Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases.

Briefings in Bioinformatics
Artem LysenkoChristopher John Rawlings

Abstract

The development of a systems based approach to problems in plant sciences requires integration of existing information resources. However, the available information is currently often incomplete and dispersed across many sources and the syntactic and semantic heterogeneity of the data is a challenge for integration. In this article, we discuss strategies for data integration and we use a graph based integration method (Ondex) to illustrate some of these challenges with reference to two example problems concerning integration of (i) metabolic pathway and (ii) protein interaction data for Arabidopsis thaliana. We quantify the degree of overlap for three commonly used pathway and protein interaction information sources. For pathways, we find that the AraCyc database contains the widest coverage of enzyme reactions and for protein interactions we find that the IntAct database provides the largest unique contribution to the integrated dataset. For both examples, however, we observe a relatively small amount of data common to all three sources. Analysis and visual exploration of the integrated networks was used to identify a number of practical issues relating to the interpretation of these datasets. We demonstrate the utility of the...Continue Reading

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Citations

Apr 13, 2010·Journal of Plant Research·Takeshi Obayashi, Kengo Kinoshita
Nov 10, 2010·Briefings in Bioinformatics·Anália LourençoIsabel Rocha
Sep 29, 2011·Briefings in Bioinformatics·Yves Sucaet, Taru Deva
May 11, 2013·Database : the Journal of Biological Databases and Curation·Jonathan VincentPierre Martre
Apr 27, 2012·BMC Bioinformatics·Luna De FerrariIgor Goryanin
Apr 10, 2013·International Journal of Molecular Sciences·Nyuk Ling MaSu Shiung Lam
Jul 28, 2016·BioData Mining·Artem LysenkoCharles Auffray

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