PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways

Date
2002-06
Advisor
Instructor
Source Title
Bioinformatics
Print ISSN
1367-4803
Electronic ISSN
1367-4811
Publisher
Oxford University Press
Volume
18
Issue
7
Pages
996 - 1003
Language
English
Type
Article
Journal Title
Journal ISSN
Volume Title
Abstract

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.

Course
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Book Title
Keywords
Automation, Cell function, Computer graphics, Computer interface, Computer program, Controlled study, Data analysis, DNA microarray, Factual database, Gene function, Gene identification, Gene sequence, Genome, Information processing, Information retrieval, Molecular Biology, Priority journal, Proteomics, Cell Physiology, Database Management Systems, Databases, Information storage and retrieval, Internet, Software design, User-computer interface
Citation
Published Version (Please cite this version)