preparing electronic health records for multi-site cer studies michael g. kahn 1,3,4, lisa schilling...
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![Page 1: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/1.jpg)
Preparing Electronic Health Recordsfor Multi-Site CER Studies
Michael G. Kahn1,3,4, Lisa Schilling2
1Department of Pediatrics, University of Colorado, Denver2Department of Medicine, University of Colorado, Denver
3Colorado Clinical and Translational Sciences Institute 4Department of Clinical Informatics, Children’s Hospital Colorado
AcademyHealth Annual Research MeetingBuilding a Data Infrastructure for Multi-stakeholder Comparative Effectiveness Research
26 June [email protected]
Funding provided by AHRQ 1R01HS019908 (Scalable Architecture for Federated Translational Inquiries Network)
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Setting the context:AHRQ Distributed Research Networks
• AHRQ ARRA OS: Recovery Act 2009: Scalable Distributed Research Networks for Comparative Effectiveness Research (R01)
• Goal: enhance the capability and capacity of electronic health networks designed for distributed research to conduct prospective, comparative effectiveness research on outcomes of clinical interventions.
Funding provided by AHRQ 1R01HS019908 (Scalable Architecture for Federated Translational Inquiries Network)
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AHRQ Distributed Research Networks Funded Projects
• SAFTINet: Scalable Architecture for Federated Therapeutic Inquiries Network– Lisa M. Schilling, University of Colorado Denver
(R01 HS19908-01)
• SCANNER: Scalable National Network for Effectiveness Research– Lucila Ohno-Machado, University of California San Diego
(R01 HS19913-01)
• SPAN: Scalable PArtnering Network for CER: Across Lifespan, Conditions, and Settings– John F. Steiner, Kaiser Foundation Research Institute
(R01 HS19912-01)
Funding provided by AHRQ 1R01HS019908 (Scalable Architecture for Federated Translational Inquiries Network)
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SAFTINet Partners• Clinical partners
– Colorado Community Managed Care Network and the Colorado Associated Community Health Information Enterprise
• Colorado Federally Qualified Health Centers– Denver Health and Hospital Authority– Cherokee Health Systems, Tennessee
• Technology partners– University of Utah, Center for High Performance Computing– QED Clinical, Inc., d/b/a CINA
• Medicaid partners– Colorado Health Care Policy & Financing– Utah Department of Public Health (partnership in development)– TennCare and Tennessee managed care organizations (partnership in
development)
• Leadership– University of Colorado Denver– American Academy of Family Physicians, National Research Network
![Page 5: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/5.jpg)
Key Differences between EHR and CER data
EHR Data CER Data EHR->CER task
Fully identified LDS or de-identified Strip identifiers; keep mappings?
Local codes and values Standardized codes and values
Terminology and value set mapping (manual!)
Broad data domains Focused data domains Filtering by patient, encounter, date, facility
Variable data quality; high level of missingness
Substantial data quality processes applied
Data profiling; iterative investigations
Lots of free text Fully coded data only NLP or ignore free text
Local access only Shared access Distributed or centralized data access
Single data source Multiple data sources Record linkage
![Page 6: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/6.jpg)
Key Differences between EHR and CER data
EHR Data CER Data EHR->CER task
Fully identified LDS or de-identified Strip identifiers; keep mappings?
Local codes and values Standardized codes and values
Terminology and value set mapping (manual!)
Broad data domains Focused data domains Filtering by patient, encounter, date, facility
Variable data quality; high level of missingness
Substantial data quality processes applied
Data profiling; iterative investigations
Lots of free text Fully coded data only NLP or ignore free text
Local access only Shared access Distributed or centralized data access
Single data source Multiple data sources Record linkage
![Page 7: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/7.jpg)
Key Differences between EHR and CER data
EHR Data CER Data EHR->CER task
Fully identified LDS or de-identified Strip identifiers; keep mappings?
Local codes and values Standardized codes and values
Terminology and value set mapping (manual!)
Broad data domains Focused data domains Filtering by patient, encounter, date, facility
Variable data quality; high level of missingness
Substantial data quality processes applied
Data profiling; iterative investigations
Lots of free text Fully coded data only NLP or ignore free text
Local access only Shared access Distributed or centralized data access
Single data source Multiple data sources Record linkage
![Page 8: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/8.jpg)
Key Differences between EHR and CER data
EHR Data CER Data EHR->CER task
Fully identified LDS or de-identified Strip identifiers; keep mappings?
Local codes and values Standardized codes and values
Terminology and value set mapping (manual!)
Broad data domains Focused data domains Filtering by patient, encounter, date, facility
Variable data quality; high level of missingness
Substantial data quality processes applied
Data profiling; iterative investigations
Lots of free text Fully coded data only NLP or ignore free text
Local access only Shared access Distributed or centralized data access
Single data source Multiple data sources Record linkage
![Page 9: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/9.jpg)
Key Differences between EHR and CER data
EHR Data CER Data EHR->CER task
Fully identified LDS or de-identified Strip identifiers; keep mappings?
Local codes and values Standardized codes and values
Terminology and value set mapping (manual!)
Broad data domains Focused data domains Filtering by patient, encounter, date, facility
Variable data quality; high level of missingness
Substantial data quality processes applied
Data profiling; iterative investigations
Lots of free text Fully coded data only NLP or ignore free text
Local access only Shared access Distributed or centralized data access
Single data source Multiple data sources Record linkage
![Page 10: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/10.jpg)
Key Differences between EHR and CER data
EHR Data CER Data EHR->CER task
Fully identified LDS or de-identified Strip identifiers; keep mappings?
Local codes and values Standardized codes and values
Terminology and value set mapping (manual!)
Broad data domains Focused data domains Filtering by patient, encounter, date, facility
Variable data quality; high level of missingness
Substantial data quality processes applied
Data profiling; iterative investigations
Lots of free text Fully coded data only NLP or ignore free text
Local access only Shared access Distributed or centralized data access
Single data source Multiple data sources Record linkage
![Page 11: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/11.jpg)
Key Differences between EHR and CER data
EHR Data CER Data EHR->CER task
Fully identified LDS or de-identified Strip identifiers; keep mappings?
Local codes and values Standardized codes and values
Terminology and value set mapping (manual!)
Broad data domains Focused data domains Filtering by patient, encounter, date, facility
Variable data quality; high level of missingness
Substantial data quality processes applied
Data profiling; iterative investigations
Lots of free text Fully coded data only NLP or ignore free text
Local access only Shared access Distributed or centralized data access
Single data source Multiple data sources Record linkage
![Page 12: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/12.jpg)
A common data model is critical!
CINACDR
Other EHR
Local Data
Warehouse
Other EHR
ExistingClinical
Registries
Other EHR
Limited Data SetCommon Data Model
Common Terminology
Common Query Interface
Limited Data SetCommon Data Model
Common Terminology
Limited Data SetCommon Data Model
Common Terminology
Crossing the CER chasm !!CER
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ROSITA-GRID-PORTAL
![Page 14: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/14.jpg)
Grid Portal
![Page 15: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/15.jpg)
Why ROSITA?
• ROSITA: Reusable OMOP and SAFTINet Interface Adaptor
• ROSITA: The only bilingual Muppet
• Converts EHR data into research limited data set1. Replaces local codes with standardized codes2. Replaces direct identifiers with random identifiers3. Supports clear-text and encrypted record linkage4. Provides data quality metrics5. Pushes data sets to grid node for distributed queries
![Page 16: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/16.jpg)
ROSITA: transforming EHR data for comparative effectiveness research
ETLXML
ETLXMK
ROSITA
JDBC
JDBC
OMOP CDM V3Grid Data Service
SAFTINet Data QualityData Service
Client CDW
Medicaid
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SAFTINet ETL specifications
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SAFTINet ETL Specifications
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SAFTINet ETL Specifications
![Page 20: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/20.jpg)
Transforming EHR Data:What does ROSITA do?
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What does ROSITA do?
![Page 22: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/22.jpg)
What does ROSITA do?
![Page 23: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/23.jpg)
Why ROSITA?
• Converts EHR data into research limited data set1. Replaces local codes with standardized codes2. Replaces direct identifiers with random identifiers3. Supports clear-text and encrypted record linkage4. Provides data quality metrics5. Pushes data sets to grid node for distributed
queries
![Page 24: Preparing Electronic Health Records for Multi-Site CER Studies Michael G. Kahn 1,3,4, Lisa Schilling 2 1 Department of Pediatrics, University of Colorado,](https://reader036.vdocuments.us/reader036/viewer/2022062720/56649f055503460f94c19cbf/html5/thumbnails/24.jpg)
Do not have Medicaid figured out
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ROSITA Security Discussion Framework
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ROSITA: Current Status
• Software development underway– In Phase 1: 16 week development
• clinical data only; no Medicaid– Phase 2: Medicaid + record linkage
• OMOP data model V4 finalized!– Clinical & financial extensions
• All SAFTINet partners have begun ETL activities– Two sites have provided full ETL extracts for
development and testing• Everything is/will be available
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Questions?
Funding provided by AHRQ 1R01HS019908 (Scalable Architecture for Federated Translational Inquiries Network)