An ontology for collaborative construction and analysis of cellular pathways
Author(s)
Date
2004-02-12Source Title
Bioinformatics
Print ISSN
1367-4803
Electronic ISSN
1367-4811
Publisher
Oxford University Press
Volume
20
Issue
3
Pages
349 - 356
Language
English
Type
ArticleItem Usage Stats
263
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views
202
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downloads
Abstract
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. © Oxford University Press 2004; All rights reserved.
Keywords
Cell activityComputer program
Controlled study
Factual
Gene function
Gene identification
Genome analysis
Mathematical computing
Molecular interaction
Molecular mechanics
Priority journal
Validation process
Biopolymers
Cell Physiology
Database management systems
Databases
Information storage and retrieval
Models
Signal transduction
Software
Systems Iitegration
User-computer interface
Biological