The impact of the upcoming Internet on scientific research worldwide was enormous, not the least in biomedical research. Especially the Human Genome Project was the inspiration for many biological databases publicly available via the Internet. As of now, conducting biomedical research without the Internet is nearly impossible. The information needed for analysis and interpretation of experimental results is usually scattered over a multitude of heterogeneous data sources: sequence databases, protein resources, gene expression data repositories, literature databases, functional annotation databases, etc. Many researchers depend on the Internet as the most important source of biomedical information. As the amount of available data increases at a rate never seen before, researchers are now faced with the problem of finding the information they need, in a format they can work with.
Several initiatives exist that try to integrate multiple data sources or facilitate complex bioinformatics queries and analyses. However, the integration is not always in tune with the userb of this workshop was to bring together researchers and practitioners to exchange ideas with respect to knowledge systems in bioinformatics that make extensive use of medical and biological semantics and ontologies, web services technologies, or distributed databasing and computing to tackle the issues mentioned above. Out of approximately 20 submitted papers, 10 papers were accepted for oral presentation. These are the papers you will find further on. Together they give a very nice overview of where we are now and where current research is headed. We were very pleased with the number of people interested in contributing to this workshop, both authors and reviewers. Every submission has received three outstanding reviews, which made the task of accepting papers of high quality quite easy. We hope you will enjoy reading them.