PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
Author(s)
Date
2002-06Source Title
Bioinformatics
Print ISSN
1367-4803
Electronic ISSN
1367-4811
Publisher
Oxford University Press
Volume
18
Issue
7
Pages
996 - 1003
Language
English
Type
ArticleItem Usage Stats
306
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201
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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.
Keywords
AutomationCell 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