data sharing of basic medicine in china
DESCRIPTION
THE FIFTH CHINA-US ROUNDTABLE ON SCIENTIFIC DATA COOPERATION. Data Sharing of Basic Medicine in China. Heng Wang, Professor, Director Institute of Basic Medical Sciences Chinese Academy of Medical Sciences School of Basic Medicine Peking Union Medical College , Beijing, 2011-10-27. - PowerPoint PPT PresentationTRANSCRIPT
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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