9:00/18:00 - Room 2A (Mezzanine)
W1: Biomedical Ontologies and Text Processing
Rob Gauizauskas and Chris Wroe
Biomedical literature, bio-databases and bio-ontologies all play an important role in supporting the work of biological researchers. Much of the biological knowledge in our community is held in electronic form as natural language text.
However, not all experimental data is appropriate to include in such research publications, and so is instead stored in more structured bio-databases.Bio-ontologies provide a common conceptual framework for structuring and annotating this data to enable it to be pooled across databases. These three resources contain overlapping information in different forms, and the inter-ependencies between them are complex.
The goal of this workshop is to bring together researchers from the bio-ontology community with those from the biomedical text processing community with a view to furthering their understanding each other's needs and capabilities. Previous workshops in the area have tended focus more either on bio-ontologies or on bio-text processing. While some research has attempted to bridge this gap the aim of current workshop is to focus explicitly on the relationship between bio-ontologies and bio-text processing.
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9:00/18:00 - Room 2B (Mezzanine)
W2: Current approaches for function prediction during genome annotation
Rob Russell and Alex Stark
This workshop brings together experts from around the world to speak on the functional aspects of genome annotation. Despite many years of research there are still many unanswered questions in assigning functions to genes and proteins in silico. There will be four main sessions:
1. Protein binding sites, functional sites & specificity
2. Interactions, networks & pathways
3. Regulation of transcription, translation & splicing (Including transcription factors & microRNAs)
4. The next generation of comparative genomics (Including contextual predictions of protein function)
9:35 - 9:40 Welcome Rob Russell, EMBL Heidelberg
9:40 - 9:50 About Biosapiens TBA
Protein binding sites, functional sites & specificity
Chair: Rob Russell
9:50 - 10:20 Function prediction at CASP6 Anna Tramontano, Univeristy of Rome
10:20 - 10:50 Protein feature prediction and data integration Soren Brunak, CBS Copenhagen
10:50 - 11:10 Coffee Break
11:10 - 11:40 Specificity-determining positions in protein alignments Mikhail Gelfand, Institute for Information Transmission Problems, RAS, Moscow
11:40 - 12:10 Title TBA Mike Sternberg, Imperial College London
12:10 - 12:40 Variability of functional sites Joerg Schultz, University of Wuertzburg
Interactions, networks & pathways
Chair: Joerg Schultz
12:40 - 13:10 Modeling the dynamics of the yeast cell cycle interactome through integration of high-throughput data Ulrik de Lichtenberg, CBS Copenhagen
13:10 - 14:00 Lunch
14:00 - 14:30 Gene function prediction: utilising the genomic context and a new generation of oligonucleotide tiling arrays Jan Korbel, Yale University
Regulation of transcription, translation & splicing
Chair: Ulrik de Lichtenberg
14:30 - 15:00 Finishing the human gene set Roderic Guigo IMIM, Barcelona
15:00 - 15:30 microRNAs: Conferring Fidelity to Gene Expression Alex Stark, EMBL Heidelberg
15:30 - 15:45 Coffee
The next generation of comparative genomics
Chair: Alex Stark (EMBL Heidelberg)
15:45 -16:15 Title TBA Ewan Birney, EBI Hinxton
16:15 - ? General Discussion Everybody
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