BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology
Abstract
Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently requires input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities such as wikis for the description, discussion and annotation of the functions of genes and gene products [Wang, 2006, Hoehndorf et al., 2006, Giles, 2007]. However, an open approach like wikis frequently raises concerns regarding the quality of the information captured. The information represented in the wiki should adhere to particular quality criteria such as internal consistency (the wiki content does not contain contradictory information) and consistency with biological background knowledge (the wiki content should be semantically correct). To address some of these concerns, logic-based tools can be employed. We have developed the BOWiki, a wiki system that uses a core ontology together with an automated reasoner to maintain a consistent knowledge base. It is specifically targeted at small- to medium-sized communities. to collaboratively integrate information and annotate data. The BOWiki and supplementary material is available at http://www. bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki. Contact: bowiki-users@lists.informatik.uni-leipzig.de