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...

Show MeSH

Related in: MedlinePlus

Illustration of Reflect mark-up of a Biochemical Journal articleThe text, from [59], shows tagged protein (blue) and chemical (gold) entities, and those for which both protein and chemical names are available (purple); clicking on a tagged entity invokes a pop-up summary, including links to features such as the structure of the protein (or chemical), its domain composition, its sequence, etc. The system is tuned for speed over accuracy, so users need to be aware of likely errors. (http://reflect.ws/).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2805925&req=5

Figure 8: Illustration of Reflect mark-up of a Biochemical Journal articleThe text, from [59], shows tagged protein (blue) and chemical (gold) entities, and those for which both protein and chemical names are available (purple); clicking on a tagged entity invokes a pop-up summary, including links to features such as the structure of the protein (or chemical), its domain composition, its sequence, etc. The system is tuned for speed over accuracy, so users need to be aware of likely errors. (http://reflect.ws/).

Mentions: The winners of the contest developed a tool (Reflect) that addresses the routine need of life scientists to be able both to jump from gene or protein names to their molecular sequences, and to understand more about particular genes, proteins or small molecules encountered in the literature [44]. With a single mouse click, Reflect tags such entities when they occur in webpages; it does this by drawing on a large, consolidated dictionary (containing 4.3 million small molecules and >1.5 million proteins from 373 organisms) that links names and synonyms to source databases. When clicked on, the tagged items invoke pop-ups (see Figure 8) displaying brief summaries of key features (domain structures, small-molecule structures, interaction partners, etc.), and allow navigation to core biological databases like UniProtKB.


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)

Illustration of Reflect mark-up of a Biochemical Journal articleThe text, from [59], shows tagged protein (blue) and chemical (gold) entities, and those for which both protein and chemical names are available (purple); clicking on a tagged entity invokes a pop-up summary, including links to features such as the structure of the protein (or chemical), its domain composition, its sequence, etc. The system is tuned for speed over accuracy, so users need to be aware of likely errors. (http://reflect.ws/).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Illustration of Reflect mark-up of a Biochemical Journal articleThe text, from [59], shows tagged protein (blue) and chemical (gold) entities, and those for which both protein and chemical names are available (purple); clicking on a tagged entity invokes a pop-up summary, including links to features such as the structure of the protein (or chemical), its domain composition, its sequence, etc. The system is tuned for speed over accuracy, so users need to be aware of likely errors. (http://reflect.ws/).
Mentions: The winners of the contest developed a tool (Reflect) that addresses the routine need of life scientists to be able both to jump from gene or protein names to their molecular sequences, and to understand more about particular genes, proteins or small molecules encountered in the literature [44]. With a single mouse click, Reflect tags such entities when they occur in webpages; it does this by drawing on a large, consolidated dictionary (containing 4.3 million small molecules and >1.5 million proteins from 373 organisms) that links names and synonyms to source databases. When clicked on, the tagged items invoke pop-ups (see Figure 8) displaying brief summaries of key features (domain structures, small-molecule structures, interaction partners, etc.), and allow navigation to core biological databases like UniProtKB.

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