27 open source projects by OHDSI

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data

PALLAS: Build process for OMOP Standardized Vocabularies. Currently not available as independent release. Therefore, do not clone or try to replicate. It is work in progress and not ready for replication.

An R package for performing patient level prediction in an observational database in the OMOP Common Data Model.

Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES) - descriptive statistics about a OMOP CDM database

OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications

Usagi is an application to help create mappings between coding systems and the Vocabulary standard concepts.

This repository is for developing study packages for OHDSI studies. Once completed, they can be moved to the StudyProtocols repository.

Interactive web site for reviewing the results of the Achilles R package.

[Under development] CIRCE is a cohort definition and syntax compiler tool for OMOP CDMv5

Definition and DDLs for the OMOP Common Data Model (CDM)

Automation code and documentation for standing up the OHDSI toolstack in an AWS environment

[in development]

An R package for performing new-user cohort studies in an observational database in the OMOP Common Data Model.

A repository to store, organize and maintain the content of the OHDSI Phenotype library.

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.

A tool to help improve data quality standards in observational data science.

Repository of OHDSI Collaborative Research Protocols

An R package for generating features (covariates) for a cohort using data in the Common Data Model.

A command line Java application for parsing MEDLINE XML files and inserting the data into a relational database

ETL-CDMBuilder is a repo containing a .NET Core application to perform ETL to OMOP CDM for multiple databases

Virtual Machine containing SynPUF data in OMOP CDM, a RDBS including query client, WebAPI, ATLAS, R and Python.

[Under development] Random classification and regression trees

Workproducts to ETL CMS datasets into OMOP Common Data Model

Shiny apps in this repository will be automatically deployed to the OHDSI Shiny server.

This is an R package and Java library for rendering parameterized SQL, and translating it to different SQL dialects.

Common Evidence Model (CEM) is a structure for standardizing evidence about drug-outcome relationship across disparate evidence sources.

Source code used to develop the OHDSI knowledge base of sources with information relevant for assessing assocations between drugs and health outcomes of interest.