Article

Pathways database system: an integrated set of tools for biological pathways

Authors:

L. Krishnamurthy,

W. XuAuthors Info & Claims

SAC '03: Proceedings of the 2003 ACM symposium on Applied computing

Pages 96 - 102

https://doi.org/10.1145/952532.952555

Published: 09 March 2003 Publication History

Abstract

During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. In this paper we present an integrated system, called Pathways Database System, with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: a) genomic information integrated with other biological data and presented from a pathway, rather than from the DNA sequence, perspective; b) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; c) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels, and to pose predetermined queries; and d) an implementation that allows for web(XML)-based dissemination of query outputs (i.e., pathways data) to researchers in the community, giving them control on the use of pathways data.

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Digital Library

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Cited By

Hu FMa LZhan XZhou YLiu CZhao HZhang Z(2021)The aging effect in evolving scientific citation networksScientometrics10.1007/s11192-021-03929-8Online publication date: 12-Mar-2021
https://doi.org/10.1007/s11192-021-03929-8
Christodoulou EDalamagas TSellis T(2006)NaviMozProceedings of the 2006 international conference on Current Trends in Database Technology10.1007/11896548_60(801-813)Online publication date: 26-Mar-2006
https://dl.acm.org/doi/10.1007/11896548_60
Yu WOzsoyoglu ZOzsoyoglu G(2003)XML Restructuring and Integration for Tabular DataDatabase and Expert Systems Applications10.1007/978-3-540-45227-0_24(233-243)Online publication date: 2003
https://doi.org/10.1007/978-3-540-45227-0_24

Pathways database system: an integrated set of tools for biological pathways
1. Applied computing
  1. Life and medical sciences

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Published In

cover image ACM Conferences

SAC '03: Proceedings of the 2003 ACM symposium on Applied computing

March 2003

1268 pages

ISBN:1581136242

DOI:10.1145/952532

Conference Chair:
Gary B. Lamont
Air Force Institute of Technology
,
Program Chairs:
Hisham Haddad
Kennesaw State University
,
George A. Papadopoulos
University of Cyprus, Cyprus
,
Publications Chair:
Brajendra Panda
University of Arkansas

Copyright © 2003 ACM.

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Published: 09 March 2003

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Cited By

Hu FMa LZhan XZhou YLiu CZhao HZhang Z(2021)The aging effect in evolving scientific citation networksScientometrics10.1007/s11192-021-03929-8Online publication date: 12-Mar-2021
https://doi.org/10.1007/s11192-021-03929-8
Christodoulou EDalamagas TSellis T(2006)NaviMozProceedings of the 2006 international conference on Current Trends in Database Technology10.1007/11896548_60(801-813)Online publication date: 26-Mar-2006
https://dl.acm.org/doi/10.1007/11896548_60
Yu WOzsoyoglu ZOzsoyoglu G(2003)XML Restructuring and Integration for Tabular DataDatabase and Expert Systems Applications10.1007/978-3-540-45227-0_24(233-243)Online publication date: 2003
https://doi.org/10.1007/978-3-540-45227-0_24

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