Programme

09:00am-09:30am

registration (and during the coffee and lunch breaks)

11:30am-01:00pm

morning tutorials (cont.)  

03:30pm-04:00pm

coffee break

08:30am-09:00am

registration (and during the coffee and lunch breaks)

opening session

Sophia Ananiadou, Juliane Fluck (session chairs)

Udo Hahn (local organiser) 

Klaus Dicke (rector of the Friedrich-Schiller-Universität)

Jürgen Sühnel (JCB)

12:30pm-01:30pm

lunch

02:30pm-04:00pm

paper presentation (chair: Udo Hahn, JULIE Lab)

Rinaldi, F.; Schneider, G.; Kaljurand, K.; Hess, M.; Romacker, M.:
An Environment for Relation Mining over Richly Annotated Corpora:
the case of GENIA

Chun, H.-W.; Tsuruoka, Y.; Kim, J.-D.; Shiba, R.; Nagata, N.; Hishiki, T.; Tsujii, J.:
Automatic Recognition of Topic-Classified Relations between Prostate Cancer and Genes from Medline Abstracts

04:00pm-04:30pm

coffee break

poster presentation (chair: Nigel Collier, Nat. Inst. of Informatics)

Hakenberg, J.; Leser, U.; Kirsch, H.; Rebholz-Schuhmann, D.:
Collecting a Large Corpus from all of Medline

Knüpfer, C.; Beckstein, C.; Dittrich, P.:
Towards a Semantic Description  of Bio-Models: Meaning Facets -
A Case Study

Milward, D.; Blaschke, C.; Neefs, J.-M.; Ott, M.-C.; Verbeeck, R.; Stubbs, A.:
Flexible Text Mining Strategies for Drug Discovery

Friedrich, C. M.; Revillion, T.; Hofmann, M.; Fluck, J.:
Biomedical and Chemical Named Entity Recognition with Conditional
Random Fields: The Advantage of Dictionary Features 

Jilani, I.; Grabar, N.; Jaulent, M.-C.: 
Fitting the finite-state automata platform for mining gene functions from biological scientific literature

Sanchez, O.; Poesio, M.; Kabadjov, M. A.; Tesar, R.:
What kind of problems do protein interactions raise for anaphora
resolution? - A preliminary analysis

08:30am-09:00am

registration (and during the coffee and lunch breaks)

invited talk

Lynette Hirschman (MITRE):
"Evaluating What Biologists Want: Designing Challenge Evaluations for Text Mining"

10:00am-10:30am

coffee break

paper session (chair: Sophia Ananiadou, NaCTeM)

Mougin, F.; Burgun, A.; Bodenreider, O.:
Data Integration through data elements: Mapping data elements to terminological resources

Vizenor, L.; Bodenreider, O.:
Using Dependence Relations in MeSH as a Framework for the Analysis of Disease Information in Medline

Kremer, G.; Anstein, S.; Reyle, U.:
Analysing and Classifying Names of Chemical Compounds with CHEMorph

12:30pm-01:30pm

lunch

industrial talk (chair: Juliane Fluck, SCAI)

TEMIS (Geißler, S.)

Biomax (Wiehler, J.)

Sun Microsystems (Köhler, A.)

02:30pm-04:00pm

industrial exhibition (with coffee break)

panel discussion

Ananiadou, S. (NaCTeM); Hahn, U. (BioTeM);  Vachon, T. (Novartis); Hirschman, L. (MITRE):
Why do we need text mining centres for the Life Science domain and how could they support us?

08:30am-09:00am

registration (and during the coffee break)

invited talk

Judith Blake (Jackson Lab):
"Beyond the Data Deluge: Bio-Ontologies and Biomedical Research"

10:00am-10:30am

coffee break

10:30am-12:00pm

paper session (chair: Stefan Schulz, Freiburg University Hospital)

Davis, N.; Harkema, H.; Gaizauskas, R.; Guo, Y.; Ghanem, M.; Barnwell, T.; Guo, Y.; Ratcliffe, J.: 
Three Approaches to GO-Tagging Biomedical Abstracts

Lin, K. H.-Y.; Hou, W.-J.; Chen, H.-H.:
Gene Ontology Annotation Using Word Proximity Relationship