preparing electronic health records for multi-site cer studies michael g. kahn 1,3,4, lisa schilling...

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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, Denver 2 Department of Medicine, University of Colorado, Denver 3 Colorado Clinical and Translational Sciences Institute 4 Department of Clinical Informatics, Children’s Hospital Colorado AcademyHealth Annual Research Meeting Building a Data Infrastructure for Multi-stakeholder Comparative Effectiveness Research 26 June 2012 [email protected] Funding provided by AHRQ 1R01HS019908 (Scalable Architecture for Federated Translational Inquiries Network)

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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,

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)

Page 2: 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,

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)

Page 3: 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,

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)

Page 4: 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,

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,

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,

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,

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,

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,

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,

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,

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,

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

Page 13: 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,

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,

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,

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,

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

Page 17: 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,

SAFTINet ETL specifications

Page 18: 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,

SAFTINet ETL Specifications

Page 19: 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,

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,

Transforming EHR Data:What does ROSITA do?

Page 21: 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,

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,

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,

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,

Do not have Medicaid figured out

Page 25: 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,

ROSITA Security Discussion Framework

Page 26: 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,

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

Page 27: 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,

Questions?

[email protected]

Funding provided by AHRQ 1R01HS019908 (Scalable Architecture for Federated Translational Inquiries Network)