Eos

Note

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!

Introduction

Setup

Prerequisites

• 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

Setting up Eos

1. clone repo git clone --recursive
2. 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).
3. 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.

With Docker

4. Check if the OMOP_CDM_vocabulary_load sql script contains all your csvs.
5. choose a docker-compose profile of your liking which can be found in setup/.
   For the entire stack run: docker-compose --profile eos --profile cdm --profile ehrbase up.
   Setup may take a while since all the vocabularies are loaded into the database

Without Docker

4. 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)

5. execute the command in setup/ddls

   $ psql -h localhost --port=5433 -U postgres -W --dbname=YOUR_DB_NAME --file=db_setup.sql

you can empty the folder setup/vocab afterwards if you wish

Running Eos

1. Make sure a openEHR platform and the database is running

2. Build the application

$ mvn clean install

2. 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

3. configure openEHR platform in src/main/resources/application.yml.

  ehrbase:
    base-url: YOUR_PLATFORM_URL
    security:
      type: basic # you can also use other sec depending on what you want
      user:
        name: YOUR_USERNAME
        password: YOUR_PASSWORD

4. configure cronjob for eras or leave them for manual execution

5. POSTMAN examples can be found in .config/

Mappings

We currently support CDM v5.4, if more tooling is provided v6 will be added in the future.

configured Mappings

See here

Usable with declarative mappings

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

DISCLAIMER:

• 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.

Special thanks

We thank the Georgia Tech Research Institute for providing jpa classes for OMOP and vita systems for their free accessible openEHR tooling.