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BMC Bioinformatics. 2009 Sep 16;10:291. doi: 10.1186/1471-2105-10-291.

Automated seeding of specialised wiki knowledgebases with BioKb.

Author information

1
Centres for Cardiovascular Science and Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ, UK. jmanning@staffmail.ed.ac.uk

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 as a plugin for the TWiki engine.

PMID:
19758431
PMCID:
PMC2753848
DOI:
10.1186/1471-2105-10-291
[Indexed for MEDLINE]
Free PMC Article

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