Bilgisayar destekli hücresel yolak modellemesi

Cellular processes form the hardware layer of living organisms. Malfunctions incellular processes are responsible for most of the currently incurable diseases. Notsurprisingly, knowledge about cellular processes are growing at an enormous rate.However, today?s molecular biology suffers from lack of a formal representationsystem for cellular processes. Most of the knowledge is locked in literature, thatare not accessible to computational analysis and modeling. Given the complexityof the system we are attacking, the need for a representation system and modelingtools for cellular processes are clear.In this dissertation, we describe an ontology for modeling processes. Ourontology possesses several unique features, including ability to represent abstrac-tions and multiple levels of detail, cellular compartments and molecular states.Furthermore, it was designed to meet several user and system requirements, in-cluding ease of integration, querying, analysis and visualization.Based on this ontology we also implemented a set of software tools withinthe Patika project. Primary use cases of Patika are integration, querying andvisualization, and we have obtained satisfactory results proving the feasibility ofour ontology.Compared with existing alternative methods of representing and querying in-formation about cellular processes, Patika provides several advantages, includinga regular representation system, powerful querying options, an advanced visual-ization. Moreover Patika models can be analyzed by computational methodssuch as flux analysis or pathway activity inference. Although it has a more steeplearning curve compared to existing ad hoc representation systems, we believethat tools like Patika will be essential for molecular biology research in thefuture.ivvKeywords: bioinformatics, ontology, pathway.