Towards a Semantic Web for Bioinformatics

Nowadays, biologists use biological data sources and tools to find relevant information for their research. However, with the explosion of the amount of online accessible data and tools, finding the relevant information is not an easy task and systems integration has become important for further progress. The vision of a Semantic Web facilitates the integration of data sources and tools. It is an extension of the current Web in which information is given a well-defined meaning by annotating web content, by standardizing terminology and by providing adequate reasoning languages. It enables computers and people to work better in cooperation and supports discovery, automation, integration and reuse across applications. In this talk we discuss the Semantic Web vision (as proposed in the EU Network of Excellence REWERSE work group on bioinformatics) and focus on two important and related technologies ontologies and knowledge representation languages, that are needed to make this vision happen.

[1]  Patrick Lambrix,et al.  Evaluation of Ontology Merging Tools in Bioinformatics , 2002, Pacific Symposium on Biocomputing.

[2]  Pedro Barahona,et al.  PSICO: Solving Protein Structures with Constraint Programming and Optimization , 2002, Constraints.

[3]  L. Krippahl,et al.  BiGGER: A new (soft) docking algorithm for predicting protein interactions , 2000, Proteins.

[4]  Patrick Lambrix,et al.  Towards Transparent Access to Multiple Biological Databanks , 2003, APBC.

[5]  Patrick Lambrix Ontologies in Bioinformatics and Systems Biology , 2004, Artificial Intelligence Methods And Tools For Systems Biology.

[6]  Liviu Badea,et al.  Integrating Biological Process Modelling with Gene Expression Data and Ontologies for Functional Genomics , 2003, CMSB.

[7]  Rolf Apweiler,et al.  A collection of well characterised integral membrane proteins , 2000, Bioinform..

[8]  François Fages,et al.  Symbolic Model Checking of Biochemical Networks , 2003, CMSB.

[9]  Rolf Backofen,et al.  Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets , 1999, Bioinform..

[10]  Ulf Leser,et al.  EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation , 1999, German Conference on Bioinformatics.

[11]  Liviu Badea,et al.  Functional Discrimination of Gene Expression Patterns in Terms of the Gene Ontology , 2002, Pacific Symposium on Biocomputing.

[12]  Peer Kröger,et al.  A Computational Biology Database Digest: Data, Data Analysis, and Data Management , 2004, Distributed and Parallel Databases.