UCSF Clinical and Translational Sciences Institute

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UCSFClinical and Translational Sciences Institute
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UCSFClinical and TranslationalSciences Institute

• Broad campus initiative
• Bench to Bedside to Community
• 2 GCRCs, 1 PCRC
• Multiple clinical research IS
• 3 teaching hospitals, Kaiser, community sites

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UCSFOffice of Academic and AdministrativeInforma
tion Systems Major new institutional investment
for research and educationalinformation systems
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UCSF CTSIBiomedical Informatics Program

• Mark Segal, PhDProfessor of Epidemiology and
  BiostatisticsDirector, Center of Bioinformatics
  Molecular Biostatistics
• Jonathan Showstack, PhD, MPH
• Professor of Medicine and Health Policy
• Assistant Vice Chancellor and Co-CIO
• Michael Kamerick
• Director, Academic Research Systems
• Office of Academic and Administrative Information
  Systems

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UCSF CTSIBiomedical Informatics Program

• Aim 1 Expand database development and management
  services
• Aim 2 Develop cutting-edge bioinformatics data
  analytic services
• Aim 3 Develop a translational data environment
• Aim 4 Expand education and training opportunities

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UCSF Biomedical Informatics ProgramBioinformatics
Data Analytic Services

• 1. Consolidate expand Bioinformatics Core
  services
• Consolidated Genomics core
• Cancer Center Bioinformatics core
• San Francisco General Hospital Microarray core
• Statistical Genetics service of the Human
  Genetics program
• 2. Expanded core services for analysis of
• proteomic data
• flow cytometric data
• novel imaging techniques

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UCSF Biomedical Informatics ProgramDatabase
Development and Management Services

• 1. Consultation for investigators, assessing data
  management needs and orienting to available
  resources
• 2. Assist with data management sections of grant
  proposals
• 3. Develop study-specific normalized schemas,
  provide data validation and integrity
  constraints, and capture data while accommodating
  evolving study designs and workflows
• 4. Design and program user interfaces (data entry
  forms, reports)
• 5. Assist and train investigators in querying
  against their data
• 6. Employ standardized vocabularies and uniform
  data encoding conventions to lower barriers to
  intra- and extramural data sharing

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UCSF Biomedical Informatics ProgramEducation and
Training Opportunities

• UCSF Center for Clinical and Translational
  Informatics
• New medical informatics PhD training program
• Microarrays course to include more material on
  recently developed platforms
• Research overview course to include new material
  on sequence data analysis
• New case studies course introduced in Fall 2006
• New graduate course on inferring gene/protein
  interaction networks and pathways in Fall 2007
• New specialized courses on data analytic issues
  in proteomics and imaging

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UCSF Biomedical Informatics ProgramTranslational
Data Environment

• Research database hosting as a core service
• Mediated access to clinical data with appropriate
  safeguards
• Integration of non-UCSF clinical data for
  research purposes
• Terminology services
• Knowledge management
• Web interfaces for data extraction and
  exploration
• Data access APIs for study-specific applications
  development

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Research Data (non-API)
Research Data, Research Applications, Data
Exploration GUI
Applications Programming Interface
Non-UCSF Research Data
Research Data Sets (SAS, etc.)
UCare
De-identification Knowledge Representation
PACS
Data Repository
Clinical Data Sources (Lab, etc)
Integration Engine
STOR
Master Person Index
Terminology Services
Document Indexing
TSI, Chart Abstracts, and Other Systems
UCSF Translational Data Environment Example
Conceptual Architecture