Data Sharing of Basic Medicine in China

Data Sharing of Basic Medicine in China

Heng Wang, Professor, DirectorInstitute of Basic Medical Sciences

Chinese Academy of Medical Sciences

School of Basic Medicine

Peking Union Medical College

， Beijing, 2011-10-27

THE FIFTH CHINA-US ROUNDTABLE ON SCIENTIFIC DATA COOPERATION

ABOUT BMICC

BioMedical Informatics Center of China

Molecule --Individual--Population

Scientists in all of the world

24 hour service

Original scientific data

produced in China

29 databases ◙ Population Survey Database (8)

◙ Molecular Mechanism Database

(14)

◙ Biomodel Organism Database (5)

◙ Experiment Material Data Resource (2)

Integrated and Shared

Sharing Database (1)

Database Sub-centers

(1) Physiological Reference Database of Chinese

IBMS

(2) Psychological Reference Database of Chinese

IBMS

(3) Chinese Visible Human Third Military Medical

University

(4) Sub-health database of Chinese IBMS

(5) Maternal and Child Nutrition Reference Database

Capital Institute of Pediatrics

Database Sub-centers

(6) NcRNA (The database of all kinds of noncoding RNA)

ICT CAS

(7) NPInter ( Functional interactions between noncoding RNAs and proteins Database)

IB CAS

(8) ATID (Alternative Translational Initiation Database)

TsinghuaUniversity

(9) dbRES (dbRES: A web-oriented database for annotated RNA Editing Site)

Tsinghua University

Sharing Database (2)

Database Sub-centers

(10) dbNEI(database for Neuro-Endocrine-Immune)

Tsinghua

University

(11) SPD(Secreted Protein Database) Peking Universi

ty

(12) SynDB(Synapse Database) Peking Universi

ty

(13) The Biology Database FTP Mirror Site Peking Universi

ty

(14) Human Urinary Proteome Database IBMS

(15) Database of potential target genes for clinical diagnosis and immunotherapy of human carcinoma

ICT CAS

(16) Natural sense-antisense transcripts database   

Peking Universi

ty

Sharing Database (3)

Database Sub-centers

(17) Natural sense-antisense transcripts database

PekingUniversity

(18) ChickVD(Chicken Variation Database) BeijingGenomicsInstitute

(19) SilkDB(Silkworm Knowledgebase) BeijingGenomicsInstitute

(20) PigGIS(Pig Genomic Informatics System)

BeijingGenomicsInstitute

(21) TFDB(Transcription Factor Databases) PekingUniversity

Sharing Database (4)

Database Sub centers

(22) China National Cell Resources Confederation

IBMS

(23) Phenotype Database for Genetically Engineered Mouse Disease Models

Model Animal Research Certer

of NanjingUniversity

(24) Liver Expression Profile Beijing Proteome

Research Center

(25) A Multi-center Survey on Cardiovascular Diseases in Chinese

CAMS

(26) Database on antiCODE IB CAS

Sharing Database (5)

New Database in 2011 Sub centers

(1) Tetrahymena Gene Expression Database

Institute of Hydrobioloty , CAS

(2) Health Survey Database of Yi People, China

IBMS, CAMS

(3) Health Survey Database of Chinese Children and teenagers

Capital Institute of Pediatrics

Sharing Database (6)

Online Tools

◙ MiRAlign

◙ MethCGI

◙ SubMito

◙ PhoScan

Resources of Data

Requirements

Original

Quality

Data from Laboratory

Data from

Cell Laboratory

Data from Health Survey

Chinese physiological reference dataset

Population: 130,000

Provinces: 9

Races: 8

Variables in dataset: 247

Zhejiang

Heilongjiaang

Inner Mongolia

Heb

ei

Sichuan

Guangxi

Hu

na

n

Yunnan

Distribution of areas

for physiological reference survey in China

Ningxia

Yan Huang database

Yan Huang database

  (Beijing Genomics Institute at Shenzhen )

• The genome, named as YH, is a very start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years.

• To illustrated the personal genome data in a MapView, which is powered by GBrowse.

• A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads.

Yan Huang database • Efforts on designing the YH database

are helpful attempts to organize and present personal genome data, which is a useful resource for genomic and medical researches.

• As the third published personal genome, YH diploid genome accelerates the discovery of disease gene and mutation in Asian population.

Yan Huang database

Data Statistics

Nucleotide

Total 117.7Gbp

Map to genome 102.9Gbp

Coverage of genome 99.97%

Polymorphism

SNP 3.07M

Indel 135262

Structural Variation 2682

Maternal and Child Nutrition Reference Database

Maternal and Child Nutrition Reference Database

• Population

Child and women in 14 provinces, China

• Information

Incidence of low birth weight

Incidence of anaemia in reproductive aged

women

Prevalence of Vitamin A deficiency in child

• Self-evaluation

Fetus weight

Anaemia in reproductive aged women

Vitamin A deficiency in child

A database on genetically engineered

mouse and mouse models

• Introduction• Reproductive information• disease models• Special use• Reference

News of research on life sciences

GOAL OF BMICC

★ To create a national scientific data sharing center for biomedical information★ To establish the technical platform for integrating and sharing the scientific

data★ To collect and integrate more valuable and available databases related to the study on health and diseases in China ★ To provide the data sharing services for various users in different requirements

• Institute of Basic Medical Sciences, CAMS

• Center for Bioinformatics in Peking University;

• Institute of Biophysics of CAS;• Institute of Computing Technology of

CAS ;  • Beijing Genomics Institute ;• Beijing Genomics Institute at Shenzhen • Bioinformatics Division Tsinghua

University;

Co-Units

13 institutes/universities, 5 provinces,

• Beijing Proteome Research Center;

• Model Animal Research Certer of

Nanjing University

• Capital Institute of Pediatrics;

• Third Military Medical University ;

• Fuwai Hospital, CAMS

• Institute of Hydrobioloty , Chinese

Academy of Sciences

Co-Units

Sharing & service

Browse Record Distribution by Month

Browse Record Distribution by Countries

Distribution of users all of the world

--- Oct. 20th, 2011

520,596 person-times

VISITERS from all of the world

• Scientists / specialists

• Health officials

• Students

• Public

User groups in China

Administration Model

Institutes in CAMS & PUMC

• Institute of Basic Medical Sciences

• Institute of Medical Information

• Institute of Laboratory Animal Science

• Institute of Clinical Medicine

• Institute of Oncology

• Institute of Cardiovascular Disease

• Institute of Plastic Surgery

• Institute of Hematology

• Institute of Dermatology

• Institute of Materia Medica

• Institute of Medicinal Biotechnology

• Institute of Medicinal Plants

– Yunan Branch

– Hainan Branch

• Institute of Microcirculation

• Institute of Radiation Medicine

• Institute of Blood Transfusion

• Institute of Medical Biology

• Institute of Biomedical Engineering

• Institute of Pathogen Biology

Standards

Resource system Technology platform

BMICCClinicalCenter

Public Health Center

Traditional

Medicine

DrugCenter

Monitor and evaluation

LocalLink

Users

InternetInternet

Users

National Medical Scientific data Sharing Network www.ncmi.cn

交换机

JOINY CONFERENCE

Authoritativeness

◘ Strategies

◘ Aim and assignment

of the sub-centers

◘ Financial plan

MANAGEMENT OFFICE

Implementation

◘ Routine activities

◘ Collect and integrate database

◘ Maintain the work on technique

platform and network

ACADEMIC COMMITTEE

Academic activities

◘ Technical advisory

◘ Monitor and revise

◘ Evaluation

Work team

RULES AND STANDARDS (1)

☆ Technical standards for data sharing

☆ The metadata standards

☆ The terminological standards in

medicine

☆ The standards on the quality control for

data searching

☆ The service guide

☆ A manual for developing technique

framework

☆ Guide for data set execution.

☆ A rule for data backup management

RULES AND STANDARDS (2)

Challenge and development

Challenge

★ Impact on biomedical researchers

★ Weaker consciousness on sharing among

researchers

★ Requirement for specialists on cross-

sciences (biomedical and computer

science)

★ Financial support on maintaining the

network for a long term development

★ Continuing to search new data

★ To improve performance of technique

platform

★ To develop the conjunction among

datasets

★ International communication & cooperation

★ Wireless access supporting

★ Online self-evaluation on health

Plan for the next step

OUTLINE

★ About

★ Administration model

★ Implementation and Progress

★ Sharing and service

★ Challenge and development

• 　

• To initiate the data sharing center from 2006.

• One of the national scientific data sharing projects supported by the Ministry of Sciences and Technology of China.

National Medical Scientific Data Sharing Network (2006-2009)

National Scientific Data Sharing Network for Population and Health (2009)

National Biomedicine Database (2001-2006)

BioMedical Information Center of China (BMICC) (2006 -)

Review

Research Funding

National Science Fund of China (NSFC)

National Science Fund for Distinguished Young Schoolars, NSFC

Beijing Natural Sciences Foundation

The National Program for Key Basic Research Projects ( 973)

The National High Technology Research and Development Program (863)

The Research Fund for Doctoral Program of Higher Education

Project of Ministry of Science and Technology

International cooperation program from NIH, US

International Cooperation program between China and Europe

Chinese Medical Board (CMB) from America

Implementation & Progress

The categories of variables surveyed• Characteristics of demography• Anthropometric measures • Account of blood cells• 血生化检验• 尿常规检验• 心电图检查• 免疫学检查• 循环系统• 呼吸系统

Data profile of Chinese physiological reference

未来

• 规范管理• 提升优质服务水平• 对外宣传扩大影响• 服务质量监督

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