Graph-based sequence annotation using a data integration approach

Robert Pesch 1 , Artem Lysenko 2 , Matthew Hindle 2 , Keywan Hassani-Pak 2 , Ralf Thiele 1 , Christopher Rawlings 2 , Jacob Köhler 3 ,  and Jan Taubert 2
  • 1 Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Germany
  • 2 Department of Biomathematics and Bioinformatics, Rothamsted Research, United Kingdom of Great Britain and Northern Ireland
  • 3 Protein Research Group, University of Tromsø, Norway


The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara- Cyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation.

The methods and algorithms presented in this publication are an integral part of the ONDEX system which is freely available from

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Journal + Issues

The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.