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CommonDataModel
Definition and DDLs for the OMOP Common Data Model (CDM)Atlas
ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational dataVocabulary-v5.0
Build process for the OHDSI Standardized Vocabularies. Currently not available as independent release.PatientLevelPrediction
An R package for performing patient level prediction in an observational database in the OMOP Common Data Model.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.DataQualityDashboard
A tool to help improve data quality standards in observational data science.WebAPI
OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applicationsAchilles
Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES) - descriptive statistics about a OMOP CDM databaseTheBookOfOhdsi
The Book of OHDSI repositoryETL-Synthea
A package supporting the conversion from Synthea CSV to OMOP CDMUsagi
Usagi is an application to help create mappings between coding systems and the Vocabulary standard concepts.ETL-CMS
Workproducts to ETL CMS datasets into OMOP Common Data ModelCohortMethod
An R package for performing new-user cohort studies in an observational database in the OMOP Common Data Model.SqlRender
This is an R package and Java library for rendering parameterized SQL, and translating it to different SQL dialects.OHDSIonAWS
Automation code and documentation for standing up the OHDSI toolstack in an AWS environmentBroadsea
Broadsea deploys the core OHDSI technology stack (Atlas & R Hades), using cross-platform Docker container technology.MIMIC
MIMIC (Medical Information Mart for Intensive Care) is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. This repository contains the ETL to the OMOP CDM.Athena
Web application for distributing and browsing the Standardized Vocabularies for all instances of an OMOP CDMFeatureExtraction
An R package for generating features (covariates) for a cohort using data in the Common Data Model.OncologyWG
Oncology Working Group RepositoryKnowledgeBase
Source code used to develop the OHDSI knowledge base of sources with information relevant for assessing assocations between drugs and health outcomes of interest.DatabaseConnector
An R package for connecting to databases using JDBC.Criteria2Query
[In Development] An application to parse freetext inclusion criteria and produce a structured cohort definition that can be executed against OMOP CDMETL-CDMBuilder
ETL-CDMBuilder is a repo containing a .NET Core application to perform ETL to OMOP CDM for multiple databasesOHDSI-in-a-Box
Virtual Machine containing SynPUF data in OMOP CDM, a RDBS including query client, WebAPI, ATLAS, R and Python.Tutorial-ETL
Course materials for OHDSI ETL tutorialEunomia
An R package that facilitates access to a variety of OMOP CDM sample data sets.CohortDiagnostics
An R package for performing various cohort diagnostics.PhenotypeLibrary
A repository to store, organize and maintain the content of the OHDSI Phenotype library. OHDSI Forum post https://forums.ohdsi.org/t/ohdsi-phenotype-library-announcements/16910StudyProtocols
Repository of OHDSI Collaborative Research ProtocolsCyclops
Cyclops (Cyclic coordinate descent for logistic, Poisson and survival analysis) is an R package for performing large scale regularized regressions.Aphrodite
[in development]NLPTools
[in development] Tools to support Natural Language Processing of freetext to create structured data elements for analysisStudyProtocolSandbox
This repository is for developing study packages for OHDSI studies. Once completed, they can be moved to the StudyProtocols repository.Perseus
[under development] Tools for ETL into OMOP CDM and deployment of OHDSI toolstackThemis
Repository for OMOP CDM conventions as defined by THEMIS. These can be reference lists of concepts, pieces of standardized code for data generation or quality certification, and debates.ShinyDeploy
Shiny apps in this repository will be automatically deployed to the OHDSI Shiny server.OMOP-Queries
Hades
Health Analytics Data-to-Evidence Suite (HADES): A collection of R packages for performing analytics against the Common Data Model.Tutorial-CDM
Training materials for Vocabulary & CDM Tutorial.ClinicalTrialsWGETL
[under development] ETL materials to support proposal for CDM enhancements for clinical trial dataAchillesWeb
Interactive web site for reviewing the results of the Achilles R package.bayes-bridge
Bayesian sparse regression with regularized shrinkage and conjugate gradient accelerationGenomic-CDM
Repository for development of the genomic module of the CDM.PheValuator
An R package for evaluating phenotype algorithms.Radiology-CDM
Pilot model and converter for integration of radiology data into OMOP-CDMFhirToCdm
Conversion from FHIR HL7 to OMOP CDMFuzzyForest
[Under development] Random classification and regression treesCapr
Cohort definition Application Programming in Rdbt-synthea
[Under development] A dbt ETL project to convert a Synthea synthetic data set into the OMOP CDMCommonEvidenceModel
Common Evidence Model (CEM) is a structure for standardizing evidence about drug-outcome relationship across disparate evidence sources.InspectOMOP
InspectOmop is a lightweight python 3 package that assists in the extraction of electronic health record(EHR) data from relational databases following the OHDSI OMOP Common Data Model(CDM) standard v>=5.ArachneUI
Network infrastructure for collaborative studies across disparate data nodes and researchesETL-LambdaBuilder
CDM Builder leveraging AWS LambdaCureIdRegistry
SelfControlledCaseSeries
An R package for performing Self-Controlled Case Series (SCCS) analyses in an observational database in the OMOP Common Data Model.QueryLibrary
This is an R package that implements a library of standard queries that run against the OMOP-CDM.Covid-19
The OHDSI repository to provide comprehensive evidence for the covid-19OMOP-Standardized-Vocabularies
This repository is not longer active. It used to have the only purpose of creating releases of the Standardized Vocabularies, i.e. the content, not those of the Pallas Vocabulary Build System itself. As of 17-July-2018, vocabulary releases are also processed by Pallas. Please visit https://github.com/OHDSI/Vocabulary-v5.0/releases.RcppXsimd
R package wrapper for the C++ header-only library Xsimd that provides parallelized math implementations using SIMDAres
A Research Exploration SystemCohortGenerator
Cohort Generation for the OMOP Common Data ModelAndromeda
AsynchroNous Disk-based Representation of MassivE DAta: An R package aimed at replacing ff for storing large data objects.Apollo
[Under development] Assessment of Pre-trained Observational Large Language-models in OHDSI (APOLLO)DeepPatientLevelPrediction
An R package for performing patient level prediction using deep learning in an observational database in the OMOP Common Data Model.ROhdsiWebApi
An R package for interfacing with a WebAPI instanceGIS
EmpiricalCalibration
An R package for performing empirical calibration of observational study estimatesParallelLogger
An R package for easy parallel computing, logging, and function call automation.Broadsea-WebTools
A Docker container that includes the OHDSI WebAPI (running in Apache Tomcat) and the OHDSI web applications.circe-be
CIRCE is a cohort definition and syntax compiler tool for OMOP CDMv5Koios
Tool to identify concept in the OMOP Genomic vocabulary from VCF and other files as well as HGVS notationsVisualizations
[Under development] Visualizations is a collection of JavaScript modules to support D3 visualizations in web-based applicationsETL-German-FHIR-Core
ETL process from FHIR (defined by the German Medical Informatics Initiative) to OMOPTutorial-PLP
OMOPV4_PCORNetV1_ETL
ETL script to transform data from OMOP v4 CDM to PCORNet V1 CDMCaseControl
An R package for performing (nested) matched case-control analyses in an observational database in the OMOP Common Data Model.EvidenceSynthesis
An R package for combining evidence from multiple sources (e.g. multiple data sites)OhdsiShinyModules
An R package containing Shiny modules used by various OHDSI Shiny appsNostos
Navigate OMOP-structured data via text-to-SQLETL---Korean-NSC
ETL code for converting Korean National Sample Cohort (NSC) derived from national insurance health service into OMOP-CDM v5 developed by Ajou UniversityImageWG
Repository for medical image working groupOSIM-v5
An updated version of OSIM for CDM v5Strategus
[Under development] An R packages for coordinating and executing analytics using HADES modulesAthenaUI
UI of web application for distributing and browsing the Standardized Vocabularies for the OMOP CDMBigKnn
An R package implementing a large scale k-nearest neighbor classifier using the Lucene search engineIcTemporalPatternDiscovery
An R package for performing the IC Temporal Pattern Discovery method.Legend
An R package implementing Large-Scale Evidence Generation and Evaluation in a Network of Databases (LEGEND).OhdsiRTools
An R package of support tools that didnβt fit other categories, including tools for maintaining R libraries.DbDiagnostics
Package to profile a database and execute data diagnostics based on individual analysis settingsCohortIncidence
Contains the Java and R assets to perform Incidence calculations on a CDMCirceR
R package wrapper for CIRCESelfControlledCohort
An R package for performing self-controlled cohort analyses, a method to estimate risk by comparing time exposed with time unexposed among the exposed cohort.MethodEvaluation
An R package for the evaluation of estimation methodsHermes
(DEPRECATED) HERMES is a vocabulary browser tool for OMOP CDM v5Hestia
Hestia is an API for function calling on the OMOP CDM.Circe
[Under development] CIRCE is a cohort definition and syntax compiler tool for OMOP CDMv5EunomiaDatasets
Hosting of sample CDM datasets in CSV format for use in testing throughout the OHDSI community. Eunomia R package to manage the datasets can be accessed at https://github.com/OHDSI/Eunomia.ArachneCentralAPI
Arachne Central middle-tier including Service API.StandardizedAnalysisAPI
Interfaces for standardized OHDSI analyses (Cohort Characterization, TxPathway, Incidence Rate etc.) used as an exchange standard or implementation guideLove Open Source and this site? Check out how you can help us