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Bioinformatics 20(3) © Oxford University Press 2004; all rights reserved.

An ontology for collaborative construction and analysis of cellular pathways

E. Demir 1,2, O. Babur 1,2, U. Dogrusoz 1,2,*, A. Gursoy 2, A. Ayaz 1,2, G. Gulesir 1,2, G. Nisanci 1,2 and R. Cetin-Atalay 1,3

1 Center for Bioinformatics, 2 Computer Engineering Department and 3 Department of Molecular Biology and Genetics, Bilkent University, Ankara 06533, Turkey

Received on March 25, 2003 ; revised on July 9, 2003 ; accepted on August 5, 2003

Motivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated.

Results: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here 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 is provided. Lastly, our ontology supports efficient querying of large amounts of data.

We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology.

Availability: PATIKA version 1.0 beta is available upon request at http://www.patika.org

Contact: patika{at}cs.bilkent.edu.tr

* To whom correspondence should be addressed.


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