Research

Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database

Masanori Arita^1,2,3 and Kazuhiro Suwa¹

¹  Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5 CB05, Kashiwa, Japan

²  Metabolome Informatics Unit, Plant Science Center, RIKEN, Japan

³  Institute for Advanced Biosciences, Keio University, Japan

author email corresponding author email

BioData Mining 2008, 1:7doi:10.1186/1756-0381-1-7

Published:	17 September 2008

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. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available.

Conclusion

This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.