Meeting Schedule

Biocuration 2013 Conference Preliminary Agenda

Sunday 7th April

Registration from 1pm

3pm Walking Tour

6pm Conference opens

6:20pm The EMBO LECTURE: Sir Rich Roberts "Annotation by sequencing", in the Wolfson Lecture Hall

7:30pm Opening reception

Monday 8th April

9am-10am Keynote lecture: Ewan Birney, in the Wolfson Lecture Hall

10am-10:40am Morning Session: Functional Annotation. Chairs: Claire O'Donovan & Owen White, in the Wolfson Lecture Hall

Talks:

1. Gemma Holliday, UCSF. Protein function curation: linking sequence & chemical reaction spaces in the SFLD
2. Matthew Campbell, Macquarie University. UniCarbKB: curating site-specific glycosylation knowledge
3. Prudence Mutowo, EMBL-EBI. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans
4. Jeremy Edwards, Boyce Thompson Institute. Manual curation and visualization of gene families and networks for the Solanaceae plant family
5. Jen Harrow, Wellcome Trust Sanger Institute. What is there new to find?

10:40am-11am Break

11am-12pm Morning Session continued

12pm-1pm Lunch

1pm-2:40pm Afternoon session: Community Annotation. Chairs: Cathy Wu & Mike Cherry, in the Wolfson Lecture Hall

Talks:

1. Andrew Oberlin, Miami University. Biological Database of Images and Genomes: tools for community annotations linking image and genomic information
2. Zhang Zhang, Beijing Institute of Genomics, Chinese Academy of Sciences. Community curation in biological knowledge wikis
3. Monica Munoz-Torres, Lawrence Berkeley National Laboratory. WebApollo: A Web-based Sequence Annotation Editor for Distributed Community Annotation.
4. Anurag Priyam, Queen Mary, University of London. Crowdsourcing Genome Annotation
5. Daniel Lawson, EMBL-EBI. A system of community annotation for arthropod genomes

2:40pm-3pm Break

3pm-5pm Afternoon Workshops: 

Go Galaxy: Suzi Lewis & Dave Clements. In the Wolfson Lecture Hall

On Sequence Similarity Searching and using Web Services for biocuration: Dr William Pearson, Rodrigo Lopez and Hamish McWilliam. In the Fellows Dining Room (Max Capacity 70)

Variation annotation LOVD: Raymond Dagleish & Peter Taschner. In the Bevin Room (Max Capacity 42)

5pm-7pm Poster session 1 with light refreshments. 

Tuesday 9th April

9am-10am Keynote lecture: Fiona Brinkman, in the Wolfston Lecture Hall

10am-10:40am Morning Session: Data integration: Interactions, pathways and networks. Chairs: Carsten Kettner & Sandra Orchard, in the Wolfston Lecture Hall

Talks:

1. Sandra Orchard, EMBL-EBI. How the use of common data standards and formats resulted in increased data sharing – the IMEx Consortium
2. David Cohen, Institut Curie. BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps
3. Carsten Kettner, Beilstein-Institut. STRENDA – Proposing a Repository System for Minimum Information on Enzyme Kinetics Experiments
4. Vijayalakshmi Chelliah, EMBL-EBI. BioModels Database: curated computational models of biological systems
5. Karen Ross, University of Delaware. Construction of Protein Phosphorylation Networks by Data Mining, Text Mining, and Ontology Integration: Analysis of the Spindle Checkpoint

10:40am-11am Break

11am-12pm Morning Session continuted

12pm-1pm Lunch

1pm-2:40pm Afternoon Session: Ontologies and Standards. Chairs: Judy Blake & Tatiana Tatusova, in the Wolfston Lecture Hall

Talks:

1. Chris Mungall, Genomics Division, Lawrence Berkeley National Laboratory. Gene Ontology Annotation Extensions: Increasing the expressivity of GO
2. Frederic Bastian, Swiss Institute of Bioinformatics - University of Lausanne. Maintaining up-to-date annotations to an unified cross-species anatomy ontology: use and tracking of Uberon in Bgee
3. Manuel Corpas, The Genome Analysis Centre. SASI: A Scientific Announcement Standards Initiative for the Life Sciences
4. Melisa Haendel, OHSU. A merger of multi-species anatomy ontologies
5. Mauno Vihinen, Lund University. Variation Ontology for annotation of variation effects and mechanisms

2:40pm-3pm Break

3pm-5pm Afternoon Workshops:

Emerging standards for genome annotation and curation in the era of high throughput sequencing: Kim Pruitt. In the Fellows Dining Room (Max Capacity 70)

Biocreative Text Mining for Biocuration: Cecilia Arighi, Kevin Cohen, Martin Krallinger & Zhiyong Lu. In the Bevin Room (Max Capacity 42)

Biocuration and scholarly communication cycle, roles and opportunities for biocurators: Susanna Sansone & Carsten Kettner. In the Wolfson Lecture Hall

5pm-7pm Poster session 2 with light refreshments.

7:30pm Conference Dinner St John’s College Cambridge, drinks reception from 7:30pm, sit down 8pm

Wednesday 10th April

9am-10am Keynote lecture: Richard Cotton "Human Variome Project – Current Overview", in the Wolfson Lecture Hall

10am-10:40am Morning Session: Lightning Talks / hot topics. Chairs: Jen Harrow & Francis Ouellette, in the Wolfson Lecture Hall

Talks:

1. Damian Smedley, Wellcome Trust Sanger Institute.  PhenoDigm: analyzing curated annotations to associate animal models with     human diseases
2. Stacia Engel, Stanford University. Sequencing and annotation of multiple Saccharomyces cerevisiae strains at SGD
3. Stanley Laulederkind, Medical College of Wisconsin. PhenoMiner: Curating Annotations with Five Ontologies/Vocabularies Simultaneously
4. Imtiaz Khan, Cardiff University.  ProtocolNavigator: repairing the data curation and consumption imbalance
5. Daniel Jamieson, University of Manchester. Cataloging the biomedical world of pain through semi-automated curation of molecular interactions
6. Louise Takeshita, Institute of Integrative Biology, University of Liverpool. A database for curating the associations between killer-cell immunoglobulin-like receptors and diseases in worldwide populations
7. Juergen Haas, Swiss Institute of Bioinformatics/Biozentrum University of Basel. The Protein Model Portal - a comprehensive resource for protein structure information
8. Charles Steward, Wellcome Trust Sanger Institute. The non-obese diabetic (NOD) mouse sequence and annotation resource: an aid for investigating type 1 diabetes
9. Heiko Dietze, Genomics Division, Lawrence Berkeley National Laboratory.  TermGenie - Granting Biocurators’ Wishes for the Gene Ontology
10. Raja Mazumder, George Washington University. Biocuration of next-generation sequence data: Infrastructure and proof-of-principle using cancer genomics data.

10:40am-11am Break

11am-12pm Morning Session continued:

12pm-1pm Lunch

1pm-2:40pm Afternoon Session: Data mining and automated prediction. Chairs: Max Hauessler & Jo McEntyre, in the Wolfson Lecture Hall

Talks:

1. Fabio Rinaldi, University of Zurich Digital Curation Experiments for RegulonDB,
2. Yalbi I. Balderas-Martínez, Centro de Ciencias Genómicas. UNAM. Major challenges for a precise curation of knowledge of gene regulation in bacteria
3. Max Haeussler, Univ of Manchester. Large-scale genome annotation and triage of full text articles
4. Gully Burns, USC/Information Sciences Institute, Marina Del Rey, California. Practical approach and infrastructure for the accelerated construction of biocuration systems
5. Mariana Neves, Humboldt-Universitaet zu Berlin. Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

2:40pm-3pm Break

3pm-5pm Afternoon Workshops:

Reusing curated data to perform annotation with biomedical ontologies: James Malone, Simon Jupp & Tony Burdett. In the Fellows Dining Room (Max Capacity 70)

Handling Metagenomics Data: Maria Martin & Peter Sterk. In the Bevin Room (Max Capacity 42)

Connecting scientific articles with research data: Simone Groothuis & Elena Zudilova-Seinstra (includes panel discussion – panel members: Mary Shimoyama (Rat Genome Database) and Judith Blake (Mouse Genome Informatics). In the Wolfson Lecture Hall

5pm-5:30pm Closing Session

Conference End