Venue & Access

Biocuration2010, October 11-14, 2010
Program (as of September 13)

[October 11th, Monday]   AIST Tokyo Waterfront, Bio-IT Bldg. 11F

12:00 - 18:00 Registration desk opens at AIST Tokyo Waterfront, Bio-IT Bldg.
13:00 - 15:45  
Satellite Meeting :
National Institute of Genetics (NIG) International Symposium "Future Perspectives of Biological Databases"
Chairpersons : Kazuho Ikeo (National Institute of Genetics, Japan)
13:00 Introduction to the NIG International Symposium
Kazuho Ikeo (National Institute of Genetics, Japan)
SA1/13:05 Bioinformatics for Human Proteomics: Current State and Future Status
Amos Bairoch (Swiss Institute of Bioinformatics, Switzerland)
SA2/13:25 Harnessing Wikipedia for Biocuration
Alex Bateman (Wellcome Trust Sanger Institute, UK)
SA3/13:45 An Equation For a Vibrant Database: Curators + Journals + Community = Success
Tanya Berardini (Carnegie Institution for Science, USA)
SA4/14:05 A community of biocurators
Pascale Gaudet (Northwestern University, USA)
SA5/14:25 The Data Shareing Challenge. Learning Community from Consortia
Winston Hide (Harvard School of Public Health, USA)
SA6/14:45 Coping with Increasingly Large Datasets - (Semi-)Automated Spatial Curation
Lorna Richardson (MRC Human Genetics Unit, UK)
SA7/15:05 Lessons Learned from Data Management for the Human Microbiome Project
Owen White (University of Maryland School of Medicine, USA)
SA8/15:25 Closer Cooperation between Journals and Databases
Yukiko Yamazaki (National Institute of Genetics, Japan)
15:45 - 16:00 Coffee Break
16:00 - 16:30  
Opening Remarks
Pascale Gaudet (Northwestern University, USA)
Takashi Gojobori (National Institute of Genetics, Japan)
16:30 - 17:30  
Plenary Talk 1
PL1/16:30 Molecular Network Based Annotation of Genomes and Metagenomes
Minoru Kanehisa (Kyoto University, Bioinformatics Center, Japan)
18:00 - 20:00  
Restaurant LA TERRE in Miraikan (National Museum of Emerging Science and Innovation)



[October 12th, Tuesday]   Tokyo International Exchange Center

8:30 - 17:00 Registration desk opens at Tokyo International Exchange Center
9:30 - 10:30  
Plenary Talk 2
PL2/9:30 Evolutionary Relationships as a Paradigm for Integrating Biological Knowledge
Paul D. Thomas (University of Southern California, USA)
10:30 - 12:30  

Session 1 : Large Scale, Automated, and Predictive Annotations

Chairpersons :
Claire O'Donovan (EBI) and Barend Mons (Netherlands Bioinformatics Centre)
S1-1/10:30 Comparison of Computationally- and Manually-Assigned Gene Ontology Annotations to Improve Functional Characterization of Gene Products
Maria C. Costanzo (Stanford University, USA)
S1-2/11:00 Automatic Protein Clustering as a Basis of Automatic Annotation
Naoki Sato (The University of Tokyo, Japan)
S1-3/11:30 Transcriptome in a Dynamic System with Next Gen Sequencers
Hideya Kawaji (RIKEN Omics Science Center, Japan)
S1-4/12:00 UniRule - Automatic Annotation In UniProtKB
Alan Bridge (SIB, Switzerland)
12:30 - 13:30 Lunch
13:30 - 15:30  

Session 2 : Outreach to User Communities & Community Annotation

Chairpersons :
Maria Costanzo (Stanford University), Mike Cherry (Stanford University) and Winston Hide (Harvard School of Public Health)
S2-1/13:30 Community Annotation in Biology
Raja Mazumder (PIR, Georgetown University Medical Center, USA)
S2-2/14:00 Nanopublication by Community Annotation in the ConceptWiki
Christine Chichester (Netherlands Bioinformatics Centre, Netherlands)
S2-3/14:15 The Challenge of Eukaryote Genome Annotation At Genoscope
Betina Porcel (Genoscope, France)
S2-4/14:30 The Neuroscience Information Framework: A Unified Semantic Framework for Discovery and Integration of Biomedical Data and Resources on the Web
Jeffrey Grethe (UCSD, USA)
S2-5/14:45 Incorporating Community Annotation Interfaces into the CIPRO2.5 Database with Comprehensible Sketches to Support Quick Annotations of Proteome Data
Keisuke Ueno (Hokkaido University, Japan)
15:00 Panel Discussion: Outreach to User Communities - Who are they and what do they need?
15:30 - 15:45 Coffee Break
15:45 - 17:15 Concurrent Workshops 1 & 2

Workshop 1 : Curation of Protein Structure and Chemicals (4F)

Chairpersons :
Susumu Goto (Kyoto Univ, Japan) and Akira R. Kinjo (Osaka Univ, Japan)
W1-1/15:45 Comparative Protein Structure Modeling: An Effective Means to Explore Protein Function
Česlovas Venclovas (Inst Biotech, Lithuania)
W1-2/16:15 Biomacromolecular Structure Annotation
Jasmine Young (RCSB PDB, Rutgers University, USA)
W1-3/16:30 ChEBI, an Open-access Chemistry Resource for the Life Sciences: Facilities for On-line Submission and Curation
Marcus Ennis (EBI, UK)
W1-4/16:45 Functional Annotation of Sugar Databases
Frederique Lisacek (SIB, Switzerland)
W1-5/17:00 Data Standardization for Glyco-informatics
Kiyoko Aoki-Kinoshita (Soka University, Japan)

Workshop 2 : Curation Interface and Software (3F)

Chairpersons :
Xiaodong Wang (WormBase, CalTech, USA) and Kimberly Van Auken (WormBase, CalTech, USA)
W2-1/15:45 Curation of Protein Domain Models for the Conserved Domain Database (CDD)
Aron Marchler-Bauer (NCBI, USA)
W2-2/16:00 InterPro Curation: Integrating Predictive Protein Signatures into Biological Hierarchies
Sarah Burge (EMBL-EBI, UK)
W2-3/16:15 Manual Biocuration, a UniProtKB/Swiss-Prot Perspective
Sylvain Poux (SIB, Switzerland)
W2-4/16:30 ISA Software Suite: Supporting Standards-Compliant Experimental Annotation and Enabling Curation at the Community Level
Philippe Rocca-Serra (University of Oxford, OeRC, UK)
W2-5/16:45 Ontology-based Tools to Enhance the Curation Workflow
Patricia Whetzel (Stanford University, USA)
W2-6/17:00 Gene Curation Software at the Rat Genome Database
Stan Laulederkind (Medical College of Wisconsin, USA)
17:30 - 18:30  

Poster Presentations (odd number)

18:30 - 19:30  

Poster Presentations (even number)



[October 13th, Wednesday]   Tokyo International Exchange Center

8:30 - 17:00 Registration desk opens at Tokyo International Exchange Center
9:00 - 10:00  
Plenary Talk 3
PL3/9:00 A Few Hundred Minds, a Million Minds or Millions of Minds?
Barend Mons (Netherlands Bioinformatics Centre, Netherlands)
10:00 - 12:00  

Session 3 : Biocuration in Metabolomics and Systems Biology

Chairpersons :
Kazuki Saito (RIKEN) and Seung Yon Rhee (Carnegie Institution for Science, USA)
S3-1/10:00 Combining Computational Prediction and Manual Curation to Create Plant Metabolic Pathway Databases
Peifen Zhang (Carnegie Institution for Science, USA)
S3-2/10:30 KaPPA-View4: A Pathway Database for Gene Co-expression and Metabolite Co-acculumation Analysis
Nozomu Sakurai (Kazusa DNA Research Institute, Japan)
S3-3/10:55 MassBank: A Reference Database for Chemical Identification of Metabolites Detected by Mass Spectrometry
Takaaki Nishioka (Keio University, Japan)
S3-4/11:20 Plant Metabolic Data Curation and Its Integration into Solanaceae Genomic Databases
Anuradha Pujar (Boyce Thompson Institute for Plant Research, USA)
S3-5/11:40 The EcoCyc Database - Integrating and Transferring Knowledge about E. coli
Ingrid Keseler (SRI International, USA)
12:00 - 12:15 Group Photo
12:15 - 13:30 Lunch
13:30 - 15:30  

Session 4 : Asian Models of Biocuration-Related Activities

Chairpersons : Takashi Gojobori (NIG)
S4-1/13:30 Curation for Systems Biology Resources in an Academic Model
Keshava Prasad (Institute of Bioinformatics, India)
S4-2/13:55 Identification Of Causative Variations Based On The Technology Of Next Generation Sequencing
Yixue Li (Shanghai Center for Bioinformation Technology, China)
S4-3/14:20 Asian Models of Micorbial Resource Information Network
Juncai Ma (Institute of Microbiology, CAS, China)
S4-4/14:45 Biocuration of Genomic Data of Non-model Species in Taiwan
Tzen-Yuh Chiang (National Cheng Kung University, Taiwan)
S4-5/15:10 Data Integration Model and GUIs Used in Human Genome Network Platform
Kazuho Ikeo (National Institute of Genetics, Japan)
15:30 - 15:45 Coffee Break
15:45 - 17:15 Concurrent Workshops 3 & 4

Workshop 3: Crop/Plant Genome Curation (4F)

Chairpersons : Takeshi Itoh (NIAS, Japan) and Mary L. Schaeffer (USDA-ARS, USA)
W3-1/15:45 Data Curation Infrastructure in the iPlant Discovery Environment
Chris Jordan (The University of Texas at Austin, USA)
W3-2/16:15 Application of Next-Generation Sequence Data for Rice Genome Analyses
Yoshihiro Kawahara (NIAS, Japan)
W3-3/16:30 MAIZEGDB.ORG, the Maize Genetics Cooperation and the 2500 MB B73 Genome-Generated Tsunami
Mary L. Schaeffer (USDA-ARS, USA)
W3-4/16:45 Arabidopsis thaliana: Further Exploiting This Plant Reference Genome
Mara Sangiovanni (University of Naples Federico II, Italy)
W3-5/17:00 A New QTL Curation Approach, Analysis and Linking QTLs to Genomes at SGN
Isaak Tecle (Cornell University, USA)

Workshop 4 : New Approaches Towards Database Integration (3F)

Chairpersons :
Chisato Yamasaki (BIRC, AIST, Japan) and Simon Twigger (Medical College of Wisconsin, USA)
W4-1/15:45 Hyperlink Management System for Creating Maintenance-Free Hyperlinks among Major Biological Databases
Tadashi Imanishi (BIRC, AIST, Japan)
W4-2/16:00 Semantic Encoding of Complex Information
Steven Vercruysse (Norwegian University of Science and Technology, Norway)
W4-3/16:15 NamesforLife Semantic Resolution Services for the Life Sciences: Moving towards an Extensible and Interoperable System for Naming
George M. Garrity (NamesforLife, LLC and Michigan State University, USA)
W4-4/16:30 Bio2RDF: Convert, Provide and Reuse
Marc-Alexandre Nolin (Laval University, Canada)
W4-5/16:45 RIKEN SciNetS: A Cloud of World's First Publication Medium of Databases on the Semantic Web
Tetsuro Toyoda (RIKEN BASE, Japan)
W4-6/17:00 TogoDB + TogoWS: a data integration platform for the Semantic Web
Toshiaki Katayama (Univ Tokyo, Japan) and Mitsuteru Nakao (DBCLS, Japan)
17:30 - 18:30  

Poster Presentations (even number)

18:30 - 19:30  

Poster Presentations (odd number)



[October 14th, Thursday]   Tokyo International Exchange Center

8:30 - 13:00 Registration desk opens at Tokyo International Exchange Center
9:00 - 10:30  

Session 5 : Data Integration Platforms and Data Sharing

Chairpersons : Amos Bairoch (SIB) and Pascale Gaudet (Northwestern University)
S5-1/9:00 Omics Data Sharing
Susanna Sansone (University of Oxford, OeRC, UK)
S5-2/9:30 H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome
Chisato Yamasaki (BIRC, AIST, Japan)
S5-3/9:45 Literature Curation of Protein Interactions: Measuring Agreement Across Major Public Databases
Andrei Turinsky (Hospital for Sick Children, Canada)
S5-4/10:00 neXtProt, a New Human-Centric Protein Knowledge Resource
Lydie Lane (University of Geneva, Switzerland)
S5-5/10:15 UniProt Knowledgebase: A Hub of Integrated Protein Data
Michele Magrane (European Bioinformatics Institute, UK)
10:30 - 10:45 Coffee Break
10:45 - 12:20  

Session 6 : Future Directions and Challenges for Biocuration

Chairpersons : Renate Kania (HITS gGmbH) and Tadashi Imanishi (BIRC, AIST)
S6-1/10:45 MetaCuration Standards and Minimum Information about a Bioinformatics Investigation
Tin Wee Tan (National University of Singapore)
S6-2/11:10 Utopia Documents: Linking Literature and Data
Steve Pettifer (The University of Manchester, UK)
S6-3/11:35 AMIS, the Article Minimum Information Standard
Delphine Dauga (Inst Dev Biol Marseille-Luminy, France)
S6-4/11:50 Publishing Interactive Articles: Integrating Journals and Biological Databases
Karen Yook (WormBase Curator,USA)
S6-5/12:05 The SciKnowMine System: Infrastructure for Biocuration Applied to MGI Document Triage
Gully Burns (USC/ISI, USA)
12:20 - 12:30  
Closing Remark
Tadashi Imanishi (BIRC, AIST, Japan)
12:30 - 13:00 Poster presenters remove posters from boards
12:30 - 13:30 Lunch
13:30 - 16:30  
Satellite Meeting :
NIAS Symposium "7th Rice Annotation Project Meeting"
13:30 Opening Remarks
Takuji Sasaki (National Institute of Agrobiological Sciences, Japan)
13:35 Chromosomal Genomics: Unlocking the 5GB Barley Genome
Klaus Mayer (MIPS, German Research Center for Environmental Health, Germany)
14:15 The Rice Annotation Project Database for Comparative Genomics
Tsuyoshi Tanaka (National Institute of Agrobiological Sciences, Japan)
14:35 Maize Genome Annotation: Transitioning from the Sequencing Project to MaizeGDB
Mary Schaeffer (MaizeGDB USDA/ARS Plant Genetics Research Unit, USA)
14:55-15:05 Break
15:05 DDBJ Read Annotation Pipeline: A Cloud Computing Based Analytical Tool for Next-generation Sequencing Data
Yasukazu Nakamura (National Institute of Genetics, Japan)
15:45 Annotation of Plant Proteins in UniProtKB/Swiss-Prot
Damien Lieberherr (Swiss Institute of Bioinformatics, Switzerland)
16:05 Characterizing Genetic Diversity and Creating Novel Gene Pools in Rice for Trait Dissection and Gene Function Discovery
Ramil P. Mauleon (International Rice Research Institute, Philippines)
18:00 - 21:00 Excursion : Tokyo Bay Dinner Cruise by Yakatabune