PATIKA: Pathway Analysis Tool for Integration and Knowledge Acquisition

Emek Demir1, Ozgun Babur2, Ugur Dogrusoz, Attila Gursoy, Asli Ayaz, Gurcan Gulesir, Gurkan Nisanci, Rengul Cetin-Atalay, and Mehmet Ozturk, BCBI;, BCBI

PATIKA (Pathway Analysis Tool for Integration and Knowledge Acquisition) is an ongoing research and development project for collaborative construction and analysis of cellular pathways. We have defined an ontology for an intuitive, comprehensive, and uncomplicated representation of cellular events. The ontology enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies are provided. Lastly, our ontology supports efficient querying of large amounts of data. We have also developed a software tool based on this ontology providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA can be accessed freely for non-commercial use at