Bioinformatics Vol. 18 no. 7 2002
Pages 996-1003
© 2002 Oxford University Press
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
1 Department of Molecular Biology and Genetics
2 Computer Engineering Department
3 Center for Bioinformatics, Bilkent University, Ankara 06533, Turkey
Received on October 12, 2001
; revised on December 11, 2001
; accepted on February 1, 2002
Motivation: Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively.
Results: We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named Patika (Pathway Analysis Tool for Integration and Knowledge Acquisition). Patika is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface.
We expect that Patika will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development.
Availability: A prototype of Patika is available upon request from the authors.
Contact: patika{at}cs.bilkent.edu.tr
* To whom correspondence should be addressed.
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