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

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.

Figure 1

A) Correspondence between relation table in RDB and pages in MediaWiki;. One tuple corresponds to one page whose title is the primary key. Together, pages in the same namespace constitute the original relation table. In Wiki pages, attributes are separated by user-defined separator symbols. In this example, && is the separator. B) Basic schema of flavonoid database; A table for reference information connects tables for metabolite and plant species. The link is used for Metabolite-Species table in Wiki pages.

Figure 2

The molecule view of (+)-catechin;. Red stars indicate information written on the Wiki page. Other information and formatting are provided by the templates. Users need not be aware of the software code in the background. The page is accessible at . Its source code is shown by clicking the 'View Source' tab. 1. Page title: The 12-digit ID describing the structural category of (+)-catechin. 2. Class hierarchy: This information and links are automatically generated from the ID and class information in other Wiki pages. 3. Molecular structure: This picture is generated from the MOL-format file on the server associated with this page. 4. Molecular information: These values are automatically generated from the MOL-format file.