construction model of data sharing network for basic ......of human disease genes, genetic markers,...
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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).
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