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Text Mining Hands-on course and Training seminar EBI, Hinxton, Cambridge, U.K. 21st-22nd April 2010
The European Bioinformatics Institute (EBI) is organising a 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.
Registration:
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
Wednesday 21st April 2010
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09.00 -10.30
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Feature extraction from biomedical text for data integration
(D. Rebholz-Schuhmann)
The starter kit:Extraction of tokens, terms and named entities, from documents to profiles, similarity measures, language models,use in biomedical text mining
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10.30-11.00
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Coffee break
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11.00-12.30
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Natural language processing(Ian Lewin)
Syntactical structure of sentences, parsing techniques, relation extraction.This presentation gives insights on the use of grammars and syntactical analyses to filter out explicit relations and other information from the literature.
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12.30-13.30
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Lunch
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13.30 -15.00
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Access to literature for biologists and bioinformaticians
(D. Rebholz-Schuhmann)
Presentation and explanations to EBI's Literature Services: CiteXplore, EbiMed, MedEvi, Whatizit.
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15.00-15.30
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Coffee break
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15.30-17.00
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Text Mining in Biomedicine (Prof. Sophia Ananiadou, NaCTeM)
NaCTeM is providing TM services to the public: KLEIO, FACTA, MEDIE,TerMine,Acromine. The solutions will be presented and explained.-->
Information extraction using UIMA and a biomedical type system
(Prof. Udo Hahn, University of Jena)
UIMA is a Java-based software package that contains a number of text mining solutions.Tokens and entities are linked to a semantic type and advanced parsing methods can be applied to the identified entities. The part of the workshop gives insights into the usage of UIMA .
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17.00-18.00
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Discussion
Time for questions, expectations for the future
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Thursday 22nd April 2010
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09.00 -10.30
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Use of ontological resources for Text Mining:
(D.Rebholz-Schuhmann)
Exploitation of biomedical semantic resources: overview of resources, biolexicon, bio-ontologies. Use of ontological resources for information extraction.
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10.30-11.00
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Coffee break
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11.00-12.30
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Success stories in biomedical text mining
(D. Rebholz-Schuhmann)
Use of the programmatic text mining infrastructure at the EBI: calling text mining services.Text mining solutions for bioinformaticians and biomedical challenges. Examples of knowledge discovery through text mining. Overview into ongoing work and future developments.
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12.30-13.30
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Lunch
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Organizers
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Dietrich Rebholz-Schuhmann, MD, PhD
Research Group Leader
European Bioinformatics Institute
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