http://precedings.nature.com/tags/scientific%20method Recently posted documents tagged with 'scientific method' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3867.1 The exponentially increasing number of published papers (1.4 million per year by one estimate) makes it more and more difficult for us to manage the flood of scientific information. Each of us has acquired some protocol to find and organize journal articles and other references over the course of our careers. Most of those protocols are likely to have been formed by old routines or idleness rather than a structured approach to save time and frustration over the long run. Furthermore, with the Web 2.0 revolution, new ways of handling information are emerging (O’Reilly 2005). For example, traditional standalone tools for reference management like EndNote are being supplemented by centralized resources like RefWorks and social bookmarking sites as described subsequently. This fusion of personal and public information offers the promise of efficiency through better organization, which in turn leads to better science.How can seasoned scientists do better using these tools and those newer to the field start off in the right way? To start to answer that question, I present ten simple rules to master the search and organization of new literature. This is not meant to be comprehensive. It represents the experiences of a few and I welcome your thoughts, through comments to this article, on what you do to keep your references organized. http://dx.doi.org/10.1038/npre.2009.3867.1 Fri, 16 Oct 2009 08:50:12 UTC Ten Simple Rules for Searching and Organizing the Scientific Literature doi:10.1038/npre.2009.3867.1 2009-10-16 Denis C. Bauer Nature Precedings 2009-10-16T08:50:12Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2027/version/2 Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology develop¬ment work being undertaken in support of scientific research. Ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But the ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, ontologies such as the GO are in different respects comparable to scientific theories, to scientific databases, and to scientific journal publications. Such a view implies a new conception of what is involved in the author¬ing, maintenance and application of ontologies in scientific contexts, and therewith also a new approach to the evaluation of ontologies and to the training of ontologists. http://precedings.nature.com/documents/2027/version/2 Wed, 16 Jul 2008 15:49:38 UTC Ontology (Science) hdl:10101/npre.2008.2027.2 2008-07-16 Barry Smith Nature Precedings 2008-07-16T15:49:38Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2027.1 Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But these ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, we shall argue, ontologies such as the GO are comparable to scientific theories, to scientific databases, or to scientific journal publications. Such a view implies a radically new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a radically new approach to the evaluation of ontologies and to the training of ontologists. http://dx.doi.org/10.1038/npre.2008.2027.1 Tue, 01 Jul 2008 16:43:36 UTC Ontology (Science) doi:10.1038/npre.2008.2027.1 2008-07-01 Barry Smith Nature Precedings 2008-07-01T16:43:36Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/