Ondex

Publications

• Thompson, P., Nawaz, R., McNaught, J. and Ananiadou, S.. (2011) Enriching a biomedical event corpus with meta-knowledge annotation. In: BMC Bioinformatics, 12, 393, 2011
• Kolluru, B., Nakjang, S., Hirt, R. P, Wipat, A. and Ananiadou, S.. (2011) Automatic extraction of microorganisms and their habitats from free text using text mining workflows. In: Journal of Integrative Bioinformatics, 8(2), 184, 2011
• Victor Lesk, Jan Taubert, Chris Rawlings, Stuart Dunbar and Stephen Muggleton (2011) WIBL: Workbench for Integrative Biological Learning. Journal of Integrative Bioinformatics, 8(2):156, 2011
• Lysenko, A., Defoin-Platel, M., Hassani-Pak, K., Taubert, J., Hodgman, T.C., Rawlings, C.J. and Saqi, M. (2011) Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. BMC Bioinformatics 12:203, May 2011
• Kolluru, B., Hawizy, L., Murray-Rust, P., Tsujii, J. and Ananiadou, S. (2011) Using Workflows to Optimise Named Entity Recognition for Chemistry. Plos ONE, Volume 6, Issue 5, May 2011
• Jochen Weile, Matthew Pocock, Simon J. Cockell, Phillip Lord, James M. Dewar, Eva-Maria Holstein, Darren Wilkinson, David Lydall, Jennifer Hallinan, and Anil Wipat (2011) Customizable views on semantically integrated networks for systems biology. Bioinformatics 2011 27: 1299-1306; doi:10.1093/bioinformatics/btr134.
• Stephen Muggleton, Jianzhong Chen, Hiroaki Watanabe, Stuart J. Dunbar, Charles Baxter, Richard Currie, José Domingo Salazar, Jan Taubert and Michael J. E. Sternberg (2010) Variation of Background Knowledge in an Industrial Application of ILP. ILP 2010: 158-170
• Nobata, C., Dobson, P., Iqbal, S. A., Mendes, P., Tsujii, J., Kell, D. B. and Ananiadou, S. (2010) Mining Metabolites: Extracting the Yeast Metabolome from the Literature. In Metabolomics 1573-3882, 2010.
• Ananiadou, S., Thompson, P., Nawaz, R. (2010) Improving Search Through Event-based Biomedical Text Mining. In Proceedings of the 1st Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts (AMICUS) workshop.
• Nawaz, R., Thompson, P., Ananiadou, S. (2010) Event Interpretation: A Step towards Event-Centred Text Mining. In Proceedings of the 1st Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts (AMICUS) workshop.
• Kano, Y., Dobson. P., Nakanishi, M., Tsujii T., Ananiadou, S. (2010) Text Mining Meets Workflow: Linking U-compare with Taverna, Bioinformatics (In Press) Advance Access.
• Simon J Cockell, Jochen Weile, Phillip Lord, Claire Wipat, Dmytro Andriychenko, Matthew Pocock, Darren Wilkinson, Malcolm Young and Anil Wipat (2010) An integrated dataset for in silico drug discovery, Journal of Integrative Bioinformatics, 7(3):116, 2010.
• Hassani-Pak, K., Legaie, R., Canevet, C., van den Berg, H.A., Moore, J.D., Rawlings, C. J. (2010) Enhancing Data Integration with Text Analysis to Find Genes Implicated in Plant Stress Response, Journal of Integrative Bioinformatics, 7(3):121, 2010.
• Yoshinobu Kano, Ruben Dorado, Luke McCrohon, Sophia Ananiadou, Jun’ichi Tsujii (2010) U-Compare: an integrated language resource evaluation platform including a comprehensive UIMA resource library, Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC 2010), pp. 428--434.
• Raheel Nawaz, Paul Thompson, Sophia Ananiadou (2010) Evaluating a meta-knowledge annotation for bio-events, Proceedings of the Workshop on Negation and Speculation in Natural Language Processing 2010, pp. 69--77.
• Raheel Nawaz, Paul Thompson, John McNaught, Sophia Ananiadou (2010) Meta-Knowledge Annotation of Bio-Events, 7th international conference on Language Resources and Evaluation (LREC 2010), Malta.
• Artem Lysenko, Matthew Hindle, Jan Taubert, Mansoor Saqi and Christopher Rawlings (2009) Data integration for plant genomics -- exemplars from the integration of Arabidopsis thaliana databases, Briefings in Bioinformatics 2009 10: 676-693.
• Splendiani, A., Kuiper, M. and Rawlings, C. J. (2009) Toward a new paradigm for user interaction on the semantic web to support life sciences investigation, Proceedings of the 6th International Workshop on Semantic Web User Interaction (SWUI 2009), CEUR-WS Vol. 544, Washington DC, October 2009.
• Jan Taubert, Matthew Hindle, Artem Lysenko, Jochen Weile, Jacob Kohler and Christopher Rawlings (2009) Linking life sciences data using graph-based mapping, Proceedings of Data Integration in the Life Sciences (DILS) 2009.
• Robert Pesch, Artem Lysenko, Matthew Hindle, Keywan Hassani-Pak, Ralf Thiele, Christopher Rawlings, Jacob Köhler and Jan Taubert (2008) Graph-based sequence annotation using a data integration approach, Journal of Integrative Bioinformatics, 5(2):94, 2008.
• Jan Taubert, Klaus Peter Sieren, Matthew Hindle, Berend Hoekman, Rainer Winnenburg, Stephan Philippi, Chris Rawlings, Jacob Köhler (2007) The OXL format for the exchange of integrated datasets, Journal of Integrative Bioinformatics, 4(3):62, 2007.
• 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.

Presentations

• Automatic extraction of microorganisms and their habitats from free text using text-mining workflows, Kolluru, B. (2011) at Integrative Bioinformatics 2011
• Using the Ondex system for exploring Arabidopsis regulatory networks, Artem Lysenko (2011) at UK Plant Systems Biology Workshop 2011
• Creating an integrated Ondex knowledge base for comparative gene function analysis, Keywan Hassani-Pak (2011) at UK Plant Systems Biology Workshop 2011
• Ondex: Data integration and visualisation, Catherine Canevet (2010), May 2010 tech meet at London Biogeeks
• An integrated dataset for in silico drug discovery, Simon Cockell (2010), International Symposium on Integrative Bioinformatics 2010
• Enhancing Data Integration with Text Analysis to Find Genes Implicated in Plant Stress Response, Keywan Hassani-Pak (2010), International Symposium on Integrative Bioinformatics 2010
• Investigating plant systems using data integration and network analysis, Chris Rawlings (2009), Nottingham Plant Bioinformatics, Systems and Synthetic Biology Summer School 2009
• BioPAX for semantic web based data integration, Andrea Splendiani (2009), Combined CellML, MIASE, SBO, SBGN BioPAX Meeting 2009
• The Ondex data integration framework, Jan Taubert (2007), The 8th annual Bioinformatics Open Source Conference BOSC 2007

Posters

• Ondex: data integration and visualisation for the Semantic Web, Catherine Canevet, Andrea Splendiani, Shao Chih Kuo, Robert Stevens, Phil Lord, Chris Rawlings (2009)
• The Ondex SABR project (Poster explained in Video), The Ondex consortium (2009)
• From data to knowledge – the Ondex System for integrating Life Sciences data sources, C. Rawlings, A. Karp, C. Goble, R. Stevens, S. Ananiadou, D. Kell, A. Wipat, D. Wilkinson, P. Lord, D. Lydall , C. Canevet (2008)