Automated structure extraction and XML conversion of life science database flat files

Philippi, S. and Koehler, J. 2006. Automated structure extraction and XML conversion of life science database flat files. IEEE Transactions on Information Technology in Biomedicine. 10, pp. 714-721. https://doi.org/10.1109/TITB.2006.875653

Related outputs

Arabidopsis sucrose non-fermenting-1-related protein kinase-1 and calcium-dependent protein kinase phosphorylate conserved target sites in ABA response element binding proteins

A - Papers appearing in refereed journals

Zhang, Y., Andralojc, P. J., Hey, S. J., Primavesi, L. F., Specht, M., Koehler, J., Parry, M. A. J. and Halford, N. G. 2008. Arabidopsis sucrose non-fermenting-1-related protein kinase-1 and calcium-dependent protein kinase phosphorylate conserved target sites in ABA response element binding proteins. Annals of Applied Biology - AAB. 153 (3), pp. 401-409. https://doi.org/10.1111/j.1744-7348.2008.00302.x

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 .

Ontology based text indexing and querying for the semantic web

A - Papers appearing in refereed journals

Koehler, J., Philippi, S., Specht, M. and Ruegg, A. 2006. Ontology based text indexing and querying for the semantic web. Knowledge-Based Systems. 19, pp. 744-754. https://doi.org/10.1016/j.knosys.2006.04.015

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

Addressing the problems with life-science databases for traditional uses and systems

A - Papers appearing in refereed journals

Philippi, S. and Koehler, J. 2006. Addressing the problems with life-science databases for traditional uses and systems. Nature Reviews Genetics. 7, pp. 482-488. https://doi.org/10.1038/nrg1872

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

Quality control for terms and definitions in ontologies and taxonomies

A - Papers appearing in refereed journals

Koehler, J., Munn, K., Ruegg, A., Skusa, A. and Smith, B. 2006. Quality control for terms and definitions in ontologies and taxonomies. BMC Bioinformatics. 7, p. 212. https://doi.org/10.1186/1471-2105-7-212

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

Extraction of biological interaction networks from scientific literature

A - Papers appearing in refereed journals

Skusa, A., Ruegg, A. and Koehler, J. 2005. Extraction of biological interaction networks from scientific literature. Briefings in Bioinformatics. 6 (3), pp. 263-276. https://doi.org/10.1093/bib/6.3.263

Bioinformatic and molecular genetic tools for identifying genes involved in the pathogenicity of Fusarium graminearum on wheat ears

C2 - Non-edited contributions to conferences

Baldwin, T. K., Winnenburg, R., Koehler, J., Urban, M. and Hammond-Kosack, K. E. 2005. Bioinformatic and molecular genetic tools for identifying genes involved in the pathogenicity of Fusarium graminearum on wheat ears. Abstracts Molecular Biology of Plant Pathogens Meeting, Ambleside, 19-21 September 2005 .

Bioinformatic and molecular genetic tools for identifying genes involved in the pathogenicity of Fusarium graminearum on wheat ears

C2 - Non-edited contributions to conferences

Baldwin, T. K., Winnenburg, R., Koehler, J., Urban, M. and Hammond-Kosack, K. E. 2005. Bioinformatic and molecular genetic tools for identifying genes involved in the pathogenicity of Fusarium graminearum on wheat ears. Abstracts ESF-EMBO Symposium on the Comparative Genomics of Eukaryotic Microorganisms, Sant Feliu de Guixols, 12-17 November 2005 .

Relations in biomedical ontologies

A - Papers appearing in refereed journals

Smith, B., Ceusters, W., Klagges, B., Koehler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A. L. and Rosse, C. 2005. Relations in biomedical ontologies. Genome Biology. 6, p. R46 (15 pages).

Modelling root activity to narrow the gene-environment gap

C1 - Edited contributions to conferences/learned societies

Richter, G. M., Steuernagel, B. and Koehler, J. 2005. Modelling root activity to narrow the gene-environment gap. Roots and the Soil Environment II. Aspects of Applied Biology 73 . pp. 133-140

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.

Using XML technology for the ontology-based semantic integration of life science databases

A - Papers appearing in refereed journals

Philippi, S. and Koehler, J. 2004. Using XML technology for the ontology-based semantic integration of life science databases. IEEE Transactions on Information Technology in Biomedicine. 8 (2), pp. 154-160. https://doi.org/10.1109/TITB.2004.826724