Training

The European Bioinformatics Institute (EBI) is organising a training event at the EBI. The purpose of this event is to teach basic solutions in information retrieval (IR) and information extraction (IE) in the biomedical domain, to enable the programmatic use of available IT infrastructures (Whatizit, UIMA-basedTM solutions) and to give insights into knowledge discovery through text mining solutions.

Who should attend: Biomedical researchers, biocurators, bioinformaticians, medical informaticians and any other researcher active in biomedical research.

Objectives

• Learn how to use existing TM solutions: through interactive and programmatic access
• Get background information and theoretical support on the exploitation of the scientific literature
• Differentiate different existing solutions concerning their exploitation in daily research work
• Express needs for future developments

Wednesday 27th October 2010 (Full day)

Presenters: Olivier Bodenreider(NLM), Dietrich Rebholz-Schuhmann

• Introduction and overview on biomedical text mining
• Feature extraction from the scientific literature, basic statistical approaches, tokenisation
• Terminological resources for the biomedical and chemical domain (BioLexion, UMLS)
• Use of the terminological resources for information extraction

Thursday 28th October 2010 (Full day)

Presenters: Sophia Ananiadou, Ian Lewin, Fabio Rinaldi, Dietrich Rebholz-Schuhmann (+ external speaker)

• Syntactical analysis of text (parsing, theory and practice)
• Text processing with publicly available means Tools and solutions for biomedical text mining (UIMA-based, Whatizit infrastructure)

Friday 29th October 2010 (1/2 day)

Presenters: Anika Oellrich, Senay Kafkas, Dietrich Rebholz-Schuhmann

• Use of ontological resources for literature analysis and knowledge discovery
• Complex systems for biomedical literature analysis: relation and event extraction from text
• Success stories of biomedical knowledge discovery from the scientific literature