appropriate mark-up tools and appropriate levels of manual intervention to make this information usefully accessible to readers: mark-up too much information, and the reader is overwhelmed; mark-up too little, and the reader is denied access to the full semantic richness of the article. For readers viewing this article using UD, click on the UD logo.

Mentions: To gain the most from electronic articles, and especially from dormant document archives, semantic mark-up of content is clearly necessary. But retrospective addition of semantics to legacy data is complex, labour-intensive and costly. A balance must therefore be found between the degree of automation it is possible to introduce to the process, and the degree of cultural change it is reasonable to expect in a research community that has not hitherto considered the relationship between data and published articles, and has hence not been concerned about providing the semantic context necessary to unite them. In the long-run, it is to be hoped that the benefits of semantic mark-up, and the availability of the right tools, will together help to seed this much-needed cultural change: compare and contrast, for example, the pages shown in Figure 12.


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)

Comparison of a page from a ‘naked’ 2003 BJ article [59] (a) with a semantically enriched counterpart (b), annotated using more than 100 different ontologiesThe colour overlay denotes the number of semantic relationships for particular areas (green areas having the least and red the most), illustrating the extent of the opportunities for mark-up that exist on a single page, and hence the need to balance both appropriate mark-up tools and appropriate levels of manual intervention to make this information usefully accessible to readers: mark-up too much information, and the reader is overwhelmed; mark-up too little, and the reader is denied access to the full semantic richness of the article. For readers viewing this article using UD, click on the UD logo.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 12: Comparison of a page from a ‘naked’ 2003 BJ article [59] (a) with a semantically enriched counterpart (b), annotated using more than 100 different ontologiesThe colour overlay denotes the number of semantic relationships for particular areas (green areas having the least and red the most), illustrating the extent of the opportunities for mark-up that exist on a single page, and hence the need to balance both appropriate mark-up tools and appropriate levels of manual intervention to make this information usefully accessible to readers: mark-up too much information, and the reader is overwhelmed; mark-up too little, and the reader is denied access to the full semantic richness of the article. For readers viewing this article using UD, click on the UD logo.
Mentions: To gain the most from electronic articles, and especially from dormant document archives, semantic mark-up of content is clearly necessary. But retrospective addition of semantics to legacy data is complex, labour-intensive and costly. A balance must therefore be found between the degree of automation it is possible to introduce to the process, and the degree of cultural change it is reasonable to expect in a research community that has not hitherto considered the relationship between data and published articles, and has hence not been concerned about providing the semantic context necessary to unite them. In the long-run, it is to be hoped that the benefits of semantic mark-up, and the availability of the right tools, will together help to seed this much-needed cultural change: compare and contrast, for example, the pages shown in Figure 12.

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