actsi bip overview jan 2011
DESCRIPTION
Overview of Atlanta Clinical and Translational Institute Biomedical Informatics ProgramTRANSCRIPT
Biomedical Informatics Program
Atlanta Clinical and Translational Science Institute
Joel Saltz MD, PhD Director
Specific Aims Aim 1: Develop and deploy a standards-based ACTSI-wide
federated system that will link inter and intra-institutional biomedical research databases collected, referenced, and managed by ACTSI institutions.
Aim 2: Deploy and support a suite of common applications for management of clinical, omics, imaging, ECG, and tissue data and for integrative analysis of these datasets.
Aim 3: Engage ACTSI investigators to maximize the impact of ACTSI investigator studies and proposals through coordinated use of bioinformatics, biostatistics, and informatics.
Aim 4: Develop an enhanced training program to educate clinicians and researchers on the principles and best practices of biomedical informatics and train them on biomedical tools and infrastructures.
Progress to Build From
• Saltz recruited and named Program Director of BIP
• Establishment of Center for Comprehensive Informatics
• Investment of $1M/year in Research IT
• BIP Architecture initiated
• Diabetes Integrated Mobile Health Solution (e-HealthyStrides) awarded
• GA Tech RFP Awards in Information Security and Testing
• Biomedical Informatics Department approved
• Studios launch
• Laboratory Information Mgmt System launch
• eCRF platform launch
• Resource discovery (eBIRT) launch
• MSM i2b2 deployed
• Minority Health Grid initiative awarded
• Cardiovascular Registry launch
• Emory i2b2 deployed
• MSM Clinical and Translational Research Web Portal launch
• Pathology Analytical Imaging Standard (PAIS) project launch
GY01-02 GY03-04 GY04
Over 347 studies leveraging BIP
Expand and Sustain Integrated BIP Collaboration between Emory, Georgia Tech, and Morehouse
School of Medicine Draw on the complementary strengths of partner organizations in
computer science, biomedical informatics, bioinformatics, and translational research
Strategy: Steering committee with CIN, BERD, and BIP leadership Architecture: Weekly working group to establish standards and
pathways to integration Institution: Key leadership at Morehouse, Emory, and GA Tech.
Integrated with Emory Informatics and Research IT Governance structures
Infrastructure and Data: Shared and integrated systems and capacities. Research, laboratory and clinical data sources
Integrated BIP Architecture working group to design a common architecture Collaborative projects
Security infrastructure Testing framework Bioinformatics support Registry implementation at Grady for quality improvement and
cardiovascular research LIMS deployment for biospecimen management i2b2 deployment for clinical data
Leverage institutional strengths for education and training Leverage over $3.8M in grant and internal funding this year
Aim 1: ACTSI-wide Federated Data Warehouse System Develop integrative, federated ACTSI information warehouse
Integrated clinical/imaging/”omic”/biomarker/tissue information should always be available
A virtually centralized, big Atlanta wide information warehouse that has all relevant data
Patients seen and information gathered at any ACTSI site, specimens sent to any affiliated core, imaging carried out at any affiliated site Give me all gene expression, SNP, virtual slide images, hematology
studies and CMV serologies for kidney transplant candidates accrued into Study X or Study Y between Feb 2011 and Jan 2012 who were on the kidney transplant waiting list as of November 1, 2010.
Development efforts Security, Web Portal, Common Data Elements & Vocabularies,
Identifiers, High-performance Computing middleware, Testing framework.
ACTSI-wide Federated Research Data
Aim 2: Deploy and Support a Suite of Common Applications
A suite of interoperable repositories Clinical registries: Initially for cardiovascular disease, diabetes and co-
morbidities. Data sources: Emory Healthcare Clinical Data Warehouse and the Grady Health System Diabetes Patient Tracking System.
Image repositories: Radiology images, Pathology images, image markup and annotations
Biospecimen repositories: Nautilus LIMS and caTissue Genomic data repositories: Gene expression datasets, microarray data,
next generation sequencing data Continued support for existing systems
CR-Assist, eBIRT: Extensions and integration with the ACTSI data warehouse infrastructure
Deployment of software from other CTSAs i2b2, REDCap
Aim 2: Common Applications (Current and Future) Infrastructure Release Key Metric # of Sites Future Plans
Resource Discovery (eBIRT)
July 2010 421 services55 cores1,263 searches
4 Integrate with VIVO and Eagle Eye. Add new data types (e.g., collaborators)
Electronic data capture forms
April 2010 19 studies508 forms
4 Expand clinical data integration/import capacity, integrate form library with common data element infrastructure
Laboratory Information Management (LIMS)
July 2010 323 studies350,000 samples/aliquots
3 Implement within new laboratories across the ACTSI institutions. Integrate into overall BIP distributed query architecture
MSM i2b2 Oct 2010 468,000 patients 2 Integrate with Emory i2b2. Expand data sources. Open up to investigators. Explore integration with LIMS.
CIN Participant tracking scheduling (CR-Assist)
Dec. 2005 119 active studies4,185 participants243 users
4 Expand functionality based on CIN needs
Common Applications (Future)
Infrastructure Estimated Release Date
Key Metric Future Direction
MSM Research Portal
February 2011 # of active users# of active projects
Integrate with ACTSI Web portal; Implement a web mash-up for multiple databases within the portal; Searchable research projects library
Emory I2b2 March 2011 # of studies supported# of data elements# of queries
Integrate with MSM i2b2; Implement Clinical Registries databases and user interface with i2b2; Integrate with ACTSI security infrastructure
Clinical Registries March 2011 # of studies supported# of data elements
Implement Cardiovascular, Diabetes and Co-morbidities Registries; Implement direct query by investigators; Support export into statistical apps; Support queries through ACTSI Web portal
Research PACS May 2012 # of studies# of images
Integrate with clinical data via the Registries; Implement combined clinical/image data views
Aim 3: Engage ACTSI investigators and research teams
Goal: Maximize the impact of ACTSI investigator studies and proposals through coordinated use of bioinformatics, biostatistics, and informatics.
Engagement being carried out via Studio program, coordinated effort between CIN, BERD,
and BIP Interactions with investigators and research groups by the
BIP, BERD, and CIN participants Contributions of Informatics support functions to
investigator proposals
Aim 3: Engage ACTSI investigators and research teams
Examples include: Metadata Analysis of Glycan Structures: Develop a custom-built system to
help visualize, identify, and cluster glycan structures in order to help discover glycan structures
Translational CardioVascular Research: Minority Health Grid and CardioVascular Research Grid: Develop new CV-related data management and analysis tools and resources
Integrated Mobile Health Solution: Develop tools based on Microsoft Health Vault to empower the diabetic patient, to manage his/her diabetes with the help of a physician and a health coach
Aim 4: Informatics Training Program Leverage existing expertise and programs at partner institutions Coordinate with RETCD Masters of Science in Clinical Research Establish an informatics academy for research and clinical
leadership to learn key informatics principles, best practices, and tools
Establish Biomedical Informatics PhD track in Computer Science and Informatics PhD Program
Establish learning material based on national competencies and initiatives, such as the AMIA 10x10
Establish an Informatics certificate training program in clinical informatics
Align with subspecialty board certification in informatics and Emory Department of Biomedical Informatics
Implementation of BIP
Exec. Committee• Priorities• Policies
Exec. Committee• Priorities• Policies
BIP Architecture• Standards• Interoperability• Privacy and Security
BIP Architecture• Standards• Interoperability• Privacy and Security
Infrastructure• Systems and Tools• Services
Infrastructure• Systems and Tools• Services
Investigators• Research• Proposals• Studios
Investigators• Research• Proposals• Studios
Informs Prioritizes
Informs
Utilizes Informs
Evaluates
Implementation of BIP Examples of initial set of projects to be targeted:
In Silico Study of Brain Tumors Cardiovascular Studies Minority Health Genomics and Translational Research
Bio-Repository Database (MH-GRID) Early Hospital Readmission CFAR (Center for AIDS Research) HIV Data Integration Clinical Interaction Network (CIN) Repositories Metadata Analysis of Glycan Structures Integrated Mobile Health Solution (eHealthyStrides)
National Contributions Cardiovascular Research Grid (NHLBI): Cardiovascular data
registries, security, data federation caBIG (NCI): Development of core caGrid, imaging, security
infrastructure, caGrid 2.0 design HL-7: Liaison between HL-7 and NCI National Center for Biomedical Oncology (NCBO): Semantic
modeling in transplant studies Southeastern CTSA Consortium Advanced Technology Consortium: Image and RT treatment
quantification TRIAD: CTSA data federation Kaiser NLP initiative (CERhub): Multi-site NLP analysis of
asthma, smoking cessation