CARE-SM to OMOP-CDM Mapping Service

Overview

The CARE-SM to OMOP-CDM Mapping Service is designed to facilitate the integration of clinical and research data from CARE-SM into the OMOP Common Data Model (CDM).

CARE2OMOP ETL workflow

Table of Contents

• CARE-SM to OMOP-CDM Mapping Service
  • Overview
  • Table of Contents
  • Usage
  • Docker and API
  • License

Usage

1. Configure the service: Create the configuration file (config.yaml) with your Triplestore credentials details.

   TRIPLESTORE_URL: https://graphdb.triplestore/endpoint
   TRIPLESTORE_USERNAME: username
   TRIPLESTORE_PASSWORD: password

2. Execute main.py:

   python main.py

   configuration.yaml needs to be in the same path as main.py:

   care2omop/
   ├── configuration.yaml
   ├── main.py
   

Docker and API

Docker and API as a web service is under development.

License

This project is licensed under the MIT License. See the LICENSE file for details.

---

Data element	OMOP table(s)
Birthdate, Birthyear	person
Deathdate	death
Sex	person
Country	location (via person)
Status	observation / death
First_visit	visit_occurrence
Diagnosis	condition_occurrence
Phenotype	condition_occurrence / observation / measurement
Symptoms_onset	condition_occurrence / observation
Examination	measurement
Laboratory	measurement
Prescription	drug_exposure
Medication	drug_exposure
Surgery	procedure_occurrence
Hospitalization	visit_occurrence
Biobank	specimen
Questionnaire	observation
Disability	observation

Birthyear Clinical_trial Genetics