Literature DB >> 18819940

Databases, data tombs and dust in the wind.

Jonathan D Wren, Alex Bateman.   

Abstract

UNLABELLED: As biomedical data accumulates, the need to store, share and organize it grows. Consequently, the number of Internet-accessible databases has been rapidly growing on an annual basis. Bioinformatics regularly publishes descriptions of biomedically relevant databases, Nucleic Acids Research has published an annual database issue since 1996 and now a new open-access journal, DATABASE: The Journal of Biological DATABASEs and Curation, will soon be launched by Oxford University Press in 2009 (http://www.oxfordjournals.org/our_journals/databa/). Since databases can be made publicly available on the Internet without publication, it is worth considering what factors prioritize publication of database descriptions in a peer-reviewed journal. In general, publication of a database description in a journal advertises it as a valuable resource for scientific research. Implicitly, it is assumed that this resource is publicly available (most likely for free) and will be maintained. However, therein lies the problem: DATABASE papers are simply not of the same nature as regular research articles. Over time, some databases simply become inaccessible, some are created but not maintained or updated, and some databases are never used (Galperin, 2006). Thus, for database creators, reviewers and journal editors, there are several additional considerations to judge, prior to publication, how potentially valuable these new databases may be.

Mesh:

Year:  2008        PMID: 18819940     DOI: 10.1093/bioinformatics/btn464

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  14 in total

1.  Human platelet microRNA-mRNA networks associated with age and gender revealed by integrated plateletomics.

Authors:  Lukas M Simon; Leonard C Edelstein; Srikanth Nagalla; Angela B Woodley; Edward S Chen; Xianguo Kong; Lin Ma; Paolo Fortina; Satya Kunapuli; Michael Holinstat; Steven E McKenzie; Jing-Fei Dong; Chad A Shaw; Paul F Bray
Journal:  Blood       Date:  2014-02-12       Impact factor: 22.113

Review 2.  Single-nucleotide polymorphism bioinformatics: a comprehensive review of resources.

Authors:  Andrew D Johnson
Journal:  Circ Cardiovasc Genet       Date:  2009-10

3.  bioNerDS: exploring bioinformatics' database and software use through literature mining.

Authors:  Geraint Duck; Goran Nenadic; Andy Brass; David L Robertson; Robert Stevens
Journal:  BMC Bioinformatics       Date:  2013-06-15       Impact factor: 3.169

4.  The annotation and the usage of scientific databases could be improved with public issue tracker software.

Authors:  Giovanni Marco Dall'Olio; Jaume Bertranpetit; Hafid Laayouni
Journal:  Database (Oxford)       Date:  2010-12-23       Impact factor: 3.451

5.  Data issues in the life sciences.

Authors:  Anne E Thessen; David J Patterson
Journal:  Zookeys       Date:  2011-11-28       Impact factor: 1.546

Review 6.  The need for novel informatics tools for integrating and planning research in molecular and cellular cognition.

Authors:  Alcino J Silva; Klaus-Robert Müller
Journal:  Learn Mem       Date:  2015-08-18       Impact factor: 2.460

Review 7.  Biological databases for human research.

Authors:  Dong Zou; Lina Ma; Jun Yu; Zhang Zhang
Journal:  Genomics Proteomics Bioinformatics       Date:  2015-02-21       Impact factor: 7.691

8.  CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria.

Authors:  Sefa Kiliç; Elliot R White; Dinara M Sagitova; Joseph P Cornish; Ivan Erill
Journal:  Nucleic Acids Res       Date:  2013-11-14       Impact factor: 16.971

9.  Tollip or not Tollip: what are the evolving questions behind it?

Authors:  Denis Prudencio Luiz; Célio Dias Santos Júnior; Ana Maria Bonetti; Malcom Antônio Manfredi Brandeburgo
Journal:  PLoS One       Date:  2014-05-14       Impact factor: 3.240

10.  A Survey of Bioinformatics Database and Software Usage through Mining the Literature.

Authors:  Geraint Duck; Goran Nenadic; Michele Filannino; Andy Brass; David L Robertson; Robert Stevens
Journal:  PLoS One       Date:  2016-06-22       Impact factor: 3.240

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