Querying KEGG pathways in logic

Kazi Zakia Sultana, Anupam Bhattacharjee, Hasan Jamil

Research output: Contribution to journalArticle

4 Scopus citations

Abstract

Understanding the interaction patterns among biological entities in a pathway can potentially reveal the role of the entities in biological systems. Although considerable effort has been contributed to this direction, querying biological pathways remained relatively unexplored. Querying is principally different in which we retrieve pathways satisfying a given property in terms of its topology, or constituents. One such property is subnetwork matching using various constituent parameters. In this paper, we introduce a logic based framework for querying biological pathways using a novel and generic subgraph isomorphism computation technique. We develop a graphical interface called IsoKEGG to facilitate flexible querying of KEGG pathways based on isomorphic pathway topologies as well as matching any combination of node names, types, and edges. It allows editing KGML represented query pathways and returns all isomorphic patterns in KEGG pathways satisfying a given query condition for further analysis.

Original languageEnglish
Pages (from-to)1-21
Number of pages21
JournalInternational Journal of Data Mining and Bioinformatics
Volume9
Issue number1
DOIs
StatePublished - Feb 24 2014

All Science Journal Classification (ASJC) codes

  • Information Systems
  • Library and Information Sciences
  • Biochemistry, Genetics and Molecular Biology(all)

Keywords

  • Graph matching
  • Logic based system
  • Lookup queries
  • Pathways
  • Query language
  • Subgraph isomorphism
  • Visual interface

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