Plan/Method: Search across the following places and uncover existing work or findings on OpenMRS & OMOD:
Google Scholar
OpenMRS Forum (Talk), OpenMRS Slack
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: https://www.sciencedirect.com/science/article/pii/S2666990023000277
ETL approach to convert OMRS to OMOP: https://link.springer.com/article/10.1186/s12911-022-01965-9
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
https://talk.openmrs.org/tag/omop & https://talk.openmrs.org/search?q=omop
There was a previous attempt in 2015 to map OpenMRS to OMOP CDM: https://talk.openmrs.org/t/designing-the-openmrs-ohdsi-module/2251 Question to answer: Why didn’t this get more traction?
Andy Kanter, Burke Mamlin, and Julianna Kohler come up as the people most interested in the topic.
Google Generic
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).
FHIR Community (Possibly Helpful for Mapping)
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