Construction Modelof Data Sharing Network

for Basic Medicine

Construction Modelof Data Sharing Network

for Basic Medicine

Institute of Basic Medical SciencesChinese Academy of Medical Sciences

School of Basic MedicinePeking Union Medical College

OUTLINE

• About Bmicc• Administration mechanism• Implementation and Progress• Sharing database and service• Challenge and development

•

ABOUT BMICC

• Is one of the national scientific data sharingprojects.

• Based on the data resource whichdistributed at universities,researchinstitutes and scientists,as well as the datafrom research projects were integrated .

• Have been set up the rules for technicalstandards ,data sharing, managementrules ,quality control of the databases andservice guide.

GOAL OF BMICC

• Establish the technical platform releasingto the entire society to push forwardChina's scientific data sharing;

• assemble more valuable and availabledatabases especially for pathogeny of theserious diseases;

• Build database integration for specialresearch field in order to give moreconvenience to users.

• Institute of Basic Medical Sciences

• PUMC School of Basic Medicine

More than 300 facultymembers in 13

academicdepartments

114 full and associateprofessors

5 academy members

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

• Beijing Genomics Institute ;• Center for Bioinformatics in Peking University;

• Bioinformatics Division Tsinghua University;• Beijing Proteome Research Center;

• Model Animal Research Certer of Nanjing University• Capital Institute of Pediatrics;

• Third Military Medical University ;

SUB-CENTER

Sharing Network

BMICC.CN

Data-base

Client

• 25 databases have been recruited

• Human Database (6)

• Molecular Mechanisms Database (13)

• Biomodel Organism Database (4)

• Experiment Material Data Resource(2)

• Online Tools (4)

DATA SHARING

Administrationmechanism

ADMINISTRATION MODEL

JOINYCONFERENCEAuthoritativeness

Strategies. Aim and assignment of

the sub-centers. Financial plan.

Evaluation

ACADEMICCOMMITTEEAcademic activities

Technical advisory

Examine and revise

Evaluation

MANAGEMENTOFFICE

Organize, coordinate,

ensure , carry out the

routine activities.

SUB-CENTER

Design, database, renew

and take responsibility to

the quality of the database.

RULES AND STANDARDS

• technical standards for data sharing;• the metadata standards of the BMICC;

• The terminological standards in medicine,

pharmaceutical and hygiene;

• the rules for the quality control of thedatabases ;

• the service guide.

• The Manual of the Data Sharing Framework

• Guide for data set execution.

• The rule for data backup management

Implementation andProgress

AVAILABLE DATABASE

CapitalInstitute ofPediatrics

Maternal and Child Nutrition Reference

DatabaseofChina http://www.bmicc.org.cn/web/share/search/eys

Database Subcenters

Physiological Reference Database of Chinese

http://www.bmicc.org.cn/web/share/search/intros

IBMS

Psychological Reference Database of Chinesehttp://www.bmicc.org.cn/web/share/search/itemintro

IBMS

Chinese Visible Humanhttp://www.bmicc.cn/web/share/search/cvh

ThirdMilitaryMedica

University

Sub-health database of Chinesehttp://www.bmicc.org.cn/web/share/search/subhealt

IBMS

AVAILABLE DATABASEDatabase Sub

centers

NcRNA(The database of all kinds of noncoding RNA)http://www.noncode.org/

ICT CAS

NPInter( Functional interactions between noncoding

RNAs and proteins Database)http://bioinfo.ibp.ac.cn/NPInter/demo

IB CAS

ATID(Alternative Translational Initiation Database)http://bioinfo.au.tsinghua.edu.cn/atie/

TsinghuaUniversity

dbRES(dbRES: A web-oriented database forannotated RNA Editing Site)http://bioinfo.au.tsinghua.edu.cn/dbRES/

TsinghuaUniversity

AVAILABLE DATABASE

IBMSHuman Urinary Proteome Databasehttp://www.bmicc.cn/web/share/search/hupd

ICT CASdatabase of potential target genes for clinical diagnosisand immunotherapy of human carcinomahttp://www.bioinfo.org.cn/hptaa/

Database Subcenters

dbNEI(database for Neuro-Endocrine-Immune)http://bioinfo.au.tsinghua.edu.cn/dbNEIweb/

TsinghuaUniversity

SPD(Secreted Protein Database)

http://spd.cbi.pku.edu.cn/

PekingUniversity

SynDB(Synapse Database)

http://syndb.cbi.pku.edu.cn/

PekingUniversity

The Biology Database FTP Mirror Site

ftp://ftp.cbi.pku.edu.cn /PekingUniversity

AVAILABLE DATABASE

PekingUniversity

TFDB(Transcription Factor Databases)http://planttfdb.cbi.pku.edu.cn/

Database Subcenters

natural sense-antisense transcripts database

http://natsdb.cbi.pku.edu.cn

PekingUniversity

ChickVD(Chicken Variation Database)

http://chicken.genomics.org.cn

BeijingGenomicsInstitute

SilkDB(Silkworm Knowledgebase)http://silkworm.genomics.org.cn

BeijingGenomicsInstitute

PigGIS(Pig Genomic Informatics System)

http://pig.genomics.org.cn

BeijingGenomicsInstitute

AVAILABLE DATABASE

IB CAS人类天然转录基因及反向转录基因数据库

Database Sub centers

China National Cell Resources Confederation

http://www.bmicc.org.cn/web/share/search/cell

IBMS

Phenotype Database for Genetically EngineeredMouse Disease Modelshttp://218.2.105.149:8011/wsjxc.asp

Model AnimalResearchCerter ofNanjing

University

Liver Expression Profile Beijing ProteomeResearchCenter

中国人群心血管健康多中心合作研究 CAMS

ASSEMBLE MORE VALUABLE ANDAVAILABLE DATABASE

• Yan Huang database(Genomics Institute at Shenzhen )

• The database for Yanhuang1 is designed for presentingthe entire DNA sequence of the first asian. A wellstructed browser and a platform for primitive personalmedicine research is included .

• in order to solve the problems, especially forthose Chinese-specific genetic diseases

• Yan Huang database will build the mirror site in BMICC.

DATABASE INTEGRATION

Initiate two projects for Database integration

● human liver cancer intergreted database

● the application of bioinformatics database

cluster and integration

Sharing databaseand service

• Accentuate the service capacity

• Set up Information collection system.

for tryout and getting feedback from users inorder to improve the function and efficiency ofdata sharing service.

The Total Visits 170300 person-time

United States 97322 person-timeAustralia 36688China 30567Germany 2936Japan 737Great Britain 423South Korea 351

( 1 /2008--- 3 /2009 )

VISITERS FROM ALL OF THEWORLD

Challenge anddevelopment

• Database integration• Service integration (grid service, web

service)• Tools integration (command line, User

Interface… )• Data warehouse• Set mirror site in BMICC

INTEGRATION SOLUTION

• Resource searching• Database combined searching• User subscription• Online learning and education• Information push service• Analysis, statistic and reporting• Wireless access supporting• Help center

APPLICATIONS & SYSTEMS

• Professionals will be trained by thisprogram to have the expertise for themanagement of this center.

• More efficacious administrationsystem.

TEAM OF PROFESSIONALS

• Standard for data collection and managementbetween US & China

• Standard for the construction of the data sharingplatform

• Strategies and mechanism of the data sharingsystem

• A professional team fully supported by thegovernment is necessary for the program.

The crucial questions about theInternational data sharing for Biomedicine

•加入1-2张生理心理数据库的图片和资料

• The newest personal data collected from more than

40,000 healthy Chinese living in different areas,

including urban, countryside, highlands and coastland,

with 30-55 items each person.

Physiological & PsychologicalReference of Chinese

(Institute of Basic Medical Sciences,CAMS)

http://www.bioinfo.org.cn/NONCODE/Database of NONCODE

(Chinese Academy of Sciences)

A brand-new database of all kinds of noncoding RNAs(except tRNAs and rRNAs) distinguished from otherncRNA databases by:

• big, and almost all traditional ncRNA classes areincluded;

• >80% data are from experiments;• Use a new classification system--process function

classification system, which based on the cellularprocess it takes part in;

• provides an efficient search option, allowing recoveryof sequence, related publications and other information.

http://www.bioinfo.org.cn/NPInter/(Chinese Academy of Sciences)

•A new database covering eight category

functional interactions between noncoding

RNAs (except tRNAs and rRNAs) and

proteins related biomacromolecules (proteins,

mRNAs and genomic DNAs) in six model

organisms, E. coli, yeast, worm, fly, mouse

and human

http://chicken.genomics.org.cnChicken Variation Database, ChickVD

(Beijing Genomics Institute )

• ChickVD hosts the high-quality sequence variation data, variationanalysis in the context of chicken genes, cDNAs, chicken orthologsof human disease genes, genetic markers, quantitative trait loci(QTLs) etc .

• All data are uniquely mapped onto the RJF draft genome andgraphically represented in MapView, an efficient visualization toolthat allows users to browse sequence variations in the genomic andfunctional context.

• The sub-viewer TraceView assists users to view the vivid graphicsof the original traces around the detected SNP.

http://bioinfo.au.tsinghua.edu.cn/atie/Alternative Translational Initiation Database

(Tsinghua University)

• The use of alternative translation initiation codons in asinge mRNA contributes to the generation of proteindiversity. The genes produce two or more versions of theencoded proteins, and the shorter version, initiated froma downstream in-frame start codon, lacks the N-terminalamino acids fragment of the full-length isoform version.ATID is established to provide data of publicly availablegenes, alternatively translational isoforms and theirdetailed annotation......

http://bioinfo.au.tsinghua.edu.cn/dbNEIweb/http://bioinfo.au.tsinghua.edu.cn/dbNEIweb/about.php

database for neuro-endocrine-immune (dbNEI)

(Tsinghua University)

• A web-based knowledge resource specific for the NEI systems. It

provides a knowledge environment for understanding the main

regulatory systems of NEI in a molecular level. dbNEI collects 1,058

NEI related signal molecules, their 940 interactions and 72 affiliated

tissues from the Cell Signaling Networks database, manually selects

982 NEI papers from PubMed, and gives links to 27,848 NEI related

genes from UniGene database.

http://spd.cbi.pku.edu.cn/Secreted Protein Database, SPD

(Peking University)

• Secreted proteins from Human, Mouse and Ratproteomes, which includes sequences from SwissProt,Trembl, Ensembl and Refseq. Such a collection isnamed as SPD, Secreted Protein Database.

• The 18152 entries were classified into fourteenfunctional categories, including "apolipoprotein","cytokine", "protease", "toxin", etc.

• To make the dataset more comprehensive, nine relateddatasets were also collected, such as SPDI, Rikenmouse secretome, SwissProt vertebrate secretedproteins, SubLoc etc.

http://datf.cbi.pku.edu.cn/Database of Arabidopsis

Transcription Factors, DATF(Peking University)

• collects all arabidopsis transcription factors (totally 1922 Loci; 2290Gene Models) and classifies them into 64 families.

• It uses not only locus (gene), but also gene model (transcript,protein) and the detail information is for each gene model not forlocus.

• It add multiple alignment of the DNA-binding domain of each family,Neighbor-Joining phylogenectic tree of each family, the GOannotation, homolog with the Database of Rice TranscriptionFactors (DRTF).