Plan/Method: Search across the following places and uncover existing work or findings on OpenMRS & OMOD: Google Scholar; OpenMRS Forum (Talk), OpenMRS Slack, OpenMRS Wiki, and Google generic.

Google Scholar

Search terms: OpenMRS OMOP, and “OpenMRS” “OMOP” (link here)

Directly relevant & helpful:

• “Standardizing OpenMRS HIV Patient Data to OMOP CDM for Enhanced Analytics and Patient-Level Insights” by Moses Gwaza https://github.com/M-Gwaza/OpenMRS-to-OHDSI

• Barry Levine: OpenMRS-OMOP Mapping & ETL paper and their findings: “Development of an OpenMRS-OMOP ETL Tool to Support Informatics Research and Collaboration in LMICS” https://www.sciencedirect.com/science/article/pii/S2666990023000277

  • Juan Espinoza, Children's Hospital Los Angeles; Abu Sikder; Armine Lulejian, University of Southern California; Barry Levine

  • https://github.com/sikder-sab/OPENMRS_OMOP_PROJECT

  • Citations here.

• ETL approach to convert OMRS to OMOP: https://link.springer.com/article/10.1186/s12911-022-01965-9 or here

  • Poster: Implementation of the ARES application to monitor network-wide data quality and mapping coverage for 16 unique OMOP sources across Rwanda https://ohdsi-europe.org/images/symposium-2023/posters/houghtaling_laisdararesposter_2023_-_Jared_Houghtaling.pdf

Indirectly helpful:

• This group outlines reasons they think OpenMRS can be difficult for researchers to query, and propose their own simpler EMR to make life easier for Researchers. We should review to see what we can learn from this: A simple electronic medical record system designed for research https://academic.oup.com/jamiaopen/article/4/3/ooab040/6332673?login=false

OpenMRS Forum (Talk) & Slack & Wiki

• Talk Search: https://talk.openmrs.org/tag/omop & https://talk.openmrs.org/search?q=omop

  • 2015 OMOD Project: There was a previous attempt in 2015 to map OpenMRS to OMOP CDM, looks like it was led by Suaranga and Maurya: https://talk.openmrs.org/t/designing-the-openmrs-ohdsi-module/2251 Question to answer: Why didn’t this get more traction?

    • https://github.com/maurya/openmrs-module-ohdsi ← Repo

    • “Mapping between the OpenMRS database and the OHDSI CDM schema were completed by experts during a face to face meeting. You can find this at:” https://openmrs.atlassian.net/wiki/download/attachments/26935841/OpenMRS ETL.docx?api=v2

    • https://openmrs.atlassian.net/wiki/spaces/projects/pages/26935877

    • https://openmrs.atlassian.net/wiki/spaces/projects/pages/26935841

    • https://openmrs.atlassian.net/wiki/spaces/projects/pages/26935841

  • People of Interest:

    • Andy Kanter, Burke Mamlin, and Julianna Kohler come up as the people most interested in the topic.

    • a member of the OHDSI community named Lee Evans (evans@ohdsi.org) developed a standard ETL script to move between OpenMRS and OMOP CDM in 2018: https://talk.openmrs.org/t/openmrs-and-ohdsi/24930/3

    • Member Shawn Dolley was interested in an initiative like this back in 2020: https://talk.openmrs.org/t/welcome-please-introduce-yourself/32/3350 . See also his post to the OHDSI community in 2016: https://forums.ohdsi.org/t/omop-use-in-global-epi-for-cdc-gates-foundation/1779

    • In 2021 OHDSI Africa Chapter First Meeting discussed how OMRS implementations would be able to port their data in OMOP: https://talk.openmrs.org/t/new-africa-ohdsi-group-start-up-for-people-interested-in-health-research-in-africa-thursday/33987

    • Nega Gebreyesus, Africa OHDSI Leader, was interested in 2022: https://talk.openmrs.org/t/africa-ohdsi-leader-in-malawi-this-month-april-may-2022-wants-to-meet-with-openmrs-implementers/36467

• Wiki: https://openmrs.atlassian.net/wiki/search?text=ohdsi%20OR%20omop

• Slack:

  • July 2024: Suggestion from Jan to review Health Data Research Gateway (done - see Other Helpful Tools below)

Other Possibly Helpful Tools

• OMOP CDM FAQs: https://ohdsi.github.io/CommonDataModel/faq.html

• OMOP Community Tool “WhiteRabbit”: WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit. https://github.com/OHDSI/whiterabbit

• Recommended by Health Data Research Gateway: This website somebody here shown to Jan at the Boston CZI grantees meeting: “gave me where she’s been helping to map clinical data to omop for a UK initiative. Said to github has some pipeline tools we might be interested in:  https://www.healthdatagateway.org “ https://github.com/HDRUK ; Health Data Research Technology Community Slack channel

  • Carrot-Mapper: Carrot-Mapper enables conversion of data to the OMOP Common Data Model, without data being egressed from its secure location, nor requiring access to the secure location. Carrot-Mapper automates as much of the process as possible, and also enables users to reuse each others' mappings. Carrot-Mapper pairs with Carrot-CDM to complete the OMOP conversion process.

  • CaRROT-CDM: The primary purpose of the CaRROT-CDM package is to Extract input datasets and Transform them using mapping rules defined in a json file, outputting formatted datasets in tsv format that can be Loaded into a database or other destination (ETL).

• What You Need to Know Before Implementing a Clinical Research Data Warehouse: Comparative Review of Integrated Data Repositories in Health Care Institutions (Mentions OMOP and OpenMRS) https://formative.jmir.org/2020/8/e17687

Google Generic Findings

• Publications that nicely set the stage for this work:

  • “Conclusions: It is feasible to develop a free, open-source ETL pipeline to transform clinical data in OpenMRS instances into OMOP.” The OpenMRS System: Collaborating Toward an Open Source EMR for Developing Countries https://www.researchgate.net/publication/6563847_The_OpenMRS_System_Collaborating_Toward_an_Open_Source_EMR_for_Developing_Countries

  • OpenMRS & OHDSI Report by Andy Kanter, 2022: https://www.ohdsi.org/wp-content/uploads/2023/10/36-Kanter-OHDSIbriefreport.pdf

FHIR Community (Not specific to OpenMRS; Possibly Helpful for Mapping)

• Short PPT uploaded to OpenMRS years ago with tips on FHIR Resource <--> OMOP Mappings: https://openmrs.atlassian.net/wiki/pages/viewpageattachments.action?pageId=26937742&preview=%2F26937742%2F26973127%2Fomop.pdf

• GT-FHIR2, the OMOP on FHIR Project, (n.d.). http://omoponfhir.org/ (accessed March 27, 2019).

• M. Choi, R. Starr, M. Braunstein, and J. Duke, OHDSI on FHIR Platform Development with OMOP CDM mapping to FHIR Resources, in: OHDSI Symposium, Observational Health Data Sciences and Informatics, Washington, DC, 2016. https://www.ohdsi.org/web/wiki/lib/exe/fetch.php?media=resources:ohdsionfhir_gatech_v1.pdf