Second CALBC Workshop – 16/17/18 March 2011 – EBI, Hinxton
Day 1 (Wednesday – March 16th, 2011)
Session 1: Introduction to the CALBC challenges, setup, participation
Overview: Setup of the first and the second CALBC challenge, overview on the analyses (D. Rebholz-Schuhmann, EBI, U.K.) (
Methods for Matching of Annotations, Harmonisation and Evaluation (Jan Kors, Erasmus University Medical Center, Rotterdam, Nl) (
Concept identification by machine learning aided dictionary-based named entity recognition and rule-based entity normalisation (György Móra, University of Szeged, Hu) (
Annotating the CALBC corpus with a machine learning harmonization approach (David Campos, Universidade de Aveiro, Pt) (
Annotating large corpora with concept retrieval (Rafael Berlanga1, Universitat Jaume I, Es) (
Session 2, part 1: Annotation methods applied to the CALBC corpus
Dictionary-based concept identification with UMLS (Max De Wilde, University of Antwerp, Be) (
OntoGene at CALBC II and Some Thoughts on the Need of Document-Wide Harmonization (Simon Clematide, University of Zurich, Ch) (
Challenge I vs. Challenge II: Set-up, Participation Data and Feedback(Udo Hahn, Friedrich-Schiller-University, Jena, De; D. Rebholz-Schuhmann) (
Recap and initial open discussion on the setup and outcome of the CALBC project and challenge (
Keynote talk: Prof. Yves Moreau (Katholieke Universiteit, Leuven, Be)
Candidate gene prioritization by genomic data fusion
Bus ride to Cambridge
Dinner, Queens College, Cambridge
Day 2 (Thursday - March 17th, 2011
Session 2, part 2: CALBC II challenge and gold standard data
Building the SSC and evaluation of the annotation systems against the SSC (I. Lewin, EBI, U.K.; J. Kors; D. Rebholz-Schuhmann) (
Evaluation of the SSC against the gold standard corpora (Senay Kafkas, EBI, U.K.; Dietrich Rebholz-Schuhmann) (
A CRF-based approach to harmonize heterogeneous gene/protein annotations (David Campos, Universidade de Aveiro, Pt) (
Use cases for improvements of annotation solutions based on the SSC (David Milward, Linguamatics, Cambridge, U.K.; Jan Kors; Erik van Mullighen) (
Keynote Talk: Lynette Hirshman (Mitre, U.S.A.)
Coupling Evaluation to End Users: Case Studies in Text Mining for Biomedicine
Session 3:Normalisation of data and Semantic Web
Normalisation of lexical entities: Jochem, LexEBI, cross-comparisons (D. Rebholz-Schuhmann et. al) (
Normalisation of the silver standard corpus using normalised lexical resources: evaluation of annotation solutions (Ernesto J. Ruiz , Oxford University, U.K.; Ian Lewin) (
A Semantic Model for Federated Queries Over a Normalized Corpus (Samuel Croset, EBI, U.K.; C. Grabmüller, EBI, U.K.) (
Integration of literature with biomedical data resources- the SESL project (Christoph Grabmüller, EBI, U.K.; Samuel Croset, EBI, U.K.; Dietrich Rebholz-Schuhmann)
Keynote Talk: Therese Vachon (Novartis Institutes for Biomedical Research, Basel, Ch)
Day 3 (Friday- March 18th, 2011)
Keynote talk: Timo Hannay (Digital Science / Nature Publishing Group, London)
When content meets technology
Session 5: Large-scale annotation – next generation?
Is the interoperability and normalisation of semantic resources solved?
Is the integration of different semantic types in the same corpus solved?
Which use cases from involving Semantic Web technology would profit from the integration of the scientific literature?
Does the CALBC approach scale in such a way that all scientific publications in the biomedical domain would be annotated with automatic means in the future?
Can we tackle the problem of multi-linguality with the CALBC approach?
What other data resources apart from the scientific biomedical literature should be annotated with the CALBC approach?
Wind-up and closing