Danielle Ziébelin

A New Approach in Object-Based Knowledge Representation: The AROM System

This paper presents AROM, a new object-based knowledge representation system. AROM is original in two ways. Firstly, in addition to classes, knowledge representation in AROM uses associations for describing links between classes instances. Secondly, AROM integrates an algebraic modeling language (AML) for describing operational knowledge (equations, constraints and queries) in a declarative way. AROM comes as a platform for knowledge representation and manipulation. It includes an interactive modeling environment, a Java API, an AML interpreter for processing queries and solving sets of equations, and a tool for consulting and editing knowledge bases on the Web.

Genepi: a blackboard framework for genome annotation

BackgroundGenome 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 systemResultsWe 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 annotation strategy. The characteristics of this framework are presented and discussed. Specific adaptations to the classical blackboard architecture have been required, such as the description of the activation patterns of the knowledge sources by using an extended set of Allens temporal relations. Although the system is robust enough to be used on real-size applications, it is of primary use to bioinformatics researchers who want to experiment with blackboard architectures.ConclusionIn the context of genome annotation, blackboards have several interesting features related to the way methodological and biological knowledge can be updated. They can readily handle the cooperative (several methods are implied) and opportunistic (the flow of execution depends on the state of our knowledge) aspects of the annotation process.