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

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

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

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

Scheme of Service Platform for Access and Sharing of Life Science Data at Shanghai Shanghai Life Science & Bio-technology service platform for full open access and sharing of scientific data Infrastructure for data resources management and services services Public internet networks & grid system Users Consulting platform Platform for collaboration and technology development

Shanghai Life Science & Bio-Technology Services Platform for Scientific Data Sharing Should Be a Core Part of National Scientific Data Sharing Project Meteorology databases Topography databases Geography databases Oceanography databases Agriculture databases Medical databases Shanghai Life Science & Bio-Technology Services Platform for Data Access and sharing ……… Central databases National Data Network and Grid National Data Network and Grid Decision making Scientific innovation Economic development Progresses in civilization Security of the country Services

Database Systems of Shanghai Life Science & Bio-Technology Services Platform for Data Access and Sharing Is Part of National Scientific Data Center Systems National data centers Database systems of Shanghai life science research Scientific data sharing networks and grid

The Localization of Life Science Database Systems in Shanghai Public Service Platform for Development of Sciences and Technologies Guiding group Executive office ExpertiseCommission Administration and service center for sharing of scientific data and information Life science data center Chemical data center ……data centers Consist of Agencies of Shanghai Municipality Consist of Agencies of Science and Technology Commission of Shanghai Municipality Located at Shanghai Center for Bioinformation Technology

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

Some Progresses － Platform construction  3 million US$ and 500 M 2 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

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.

Web pages of platform for open access scientific data and services

Some Progresses － Survey, integration and distribution of scientific data resources Issuing new policy to promote the integration of p roprietary 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 。

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.

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

Software systems developed by Life Science Service Platform  Peptide mapping system b Genome annotation system b Virus genome annotation system b Microarray data analysis and its LIMS b Protein-protein interaction analysis b Workflow technology based data analysis and visualization system b Text mining system b E-cloning system b Automatic EST analysis pipeline b etc.

Clicking the value popes out the submit page Clicking the red point Fingerprint Spectrum can be shown

BIO-Science:Workflow technology based data analysis and visualization system

Research and services b Bio-Science system developed by our service platform has gotten 100 RMB contract, development of next version will get contract with 500 RMB b EOMAS package can provide high-throughput,comprehensive 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. b Customized services for data analysis and software developments around Shanghai area b SARS-Cov research paper was published on 《 Science 》 journal  Proteome standard research work collaborated with EBI was published on journal of 《 Nature Biotechnology 》

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

Policy for the administration and sharing of scientific data and information at Shanghai

Policy for scientific data collection

Strategy for Data Security

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.

Further Strategy of services platform construction: Establishment 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.

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

Service platform Software resourcesData resourcesConsulting 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 Public servicesProfessional services User logging in Free access authorization Workflow designing Gateway system

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

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

Thanks ！