The Ondex Data Integration Framework

The ONDEX data integration framework BOSC2007, Vienna 20.07.2007 Jan Taubert ( [email_address] ) Rothamsted Research, UK

Summary

ONDEX – framework for large scale data integration, text mining & graph analysis

JAVA API and standalone application

License: GNU General Public License

Project status: early alpha

Statistics: 814 files, 159572 lines

http://ondex.sourceforge.net

University of Bielefeld, Bielefeld, Germany.

University of Koblenz, Koblenz, Germany.

University of Nottingham, Nottingham, Nottinghamshire, UK.

University of Tromsø, Tromsø, Norway.

University of Wageningen, Wageningen, Netherlands.

Rothamsted Research, Harpenden, Hertfordshire, UK.

Current members:

Jan Baumbach

Sonja Ernst

Keywan Hassani-Pak

Matthew Hindle

Berend Hoekman

Jacob Köhler

Artem Lysenko

Stephan Philippi

Chris Rawlings

Jan Taubert

Paul Verrier

Jochen Weile

Rainer Winnenburg

Tully Yates

Former members:

Jessica Butz

Sebastian Elsner

Ina Kupp

Alexander Rüegg

Klaus Peter Sieren

Andre Skusa

Michael Specht

Members

Based on

JAVA J2SE 5.0

Berkeley DB Java Edition

XFire SOAP framework

Jetty WebServer

Lucene text search engine

Taverna for workflows

combine Large Experimental Data New Insights ONDEX Motivation 100‘s of Bio-Databases

… in which nodes and edges can have different properties. enzyme kinetics protein interactions metabolic pathways protein structure relation properties ontologies Everything is a network

ONDEX: Graph of Concepts and Relations Biology: Protein interaction network Ontology of Concept Classes, Relation Types and additional Properties Properties: compound name, protein sequence, protein structure, cellular component, KM-value, PH optimum … Protein – Ligand interaction network Protein Ligand interact Protein interact Concept Concept Concept Relation Relation Concept Class: Protein Protein Ligand Relation Type: interact interact Ontology based graph

Microarray experiment result analysis map 100‘s of Bio-Databases One example application

Comp Protein Gene Enzyme EC Treat- ment Reaction Pathway

Treatments from DRASTIC Pathways from KEGG

Three steps:

Try it out, submit bugs you find

Suggest/Implement your improvements

Become a contributor and submit improvements

http://ondex.sourceforge.net Contributors will be acknowledged on the project website and in publications involving their work. Contributors are welcome to publish their work on ONDEX under their own names. How to contribute

Good : Write Flatfile parser for ONDEX Better : Provide your database in OXL (see Taubert et al. (2007) “Exchange of integrated datasets – the OXL format”, in press, IB2007) Also welcome : Provide your database in another standard (BioPax, SBML, XGMML; but may result in loss of information) http://ondex.sourceforge.net What to contribute

Algorithms : Needed for the alignment of integrated data Core : Improve persistency layer of Ontology based graph Exporter : Provide your own exchange standard Webservices : Increase compatibility http://ondex.sourceforge.net What to contribute

http://ondex.sourceforge.net Support : OXL in your application Connect : Import from web service or directly from Core API Algorithms : Graph analysis using the ONDEX Visualisation and Analysis Tool Kit (OVTK) Feedback & Feature requests : Mailing lists and Sourceforge.net What to contribute

Jun 06 – Jun 07: 1828 Downloads, 15289 page views Current SF.net rank: 1074 Subversion Activity Jan 07 – Jun 07 8904 Reads 2072 Writes 4821 File Uploads Developer mailing list : [email_address] User mailing list : [email_address] Current release : 0.9alpha1 Sourceforge.net

J Taubert, R Winnenburg, M Hindle, J Weile, J Baumbach, S Philippi, C Rawlings and J Köhler (2007) “Data integration, information filtering and knowledge extraction with ONDEX”, Paper in preparation J Taubert, K P Sieren, M Hindle, B Hoekman, R Winnenburg, S Philippi, C Rawlings and J Köhler (2007) “Exchange of integrated datasets – the OXL format”, Submitted Paper, 4th integrative bioinformatics workshop (IB2007) Jacob Köhler, Stephan Philippi, Michael Specht and Alexander Rüeg (2006) "Ontology based text indexing and querying for the semantic web", Knowledge-Based Systems, Volume 19, Issue 8 Jacob Köhler, Jan Baumbach, Jan Taubert, Michael Specht, Andre Skusa, Alexander Rüegg, Chris Rawlings, Paul Verrier and Stephan Philippi (2006) "Graph-based analysis and visualization of experimental results with ONDEX", Bioinformatics 22(11) Skusa, A., Rüegg, A., Köhler, J. (2005) "Extraction of biological networks from scientific literature", Briefings in Bioinformatics 6(3) Köhler, J., Rawlings, C., Verrier, P., Mitchell, R., Skusa, A., Rüegg, A. and Philippi, S. (2004), "Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalized Data Structures", In Silico Biol, Volume 5, Special Issue: Ontology and Genome, Manuscript number in online journal: 0005. Publications

Centre for Mathematical and Computational Biology Department of Biomathematics and Bioinformatics Rothamsted Research Dr Jacob Köhler, Principle Investigator Prof Chris Rawlings, Head of Department Rothamsted Research is supported by the BBSRC Travel grants and scholarships by Acknowledgements

4 th Integrative Bioinformatics workshop 10th to 12th September 2007 University of Ghent, Belgium http://www.rothamsted.bbsrc.ac.uk/bab/conf/ib07/ Invited speakers: Prof Carole Goble, School of Computer Science, University of Manchester, UK Prof Søren Brunak, BioCentrum-DTU, Technical University of Denmark, Denmark Dr David Searls, Senior Vice President, Informatics, GlaxoSmithKline Pharmaceuticals, USA Dr Luis Serrano, EMBL, Heidelberg, Germany Organising committee : Prof Ralf Hofestädt, University of Bielefeld, Germany (Co-chair) Dr Jacob Koehler, Rothamsted Research, UK (Co-chair) Prof Martin Kuiper, University of Ghent, Belgium (Local organisation) Paul Verrier, Rothamsted Research, UK (Local organisation) Poster submission deadline 27 th August 2007 Registration deadline 13 th August 2007