Talking Biology in Logic, and Back

While computation of biological information takes center stage in today's research, knowledge-based query processing in biological databases has not gained much attention. The complex relationship among biological entities, and the numerous possibilities make it extremely difficult for a user to query data repositories in traditional ways since the information users seek are often not stored directly as extents. Thus, to meaningfully query such repositories, users often write complex applications to compute the needed response based on universal knowledge, or user specific hypothesis. In this paper, we propose a new data model based on object-oriented deductive databases and ontological concepts to allow knowledge-based querying. We propose a new query language called Con Log (for Concept Logic) in the direction of the acclaimed F-Logic and show that Con Log is able to express biological information and support queries in intuitive and user specific ways.