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: Till September 10th, 2009

Please Register here

Please contact Alison Barker in case of questions.

Objectives

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

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 TmWorkshop_Part3_HandsOnSolutions_DRS.pdf
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) TmWorkshop_Part5_Resources_JJK.pdf
10.30-11.00	Coffee break
11.00-12.30	Success stories in biomedical text mining (Hands-on/Theory) Solutions for bioinformaticians, biomedical challenges TmWorkshop_Part6_Computational_AJY.pdf
12.30-13.30	Lunch

Pre-meeting seminar

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 TmWorkshop_Part0_Intro_DRS.pdf TmWorkshop_Part1_TextFeatures_PP.pdf
10.30-11.00	Coffee break
11.00-12.30	Natural language processing (Theory) Syntactical structure of sentences, parsing techniques, relation extraction TmWorkshop_Part2_NLP_IL.pdf

Organizers

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 Email: Rebholz@ebi.ac.uk	Prof. Sophia Ananiadou School of Computer Science Director, National Centre for Text Mining Manchester Interdisciplinary Biocentre University of Manchester 131 Princess Street, M1 7DN www.nactem.ac.uk