OHDSI/Atlas

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Created over 9 years ago
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OHDSI/Atlas

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

ATLAS

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data converted to the OMOP Common Data Model V5. Researchers can create cohorts by defining groups of people based on an exposure to a drug or diagnosis of a particular condition using healthcare claims data. ATLAS has vocabulary searching of medical concepts to identify people with specific conditions, drug exposures etc. Patient profiles can be viewed within a specific cohort allowing visualization of a particular subject's health care records. Population effect level estimation analyses allows for comparison of two different cohorts and leverages R packages.

Resources

Atlas (ohdsi.org) Please note: Google Chrome is the recommended browser for ATLAS.
Documentation
Releases

Technology

ATLAS is built using HTML, CSS and Knockout JavaScript. For more information on using Atlas, please refer to the setup guide.

Dependencies

WebAPI

Getting Involved

Developer questions/comments/feedback: OHDSI Forum
We use the GitHub issue tracker for all bugs/issues/enhancements

License

ATLAS is licensed under Apache License 2.

CommonDataModel

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

Vocabulary-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 applications

Achilles

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

TheBookOfOhdsi

The Book of OHDSI repository

ETL-Synthea

A package supporting the conversion from Synthea CSV to OMOP CDM

Usagi

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 Model

CohortMethod

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 environment

Broadsea

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 CDM

FeatureExtraction

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

OncologyWG

Oncology Working Group Repository

KnowledgeBase

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 CDM

ETL-CDMBuilder

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

OHDSI-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 tutorial

Eunomia

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/16910

StudyProtocols

Repository of OHDSI Collaborative Research Protocols

Cyclops

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 analysis

StudyProtocolSandbox

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 toolstack

Themis

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

Jupyter Notebook

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 data

AchillesWeb

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

bayes-bridge

Bayesian sparse regression with regularized shrinkage and conjugate gradient acceleration

Jupyter Notebook

Genomic-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-CDM

FhirToCdm

Conversion from FHIR HL7 to OMOP CDM

FuzzyForest

[Under development] Random classification and regression trees

Capr

Cohort definition Application Programming in R

dbt-synthea

[Under development] A dbt ETL project to convert a Synthea synthetic data set into the OMOP CDM

CommonEvidenceModel

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 researches

ETL-LambdaBuilder

CDM Builder leveraging AWS Lambda

CureIdRegistry

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-19

OMOP-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 SIMD

Ares

A Research Exploration System

CohortGenerator

Cohort Generation for the OMOP Common Data Model

Andromeda

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 instance

GIS

EmpiricalCalibration

An R package for performing empirical calibration of observational study estimates

ParallelLogger

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 CDMv5

Koios

Tool to identify concept in the OMOP Genomic vocabulary from VCF and other files as well as HGVS notations

Visualizations

[Under development] Visualizations is a collection of JavaScript modules to support D3 visualizations in web-based applications

ETL-German-FHIR-Core

ETL process from FHIR (defined by the German Medical Informatics Initiative) to OMOP

Tutorial-PLP

OMOPV4_PCORNetV1_ETL

ETL script to transform data from OMOP v4 CDM to PCORNet V1 CDM

CaseControl

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 apps

Nostos

Navigate OMOP-structured data via text-to-SQL

Jupyter Notebook

ETL---Korean-NSC

ETL code for converting Korean National Sample Cohort (NSC) derived from national insurance health service into OMOP-CDM v5 developed by Ajou University

ImageWG

Repository for medical image working group

Rich Text Format

OSIM-v5

An updated version of OSIM for CDM v5

Strategus

[Under development] An R packages for coordinating and executing analytics using HADES modules

AthenaUI

UI of web application for distributing and browsing the Standardized Vocabularies for the OMOP CDM

BigKnn

An R package implementing a large scale k-nearest neighbor classifier using the Lucene search engine

IcTemporalPatternDiscovery

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 didn’t fit other categories, including tools for maintaining R libraries.

DbDiagnostics

Package to profile a database and execute data diagnostics based on individual analysis settings

CohortIncidence

Contains the Java and R assets to perform Incidence calculations on a CDM

CirceR

R package wrapper for CIRCE

SelfControlledCohort

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 methods

Hermes

(DEPRECATED) HERMES is a vocabulary browser tool for OMOP CDM v5

Hestia

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 CDMv5

EunomiaDatasets

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.

Calypso

CALYPSO (Criteria Assessment Logic for Your Population Study in Observational data) is a web user interface to define, instantiate and evaluate a study population and the implications of inclusion criteria

StandardizedAnalysisAPI

Interfaces for standardized OHDSI analyses (Cohort Characterization, TxPathway, Incidence Rate etc.) used as an exchange standard or implementation guide