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Information Management People .
The organisation, integration, presentation and application of the vast amounts of (public) omics data and biomedical knowledge is crucial to advance life sciences. The heterogeneity and the size of the data offers a range of information management challenges that we address in our projects. For example, we have been working on a database for the storage of SAGE data (Van Kampen, 2000, Bioinformatics), the integration of SAGE data with the human genome to construct transcriptome maps as a cancer research tool (Caron, 2001, Science), the visualization of microarray data in the context of metabolic pathways (Luyf, 2002, Bioinformatics), the development of a peroxisome knowledge base based on semantic web technologies (Willemsen, Bioinformatics, 2008) and the comparison of metabolic pathway databases to facilitate the use and improvement of these resources (Stobbe, 2011, BMC Systems Biology).

  • van Kampen AHC, van Schaik BDC, Pauws E, Michiels EMC, Ruijter JM, Caron HN, Versteeg R, Heisterkamp SH, Leunissen JAM, Baas F and van der Mee M (2000) USAGE: a web-based approach for the analysis of SAGE data. Bioinformatics, 16(10).
  • Luyf ACM, de Gast J, van Kampen AHC (2002) Visualizing metabolic activity on a genome-wide scale Bioinformatics,18(6), 813-818.
  • Willemsen AM, Jansen GA, Komen JC, van Hooff S, Waterham HR, Brites PM, Wanders RJ, van Kampen AH (2008) Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways.Bioinformatics. 24(16), i21-7.
  • Stobbe MD, Houten SM, Jansen GA, van Kampen AH, Moerland PD (2011) Critical assessment of human metabolic pathway databases: a stepping stone for future integration. BMC Systems Biology, 5, 165

BioExpert is an example of a project that applies cutting edge Semantic Web standards (e.g., RDF, OWL, SKOS, SPARQL) in a framework that allows the construction of high quality domain-specific knowledge bases. In a first implementation of the framework, we have created the Peroxisome Knowledge Base. This integrates a set of 'concept maps' - visual representations of a limited set of connected facts in a specific context - that have been specified by leading experts in the field of peroxisomal biochemistry and related diseases.

Versions of the Peroxisome Knowledge Base


Figure 1. Example concept map from the peroxisome knowledge base. The underlying representation is RDF/OWL.
The Semantic Biosystems research is led by Prof. Dr. Antoine van Kampen . Andrew Gibson is working on the use and development of Semantic Web technologies. Dr. Gerbert Jansen is responsible for the biomedical content of the peroxisome knowledge base. Eelke van der Horst , is developing and implementing major parts of the software infrastructure. Jack Vink is responsible for the implementation of a yeast glycolysis knowledge base. Miranda Stobbe is a PhD student working on the comparison and integration of metabolic pathway databases.

Former researchers working on this topic: Serge Barth, Aviral Vatsa, Jasper Komen, Marcel Willemsen.

Topic revision: r3 - 31 Jul 2014, AngelaLuijf
 

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