Awesome OMOP 🏥

A curated list of open source OMOP (Observational Medical Outcomes Partnership) tools and resources.

What is OMOP?

The OMOP Common Data Model (CDM) is a standardized data model for observational healthcare data. It enables large-scale analytics across different healthcare systems and data sources. This list focuses on open source tools that work with OMOP CDM. It's not everything - the OHDSI organisation has over 350 repositories, so this is the interesting ones + the wider community.

Contents

• ETL & Data Processing
• Analytics & Research
• Machine Learning & AI
• Development & Infrastructure
• Vocabs
• Datasets
• Resources

Categories

• Common Data Model - The CDM itself

🗄️ ETL & Data Processing

Tools for transforming data into OMOP CDM:

• Rabbit-in-a-Blender - Full ETL tool
• Carrot - Toolset for ETL
• Data2Evidence - End to end ETL tool
• OMOP on FHIR - FHIR built on top of OMOP

Profiling

• WhiteRabbit - Data profiling tool for OMOP CDM mapping

Mapping

• Usagi - Vocabulary mapping tool
• Carrot Mapper - Community mapping tool
• OMOP2OBO - Mapping to Open Biomedical Ontologies
• Bouzyges - Semantic mapping with LLM
• ODmapper - API to map a genomic variant to the OMOP concept_id
• ODharmonizer - Suite of tools to harmonize omics data to OMOP.
• kotobuki - Update outdated mappings in Usagi
• OMOCL - Declarative mapping language for openEHR to OMOP
• Genomics England Mappings - NHS datasets mapping
• DICOM2OMOP - DICOM mapping to OMOP
• ROMOPMappingTools - Functions to validate, update, and summarise Usagi mapping files
• FinOMOP_mappings - Mapping of Finnish medical vocabularies
• ready42 - Tools for data curation and mapping into OMOP CDM
• Ariadne - Python toolkit for mapping source terminologies to standard concepts

Transformation

• ETL-Synthea - ETL for Synthea synthetic data
• Carrot Transform - Data transform to CDM
• convert-pheno - Conversion of datamodels for phenotypic data
• oxford-omop-data-mapper - Transformation of NHS datasets
• i2o-transform - PCORnet to OMOP
• fhir-omop-ig - FHIR implementation
• MEDS - Schema for medical event streams, used for EHR foundation models
• meds_etl - ETLs to MEDS, including OMOP v5
• OMOP_MEDS - OMOP to MEDS using MEDS-Transforms
• omop2meds - Fast OMOP to MEDS conversion in DuckDB
• EHR2Trace - Converts EHR exports to OMOP CDM 5.4 and MEDS from one canonical layer, with row-level lineage and output validation
• dbt-synthea - dbt project to convert Synthea synthetic data to OMOP CDM
• fhir2omop - FHIR R4 to OMOP CDM v5.4 mapping spec and ELT runtime

Validation

• DataQualityDashboard - Data quality assessment reports
• dqd-container - DQD in a Nightly Container
• ACHILLES - Data quality assessment and characterization
• Data-Quality-Analysis - Data assessment tool
• CdmInspection - R Quality control
• fastssv - Static semantic validator for OMOP CDM SQL

ETL Pipelines

• BlendedICU - ETL for ICU data
• Janssen CDM - ETL inc. CPRD
• MIMIC-OMOP - MIMIC-III ETL
• Eos - openEHR ETL
• IMI_SOPHIA_DMS_OMOP - Maastricht ETL
• ETL-Synthea - Synthea to OMOP ETL
• FinnGen/ETL - FinnGen ETL
• mimic-iv-dbt - MIMIC-IV to CDM 5.4 with DuckDB and dbt
• dbt_mimic_omop - MIMIC-IV and MIMIC-IV-Note to OMOP CDM with dbt

📊 Analytics & Research

Tools for analyzing and visualizing OMOP data:

• OmopSketch - Feasibility tool
• HADES - Large scale analytics packages
• Bunny - Cohort discovery tool
• ATLAS Data Sources - REST API for OMOP data access
• ATLAS - Web-based application for cohort definition and analysis
• Atlas3 - Updated reimplementation of OHDSI ATLAS for cohort definition and analysis
• CohortDiagnostics - Cohort characterization and diagnostics
• CohortGenerator - Cohort definition and generation
• PhenEx - Python framework for phenotype and cohort extraction, with built-in OMOP support
• Characterization - Patient and cohort characterization
• Cyclops - Large scale regularized regressions
• CohortMethod - Population-level effect estimation
• Cohort360 - Cohort builder / visualiser
• eds-scikit - Python lib for analysing OMOP
• LinkR - Web app for vis / analysing OMOP
• recruit - Clinical trial recruitment system with FHIR + OMOP
• SIDHA - Open data architecture for hidradenitis suppurativa research: EHR ingestion, computable phenotypes, diagnostic-delay analytics on OMOP CDM + FHIR R4
• Strategus - Coordinating / executing analytics
• CohortConstructor - Create study cohorts
• Picard - RWE pipelining tool favouring OHDSI tools
• OPAL - Data quality, cohort building, and concept exploration platform
• ehrapy - Python EHR analysis, with OMOP support through ehrdata
• All of Us Researcher Workbench - Research platform for the All of Us OMOP dataset
• IncidencePrevalence - Estimate incidence and prevalence
• CodelistGenerator - Find relevant concepts in the OMOP vocabularies
• PatientProfiles - Add patient-level characteristics to OMOP tables
• DrugUtilisation - Drug utilisation studies
• CohortCharacteristics - Summarise and compare cohort characteristics
• visOmopResults - Tables and plots for OMOP study results
• PSDL - Portable language for clinical scenario and cohort definitions
• omopy - Python reimplementation of the DARWIN EU R packages

🤖 Machine Learning & AI

AI/ML tools built for OMOP data:

• omop-learn - Python ML with OMOP
• Lettuce - LLM for matching drug names to OMOP concepts
• PatientLevelPrediction - Patient-level prediction models
• DeepPatientLevelPrediction - Deep learning for patient-level prediction
• CohortMethod - Population-level effect estimation
• omcp - MCP server for OMOP
• omop_mcp - MCP server for OMOP
• ascent-epi-demo - MCP agent demo for natural-language epidemiology and cohort generation on OMOP (Ascent)
• onto-llm-mapping - Ontology mapping with LLM + RAG
• Pythia - AI cohort-design advisor for ATLAS 3.0
• StudyAgent - Agentic study execution
• trex - Supabase-compatible backend with an embedded analytical engine and agent runtime
• FEMR - Framework for EHR foundation models (CLMBR, MOTOR) on OMOP data
• EDS-NLP - Clinical NLP framework from AP-HP

🛠️ Development & Infrastructure

Developer tools and infrastructure components:

• omop-lite - OMOP CDM database creator
• CDMConnector - Tidyverse connector
• DatabaseConnector - Database connection management
• dsOMOP - OMOP support for DataSHIELD
• SqlRender - SQL translation and rendering
• FeatureExtraction - Feature extraction from OMOP data
• omopcept - R package for getting OMOP concepts
• omock - Generate mock OMOP CDM data
• OHDSIonAzure - Deploy OHDSI on Azure
• Broadsea - Deploys the core OHDSI stack
• sqlalchemy_omopcdm - SQLAlchemy models for OMOP CDM
• omop-cdm - Databricks 5.3 CDM
• dzd-omop-cdm-python-models - Python data class lib for OMOP CDM
• OMOPCommonDataModel.jl - Julia implementation of the OMOP CDM
• pyomop - Useful OMOP "swiss army knife" in Python
• PatientGenerator - Synthetic data generator for OMOP
• Circepy - Python implementation of CIRCE-BE
• GIS - Geospatial and exposome data in the CDM
• gaiaDB - Staging database and transformation recipes for place-based datasets
• omop-alchemy - SQLAlchemy models for OMOP CDM
• promop - Django models for OMOP CDM and the oncology extension
• DuckCDM - DuckDB OMOP engine with SqlRender, Circe, Achilles and an ATLAS 3.0-compatible WebAPI in pure Python

Vocabs

• Vocabulary-v5.0 - Build/releases of vocabularies
• Athena - Web application for distributing vocabularies
• Hecate - Semantic search engine for OHDSI vocabularies
• CVB - Custom vocabulary builder
• omophub-python - Python SDK for the OMOPHub vocabulary API
• omophub-R - R SDK for the OMOPHub vocabulary API
• omophub-node - Node.js SDK for the OMOPHub vocabulary API
• omophub-mcp - MCP server for OMOP vocabularies

Datasets

• Eunomia - Package to access sample datasets
• EunomiaDatasets - Sample CDM
• UK-OMOP - Directory of UK OMOP data sets
• Barts Health - 10k synthetic CDM
• Synthea - 1k, 100k, 2.8m
• MIMIC-IV 100 patients
• EHRSHOT - Benchmark for EHR foundation models, with data in OMOP format

Resources

• OHDSI Website
• OMOP CDM Documentation
• OHDSI Forums
• OHDSI Book
• OHDSI Book 2nd Edition
• Tidy R programming with the OMOP Common Data Model
• HDRUK: The OMOP Common Data Model for Federated Analytics of Health Data
• linkml-omop-tutorial - LinkML schemas for OMOP

Contributing

Know a tool that should be here? Suggest it or open a pull request. See CONTRIBUTING.md.

License

This list is open source and available under the MIT License.