| 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 |
|
- Reception
- Restaurant LA TERRE in Miraikan (National Museum of Emerging Science and Innovation)
|
| 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) |
|
Click here to download the poster program (PDF)
|
| 17:30 - 18:30 |
|
|
Poster Presentations (odd number)
|
| 18:30 - 19:30 |
|
|
Poster Presentations (even number)
|
| 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) |
|
Click here to download the poster program (PDF)
|
| 17:30 - 18:30 |
|
|
Poster Presentations (even number)
|
| 18:30 - 19:30 |
|
|
Poster Presentations (odd number)
|
| 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 |
