Eos is the result of a research project. To support our research, please cite one of our papers instead of referencing our github in scientific articles. You can find an overview of papers about Eos here. If you are not sure which paper to cite, we recommend this one:
Severin Kohler, Diego Boscá, Florian Kärcher, Birger Haarbrandt, Manuel Prinz, Michael Marschollek, Roland Eils, Eos and OMOCL: Towards a seamless integration of openEHR records into the OMOP Common Data Model, Journal of Biomedical Informatics, Volume 144, 2023 (Link)
Thanks!
- JDK (>= 17)
- Apache Maven (>= 3.8.0)
- docker and docker-compose if you want to use docker
- Postgres if not using docker
- optionally: openEHR platform, otherwise there is the option to setup one down below
- clone repo
git clone --recursive(may require SSH authentication to github) - Use Common Data model sqls from
setup/ddls/or download them here. If downloaded change the file names according to the provided ones (delete the version number). - Download Vocabs from https://athena.ohdsi.org/, you need to create an Account for that, afterwards copy them
to
setup/vocab/. For recommended vocabs see Wiki.
- Check if the OMOP_CDM_vocabulary_load sql script contains all your csvs.
- choose a docker-compose profile of your liking which can be found in
setup/.
For the entire stack (including the open source EHRBase openEHR CDR) run:docker-compose --profile eos --profile cdm --profile ehrbase up.
Setup may take a while since all the vocabularies are loaded into the database
-
Start your postgres database (in this walktrough the example port is 5433, so it is not in conflict with other postgres dbs from e.g. the openEHR platform)
-
execute the command in
setup/ddls
$ psql -h localhost --port=5433 -U postgres -W --dbname=YOUR_DB_NAME --file=db_setup.sqlyou can empty the folder setup/vocab afterwards if you wish
- Build the application
$ mvn clean install- configure database in
src/main/resources/application.yml
datasource:
password: YOUR_PASSWORD
username: YOUR_USERNAME
url: jdbc:postgresql://localhost:5433/YOUR_SCHEMA #default is public- configure openEHR platform in
src/main/resources/application.yml
ehrbase:
base-url: YOUR_PLATFORM_URL
security:
type: basic # you can also use other security depending on the capabilities of your CDR
user:
name: YOUR_USERNAME
password: YOUR_PASSWORD-
configure cronjob for eras or leave them for manual execution
-
Run the application
Check the wiki for available api calls or use the POSTMAN example collection found in .config/.
0. Make sure there's an EHR in the CDR with at least one COMPOSITION. (For openEHR getting started consider https://docs.ehrbase.org/docs/category/openehr-introduction)
- Create PERSONs in the OMOP database for each (or a specific) by POSTing to EOS's '/person' endpoint with an empty body.
- Creata records in the OMOP database for each compostion using EOS's '/ehr' endpoint. (Make sure EOS has the relevant OMOCL mappings for the relevant archetypes).
We currently support CDM v5.4, if more tooling is provided v6 will be added in the future.
See here
| CDM table | Supported |
|---|---|
| OBSERVATION_PERIOD | automatically generated |
| VISIT_OCCURRENCE | automatically generated |
| VISIT_DETAIL | |
| CONDITION_OCCURRENCE | x |
| DRUG_EXPOSURE | x |
| PROCEDURE_OCCURRENCE | x |
| DEVICE_EXPOSURE | x |
| MEASUREMENT | x |
| OBSERVATION | x |
| DEATH | x |
| NOTE | |
| NOTE_NLP | |
| SPECIMEN | x |
| FACT_RELATIONSHIP | |
| DRUG_ERA | automatically generated |
| CONDITION_ERA | automatically generated |
- INTERVAL_EVENT is currently only mapping the event time
- Interval of Quantity is not supported
- Multiplication is currently only supported for DrugExposure quantity, will be added to other configs on demand.
- Dv_Proportion only type 2 is supported for unit due to lack of sample data. If samples are provided this can be added.
- CustomConverters are not supported for Person Conversions
- range low range high and operator will map normal range and magnitude status if DV Quantity is provided and NOT magnitude.
We thank the Georgia Tech Research Institute for providing jpa classes for OMOP and vita systems for their free accessible openEHR tooling.