IsoKEGG: A logic based system for querying biological pathways in KEGG

Kazi Zakia Sultana, Anupam Bhattacharjee, Hasan Jamil

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

Understanding the interaction patterns among a set of biological entities in a pathway is an important exercise because it potentially could reveal the role of the entities in biological systems. Although a considerable amount of effort has been directed to the detection and mining of patterns in biological pathways in contemporary research, querying biological pathways remained relatively unexplored. Querying is principally different in which we retrieve pathways that satisfy 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 based on a novel and generic subgraph isomorphism computation technique. We cast this technique into a graphical interface called IsoKEGG to facilitate flexible querying of KEGG pathways.We demonstrate that IsoKEGG is flexible enough to allow querying based on isomorphic pathway topologies as well as matching any combination of node names, types, and edges. It also allows editing KGML represented query pathways and returns all possible pathways in KEGG that satisfy a given query condition that the users are able to investigate further.

Original languageEnglish
Title of host publicationProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Pages626-631
Number of pages6
DOIs
StatePublished - 1 Dec 2010
Event2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 - Hong Kong, China
Duration: 18 Dec 201021 Dec 2010

Publication series

NameProceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010

Conference

Conference2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
CountryChina
CityHong Kong
Period18/12/1021/12/10

Keywords

  • Drug design
  • Hypothesis testing
  • Pathways
  • Pattern lookup
  • Subgraph isomorphism

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    Sultana, K. Z., Bhattacharjee, A., & Jamil, H. (2010). IsoKEGG: A logic based system for querying biological pathways in KEGG. In Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010 (pp. 626-631). [5706642] (Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010). https://doi.org/10.1109/BIBM.2010.5706642