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

Lysenko, A., Hindle, M. M., Taubert, J., Saqi, M. and Rawlings, C. J. 2009. Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases. Briefings in Bioinformatics. 10, pp. 676-693. https://doi.org/10.1093/bib/bbp047

Authors	Lysenko, A., Hindle, M. M., Taubert, J., Saqi, M. and Rawlings, C. J.
Year of Publication	2009
Journal	Briefings in Bioinformatics
Journal citation	10, pp. 676-693
Digital Object Identifier (DOI)	https://doi.org/10.1093/bib/bbp047
Open access	Published as bronze (free) open access
Funder project or code	Centre for Mathematical and Computational Biology (MCB)
	Project: 4918
Publisher's version	Lysenko-2009-Data-integration-for-plant-genomics (1).pdf
ISSN	1467-5463
Publisher	Oxford University Press (OUP)

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Sternberg, M. J. E., Tamaddoni-Nezhad, A., Lesk, V. I., Kay, E., Hitchen, P. G., Cootes, A., Van Alphen, L. B., Lamoureux, M. P., Jarrell, H. C., Rawlings, C. J., Soo, E. C., Szymanski, C. M., Dell, A., Wren, B. W. and Muggleton, S. H. 2013. Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach. Journal of Molecular Biology. 425 (1), pp. 186-197. https://doi.org/10.1016/j.jmb.2012.10.014

Detection of multi-clustered genes and community structure for the plant pathogenic fungus Fusarium graminearum

B - Book chapters etc edited externally

Bennett, L., Lysenko, A., Papageorgiou, L. G., Urban, M., Hammond-Kosack, K. E., Rawlings, C. J., Saqi, M. and Tsoka, S. 2012. Detection of multi-clustered genes and community structure for the plant pathogenic fungus Fusarium graminearum. in: Gilbert, D. and Heiner, M. (ed.) Computational Methods in Systems Biology Springer-Verlag Berlin Heidelberg.

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A - Papers appearing in refereed journals

Love, C. G., Andongabo, A. E., Wang, J., Carion, P. W. C., Rawlings, C. J. and King, G. J. 2012. InterStoreDB: a generic integration resource for genetic and genomic data. Journal of Integrative Plant Biology. 54 (5), pp. 345-355. https://doi.org/10.1111/j.1744-7909.2012.01120.x

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Defoin-Platel, M., Hassani-Pak, K. and Rawlings, C. J. 2011. Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits. Systems Approaches to Crop Improvement. Aspects of Applied Biology 107 . Association of Applied Biologists (AAB) Wellesbourne Warwick . pp. 79-87

Lost in translation: data integration tools meet the Semantic Web

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Splendiani, A., Rawlings, C. J., Kuo, S-C., Stevens, R. and Lord, P. 2011. Lost in translation: data integration tools meet the Semantic Web. Proceedings 1st IRAST International Conference on Data Engineering and Internet Technology (DEIT), Bali, 15-17 March 2011 . IEEE. pp. 621-625

AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations

A - Papers appearing in refereed journals

Defoin-Platel, M., Hindle, M. M., Lysenko, A., Powers, S. J., Habash, D. Z., Rawlings, C. J. and Saqi, M. 2011. AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations. BMC Bioinformatics. 12, p. 431 (13pp). https://doi.org/10.1186/1471-2105-12-431

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

A - Papers appearing in refereed journals

Lysenko, A., Defoin-Platel, M., Hassani-Pak, K., Taubert, J., Hodgman, C., Rawlings, C. J. and Saqi, M. 2011. Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. BMC Bioinformatics. 12, p. 203 (14pp). https://doi.org/10.1186/1471-2105-12-203

WIBL: Workbench for Integrative Biological Learning

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Lesk, V., Taubert, J., Rawlings, C. J., Dunbar, S. and Muggleton, S. 2011. WIBL: Workbench for Integrative Biological Learning. Journal of Integrative Bioinformatics. 8, p. 156 (9pp). https://doi.org/10.2390/biecoll-jib-2011-156

Analysis and visualisation of RDF resources in Ondex

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Canevet, C., Lysenko, A., Splendiani, A., Pocock, M. J. O. and Rawlings, C. J. 2010. Analysis and visualisation of RDF resources in Ondex. Nature Precedings. https://doi.org/10.1038/npre.2010.5430

Enhancing data integration with text analysis to find proteins implicated in plant stress response

A - Papers appearing in refereed journals

Hassani-Pak, K., Legaie, R., Canevet, C., Van Den Berg, H. A., Moore, J. D. and Rawlings, C. J. 2010. Enhancing data integration with text analysis to find proteins implicated in plant stress response. Journal of Integrative Bioinformatics. 7, p. 121 (13pp). https://doi.org/10.2390/biecoll-jib-2010-121

Ondex: Data integration and visualisation for the Semantic Web

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Canevet, C., Splendiani, A., Kuo, S-C., Stevens, R., Lord, P. and Rawlings, C. J. 2009. Ondex: Data integration and visualisation for the Semantic Web. In: CEUR Workshop Proceedings vol. 559, CEUR-WS.org, Workshop on Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2009, Amsterdam, 1/07/2009. . CEUR-WS.org.

Toward a new paradigm for user interaction on the semantic web to support life sciences investigation

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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 Workshop on Semantic Web User Interaction: Sharing Ideas for Complex Problems in User Interaction (SWUI2009), Washington DC, 25 October 2009 .

Linking life sciences data using graph-based mapping

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Taubert, J., Hindle, M. M., Lysenko, A., Weile, J., Kohler, J. and Rawlings, C. J. 2009. Linking life sciences data using graph-based mapping. in: Paton, N. W., Hedeler, C. and Missier, P. (ed.) Data Integration in the Life Sciences. DILS 2009. Lecture Notes in Computer Science Volume 564 Springer, Berlin. pp. 16-30

Analysis of the newly sequenced Fusarium genomes using PHI-Base and ONDEX

C2 - Non-edited contributions to conferences

Beacham, A. M., Cavenet, C., Taubert, J., Urban, M., Antoniw, J. F., Rawlings, C. J. and Hammond-Kosack, K. E. 2008. Analysis of the newly sequenced Fusarium genomes using PHI-Base and ONDEX.

Graph-based sequence annotation using a data integration approach

A - Papers appearing in refereed journals

Pesch, R., Lysenko, A., Hindle, M. M., Hassani-Pak, K., Thiele, R., Rawlings, C. J., Kohler, J. and Taubert, J. 2008. Graph-based sequence annotation using a data integration approach. Journal of Integrative Bioinformatics. 5(2):94, p. 15pp. https://doi.org/10.2390/biecoll-jib-2008-94

PHI-base update: additions to the pathogen-host interaction database

A - Papers appearing in refereed journals

Winnenburg, R., Urban, M., Beacham, A., Baldwin, T. K., Holland, S., Lindeberg, M., Hansen, H., Rawlings, C. J., Hammond-Kosack, K. E. and Kohler, J. 2008. PHI-base update: additions to the pathogen-host interaction database. Nucleic Acids Research. 36, pp. D572-D576. https://doi.org/10.1093/nar/gkm858

PHI-base: a database of experimentally verified pathogenicity, virulence and effector genes in fungal, oomycete and bacterial pathogens of animals and plants

C2 - Non-edited contributions to conferences

Baldwin, T. K., Winnenburg, R., Beacham, A., Urban, M., Rawlings, C. J., Koehler, J. and Hammond-Kosack, K. E. 2007. PHI-base: a database of experimentally verified pathogenicity, virulence and effector genes in fungal, oomycete and bacterial pathogens of animals and plants. Abstracts 13th International Congress on Molecular Plant-Microbe Interactions, Sorrento, 21-27 July 2007 .

Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence

A - Papers appearing in refereed journals

Mitchell, R. A. C., Castells-Brooke, N. I. D., Taubert, J., Verrier, P. J., Leader, D. J. and Rawlings, C. J. 2007. Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence. Nucleic Acids Research. 35(Web Server issue), pp. W148-W151. https://doi.org/10.1093/nar/gkm220

The Pathogen-Host Interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity

A - Papers appearing in refereed journals

Baldwin, T. K., Winnenburg, R., Urban, M., Rawlings, C. J., Koehler, J. and Hammond-Kosack, K. E. 2006. The Pathogen-Host Interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity. Molecular Plant-Microbe Interactions - MPMI. 19 (12), pp. 1451-1462. https://doi.org/10.1094/MPMI-19-1451

Graph-based analysis and visualization of experimental results with ONDEX

A - Papers appearing in refereed journals

Koehler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Ruegg, A., Rawlings, C. J., Verrier, P. J. and Philippi, S. 2006. Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 22 (11), pp. 1383-1390. https://doi.org/10.1093/bioinformatics/btl081

PHI-base: a new database for pathogen host interactions

A - Papers appearing in refereed journals

Winnenburg, R., Baldwin, T. K., Urban, M., Rawlings, C. J., Koehler, J. and Hammond-Kosack, K. E. 2006. PHI-base: a new database for pathogen host interactions. Nucleic Acids Research. 34 (1), pp. D459-D464. https://doi.org/10.1093/nar/gkj047

Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures

A - Papers appearing in refereed journals

Koehler, J., Rawlings, C. J., Verrier, P. J., Mitchell, R. A. C., Skusa, A., Ruegg, A. and Philippi, S. 2004. Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures. In Silico Biology. 5 (1), pp. 33-44.