Construction of Shanghai Life Science

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Construction of Shanghai Life Science
Bio-technology Service Platform for Data Access
and Sharing

• International Workshop on Strategies Presentation
  of and Open Access to Scientific Data
• Beijing June 22-23, 2004
• Dr. Yixue LI
• Shanghai Center for Bioinformation Technology
• Http//www.scbit.org, yxli_at_scbit.org

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Outline

• Goal and orientation of service platform
• Progresses of service platform construction
• Establishment of data centers
• Survey and integration of scientific data
  resources
• Construction of service infrastructure and
  mechanisms
• Policy for scientific data administration, access
  and sharing
• Platform structure design for open access and
  sharing of scientific data
• Development strategy of service platform
• Resource systems construction
• Service systems construction
• Data opening and sharing oriented research of
  data standards and data distribution technology

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Goal and Orientation

• To meet the comprehensive requirements of
  science, technology and economy development at
  Shanghai
• Progresses of science and technology will be a
  crucial factor for maintaining economical
  advantages of Shanghai in next 20 years
• Government dominant
• Shanghai should be a main national center for
  knowledge production and services, a national
  base for high-tech application and
  industrialization, for this purpose
• Five industrialization oriented citywide public
  platforms will be established, one of them is
  public Service Platform for Development of
  Sciences and Technologies, and the main aspect
  of which is life science data sharing system,
  this system will also be a pilot program for
  constructing whole public service platform

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Goal and Orientation

• Goal for building life science service platform
• Promoting research of life science, applications
  of science and technology, industrialization,
  economical development of Shanghai area by the
  construction of government dominant public
  scientific service platforms
• Playing a key role in scientific data collection,
  access and administration in Shanghai area

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Scheme of Service Platform for Access and Sharing
of Life Science Data at Shanghai
Users
services
Shanghai Life Science Bio-technology service
platform for full open access and sharing of
scientific data
Consulting platform
Platform for collaboration and technology
development
Infrastructure for data resources management and
services
Public internet networks grid system
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Shanghai Life Science Bio-Technology Services
Platform for Scientific Data Sharing Should Be a
Core Part of National Scientific Data Sharing
Project
Services
Central databases
Meteorology databases
Decision making
National Data Network and Grid
Topography databases
Security of the country
Geography databases
Oceanography databases
Scientific innovation
Agriculture databases
Economic development
Medical databases
Progresses in civilization
Shanghai Life Science Bio-Technology Services
Platform for Data Access and sharing

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Database Systems of Shanghai Life Science
Bio-Technology Services Platform for Data Access
and Sharing Is Part of National Scientific Data
Center Systems
Database systems of Shanghai life science research
Scientific data sharing networks and grid
National data centers
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The Localization of Life Science Database Systems
in Shanghai Public Service Platform for
Development of Sciences and Technologies
Guiding group
Consist of Agencies of Shanghai Municipality
Expertise Commission
Consist of Agencies of Science and Technology
Commission of Shanghai Municipality
Executive office
Administration and service center for sharing of
scientific data and information
Located at Shanghai Center for Bioinformation
Technology
Life science data center
Chemical data center
data centers
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Construction Strategy of platform

• Comprehensively programming, construction step by
  step
• Starts from one or two pilot systems, then extend
  through whole field
• During the time of service system construction,
  provide services synchronously
• Enhances collaboration,cooperation, contribution,
  opening, sharing and services by appreciate
  policy issued by municipality

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Some Progresses-Platform construction

• 3 million US and 500 M2 working place provided
  by Shanghai Municipality for infrastructure
  construction of life science data administration
  center
• Shanghai Center for Bioinformation Technology was
  established for promoting manipulating,
  administrating and sharing of life science data
  and information
• General environment was established for database
  and software running
• Start to survey life science data resources, to
  integrate proprietary and public data, to setup
  and develop data mining systems in our ongoing
  platform
• Several rules and policies for the administration
  of scientific data and information sharing were
  submitted to Shanghai Municipality

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Resources of data and related software
1. Submitting list of scientific resources at
Shanghai About 200 databases and datasets
around 18 research fields are listed, one can
searches, downloads the most of databases and
datasets 2. Navigation of international public
databases 5003 databases around 173 research
field are linked to our scientific resources
management platform 3. Navigation of software
resources Over 300 software packages for
data mining are collected in our platform, and
the most of them can be freely downloaded by
academic users 4. The most of above mentioned
resources are from life science research field.
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Web pages of platform for open access scientific
data and services
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Some Progresses- Survey, integration and
distribution of scientific data resources

• Issuing new policy to promote the integration of
  proprietary databases into service platform
• Carefully selection of main resources for setting
  up distributed core databases
• Developing technologies and software tools to
  facility data sharing according to the data
  access policy of Science and Technology
  Commission of Shanghai Municipality
• Setting up network links to main international
  and domestic databases
• Establishing mirror sites or physical copies of
  main international public databases systems
• Integrating scientific data from distributed
  public databases and literatures to form
  secondary databases
• Providing life science research data mining
  services?

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Some Progresses- Survey, integration and
distribution of scientific data resources

• Public databases
• Setting up network links to main international
  and domestic databases
• Over 200 life science databases are collected to
  be linked to our service platform, of them the
  most important public databases are selected to
  set up mirror sites or physical copies
• Proprietary databases
• Shanghai Life Science Bio-Technology Service
  Platform for Scientific Data Sharing consists of
  nine important research centers and institutes,
  main of them are Shanghai Center for
  Bioinformation Technology, National Human Genome
  Research Center at Shanghai, National Center for
  Microarray Engineering at Shanghai, Proteomics
  Research Center of CAS, Shanghai Life Science
  Information Center of CAS, etc., and now this
  center have over 25 million data records, main of
  them are public data ,rests are local and
  proprietary data.

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Some Progresses-Realization of Service Function

• Strategy of services
• Organization of service teams
• Building up distributed and separated service
  systems.
• Services of data analysis
• Customized services for data analysis and
  software developments
• Consultation
• Setting up online services
• Provide data analysis consultation for users
• Capacity building of knowledge services
• Data integration, data-warehousing
• Comprehensive data analysis based on workflow
  technology,knowledge discovery, etc.
• User training

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Software systems developed by Life Science
Service Platform

• Peptide mapping system
• Genome annotation system
• Virus genome annotation system
• Microarray data analysis and its LIMS
• Protein-protein interaction analysis
• Workflow technology based data analysis and
  visualization system
• Text mining system
• E-cloning system
• Automatic EST analysis pipeline
• etc.

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BIO-ScienceWorkflow technology based data
analysis and visualization system
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Research and services

• Bio-Science system developed by our service
  platform has gotten 100 RMB contract, development
  of next version will get contract with 500 RMB
• EOMAS package can provide high-throughput,comprehe
  nsive microarray data analysis services
• Being involve in HLPP, and in charge of
  construction of its bioinformation system, such
  as proteome database, protein interaction
  database, PPI, PTM analysis packages, etc.
• Customized services for data analysis and
  software developments around Shanghai area
• SARS-Cov research paper was published on
  Sciencejournal
• Proteome standard research work collaborated with
  EBI was published on journal ofNature
  Biotechnology

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Some Progresses -Administration strategy and
policy

• Shanghai Municipality also pays more attention
  for
• Policy for the administration and sharing
• of scientific data and information at Shanghai
• Policy for scientific data collection
• Strategy of Data Security

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Policy for the administration and sharing of
scientific data and information at Shanghai
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Policy for scientific data collection
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Strategy for Data Security
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Some Progresses -Service Models

• Service oriented
• Collaboration with wet labs. For resources
  accumulating
• Participating in national projects for scientific
  data access and sharing
• Setting pilot program for the research of
  scientific data sharing technology and its
  applications by Shanghai municipality
• Participating in international projects
• Collaboration with EBI, such as PSI, proteome
  database, PPI database
• Participating in setting up SNP data standard,
  meeting at Japan
• Promotes collaboration with international
  organization like CODATA, UNESCO, EBI, NIH, ISSU,
  ICP, etc.

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Further Strategy of services platform
constructionEstablishment of Fundamental
Resources System

• Confirm targets and orientation of platform
  development through scientific requirements
  classification and resources survey
• Establish several core database systems based on
  main scientific resources at Shanghai area
• HLPP proteome database system
• Microarray database system and LIMS
• Disease related genome information database
  systems
• Rice genome database system
• Silkworm genome database system
• Schistosome genome database system
• Molecular probe database system
• Etc.

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Further Strategy Services Platform System
Construction

• Construction evaluation system for service
  platform
• Attracting volunteers participating in the work
  of platform construction
• Inviting expertise to involve in service system,
  providing consulting services
• Promoting enterprise involve in service system by
  using developed platform and data resources

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User logging in
Free access
authorization
Service platform
Public services
Professional services
Gateway system
Software resources
Data resources
Consulting services
Public data services
Customized data services
Data survey, collection and integration
Customized services
Workflow based services
Commercial software services
Free access software services
Requirement analysis
Consulting and training
Data analysis
Customized software developing
Workflow designing
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Development Strategy Application Research of
Data Sharing Technology and Standard

• Standardization of life science data resources
• - such as data standards, data exchange
  models, etc.
• meta-data standards
• Scientific data sharing technology
• - in data search level, application level
  and data level

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Tasks of Data Sharing Services
Different users
Data search
Shanghai Life Science Bio-technology service
platform for data access and sharing
Technologies,standards and policies
Database1
Database2
Database3
Sharing at search level
search
search
search
Sharing at application level
application
application
application
Sharing at data level
administration
administration
administration
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Thanks!