Medical Bioinformatics

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Semantic Biosystems People
The work in Semantic Biosystems works on the basis that well-structured, accessible and integrated information is crucial for the future. Our own cross-disciplinary challenge is how to build computer systems that can support life science researchers as they try to navigate and manipulate a vast amount of available information, and then interpret it and use it. This is especially relevant for genomics and systems biology research.

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. We have started work on several other implementations that integrate knowledge of other biological systems.

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 Dr. Andrew Gibson . Dr. Gerbert Jansen is responsible for the biomedical content of the peroxisome knowledge base. Serge Barth, MSc, is developing and implementing major parts of the software infrastructure (e.g., concept map browser and editor).

Semantic Biosystems currently has several (PhD) positions to extend the research towards systems biology and the integration of biological knowledge with multivariate statistical models.

Topic revision: r16 - 21 Mar 2011, AngelaLuijf Search
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