Coming courses within FMB
Knowledge Engineering and Text Mining
November 17-18 2008 at Karolinska Institutet
The PhD Programme in Medical Bioinformatics will give a course in Knowledge Engineering and Text Mining. The course is arranged by Professor Patrick Lambrix at Linköping University. The course will take place at Karolinska Institutet November 17-18 and it will consist of both lectures and hands-on. The lecturers are both from academy and industry. Please see below for more information about the course. A more thorough schedule will come in a couple of weeks.
How to apply?
Please email Lena Lewin (lena.lewin@ki.se) if you would like to participate. Last chance to register will be October 27. The students in the PhD Programme will have priority, but other students and researchers are also welcome, also from industry.
Background
During recent years an enormous amount of biological data, such as DNA and protein sequences, and gene regulatory and protein interaction networks, has been generated. This data is spread in a large number of autonomous data sources that are often publicly available on the Web. Further, there are also numerous tools available on the Web. Researchers in various areas, e.g. medicine, agriculture and environmental sciences, use these data sources and tools for such things as developing drugs enabling treatment of diseases, studying how mutations affect functioning of different components in organisms and investigating the influence of environmental factors on human health.
Due to the explosion of the amount of online accessible data and tools, it becomes more and more difficult for researchers to find the relevant sources and tools, and retrieve the relevant information. Further, often information from different sources needs to be integrated. The vision of a Semantic Web alleviates these difficulties. The Semantic Web is an extension of the current Web in which information is given a well-defined meaning by annotating Web content with ontology terms.
In this course we discuss the vision of a Semantic Web for biomedical informatics with a focus on modeling, organization and management of biomedical data for improved access and search. We discuss two important technologies that are needed to make this vision happen: knowledge engineering and text mining. Further, we exemplify these approaches through real cases in a pharmaceutical company and demonstrate different systems.
| Introduction |
| A Semantic Web for Bioinformatics |
| Professor Patrick Lambrix |
| --------------------------------------- |
| Theme: Knowledge Engineering |
| Biomedical Ontologies and Align |
| Professor Patrick Lambrix |
| Standards for Molecular Interaction |
| Dr Lena Strömbäck |
| Probabilistic Graph Models for Gene Regulatory Networks |
| Dr José M Pena |
| --------------------------------------- |
| Theme: Text Mining |
| Gene Symbol Disambiguation |
| Dr He Tan |
| Applied Biomedical Text Mining at AstraZeneca |
| Dr Marcus Bjäreland |
