Literature mining: Speed reading

Lok, Corie

doi:10.1038/463416a

Cited by 16 publications

(11 citation statements)

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“…Here, we propose the development of semiautomated graphical and interactive tools to help neuroscientists and other biologists, including those working in molecular and cellular cognition, to track, map, and weight causal evidence in research papers. There is a great need for a concerted effort by biologists, computer scientists, and funding institutions to develop maps of causal information that would aid in integration of research findings and in experiment planning.Information in biology, including neuroscience, is growing at an unprecedented pace that demands new tools and new approaches (Lok 2010;Silva et al 2014). Because of the ever-growing number, complexity, and interconnectedness of research publications and biological concepts, it is simply no longer possible for individual biologists to be aware of even a fraction of the published findings potentially pertinent to their work.…”

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confidence: 99%

“…Information in biology, including neuroscience, is growing at an unprecedented pace that demands new tools and new approaches (Lok 2010;Silva et al 2014). Because of the ever-growing number, complexity, and interconnectedness of research publications and biological concepts, it is simply no longer possible for individual biologists to be aware of even a fraction of the published findings potentially pertinent to their work.…”

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confidence: 99%

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The need for novel informatics tools for integrating and planning research in molecular and cellular cognition

Silva

Müller

2015

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The sheer volume and complexity of publications in the biological sciences are straining traditional approaches to research planning. Nowhere is this problem more serious than in molecular and cellular cognition, since in this neuroscience field, researchers routinely use approaches and information from a variety of areas in neuroscience and other biology fields. Additionally, the multilevel integration process characteristic of this field involves the establishment of experimental connections between molecular, electrophysiological, behavioral, and even cognitive data. This multidisciplinary integration process requires strategies and approaches that originate in several different fields, which greatly increases the complexity and demands of this process. Although causal assertions, where phenomenon A is thought to contribute or relate to B, are at the center of this integration process and key to research in biology, there are currently no tools to help scientists keep track of the increasingly more complex network of causal connections they use when making research decisions. Here, we propose the development of semiautomated graphical and interactive tools to help neuroscientists and other biologists, including those working in molecular and cellular cognition, to track, map, and weight causal evidence in research papers. There is a great need for a concerted effort by biologists, computer scientists, and funding institutions to develop maps of causal information that would aid in integration of research findings and in experiment planning.Information in biology, including neuroscience, is growing at an unprecedented pace that demands new tools and new approaches (Lok 2010;Silva et al. 2014). Because of the ever-growing number, complexity, and interconnectedness of research publications and biological concepts, it is simply no longer possible for individual biologists to be aware of even a fraction of the published findings potentially pertinent to their work. The library of medicine, for example, now includes more than 25 million research papers reporting the results of at least 100 million experiments. Even a young field like Molecular and Cellular Cognition includes tens of thousands of research papers reporting millions of experiments. When the implications of what has already been published remain buried in the never-ending avalanche of published information, how can scientists reasonably optimize future research plans? Although there is a great deal of work on-going to tackle different components of this problem, from annotation of the literature, to curation of databases and automated reasoning, much remains to be done. Here, we address the need for graphical and interactive tools that track and map causal evidence in research papers (i.e., research maps). Although causal assertions are the very fabric of biology, there are currently no tools to help biologists keep track of the increasingly more complex network of causal connections derived from published findings. A causal connection is defined by ev...

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The need for novel informatics tools for integrating and planning research in molecular and cellular cognition

Silva

Müller

2015

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“…Many health care professionals are overwhelmed by the amount of literature published and find it very difficult to stay current in their fields of interest. 2 Clinical librarians can use Web 2.0 tools to provide easy access to selected information that is manageable and can be worked into a busy clinician's workflow.…”

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confidence: 99%

Collaborating and Delivering Literature Search Results to Clinical Teams Using Web 2.0 Tools

Damani

Fulton

2010

Medical Reference Services Quarterly

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“…2 However, translational neuroscience faces a strong disproportion between the immense preclinical research effort and the lack of successful clinical trials in SCI therapy: So far, no therapeutic approach has led to functional recovery in human patients (Filli and Schwab, 2012). As the vast amount of published information by far exceeds the capacity of individual scientists to read and understand the relevant knowledge (Lok, 2010), the selection of promising therapeutic interventions for clinical trials is notoriously based on incomplete information (Prinz et al, 2011;Steward et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Ontology-based Extraction of Structured Information from Publications on Preclinical Experiments for Spinal Cord Injury Treatments

Paaßen

Stöckel

Dickfelder

et al. 2014

Proceedings of the Third Workshop on Semantic Web and Information Extraction

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Preclinical research in the field of central nervous system trauma advances at a fast pace, currently yielding over 8,000 new publications per year, at an exponentially growing rate. This amount of published information by far exceeds the capacity of individual scientists to read and understand the relevant literature. So far, no clinical trial has led to therapeutic approaches which achieve functional recovery in human patients.In this paper, we describe a first prototype of an ontology-based information extraction system that automatically extracts relevant preclinical knowledge about spinal cord injury treatments from natural language text by recognizing participating entity classes and linking them to each other. The evaluation on an independent test corpus of manually annotated full text articles shows a macroaverage F 1 measure of 0.74 with precision 0.68 and recall 0.81 on the task of identifying entities participating in relations.

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Literature mining: Speed reading

Cited by 16 publications

References 0 publications

The need for novel informatics tools for integrating and planning research in molecular and cellular cognition

The need for novel informatics tools for integrating and planning research in molecular and cellular cognition

Collaborating and Delivering Literature Search Results to Clinical Teams Using Web 2.0 Tools

Ontology-based Extraction of Structured Information from Publications on Preclinical Experiments for Spinal Cord Injury Treatments

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