Software

Automated seeding of specialised wiki knowledgebases with BioKb

Jonathan R Manning , Ann Hedley , John J Mullins and Donald R Dunbar

Centres for Cardiovascular Science and Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ, UK

author email corresponding author email

BMC Bioinformatics 2009, 10:291doi:10.1186/1471-2105-10-291

Published:	16 September 2009

Abstract

Background

Wiki technology has become a ubiquitous mechanism for dissemination of information, and places strong emphasis on collaboration. We aimed to leverage wiki technology to allow small groups of researchers to collaborate around a specific domain, for example a biological pathway. Automatically gathered seed data could be modified by the group and enriched with domain specific information.

Results

We describe a software system, BioKb, implemented as a plugin for the TWiki engine, and designed to facilitate construction of a field-specific wiki containing collaborative and automatically generated content. Features of this system include: query of publicly available resources such as KEGG, iHOP and MeSH, to generate 'seed' content for topics; simple definition of structure for topics of different types via an administration page; and interactive incorporation of relevant PubMed references. An exemplar is shown for the use of this system, in the creation of the RAASWiki knowledgebase on the renin-angiotensin-aldosterone system (RAAS). RAASWiki has been seeded with data by use of BioKb, and will be the subject of ongoing development into an extensive knowledgebase on the RAAS.

Conclusion

The BioKb system is available from http://www.bioinf.mvm.ed.ac.uk/twiki/bin/view/TWiki/BioKbPlugin webcite as a plugin for the TWiki engine.