Infrastructure for the life sciences: design and implementation of the UniProt website

Article Article scientifique Article Infrastructure for the life sciences: design and implementation of the UniProt website eng 2009 author Jain Eric 639307 author Bairoch Amos Marc 0000-0003-2826-6444 21964 author Duvaud Séverine 640853 author Phan Isabelle 639323 author Redaschi Nicole 639334 author Suzek Baris E. author Martin Maria J. author McGarvey Peter author Gasteiger Elisabeth 101626 136 10.1186/1471-2105-10-136 19426475 1471-2105 http://www.biomedcentral.com/1471-2105/10/136 BACKGROUND: The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website http://www.uniprot.org was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the http://www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008. DESCRIPTION: The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. These tools include full text and field-based text search, similarity search, multiple sequence alignment, batch retrieval and database identifier mapping. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access.http://www.uniprot.org/ is open for both academic and commercial use. The site was built with open source tools and libraries. Feedback is very welcome and should be sent to help@uniprot.org. CONCLUSION: The new UniProt website makes accessing and understanding UniProt easier than ever. The two main lessons learned are that getting the basics right for such a data provider website has huge benefits, but is not trivial and easy to underestimate, and that there is no substitute for using empirical data throughout the development process to decide on what is and what is not working for your users. Databases, Protein Information Storage and Retrieval/methods Internet Proteins/chemistry Sequence Analysis, Protein User-Computer Interface Dewey 576 136 Département de biologie structurale et bioinformatique 21E false 57 Calipho 80 BMC bioinformatics 10 da53869a-6589-46d2-a940-b7ef8b8da8e1 Article (Published version) Public Article.pdf 3065629 application/pdf openAccess Faculté de médecine / Section de médecine fondamentale / Département de biologie structurale et bioinformatique

Title	Published in	Access level	OA Policy	Year	Views	Downloads

Infrastructure for the life sciences: design and implementation of the UniProt website	BMC bioinformatics			2009	1,041	2,673

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Jain, Eric