Scientific Program

April 8, 2018
Crowne Plaza Hotel

Address:Crowne Plaza Ballroom A

8:00 – 18:00 Onsite Registration

Address: Growne Plazza Ballroom, 2nd floor

08:00 - 12:00

Pre-conference Training 1:

OntoChina and OBO Foundry Meet OHDSI China:

A Roadmap of Community-based Biomedical Ontology and Vocabulary Development for Big Data Innovation [Intro]

Co-Chairs: Yongqun “Oliver” He, Guoqian Jiang

Speakers: Jie Zheng, Yongqun “Oliver” He, Suzanna Lewis, Xiaolin Yang, Yan Zhu, Wei Zhou, Mengchun Gong, Li Wang, Guoqian Jiang

12:00 - 13:30


DATABASE Editorial Board meeting

13:30 - 15:00

Pre-conference Training 2:

CIVIC team from Washington University School of Medicine

15:00 - 17:30

Pre-conference Training 3:

Real World Medicine and Real World Patients: Critical Understanding forTranslational and Precision Medicine [Intro]

Michael N. Liebman, PhD, Managing Director, IPQ Analytics, Invited Professor, Shanghai Center for Bioinformatic Technology, Adjunct Professor, Drexel College of Medicine

18:00 - 18:15

Opening Ceremony

18:15 - 19:05

Keynote Lecture 1:

Li Jin, Fudan University, China

19:05 - 20:00

Table Meal

April 9, 2018
Crowne Plaza Hotel

09:00 – 12:00    Plenary Session

Chaired by: Professor Lei Liu Fudan University

Address:Crowne Plaza Ballroom A+B

09:00 - 09:50

Keynote Lecture 2

Interpreting Newborn Genomes

Steven E. Brenner, University of California, United States

09:50 - 10:20

Invited Talk 1

Text Mining and Deep Learning for Biocuration [Intro]

Zhiyong Lu, NCBI, United States

10:20 - 10:40

Coffee Break

10:40 - 11:40

Session 1 DATABASE Paper Talk

10:40 – 11:00 Talk 1

Micropublication: Incentivizing Community Curation and Placing Unpublished Data into the Public Domain

Daniela Raciti

11:00 – 11:20 Talk 2

GEOMetaCuration: A web-based system for the accurate manual curation of Gene Expression Omnibus (GEO) metadata

Yu, Peng

11:20 – 11:40 Talk 3

CITGeneDB: a comprehensive database of mouse genes enhancing or suppressing cold-induced thermogenesis validated by perturbation experiments.

Yu, Peng

11:40 - 12:10

Invited Talk 2

Hui LV

12:10 - 13:30


13:30 - 15:30

Workshop 1

Address:Crowne Plaza Ballroom A

Careers in Biocuration: An overview of the current status, challenges and goals in the biocuration fieldBeyond [Intro]

Chaired by: Nicole Vasilevsky, Cecilia Arighi, Randi Vita

13:30-15:30   Session 2: Abstract Talk -- Functional Annotation

Chaired by Alex Bateman, European Bioinformatics Institute (EMBL-EBI)

Address:Crowne Plaza Ballroom B


Submission 7

Improvements to phenotype annotations in FlyBase.[Abstract]

Dr. Silvie Fexova,University of Cambridge, Department of Physiology, Development and Neuroscience


Submission 10

wwPDB Biocuration: A Global Enterprise Supporting High-Quality Open Biological Data. [Abstract]

Jasmine Young, RCSB Protein Data Bank


Submission 12

MeSHLabeler and GOLabeler, Recent Progress in Large-Scale MeSH Indexing and Protein Function Prediction. [Abstract]

Shanfeng Zhu, Fudan University


Submission 18

Representative functional immunoglobulin (IG) genes in UniProtKB/Swiss-Prot. [Abstract]

Sylvain Poux, Swiss-Prot


Submission 24

Surpassing the Data Deluge: Semantic Digitization of BioScience Experimental Data . [Abstract]

Pratibha Gour, Department of Plant Molecuar biology, University of Delhi, South Campus


Submission 54

The NHGRI-EBI Genome-Wide Association Studies (GWAS) Catalog - imposing structure on unstructured data.[Abstract]

Aoife McMahon, European Bioinformatics Institute (EMBL-EBI)


Submission 46

Annotare – annotating and sharing functional genomics data through ArrayExpress and Expression Atlas. [Abstract]

Anja Füllgrabe, European Bioinformatics Institute (EMBL-EBI)


Submission 48

InterMine: Integrative Analysis Across Multiple Organisms. [Abstract]

Rachel Lyne, University of Cambridge


Submission 62

Curation of rapidly-evolving and potentially controversial hypotheses of anatomical homology. [Abstract]

Frederic BASTIAN, University of Lausanne, SIB Swiss Institute of Bioinformatics


Submission 63

Gene and Protein Expression Data at the Saccharomyces Genome Database. [Abstract]

Edith Wong, Stanford University


Submission 88

Phylogenetic- based gene function prediction in the Gene Ontology Consortium. [Abstract]

Huaiyu Mi, University of Southern California


Coffee Break & Poster session 1.


Workshop 2

Address:Crowne Plaza Ballroom A
Database Resources of the BIG Data Center [Intro]

Lead organizers: Yiming Bao, Weimin Zhu, Zhang Zhang, Wenming Zhao, Jingfa Xiao

16:30 – 17:30 Session 3: Abstract Talk – Curation Standards and Best Practice; data and annotation quality

Chaired by Claire O‘Donovan, European Bioinformatics Institute

Address:Crowne Plaza Ballroom B


Submission 4

What MODs can learn from Journals - a GigaDB curator's perspective. [Abstract]

Mary Ann Tuli, GigaScience Journal. BGI-Hong Kong


Submission 47

NetworkCurator – a platform for team-based creation and annotation of networks. [Abstract]

Tomasz Konopka, Queen Mary University of London


Submission 66

The Alliance of Genome Resources, the Many work as One. [Abstract]

J. Michael Cherry, Stanford University


Submission 74

BioCode: archiving bioinformatics codes for open source projects. [Abstract]

Lili Hao, Beijing Institute of Genomics


Submission 111

SABIO-RK: a resource for manually curated biochemical reaction kinetics. [Abstract]

Andreas Weidemann, HITS gGmbH Heidelberg


Submission 116

neXtProt: a knowledgebase on human proteins. [Abstract]

Valentine Rech de Laval, SIB Swiss Institute of Bioinformatics, University of Geneva (UNIGE)

April 10, 2018
Crowne Plaza Hotel

09:00 – 12:00   Plenary Session

Chaired by Zhang Zhang, Beijing Institute of Genomics, Chinese Academy of Sciences

Address:Crowne Plaza BallroomA+B

09:00 – 09:50

Keynote Lecture 3

Big Data to Knowledge: Integrated Bioinformatics towards Systems Biology and Precision Medicine [Intro]

Cathy Wu, University of Delaware, United States

9:50 - 10:20

Invited Talk 3

Graphical curation of biomolecular pathways[Intro]

Jing-Dong Jackie Han, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

10:20 - 10:40

Coffee Break

10:40 – 11:40

Session 1 DATABASE Paper Talk

10:40 – 11:00 Talk 1

Prevention of Data Duplication for High-Throughput Sequencing Repositories

Gabdank, Idan

11:00 – 11:20 Talk 2

Updated regulation curation model at the Saccharomyces Genome Database

Engel, Stacia

11:20 – 11:40 Talk 3

Identification of Errors in the IEDB Using Ontologies

Vita, Randi

11:40 - 12:10

Invited Talk 4

Graphical curation of biomolecular pathways [Intro]

Henning Hermjakob, European Bioinformatics Institute (EMBL-EBI)

12:10 – 13:30


13:30 - 15:00

Workshop 3

Address:Crowne Plaza Ballroom A

Clinical and Translational Data Curation and Harmonization [Intro]

Dr. Reinhard Schneider, Head of Bioinformatics Core Facility, Luxembourg Centre for Systems Biomedicine (LCSB)

Dr. Samiul Hasan, Director, Data Analytics Solution Engineer, GlaxoSmithKline plc.

Dr. Martin Romacker, Principal Scientist, Roche Innovation Center Basel, Switzerland

Dr. Paul Houston, European Liaison at CDISC

13:30 - 15:00    Session 5: Abstract Talk – Data Standards and Ontologies

Chaired by Cathy Wu, University of Delaware

Address:Crowne Plaza Ballroom B

13:30 - 13:40

Submission 1

Curation of 30,000 Polysomnograms for the U.S. National Sleep Research Resource - towards a sleep data commons.[Abstract]

Guo-Qiang Zhang, Institute for Biomedical Informatics, the University of Kentucky

13:40 - 13:50

Submission 11

Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.[Abstract]

Valerio Arnaboldi, California Institute of Technology

13:50 - 14:00

Submission 14

Automation to augment the biocuration of ontologies mapping.[Abstract]

Rama Balakrishnan, Pistoia Alliance Inc

14:00 - 14:10

Submission 21

Modular-based mapping between HPO and MPO provides a new approach to decipher phenotypic mechanisms. [Abstract]

Yunxiang Liang, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University

14:10 - 14:20

Submission 25

Designing a Standard Framework for Describing Chinese Publications Based on JATS Standard. [Abstract]

Hongyu Kang, Institute of Medical Information &Library, Chinese Academy of Medical Sciences

14:20 - 14:30

Submission 69

BioThings Explorer:cross-linking biological APIs for Knowledge Exploration [Abstract]

Jiwen Xin,The Scripps Research Institute

14:30 - 14:40

Submission 43

The China Biomedical Ontology Consortium (abbreviated as “OntoChina”): Coordinating the research, development, and applications of biomedical ontologies in China. [Abstract]

Xiaolin Yang, Peking Union Medical College

14:40 - 14:50

Submission 115

Research on Metadata Standards of Biomedical Data Repository. [Abstract]

Jiawei Cui, Chinese Academy of Medical Science & Peking Union Medical College

14:50 - 15:00

submission 118

Domain annotation and combined alignment visualization enhance remotely related protein search with PSISearch2D


15:00 - 16:00

Coffee Break & Poster session 2

16:00 - 17:30

Workshop 4

Address:Crowne Plaza Ballroom A

Precision Medicine Knowledge Base [Intro]

Chaired by Lei Liu, Lei Wang

16:00 - 17:30    Session 6: Abstract Talk -- Precision Medicine

Chaired by Weidong Tian, Fudan University

Address:Crowne Plaza Ballroom B

16:00 - 16:10

Submission 3

Computational Approach to Prediction of Human Gene - Phenotype Association for Intrinsically Disordered Proteins. [Abstract]

Vladimir Perovic,Institute of Nuclear Sciences Vinca

16:10 - 16:20

Submission 31

OncoMX: a community web portal to search integrated cancer mutation and expression database for the detection of cancer biomarkers. [Abstract]

Raja Mazumder, School of Medicine & Health Sciences, The George Washington University

16:20 - 16:30

Submission 45

Systems Medicine Disease Maps: the roadmap for integrated representation of disease mechanisms. [Abstract]

Inna Kuperstein, Department of Bioinformatics and Computational Systems Biology of Cancer, Institut Curie

16:30 - 16:40

Submission 58

A strategy to create a comprehensive disease ontology for human disease curation. [Abstract]

Nicole Vasilevsky,  Oregon Health & Science University

16:40 - 16:50

Submission 81

Mining Drug Therapy Knowledge from Electronic Medical Records. [Abstract]

Haomin Li, Zhejiang University

16:50 - 17:00

Submission 87

Facilitate Data Curation in Translational Medicine: NCER-PD Data and Computing Platform for the National Centre of Excellence in Research on Parkinson’s Disease Project. [Abstract]

Reinhard Schneider, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg

17:00 - 17:10

Submission 91

de novo assembly of a northern Chinese genome. [Abstract]

Zhenglin Du, BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences

17:10 - 17:20

Submission 96

Construction of a Pragmatic Ontology in Medicine: Application to Real World Clinical Practice and Drug Development. [Abstract]

Michael Liebman, IPQ Analytics

17:20 - 17:30

Submission 98

Biocuration to Cancer Genomics. [Abstract]

Paula Carrio Cordo, University of Zurich

April 11, 2018
Crowne Plaza Hotel

09:00 – 12:00    Plenary Session

Chaired by Weimin Zhu, National Center for Protein Sciences. Beijing

Address:Crowne Plaza BallroomA+B

09:00 – 09:50

Keynote Lecture 4

Towards a Data-Driven Industry – The Emerging Importance of Data Quality and Data Curation in the Life Sciences [Intro]

Martin Romacker, Roche Innovation Center Basel, Switzerland

9:50 - 10:20

Invited Talk 5

Naming of biomedical entities and text mining[Intro]

Vladimir B. Bajic, King Abdullah University of Science and Technology (KAUST), Saudi Arabia.

10:20 – 10:45

Coffee Break

10:45 – 11:30

Session 1 DATABASE Paper Talk

10:45 – 11:05 Talk 1

FAIR principles and the IEDB: Short-term improvements and a Long-term vision of OBO-Foundry mediated machine-actionable interoperability.

Vita, Randi

11:05 – 11:25 Talk 2

Signalling maps in cancer research: construction and data analysis

Kondratova, Maria

11:30 – 12:30

Industrial Talk

Digital China Health

12:00 – 13:30


13:00-13:30  ISB general meeting

Address:Meeting Room 3

13:30 - 15:00

Workshop 5

Address:Crowne Plaza Ballroom A

Data Driven Biomedical Discovery[Intro]

Chaired by Hui Lu,Weimin Zhu,Shanghai Jiaotong University

13:30 - 15:00   Session 8: Abstract Talk – Data Integration and Visualization

Chaired by Cecilia Arighi, University of Delaware

Address:Crowne Plaza Ballroom B

13:30 - 13:40

Submission 9

Wikidata Crowdsourcing Model for Enhancing DO Curation. [Abstract]

Gregory Stupp, The Scripps Research Institute

13:40 - 13:50

Submission 16

Disease Portals at the Rat Genome Database: Disease-Focused Platforms for Rat and Disease Researchers. [Abstract]

Elizabeth Bolton, Medical College of Wisconsin

13:50 - 14:00

Submission 39

dbRED:a visualized database of A-to-I RNA editing events. [Abstract]

Chenghui Zhao, Beijing Institute of Radiation Medicine

14:00 - 14:10

Submission 76

Representing Protein Interactions in the UniProtKB database. [Abstract]

Sandra Orchard, The European Bioinformatics Institute(EMBL-EBI)

14:10 - 14:20

Submission 97

iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations [Abstract]

Jiaqi Zhou,Huazhong University of Science and Technology

14:20 - 14:30

Submission 92

dbPAF: an integrative database of protein phosphorylation in animals and fungi. [Abstract]

Shaofeng Lin, Huazhong University of Science and Technology

14:30 - 14:40

Submission 106

Integbio Database Catalog: new features and updates.[Abstract]

Tomoe Kamada-Nobusada, National Bioscience Database Center, Japan Science and Technology Agency

14:40 - 14:50

Submission 104

Bioso! RESTful Interfaces – A Programing Framework (API) for Data Annotation. [Abstract]

Benyu Zhang, National Center for Protein Science . Beijing

14:50 - 15:00

Submission 28

Data integration: overcoming challenges and creating opportunities. [Abstract]

Jana Sponarova, Nebion AG

15:00 - 15:10

Submission 23

JASPAR: a comprehensive database of transcription factor binding profiles. [Abstract]

Aziz Khan, University of Oslo

15:20 - 15:40

Coffee Break

15:40 – 16:10

Career Talk

Curating bioimaging data - lessons from the first 40 terabytes[Abstract]

Eleanor Margaret Williams, Genomics England Limited

16:10 - 16:40

Closing Session

Address:Crowne Plaza BallroomA+B

Scientific Sessions

Precision Medicine

Phenotypes, genotypes, and variants

Data Standards and Ontologies

Text Mining

Functional Annotation

Community Annotation

Data Integration and Visualization

Deep Learning in curation process

Software, Applications and Systems in biocuration

Curation Standards and Best Practice; inference from evidence; data and annotation quality