Bilkent University
Department of Computer Engineering


An Ontology for Cellular Processes


Emek Demir
Ph.D Student
Computer Engineering
Bilkent University

Cellular processes form the hardware layer of living organisms. Malfunctions in cellular processes are responsible for most of the currently incurable diseases. Not surprisingly, knowledge about cellular processes are growing at an enormous rate. However, today's molecular biology suffers from lack of a formal representation system. Most of the knowledge is locked in literature, that are not accessible to computational analysis and modeling. Given the complexity of the system we are attacking, the need for a representation system and modeling tools are clear. In this work, we describe an ontology for modeling processes. Our ontology possesses several unique features, including ability to represent abstractions and multiple levels of detail, cellular compartments and molecular states. Furthermore it was designed to meet several user and system requirements, including ease of integration, querying, analysis and visualization. We consider different aspects for a good ontology and argue that they are conflicting most of the time. Tradeoffs must be made not only based on biological phenomena at hand but also requirements of the system it was designed for. Based on this ontology we also implemented a set of software tools, Patika project. Patika's primary use cases are integration, querying and visualization, and we have obtained satisfactory results proving the feasibility of our ontology.


DATE: October5, 2005, Wednesday@ 16:00