Scientific Program

Last updated: 10:54 AM May 24, 2015 (CST)
The presentation PDFs are made publicly available by courtesy of and with permission from their corresponding speakers.
Pre-conference Biocuration Training
Free of charge for both registered and non-registered participants
Wednesday 22 April 2015
Conference Hall, Beijing Institute of Genomics, Chinese Academy of Sciences
09:00 - 10:00 Wormbase literature curation workflow [Video (575M)]
Xiaodong Wang, WormBase & California Institute of Technology, USA
10:00 - 11:00 PubChem: a case study for managing big data [PDF]
Yanli Wang, National Center for Biotechnology Information, USA
11:00 - 12:00 Overview of annotation tools and curation workflow for the GENCODE gene sets [PDF] [Video (448M)]
Mark Thomas, Wellcome Trust Sanger Institute, UK
Thursday 23 April 2015
Function Room, Building 1, Beijing Friendship Hotel
09:00 - 12:00 Biocuration of GenBank & RefSeq [PDF] [PDF] [Video (551M)] [Video (644M)]
Ilene Mizrachi and Kim Pruitt, NCBI, USA
13:30 - 16:30 Biocuration of UniProt & Proteomics Databases [PDF] [PDF] [Video (285M)] [Video (433M)]
Claire O'Donovan and Sandra Orchard, EMBL-EBI
 
Thursday 23 April 2015
Beijing Friendship Hotel
13:00 - 18:00 Arrival & Registration
Function Room, Building 1
17:00 - 17:50 Plenary Session, Chaired by Alex Bateman
Function Room, Building 1
Keynote Lecture 1
Biocuration: Driven by Functional Studies for Biology [PDF]
Guoping Zhao, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China
18:00 - 21:00 Welcome Reception
Ya Shi Ting, Building 1
18:00 - 18:15 Introduction of National Scientific Data Sharing Platform for Population and Health
Depei Liu, Chinese Academy of Medical Sciences, China Chaired Weimin Zhu
18:15 - 21:00 Buffet Dinner
 
Friday 24 April 2015
Beijing Friendship Hotel
08:30 - 08:50 Welcome and Opening Remarks
Chaired by Weimin Zhu
JuYing Ballroom, Friendship Palace

Tieniu Tan
Deputy Secretary-General of Chinese Academy of Sciences

Alex Bateman
Chair of International Society for Biocuration

Weimin Zhu, Jingchu Luo, and Zhang Zhang
Organizing Chairs of Biocuration2015

08:50 - 10:10 Plenary Session, Chaired by Weimin Zhu
JuYing Ballroom, Friendship Palace
   08:50 - 09:40 Keynote Lecture 2
Biocuration in the community [PDF]
Alex Bateman, EMBL-EBI, UK
   09:40 - 10:10 Invited Lecture 1
Challenges and Practices of Big Data in Life Science [PDF]
Yixue Li, Shanghai Center of Bioinformation Technology, China
10:10 - 10:40 Group Photo and Coffee & Tea Break
10:40 - 12:00 Session 1: Curation and Data annotation: from molecules to communities
Chaired by Suzanna Lewis, Ilene Mizrachi
JuYing Ballroom, Friendship Palace
   10:40 - 11:00 The UniRule system to enable scaling from manual curation to large data sets [PDF]
Claire O'Donovan, EMBL-EBI
   11:00 - 11:20 Functional curation of sequence data for RefSeq [PDF]
Kim Pruitt, NCBI, USA
   11:20 - 11:40 MyVariant.info: community-aggregated variant annotations as a service [PDF]
Chunlei Wu, The Scripps Research Institute, USA
   11:40 - 12:00 APOLLO: SCALABLE & COLLABORATIVE CURATION OF GENOMES [PDF]
Monica Munoz-Torres, Lawrence Berkeley National Laboratory, USA
12:00 - 13:30 Lunch
Ju He Ting, Friendship Palace
13:30 - 14:50 Plenary Session, Chaired by Jingchu Luo
JuYing Ballroom, Friendship Palace
   13:30 - 14:20 Keynote Lecture 3
neXtProt: recent developments in the context of biocuration [PDF]
Amos Bairoch, Swiss Institute of Bioinformatics, Switzerland
   14:20 - 14:50 Invited Lecture 2
Detangling transcriptional complexity in GENCODE using cutting-edge transcriptomics and proteomics data [PDF]
Jennifer Harrow, Wellcome Trust Sanger Institute
14:50 - 15:50 Session 2: Curation: from genotype to phenotype
Chaired by Ming Qi
JuYing Ballroom, Friendship Palace
   14:50 - 15:10 Large-scale semantic mining of disease-phenotype annotations [PDF]
Robert Hoehndorf, King Abdullah University of Science and Technology, Saudi Arabia
   15:10 - 15:30 Annotation of functional impact of missense mutations in BRCA1 [PDF]
Pascale Gaudet, Swiss Institute of Bioinformatics, Switzerland
   15:30 - 15:50 PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal diseases [PDF]
Shur-Jen Wang, Medical College of Wisconsin, USA
15:50 - 16:10 Coffee & Tea Break
16:10 - 17:40 Concurrent Workshops
Workshop 1: Crowd/community curation: challenges & credit attribution
Chaired by Henning Hermjakob
JuYing Ballroom, Friendship Palace
  • Todd Taylor, RIKEN Center for Integrative Medical Sciences, Japan [PDF]
Workshop 2: Data visualization & annotation
Chaired by Rama Balakrishnan and Monica Munoz-Torres
Conference Room 4, Friendship Palace
17:40 - 19:00 Poster Session 1
Conference Rooms 1, 2, and 3, Friendship Palace
 
Saturday 25 April 2015
Beijing Friendship Hotel
09:00 - 10:20 Plenary Session, Chaired by Yixue Li
JuYing Ballroom, Friendship Palace
   09:00 - 09:50 Keynote Lecture 4
Big data to small data and back again: integrating biological data with the open access literature [PDF]
Johanna McEntyre, EMBL-EBI
   09:50 - 10:20 Invited Lecture 3
Interoperable metadata leads to integrative analyses [PDF]
Mike Cherry, Stanford University, USA
10:20 - 10:40 Coffee & Tea Break
10:40 - 12:00 Session 3: Biological database, tool & framework
Chaired by Vladimir Bajic
JuYing Ballroom, Friendship Palace
   10:40 - 11:00 The human proteome in UniProtKB [PDF]
Sylvain Poux, SIB Swiss Institute of Bioinformatics, Switzerland
   11:00 - 11:20 VCGDB: a dynamic genome database of the Chinese population [PDF]
Jiayan Wu, Beijing Institute of Genomics, CAS, China
   11:20 - 11:40 Epidaurus: A Platform for Aggregation and Integration Analysis of the Epigenome [PDF]
Liguo Wang, Mayo Clinic, USA
   11:40 - 12:00 The Bgee database: large-scale multi-species expression data [PDF]
Frederic Bastian, SIB Swiss Institute of Bioinformatics & University of Lausanne, Switzerland
12:00 - 13:30 Lunch
Ju He Ting, Friendship Palace
13:30 - 14:50 Plenary Session, Chaired by Juncai Ma
JuYing Ballroom, Friendship Palace
   13:30 - 14:20 Keynote Lecture 5
Challenges in the Future and Experiences in the Past of Genome Annotation
Takashi Gojobori, King Abdullah University of Science and Technology, Saudi Arabia
   14:20 - 14:50 Invited Lecture 4
Disease causing repeats and novel repeats in eukaryotic proteins
Xiu-Jie Wang, Institute of Genetics and Developmental Biology, CAS, China
14:50 - 15:50 Session 4: Drug & disease
Chaired by Yanli Wang
JuYing Ballroom, Friendship Palace
   14:50 - 15:10 Standardization and global knowledge exchange in metabolomics [PDF]
Reza Salek, EMBL-EBI
   15:10 - 15:30 BioExpress: An integrated RNA-seq derived gene expression database for pan-cancer analysis [PDF]
Yang Pan, The George Washington University, USA
   15:30 - 15:50 Bridge up chemical genomics and genomic information resources at NCBI [PDF]
Yanli Wang, NCBI, USA
15:50 - 16:10 Coffee & Tea Break
16:10 - 17:40 Concurrent Workshops
Workshop 3: Biocuration in big data to knowledge: new strategy, process & framework
Chaired by Francis Ouellette
JuYing Ballroom, Friendship Palace
Workshop 4: International collaboration in biocuration: projects & data/expertise sharing
Chaired by Claire O'Donovan and Sandra Orchard
Conference Room 4, Friendship Palace
17:40 - 19:00 Poster Session 2
Conference Rooms 1, 2, and 3, Friendship Palace
19:00 - 21:00 Special Workshop: Biocuration in China: importance, road map & priority
Chaired by Weimin Zhu, Jingchu Luo and Zhang Zhang
Conference Room 5, Friendship Palace
 
Sunday 26 April 2015
Beijing Friendship Hotel
09:00 - 10:20 Plenary Session, Chaired by Zhang Zhang
Ya Shi Ting, Building 1
   09:00 - 09:50 Keynote Lecture 6
Genomes: The good, the bad and the ugly - the limits of automatic biocuration [PDF]
Michal Linial, The Hebrew University, Israel
   09:50 - 10:20 Invited Lecture 5
Big and better but no junk [PDF]
Jun Yu, Beijing Institute of Genomics, CAS, China
10:20 - 10:40 Coffee & Tea Break
10:40 - 12:00 Session 5: Data standards & Ontologies
Chaired by Sandra Orchard and Pascale Gaudet
Ya Shi Ting, Building 1
   10:40 - 11:00 Ontology application and use at the ENCODE DCC [PDF]
Venkat Malladi, Stanford University, USA
   11:00 - 11:20 Applying OBO Foundry ontologies to model, annotate and query longitudinal field studies on malaria [PDF]
Jie Zheng, University of Pennsylvania, USA
   11:20 - 11:40 Phylogenetic- based gene function prediction in the Gene Ontology Consortium [PDF]
Huaiyu Mi, University of Southern California, USA
   11:40 - 12:00 Standards for public health genomic epidemiology to improve infectious disease outbreak detection and investigation [PDF]
Melanie Courtot, Simon Fraser University & BC Public Health Microbiology and Reference Laboratory, Canada
12:00 - 13:30 Lunch
Ju He Ting, Friendship Palace
13:30 - 14:30 Session 6: Literature mining
Chaired by Zhiyong Lu and Cecilia Arighi
Ya Shi Ting, Building 1
   13:30 - 13:50 TextpressoCentral: A universal portal to search and curate biological literature [PDF]
Yuling Li, California Institute of Technology, USA
   13:50 - 14:10 Construction of Phosphorylation Interaction Networks by Text Mining of Full-length Articles using the eFIP System [PDF]
Cecilia Arighi, Protein Information Resource & University of Delaware, USA
   14:10 - 14:30 SourceData: integrating biocuration within the publishing process [PDF]
Thomas Lemberger, EMBO, Germany
14:30 - 15:30 Concurrent Special Sessions: Lightning Talks
Special Session I: Chaired by Jingchu Luo
Ya Shi Ting, Building 1
   14:30 - 14:40 Bioso!  A Search Engine & Annotation Framework for Biological Big Data [PDF]
Yin Huang, Beijing Proteome Research Center, China
   14:40 - 14:50 Improved Data Representation of Very Large Macromolecules at Protein Data Bank [PDF]
Jasmine Young, RCSB Protein Data Bank, USA
   14:50 - 15:00 An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools [PDF]
Anyuan Guo, Huazhong University of Science and Technology, China
   15:00 - 15:10 Gene Curation Software at the Rat Genome Database: Update 2015 [PDF]
Stanley Laulederkind, Medical College of Wisconsin, USA
   15:10 - 15:20 dbPSP: a curated database for protein phosphorylation sites in prokaryotes
Zexian Liu, Huazhong University of Science and Technology
   15:20 - 15:30 Shared Resources, Shared Costs  Leveraging Biocuration Resources [PDF]
Sandra Orchard, EMBL-EBI
Special Session II: Chaired by Zhang Zhang
Conference Room 4, Friendship Palace
   14:40 - 14:50 Improving the Consistency of Domain Annotation within the Conserved Domain Database (CDD) [PDF]
Myra Derbyshire, NCBI, USA
   14:50 - 15:00 Automated collection, curation and analysis for Transcriptional and Epigenetic Regulation Data [PDF]
Hanfei Sun, Tongji University, China
   15:00 - 15:10 mycoCLAP, the Database for Characterized Lignocellulose-Active Proteins of Fungal Origin: Resource and Text Mining Curation Support [PDF]
Gregory Butler, Concordia University, Canada
   15:10 - 15:20 dbPPT: a comprehensive database of protein phosphorylation in plants [PDF]
Han Cheng, Huazhong University of Science and Technology, China
   15:20 - 15:30 Generating a focused view of Disease Ontology cancer terms for pan-cancer data integration and analysis [PDF]
Raja Mazumder, The George Washington University, USA
15:30 - 15:50 Coffee & Tea Break
15:50 - 17:20 Concurrent Workshops
Workshop 5: Genotype-2-phenotype: Curation challenges in translational & reverse
translational informatics

Chaired by Stanley Laulederkind
Ya Shi Ting, Building 1
  • Elvira Mitraka, University of Maryland/IGS, USA [PDF]
  • Hong Sun, Shanghai Center for Bioinformation Technology, China
  • Stacia Engel, Stanford University, USA [PDF]
  • Li Ni, The Jackson Laboratory, USA [PDF]
  • Stanley Laulederkind, Medical College of Wisconsin, USA [PDF]
Workshop 6: Money for biocuration: strategies, ideas & funding
Chaired by Renate Kania, Ulrike Wittig
Conference Room 4, Friendship Palace
17:20 - 17:40 Closing Session: Discussions, Awards and Closing Remarks
Chaired by Weimin Zhu
Ya Shi Ting, Building 1