Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 26 (17), 2210-1

Biological Knowledge Bases Using Wikis: Combining the Flexibility of Wikis With the Structure of Databases

Affiliations

Biological Knowledge Bases Using Wikis: Combining the Flexibility of Wikis With the Structure of Databases

Sylvain Brohée et al. Bioinformatics.

Abstract

Summary: In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis.

Availability: The source code and its documentation are freely available on the MediaWiki website: http://www.mediawiki.org/wiki/Extension:WikiOpener.

Similar articles

See all similar articles

Cited by 2 PubMed Central articles

Publication types

LinkOut - more resources

Feedback