Epic EMR to OMOP CDM to Clinical Research Data Mart: an Unmaintained Road or a Highway?
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Poster we presented at 2017 AMIA Joint Summits on Clinical and Translational Research Informatics. In this research data delivery project, we explored a less traveled path of building a clinical data mart for a registry study on kidney transplant patients, based on the institutional instance of the EMR data, translated into the OMOP (Observational Medical Outcomes Partnership) common data model.
![RESEARCH POSTER PRESENTATION DESIGN 息 2015
www.PosterPresentations.com
Elicit data
requirements
Identify
primary data
source
Identify
needed subset
of source data
components
Identify
cohort
Build and
populate
data mart
Test and
validate data
with the user
Develop
user
manuals
In this research data delivery project, we explored a less traveled path of building a clinical data
mart for a registry study on kidney transplant patients based on our institutional OMOP database.
Background
Project Goals
The 5 Things We learned
References
1. Observational Health Data Sciences and Informatics (OHDSI) Website: https://www.ohdsi.org/
2. Huser V, DeFalco FJ, Schuemie M, Ryan PB, Shang N, Velez M, Park RW, Boyce RD, Duke J,
Khare R, Utidjian L, Bailey C. EGEMS (Wash DC). 2016 Nov 30; Multisite Evaluation of a Data
Quality Tool for Patient-Level Clinical Data Sets. 4(1):1239. doi: 10.13063/2327-9214.1239.
eCollection 2016.
3. User acceptance testing framework: https://usersnap.com/blog/types-user-acceptance-tests-
frameworks/
Acknowledgements
族 This project is supported by the UCSF Clinical and Translational Science Institute (CTSI), part of
the Clinical and Translational Science Award program funded by the National Center for Advancing
Translational Sciences (Grant Number UL1 TR000004) at the National Institutes of Health (NIH).
族 We thank UCSF pSCANNER team, PI Dr. Mary Whooley, MD, project manager Nirupama
Krishnamurthi, MPH and UCSF IT EIA team that implemented our institutions instance of OMOP
database, for all their support and inspiration to use OMOP CDM for research.
First, we supported the study by providing access to data
o Provide ongoing access to the up-to-date clinical data on kidney transplant patients that the study
team can use to answer the research questions
Second, we learned what it takes and how it could scale
o Learn about building a study data product, based on specific solution choices.
o Assess feasibility of generalizing this approach for other studies that rely on EMR data; identify
generalizable components
1,2,3,4,5,6,7,8,9,10,11University of California San Francisco, CA
Oksana Gologorskaya, MS1, Meyeon Park, MD2, Debbie Huang, MS3, Robert Hink, PhD, MBA4, Vijaykumar Rayanker5, MS, Nelson
Lee, MA, MBA6, Hasan Bijli, BS, MBA7, Govardhan Giri, MBA8, Amit Shetty, BS9, Leslie Yuan, MPH10, Mark Pletcher, MD, MPH11
EPIC EMR to OMOP CDM to Research Data Mart:
An Unmaintained Road or a Highway?
START HERE:
Researcher needs access to extensive
up-to-date clinical information on
kidney transplant patients to support
long term registry study
Solution choices, methods and the questions we had
o Delivery format: data mart built from the institutional OMOP data warehouse
o When is it appropriate to use OMOP DB as the primary source of EMR data for research?
o Data mart implementation process: what is generalizable? What recourses/time it
takes?
o What else should the research team get besides access to the data mart? E.g.
documentation (user manual, including data limitations), other resources?
o Primary data source: subset of institutional EMR (Epic) data available in OMOP DB
o What about adding other data sources, e.g. pathology data or kidney transplant data?
o Deliverables: data mart access, documentation (user manual for data access),
including data limitations
o QA and data validation: User-centered approach: user acceptance testing and data validation
procedures
o What are researchers expectations about the quality of data?
o General best practices and understanding of working with EMR data
o Important questions that came up in the process:
o How can we help the researcher use the imperfect data thats available?
o When is it right to build a data mart? What kind of projects and what kind of study
teams can fully benefit from it?
DATA REQUIREMENTS
Most of the required data are available
in the EMR DB, Epic Clarity.
Need lab results, medications, health
conditions, vitals, other observations
(imaging etc.) pre- and post-transplant
WAIT
Custom queries
getting the data
scattered all over
EMR DB, repeated
for data refresh,
would not scale.
HOW could we
meet these needs
by spending LESS EFFORT,
and getting MORE VALUE
in the future?
1. Data is never perfect but you can still trust it if you understand it!
In order to use the data in the best way, and to trust our data, we need to understand its
limitations. Present/analyze the data along with the limitations, based on the level of evidence
the data provides.
2. Study teams involvement in the quality control / validation of the data was extremely
effective.
We adopted a User Acceptance Testing method as part of our data delivery process. We
developed a user acceptance testing procedure for the research data mart that may now be used
as a model for all research data delivery projects at UCSF
3. Setting expectations with the researcher is important
Set expectations with the researcher about the quality of data, the complexity of the data and the
necessity of their involvement in the process of data delivery
4. Advantages of using OMOP-based vs. Epic CLARITY data source
端 OMOP is a research-oriented data model. Alternative to CLARITY reports, potentially faster
access, easy enough for skilled analyst to use independently
端 OMOP CDM is open source. No need to go to CLARITY training to learn the data model
端 Common data models (CDMs) shared across many organizations allow the same analytical code
to be executed on multiple distributed data sets. In some cases, adherence to a CDM is a
prerequisite for participating on a grant (or research network).[2]
5. OMOP data quality issues we found sparked internal OMOP QA initiative
Implementing research data mart what can be streamlined?
Study-specific, manual work Reusable method Reusable code, tools and deliverables and
much faster execution in repeat projects
We believe that building OMOP-based data marts is a very efficient way to deliver data for research
because for the next similar project, we can replicate this solution, plug-in a new cohort and be done!
Implementation Highlights:
族 ETL/Data integration tool: IBM InfoSphere DataStage
族 Data flow: UCSF EPIC CLARITY EMR -> UCSF OMOP DB -> Research Datamart
族 UCSF OMOP version: v4, being upgraded to v5
族 Source DB platform: SQL Server
族 Target DB: SQL Server
族 Refresh frequency: Weekly
族 datamart access for study data analysts to query directly in the DB or from SAS.
Contact
Oksana Gologorskaya
Sr. Product Manager, Research Technology
http://profiles.ucsf.edu/oksana.gologorskaya
Clinical & Translational Science Institute (CTSI)
University of California, San Francisco (UCSF)
550 16th St, 6th Floor, San Francisco, CA 94143-0558](https://image.slidesharecdn.com/amia2017ogposter-170405205018/85/Epic-EMR-to-OMOP-CDM-to-Clinical-Research-Data-Mart-an-Unmaintained-Road-or-a-Highway-1-320.jpg)
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Epic EMR to OMOP CDM to Clinical Research Data Mart: an Unmaintained Road or a Highway?
- 1. RESEARCH POSTER PRESENTATION DESIGN 息 2015 www.PosterPresentations.com Elicit data requirements Identify primary data source Identify needed subset of source data components Identify cohort Build and populate data mart Test and validate data with the user Develop user manuals In this research data delivery project, we explored a less traveled path of building a clinical data mart for a registry study on kidney transplant patients based on our institutional OMOP database. Background Project Goals The 5 Things We learned References 1. Observational Health Data Sciences and Informatics (OHDSI) Website: https://www.ohdsi.org/ 2. Huser V, DeFalco FJ, Schuemie M, Ryan PB, Shang N, Velez M, Park RW, Boyce RD, Duke J, Khare R, Utidjian L, Bailey C. EGEMS (Wash DC). 2016 Nov 30; Multisite Evaluation of a Data Quality Tool for Patient-Level Clinical Data Sets. 4(1):1239. doi: 10.13063/2327-9214.1239. eCollection 2016. 3. User acceptance testing framework: https://usersnap.com/blog/types-user-acceptance-tests- frameworks/ Acknowledgements 族 This project is supported by the UCSF Clinical and Translational Science Institute (CTSI), part of the Clinical and Translational Science Award program funded by the National Center for Advancing Translational Sciences (Grant Number UL1 TR000004) at the National Institutes of Health (NIH). 族 We thank UCSF pSCANNER team, PI Dr. Mary Whooley, MD, project manager Nirupama Krishnamurthi, MPH and UCSF IT EIA team that implemented our institutions instance of OMOP database, for all their support and inspiration to use OMOP CDM for research. First, we supported the study by providing access to data o Provide ongoing access to the up-to-date clinical data on kidney transplant patients that the study team can use to answer the research questions Second, we learned what it takes and how it could scale o Learn about building a study data product, based on specific solution choices. o Assess feasibility of generalizing this approach for other studies that rely on EMR data; identify generalizable components 1,2,3,4,5,6,7,8,9,10,11University of California San Francisco, CA Oksana Gologorskaya, MS1, Meyeon Park, MD2, Debbie Huang, MS3, Robert Hink, PhD, MBA4, Vijaykumar Rayanker5, MS, Nelson Lee, MA, MBA6, Hasan Bijli, BS, MBA7, Govardhan Giri, MBA8, Amit Shetty, BS9, Leslie Yuan, MPH10, Mark Pletcher, MD, MPH11 EPIC EMR to OMOP CDM to Research Data Mart: An Unmaintained Road or a Highway? START HERE: Researcher needs access to extensive up-to-date clinical information on kidney transplant patients to support long term registry study Solution choices, methods and the questions we had o Delivery format: data mart built from the institutional OMOP data warehouse o When is it appropriate to use OMOP DB as the primary source of EMR data for research? o Data mart implementation process: what is generalizable? What recourses/time it takes? o What else should the research team get besides access to the data mart? E.g. documentation (user manual, including data limitations), other resources? o Primary data source: subset of institutional EMR (Epic) data available in OMOP DB o What about adding other data sources, e.g. pathology data or kidney transplant data? o Deliverables: data mart access, documentation (user manual for data access), including data limitations o QA and data validation: User-centered approach: user acceptance testing and data validation procedures o What are researchers expectations about the quality of data? o General best practices and understanding of working with EMR data o Important questions that came up in the process: o How can we help the researcher use the imperfect data thats available? o When is it right to build a data mart? What kind of projects and what kind of study teams can fully benefit from it? DATA REQUIREMENTS Most of the required data are available in the EMR DB, Epic Clarity. Need lab results, medications, health conditions, vitals, other observations (imaging etc.) pre- and post-transplant WAIT Custom queries getting the data scattered all over EMR DB, repeated for data refresh, would not scale. HOW could we meet these needs by spending LESS EFFORT, and getting MORE VALUE in the future? 1. Data is never perfect but you can still trust it if you understand it! In order to use the data in the best way, and to trust our data, we need to understand its limitations. Present/analyze the data along with the limitations, based on the level of evidence the data provides. 2. Study teams involvement in the quality control / validation of the data was extremely effective. We adopted a User Acceptance Testing method as part of our data delivery process. We developed a user acceptance testing procedure for the research data mart that may now be used as a model for all research data delivery projects at UCSF 3. Setting expectations with the researcher is important Set expectations with the researcher about the quality of data, the complexity of the data and the necessity of their involvement in the process of data delivery 4. Advantages of using OMOP-based vs. Epic CLARITY data source 端 OMOP is a research-oriented data model. Alternative to CLARITY reports, potentially faster access, easy enough for skilled analyst to use independently 端 OMOP CDM is open source. No need to go to CLARITY training to learn the data model 端 Common data models (CDMs) shared across many organizations allow the same analytical code to be executed on multiple distributed data sets. In some cases, adherence to a CDM is a prerequisite for participating on a grant (or research network).[2] 5. OMOP data quality issues we found sparked internal OMOP QA initiative Implementing research data mart what can be streamlined? Study-specific, manual work Reusable method Reusable code, tools and deliverables and much faster execution in repeat projects We believe that building OMOP-based data marts is a very efficient way to deliver data for research because for the next similar project, we can replicate this solution, plug-in a new cohort and be done! Implementation Highlights: 族 ETL/Data integration tool: IBM InfoSphere DataStage 族 Data flow: UCSF EPIC CLARITY EMR -> UCSF OMOP DB -> Research Datamart 族 UCSF OMOP version: v4, being upgraded to v5 族 Source DB platform: SQL Server 族 Target DB: SQL Server 族 Refresh frequency: Weekly 族 datamart access for study data analysts to query directly in the DB or from SAS. Contact Oksana Gologorskaya Sr. Product Manager, Research Technology http://profiles.ucsf.edu/oksana.gologorskaya Clinical & Translational Science Institute (CTSI) University of California, San Francisco (UCSF) 550 16th St, 6th Floor, San Francisco, CA 94143-0558