Advanced querying interface for biochemical network databases
Authors: 
Brendan Elliott, Stephen Mayes, Ali Cakmak, Gultekin Ozsoyoglu, Z. Meral OzsoyogluAuthors Info & Claims
Brendan Elliott, Stephen Mayes, Ali Cakmak, Gultekin Ozsoyoglu, Z. Meral OzsoyogluAuthors Info & ClaimsPages 1526 - 1533
Abstract
Querying biochemical networks in flexible ways over the web is important to facilitate ongoing biological research. In this paper, we present a querying interface for biological networks, more specifically, metabolic networks. The interface allows for the specification of a large class of containment, path, and neighborhood queries with ease from a web browser. The query specification process is user-friendly, employs hierarchically arranged relationships among biological entities, and uses autocomplete features. The interface is provided as part of PathCase, a system to store, query, visualize and analyze metabolic pathways at different levels of detail.
References
[1]
AQI. 2009. Available at http://nashua.case.edu/PathwaysKegg/Web/LinkForwarder.aspx?rid=AdvancedQueryInterface&rtype=br
[2]
PathCase. (2009.a). PathCase System available at http://nashua.case.edu/pathways.
[3]
PathCase. (2009.b). PathCase Built-in Queries available at http://nashua.case.edu/PathwaysKegg/Web/LinkForwarder.aspx?rid=SimpleQueries&rtype=br
[4]
Elliott, B, Kirac, M, Cakmak, A et al. (2008). PathCase Pathways Database System. Bioinformatics 24(21):2526--2533, November 2008.
[5]
Krummenacker, M, Paley, S, Mueller, L, Yan, T, Karp, PD. Querying and Computing with BioCyc Databases, Bioinformatics 21:3454--5 2005.
[6]
Structured Advanced Query Page (2009). Available at http://biocyc.org/query.html
[7]
Durand, P., Labarre, L., Meil, A. et al. GenoLink: a graph-based querying and brows-ing system for investigating the function of genes and proteins. BMC Bioinformatics. 2006; 7: 21.
[8]
Shannon P, Markiel A, Ozier O et al. Cytoscape: a software environment for inte-grated models of biomolecular interaction networks. Gen. Res. 2003 Nov; 13(11):2498--504
[9]
Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K. F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354--357.
[10]
Dogrusoz, U. et al. (2006) PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization, Bioinformatics, 22(3), 374--375.
[11]
Zloof, M. (1977). Query by Example. IBM Systems Journal p. 324--343 No. 4.
[12]
Carey, M. et al. (1996). PESTO: An Integrated Query/Browser for Object Databases. VLDB, p. 203--214.
[13]
Leser, U. (2005). A Query Language for Biological Networks. Bioinformatics Vol. 21 Suppl. 2 p. ii33--ii39.
[14]
Croes D, Couche F, Wodak SJ, van Helden J. (2005). Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue):W326--30.
[15]
MetaPathFinding Tool, (it was offline during the preparation of this manuscript), http://www.scmbb.ulb.ac.be/Users/didier/pathfinding/metabpathfinding.php
[16]
Beasley, JE, and Planes, FJ. (2007). Recovering metabolic pathways via optimization. Bioinformatics 23:92--98 2007.
[17]
Rahman, SA et al. (2005). Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics 2005, 21: 1189--1193.
[18]
Hatzimanikatis, V, Li, C, Ionita, JA, Henry, CS, Jankowski, MD, Broadbelt, LJ. (2005). Exploring the diversity of complex metabolic networks. Bioinformatics, vol. 21, num. 8, 2005, p. 1603--1609.
[19]
Küffner R, Zimmer R, Lengauer T. Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics. 2000 Sep; 16(9):825--36.
[20]
Michal, G (1999) Biochemical Pathways Spektrum Akademischer Verlag, Heidelberg.
[21]
Balkir, H. N. et al (2002), A Graphical Query Language: VISUAL and Its Query Processing, IEEE Transactions on Knowledge and Data Eng., 14(5): 955--978.
[22]
PathCase Architecture and Data Model, 2009. Available at http://nashua.case.edu/PathwaysWeb/DataModel.aspx
[23]
Mayes, S. (2007) Advanced Interface for Querying Graph Data. Master's thesis, Case Western Reserve University, EECS Dept., Cleveland, Ohio, USA.
Index Terms
- Advanced querying interface for biochemical network databases
Recommendations
A Visual Interface for Querying Heterogeneous Phylogenetic Databases
Despite the recent growth in the number of phylogenetic databases, access to these wealth of resources remain largely tool or form-based interface driven. It is our thesis that the flexibility afforded by declarative query languages may offer the ...
Querying through a user interface
In contrast to a traditional setting where users express queries against the database schema, we assert that the semantics of data can often be understood by viewing the data in the context of the user interface (UI) of the software tool used to enter ...
Comments
Information & Contributors
Information
Published In
March 2010
2712 pages
ISBN:9781605586397
DOI:10.1145/1774088
- Conference Chairs:
- Sung Y. Shin,
- Sascha Ossowski,
- Michael Schumacher,
- Program Chairs:
- Mathew J. Palakal,
- Chih-Cheng Hung
Copyright © 2010 ACM.
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]
Sponsors
Publisher
Association for Computing Machinery
New York, NY, United States
Publication History
Published: 22 March 2010
Check for updates
Qualifiers
- Research-article
Funding Sources
Conference
SAC'10
Sponsor:
Acceptance Rates
SAC '10 Paper Acceptance Rate 364 of 1,353 submissions, 27%;
Overall Acceptance Rate 1,650 of 6,669 submissions, 25%
Contributors
Other Metrics
Bibliometrics & Citations
Bibliometrics
Article Metrics
- 0Total Citations
- 116Total Downloads
- Downloads (Last 12 months)2
- Downloads (Last 6 weeks)0
Reflects downloads up to 03 Oct 2024
Other Metrics
Citations
View Options
Get Access
Login options
Check if you have access through your login credentials or your institution to get full access on this article.
Sign in