A Semantic Web for bioinformatics: goals, tools, systems, applications

The quantity of biological information is increasing at an impressive rate. An integrated access to this huge amount of information requires complex search and retrieval software and automation of analysis processes. Automation of integration procedures mainly concerns how to link data, how to select and extract information and how to pipe retrieval and analysis steps. This automated approach to data analysis requires the adoption of new technologies and tools in the bioinformatics domain

05441 Abstracts Collection -- Managing and Mining Genome Information: Frontiers in Bioinformatics

From 30.10.05 to 04.11.05, the Dagstuhl Seminar 05441 ``Managing and Mining Genome Information: Frontiers in Bioinformatics\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Semantic browsing of pathway ontologies and biological networks with RDFScape (working paper)

Studying biological organisms at the systems level is a complex task. Computational approaches require structured representations of existing biological knowledge. This necessity has prompted the development of formal representations of specific areas of knowledge, resulting in ontologies such as Gene Ontology and BioPAX. However, only part of this formalized knowledge is exploited for the interpretation of experimental data. Specifically, it is common to use the association between entities and annotations, like genes and functions, while the structure of the annotation is not considered beyond some common features as inheritance. This is partly due to a lack of tools and methods that bridge resources related to ontologies to the ones related to data analysis. Here we present a platform that merges a semantic web toolkit with a widely adopted modular tool for systems biology investigation. We demonstrate how in this environment it is possible to query ontologies not only as a list of annotations but as a knowledge base from which new information can be derived. We also show how this knowledge can be integrated with biological data