Methods of Gene Ontology Term Similarity Analysis in Graph Database Environment

Conference paper

DOI: 10.1007/978-3-319-06932-6_33

Part of the Communications in Computer and Information Science book series (CCIS, volume 424)
Cite this paper as:
Stypka Ł., Kozielski M. (2014) Methods of Gene Ontology Term Similarity Analysis in Graph Database Environment. In: Kozielski S., Mrozek D., Kasprowski P., Małysiak-Mrozek B., Kostrzewa D. (eds) Beyond Databases, Architectures, and Structures. BDAS 2014. Communications in Computer and Information Science, vol 424. Springer, Cham

Abstract

The article presents and analyses three graph processing issues that can be identified in three methods of GO term similarity evaluation. The solutions of these problems are implemented in Neo4j graph database environment. Each of the issues can be solved directly by a single Cypher query or can be divided into several queries which results have to be merged. The comparison of the introduced solutions is presented in terms of time and memory effectivness. The results show how to implement the effective solutions of this class of issues.

Keywords

graph database Neo4j Gene Ontology GO term similarity 

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  1. 1.Institute of InformaticsSilesian University of TechnologyGliwicePoland
  2. 2.Future ProcessingGliwicePoland

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