Observational Health Data Sciences and Informatics

Login: OHDSI

Company: null

Location: null

email:

Blog: http://ohdsi.org

Members

1. Marc Suchard
2. Martijn Schuemie
3. Rae Woong Park
4. null

Repositories

Achilles

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

Achilles-Node

A Node.js Web Service for Generating Achilles SQL Scripts

AchillesWeb

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

Aegis

Application for Epidemiological Geographic Information System (AEGIS): a system for semi-automatic GIS visualization based on the OMOP Common Data Model.

Aphrodite

[in development]

ArachneCentralAPI

Arachne Central middle-tier including Service API.

ArachneCommons

Commons module contains common code re-used between all Arachne components

ArachneExecutionEngine

Arachne Execution Engine is a component used to execute remote SQL or R code. It is used by both Arachne Data Node as well as WebAPI

ArachneNodeAPI

Arachne Data Node is a component that facilitates connection and communication between local databases and Arachne Central

ArachneUI

Network infrastructure for collaborative studies across disparate data nodes and researches

ArachneUIComponents

[under development] a open repository to host ARACHNE Common UI components

Architecture

Architecture artifact repository.

Athena

Web application for distributing the Standardized Vocabularies for the OMOP CDM

AthenaUI

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

Atlas

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

BigKnn

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

bit

Fork of the R bit package

BoostCompiledLibraries

R package for several BOOST compiled libraries

Broadsea

Broadsea deploys the full OHDSI technology stack (R methods library & web tools), using cross-platform Docker container technology.

Broadsea-MethodsLibrary

null

Broadsea-Shiny

A Docker container based on rocker/shiny with added java jdk and additional R packages.

Broadsea-WebTools

A Docker container that includes the OHDSI WebAPI (running in Apache Tomcat) and the OHDSI web applications.

BrokenAdaptiveRidge

null

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

CaseControl

An R package for performing (nested) matched case-control analyses in an observational database in the OMOP Common Data Model.

CaseCrossover

An R package for performing case-crossover and case-time-control analyses in an observational database in the OMOP Common Data Model.

CdmAtlasCutover

An R package to assist in the management of multiple CDM data sources for use in Atlas

CDMTableBrowser

[under development] A GUI to explore the structure (tables, fields and other meta-data) associated with the OMOP Common Data Model v5

Centaur

An R package for performing new-user cohort studies. This package implements a more traditional approach than the one used in the CohortMethod package.

Cert

[Under development] R package for running the Comparison on Extreme Laboratory Test results (CERT) algorithm.

Chronos

Chronological Health Report for the OHDSI Network Of Subjects

Circe

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

circe-be

CIRCE is a cohort definition and syntax compiler tool for OMOP CDMv5

Clear

[Under development] R package for running the Comparison of the Laboratory Extreme Abnormality Ratio (CLEAR) algorithm.

CohortMethod

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

CommonDataModel

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

CommonEvidenceModel

Structure for standardizing evidence about drug-outcome relationship across disparate evidence soures

Community

A repo for general OHDSI issue tracking and project management

Criteria2Query

[In Development] An application to parse freetext inclusion criteria and produce a structured cohort definition that can be executed against OMOP CDM

Cyclops

Cyclops (Cyclic coordinate descent for logistic, Poisson and survival analysis) is an R package for performing large scale regularized regressions.

DatabaseConnector

An R package for connecting to databases using JDBC.

DatabaseConnectorJars

An R package containing the external JAR dependencies of the DatabaseConnector package.

Dataprint

A Novel Visualization Tool for Database Comparison

DDLgeneratr

null

drat

drat repository for OHDSI R packages

DrugExposureExplorer

null

EmpiricalCalibration

An R package for performing empirical calibration of observational study estimates

Era-Constructor

This is a repo that contains standardized code for hte construction of Drug Eras, Dose Eras and Condition Eras

ETL-CDMBuilder

ETL-CDMBuilder is a repo containing a .NET application to perform ETL to OMOP CDMv4 for multiple databases

ETL-CMS

Workproducts to ETL CMS datasets into OMOP Common Data Model

ETL-HealthVerityBuilder

ETL to take dataset from HealthVerity and convert to OMOP CDM v5 [in development, not for production use yet]

ETL---IMS-Data

ETL documentation for QuintilesIMS Data

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

EvidenceSynthesis

[Under development] An R package for combining evidence from multiple sources (e.g. multiple data sites)

f2f-dissemination

a hackathon repository for the ohdsi f2f

FeatureExtraction

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

ff

Fork of the R ff package

FuzzyForest

[Under development] Random classification and regression trees

GIS

null

Helios

Docker image for creating and initializing a SOLR based text index for use in support of vocabulary search functionality.

Heracles

[UNDER DEVELOPMENT] Health Enterprise Resource and Care Learning Exploration System (HERACLES) - descriptive statistics about a cohort in an OMOP CDM v4 or V5 database

Hercules

null

Hermes

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

Homer

[under development] Health Outcomes and Medical Effectiveness Research (HOMER) is a platform for integrating disparate analyses across a data network for exploring population-level estimates of causal effects.

IcTemporalPatternDiscovery

An R package for performing the IC Temporal Pattern Discovery method.

Iris

IRIS provides a high-level descriptive summary of a population within a OMOP CDM-compliant database

JCdmBuilder

JCdmBuilder is a Java program that can be used to transform observational datasets from their native formats and schemas into the OMOP Common Data Model.

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.

KnowledgeBaseWeb

[in development]

Legend

[Under development] An R package implementing Large-Scale Evidence Generation and Evaluation in a Network of Databases (LEGEND).

LocalControl

An R Package for Generating High Quality Comparative Effectiveness Evidence

MedlineXmlToDatabase

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

MethodEvaluation

[Under development] An R package for the evaluation of estimation methods

NLPTools

[in development] Tools to support Natural Language Processing of freetext to create structured data elements for analysis

OHDSI-Apps-Style-Guide

Initial Style Guide for OHDSI Apps

OhdsiRTools

An R package of support tools that didn?t fit other categories, including tools for maintaining R libraries.

OhdsiServiceWrapper

The OHDSI Service Wrapper is an R package that provides a layer between the OHDSI WebAPI and the R methods library. This package contains analysis specific features that leverage the methods library in order to generate evidence from OHDSI assets defined within the architecture.

OhdsiSharing

[Under development] Package for sharing of the results of the OHDSI tools

OhdsiStudy2

Treatment Pathways Study Protocol 12 Months

Olympus

[UNDER DEVELOPMENT] OLYMPUS - An OHDSI Launcher and Configurator

OMOP-Queries

null

OMOP-Standardized-Vocabularies

null

OMOPV4_PCORNetV1_ETL

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

OSIM-v5

An updated version of OSIM for CDM v5

Pace

null

PatientLevelPrediction

An R package for performing patient level prediction.

Penelope

PENELOPE (Personalized Exploratory Navigation and Evaluation for Labels Of Product Effects) [under development]

PhenotypeLibrary

A repository to store validated phenotype cohort definitions, with all associated source code, documentation, and validation results.

PredictionComparison

[Under development] An R package for comparing patient-level predictions and prediction models

PropensityScoreEvaluation

null

PublicOracle

R Interface to the OHDSI Public Web API [in development]

RcppBoostCompute

Rcpp wrapper for boost::compute, an STL algorithm-based OpenCL library

RcppBoostSimd

null

RcppCudaJitify

Compile CUDA code at run-time within an Rcpp-enabled R package

RcppVexCL

R wrapper for VexCL, an expressive C++11 header-library for OpenCL computing

RiskStratifiedEstimation

[Under development] An R package for performing effect estimation in risk strata derived from predictive models.

San

null

sandbox

Place for initial sharing of community-contributed code

SelfControlledCaseSeries

An R package for performing Self-Controlled Case Series (SCCS) analyses in an observational database in the OMOP Common Data Model.

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.

ShinyDeploy

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

Specifications

A repository for development and sharing of OHDSI specifications in the OpenAPI 3.0 format.

SqlRender

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

Statius

null

StudyProtocols

Repository of OHDSI Collaborative Research Protocols

StudyProtocolSandbox

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

Tantalus

[Under development] An R package for comparing two versions of the Vocabulary.

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.

TxPath

Treatment Pathways Unified Revision Repo

txPath-lite

null

Usagi

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

Visualizations

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

Vocab-download

Tools and features outside the Woldpress content management

Vocabulary-v4.5

The OMOP Standard Vocabulary creates a standardized representation of data in the OMOP CDM

Vocabulary-v5.0

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.

WebAPI

[Under development] OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications

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.