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Lesk: Introduction to Bioinformatics: 3e

Chapter 03

The transition to electronic publishing

Lesk, M. (2004). Understanding Digital Libraries, 2nd edn. Morgan Kaufmann Publishers, San Francisco. Introduction to the transition from traditional libraries to information provision by computer.

Berners-Lee, T. (With Mark Fischetti) (2000). Weaving the Web: The Original Design and Ultimate Destiny of the World Wide Web. Harper Business, New York.

Berners-Lee, T. and Hendler, J. (2001). Publishing on the semantic web. Nature, 410, 1023-1024. From the inventor of the Web. [DOI: 10.1038/35074206]

Gorder, P.F. (2006). Digital libraries come of age. Computing in Science and Engineering, 8(5), 6-10. [DOI: 10.1109/MCSE.2006.86]

Butler, D. and Campbell, P. (2001). Future e-access to the primary literature, Nature Web Debates, 5 April. http://www.nature.com/nature/debates/e-access/introduction.html Introduction to a continuing discussion, about the web, on the web.

Malakoff, D. (2003). Scientific publishing: opening the books on open access. Science, 302, 550-554. Description of the journals published by the Public Library of Science. [PubMed: 14576392] [DOI: 10.1126/science.302.5645.550]

Spedding, V. (2003). Great data, but will it last? Research Information, Spring, 16-20. Problems of preservation of digital information. This journal has many articles of interest to scientists whose research depends on the quality and computer accessibility of data.

Garson, L.R. (2004). Communicating original research in chemistry and related sciences. Accounts in Chemical Research. 37, 141-148. [DOI: 10.1021/ar0300017]

Winograd, S. and Zare, R.N. (1995). Wired' science or whither the printed pages. Science, 269, 615. The authors, among the most distinguished of contemporary scientists, raise questions that are still not answered after more than 10 years.

Discussions of developments in access and pricing in scientific journals

Van Orsdel, L.C. and Born, K. (2006). Journals in the time of Google. Library Journal, 131 (7), 39-44.

SQW Ltd (2004). In: Costs and Business Models in Scientific Research Publishing. Wellcome Trust, London.

King, D.W. and Tenopir, C. (2004). Scholarly journal and digital database pricing: threat or opportunity?. Available at: http://web.utk.edu/∼tenopir/pub/Chapters.html.

King, D.W. (2007). The cost of journal publishing: a literature review and commentary. Learned Publishing, 20, 85-106. [DOI: 10.1087/174148507X183551]

Dewatripont, M., Ginsburgh, V., Legros, P., Walckiers, A., Devroey, J.-P., Dujardin, M., Vadooren, F., Dubois, P., Foncel, J., Ivaldi, M. and Heusse, M.-D. (2006). Study on the Economic and Technical Evolution of the Scientific Publication Markets in Europe. European Commission, Directorate-General for Research, Brussels. A recent, and thorough exposition of the issues, and some recommendations.

Reviews of the achievements challenges and resources for applications of natural language processing in bioinformatics

Krallinger, M. and Valencia, A. (2005). Text-mining and information-retrieval services for molecular biology. Genome Biology, 6, 224. [PubMed: 15998455] [DOI: 10.1186/gb-2005-6-7-224]

Cohen, A.M. and Hersh, W.R. (2005). A survey of current work in biomedical text mining. Briefings in Bioinformatics, 6, 57-71. [PubMed: 15826357] [DOI: 10.1093/bib/6.1.57]

Shatkay, H. (2005). Hairpins in bookstacks: information retrieval from biomedical text. Briefings in Bioinformatics, 6, 222-238. [PubMed: 16212771] [DOI: 10.1093/bib/6.3.222]

Bosak, J. and Bray, T. (1999). XML and the second-generation web. Scientific American 280 (5), 89-93. An introduction to XML, including descriptions of the problems that motivated its development, and the solutions it provides.