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Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web

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      Abstract

      Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

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      Most cited references 177

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      An index to quantify an individual's scientific research output.

      I propose the index h, defined as the number of papers with citation number > or =h, as a useful index to characterize the scientific output of a researcher.
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        UniProt: the Universal Protein knowledgebase.

        To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.
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          The increasing dominance of teams in production of knowledge.

          We have used 19.9 million papers over 5 decades and 2.1 million patents to demonstrate that teams increasingly dominate solo authors in the production of knowledge. Research is increasingly done in teams across nearly all fields. Teams typically produce more frequently cited research than individuals do, and this advantage has been increasing over time. Teams now also produce the exceptionally high-impact research, even where that distinction was once the domain of solo authors. These results are detailed for sciences and engineering, social sciences, arts and humanities, and patents, suggesting that the process of knowledge creation has fundamentally changed.
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            Author and article information

            Affiliations
            [1 ]School of Chemistry, The University of Manchester, Manchester, United Kingdom
            [2 ]The Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, United Kingdom
            [3 ]School of Computer Science, The University of Manchester, Manchester, United Kingdom
            National Center for Biotechnology Information (NCBI), United States of America
            Author notes
            Contributors
            Role: Editor
            Journal
            PLoS Comput Biol
            plos
            ploscomp
            PLoS Computational Biology
            Public Library of Science (San Francisco, USA )
            1553-734X
            1553-7358
            October 2008
            October 2008
            31 October 2008
            : 4
            : 10
            2568856
            07-PLCB-RV-0748R3
            10.1371/journal.pcbi.1000204
            18974831
            (Editor)
            Hull et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
            Counts
            Pages: 14
            Categories
            Review
            Computer Science/Information Technology
            Computational Biology/Literature Analysis

            Quantitative & Systems biology

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