Search extension transforms Wiki into a relational system A case for flavonoid metabolite database 英文参考文献.docVIP

BioData Mining BioMedCentral Research Open Access Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database Masanori Arita*1,2,3 and Kazuhiro Suwa1 Address: 1Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5 CB05, Kashiwa, Japan, 2Metabolome Informatics Unit, Plant Science Center, RIKEN, Japan and 3Institute for Advanced Biosciences, Keio University, Japan Email: Masanori Arita* - arita@k.u-tokyo.ac.jp; Kazuhiro Suwa - suwa@dotrump.jp * Corresponding author Published: 17 September 2008 Received: 23 May 2008 Accepted: 17 September 2008 BioData Mining 2008, 1:7 doi:10.1186/1756-0381-1-7 This article is available from: /content/1/1/7 ? 2008 Arita and Suwa; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word database often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. Results: To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format