Text Mining Hands-on Course and Training Seminar

EBI, Hinxton, Cambridge, U.K. 5th-6th October 2009

The European Bioinformatics Institute (EBI) and the National Centre for Text Mining (University of Manchester) are organising a joint training event at the EBI. The purpose of this event is to teach basic techniques in information retrieval (IR) and information extraction (IE) in the biomedical domain and to give hands-on training on existing solutions provided by the two centres.

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

Registration is open until September 10th, 2009
Please register here


  • Learn how to use existing text mining solutions
  • Understand basic text mining techniques and get an overview of underlying technologies
  • Appreciate the variety of text mining components and the contexts in which they are used individually and in combination
  • Interact with text miners to express needs for future developments

Pre-meeting seminar (Optional)

The pre-meeting seminar takes place before the main seminar (Monday morning). It provides theoretical background information to better understand the research domain of biomedical text mining. It teaches school book knowledge on text mining applied in the biomedical domain and recent advances in the research domain. It is not required to attend the pre-meeting seminar, if you are only interested in the main seminar: the main seminar is self-explanatory. The pre-meeting seminar will give an understanding of the mathematical and linguistics approaches that are used in biomedical text mining. It addresses the need of biomedical researchers to understand the concepts behind biomedical text mining and helps to better understand the research side of it.

There are no extra charges for the pre-meeting seminar.

Monday 5th October 2009
09.00-10.30 Feature extraction from biomedical text for data integration (Theory)
Extraction of tokens, terms and named entities, from documents to profiles, similarity measures, language models
10.30-11.00 Coffee break
11.00-12.30 Natural language processing (Theory)
Syntactical structure of sentences, parsing techniques, relation extraction

Main Seminar

Monday 5th October 2009
13.30-15.00 Access to literature for biologists and bioinformaticians (Theory, Hands-on)
EBI's Literature Services: CiteXplore, EbiMed, MedEvi, Whatizit
15.00-15.30 Coffee break
15.30-17.00 Text Mining in Biomedicine (Theory, Hands-on) NaCTeM's Services: KLEIO, FACTA, MEDIE,TerMine,Acromine
17.00-18.00 Open discussion, time for questions, expectations for the future

Tuesday 6th October 2009

09.00-10.30 Exploitation of biomedical semantic resources (Theory / Hands-On)
Overview of resources, biolexicon, bio-ontologies,text mining infrastructure (U-Compare text mining workflows)
10.30-11.00 Coffee break
11.00-12.30 Success stories in biomedical text mining (Hands-on/Theory)
Solutions for bioinformaticians, biomedical challenges
12.30-13.30 Lunch


Dietrich Rebholz-Schuhmann, MD, PhD
Research Group Leader
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD,
United Kingdom
Phone: +44 (0)1223 492 594
Prof. Sophia Ananiadou
School of Computer Science
Director, National Centre for Text Mining
Manchester Interdisciplinary Biocentre
University of Manchester
131 Princess Street, M1 7DN
United Kingdom