Rolf Backofen, Mike Badea, Albert Burger, François Fages, Patrick Lambrix, Werner Nutt, Michael Schroeder, Sylvain Soliman, Sebastian Will:
Michael Schroeder (editor):
State-of-the-art in Bioinformatics.

Complete Text [
.pdf, 244KB]
In: (A2-D1)

With the explosion of online accessible bioinformatics data and tools, systems integration has become very important for further progress. Currently, bioinformatics relies heavily on the Web. But the Web is geared towards human interaction rather than automated processing. The vision of a Semantic Web facilitates this automation by annotating web content and by providing adequate reasoning languages as developed in the REWERSE project. The report summarises the state-of-the-art in bioinformatics relevant to REWERSE. First, we give a motivation by sketching the growth of data in biology, the types of data, and their distribution and availability. We introduce two fundamental classes of bioinformatics problems: alignments (of sequences or structures) and structure prediction. Next, we discuss the most important databases and approaches towards their integration. A fundamental ingredient of a Semantic Web, which transparently integrates data sources are ontologies. We discuss a number of di erent bioinformatics ontologies including GeneOntology, the most widely used one with some 19.000 terms. Finally, we show three application areas in which rules are used: Rules to implement computation tree logic to represent and query metabolic pathways; Rules as constraints for structure prediction; and rules learned by inductive logic programming to declaratively capture biological knowledge.



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