Genepi: a blackboard framework for genome annotation

Background: Genome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be executed more than once and might be subjected to several revisions as the biological (new data) or methodological (new methods) knowledge evolves. In this context, although a lot of annotation platforms already exist, there is still a strong need for computer systems which take in charge, not only the primary annotation, but also the update and advance of the associated knowledge. In this paper, we propose to adopt a blackboard architecture for designing such a system Results: We have implemented a blackboard framework (called Genepi) for developing automatic annotation systems. The system is not bound to any specific annotation strategy. Instead, the user will specify a blackboard structure in a configuration file and the system will instantiate and run this particular a...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Stéphane Descorps-Declère, Danielle Ziébelin, François Rechenmann, Alain Viari
• Keywords: Annotation, Blackboard Architectures, BMCBI 2006, Genome Annotation