Nothing Special   »   [go: up one dir, main page]

skip to main content
article

bcnQL: A query language for biochemical networks

Published: 01 October 2010 Publication History

Abstract

This paper proposes a graph data model that can represent information present in Biochemical Networks. The study presented in this paper also proposes a query language, called bcnQL, which empowers users to query entities, interactions, processes and pathways with arbitrary conditions. We then discuss the query-processing techniques, more specifically, the translation of bcnQL queries into G-algebra and a set of algebraic operators on graph objects. Some query examples are presented to demonstrate the applicability of the language for this specific domain. Finally, we provide details of a prototype implementation for the query language.

References

[1]
Amann, B. and Scholl, M. (1993) 'Gram: a graph data model and query languages', Proceedings of the ACM Conference on Hypertext, ACM Press, Milan, Italy, pp.201-211.
[2]
Bader, G.D., Donaldson, I., Wolting, C., Ouellette, B.F., Pawson, T. and Hogue, C.W. (2001) 'Bind: the bio-molecular interaction network database', Nucleic Acids Research, Vol. 29, No. 1, pp.242-245.
[3]
Bairoch, A. (2000) 'The ENZYME database in 2000', Nucleic Acids Res., Vol. 28, No. 1, pp.304-305.
[4]
Guting, R.H. (1994) 'GraphDB: modeling and querying graphs in databases', Proceedings of the 20th International Conference on Very Large Databases (VLDB), Morgan-Kaufman, pp.297-308.
[5]
He, H. and Singh, A.K. (2007) GraphQL: Query Language and Access Methods for Graph Databases, Technical Report, Department of Computer Science at University of California, Santa Barbara.
[6]
Kanehisa, M. and Goto, S. (2000) 'KEGG: Kyoto encyclopedia of genes and genomes', Nucleic Acids Res., Vol. 28, No. 1, pp.27-30.
[7]
Karp, P.D. (2000) 'An ontology for biological function based on molecular interactions', Bioinformatics, Vol. 16, No. 3, pp.269-285.
[8]
Krishnamurthy, L., Nadeau, J., Ozsoyoglu, G., Ozsoyoglu, M., Schaeffer, G., Tasan, M. and Xu, W. (2003) 'Pathways database system: an integrated system for biological pathways', Bioinformatics, Vol. 19, No. 8, pp.930-937.
[9]
Leser, U. (2005) 'A query language for biological networks', Bioinformatics, Vol. 21, Suppl. 2, pp.ii33-ii39.
[10]
Sheng, L., Ozsoyoglu, Z.M. and Ozsoyoglu, G. (1999) 'A graph query language and its query processing', Proceedings of the 15th International Conference on Data Engineering, IEEE Press, New York, NY, pp.572-581.
[11]
Takai-Igarashi, T., Nadaoka, Y. and Kaminuma, T. (1998) 'A database for cell signalling networks', J. Comput. Biol., Vol. 5, No. 4, pp.747-754.
[12]
van Helden, J., Naim, A., Mancuso, R., Eldridge, M., Wernisch, L., Gilbert, D. and Wodak, S.J. (2000) 'Representing and analysing molecular and cellular function in the computer', Biol. Chem., Vol. 381, Nos. 9-10, pp.921-935.
[13]
Venter, J.C., Adams, M.D. et al. (2001) 'The sequence of the human genome', Science, Vol. 291, No. 5507, pp.1304-1351.
[14]
Yang, H. and Sunderraman, R. (2008) bcnQL: A Query Language for Querying Graph Data, Manuscript, Department of Computer Science, Georgia State University.

Recommendations

Comments

Please enable JavaScript to view thecomments powered by Disqus.

Information & Contributors

Information

Published In

cover image International Journal of Data Mining and Bioinformatics
International Journal of Data Mining and Bioinformatics  Volume 4, Issue 5
October 2010
129 pages
ISSN:1748-5673
EISSN:1748-5681
Issue’s Table of Contents

Publisher

Inderscience Publishers

Geneva 15, Switzerland

Publication History

Published: 01 October 2010

Author Tags

  1. G-algebra
  2. biochemical networks
  3. bioinformatics
  4. graph data modelling
  5. query languages
  6. query processing

Qualifiers

  • Article

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • 0
    Total Citations
  • 0
    Total Downloads
  • Downloads (Last 12 months)0
  • Downloads (Last 6 weeks)0
Reflects downloads up to 27 Nov 2024

Other Metrics

Citations

View Options

View options

Login options

Media

Figures

Other

Tables

Share

Share

Share this Publication link

Share on social media