Observational Health Data Sciences and Informatics documentation

documentation:achilles

Anonymous (anonymous@undisclosed.example.com) — 2014-11-17T14:08:58+0000

There are 2 applications. Achilles creates JSON files and then AchillesWeb is able to display JSON data on a website.

documentation:apps

Anonymous (anonymous@undisclosed.example.com) — 2015-04-09T07:43:37+0000

Getting Started with OHDSI Apps * ACHILLES for data characterization * HERMES for vocabulary exploration * CIRCE for cohort creation * HOMER for population-level estimation * PLATO for patient-level prediction * WhiteRabbit for ETL design * Usagi source code to Vocabulary mapping

documentation:cdm-goals-2016

Anonymous (anonymous@undisclosed.example.com) — 2016-02-12T02:45:14+0000

CDM and Vocabulary Workgroup Goals 2016 1. Establish a consistent transparent process to improve and change both the CDM and the Vocabulary through: * Forum discussion * Uniform proposal submission * Peer vetting * Group approval * Documentation

documentation:cdm

Anonymous (anonymous@undisclosed.example.com) — 2024-09-02T09:39:57+0000

OMOP Common Data Model Thank you for visiting the wiki! This page has moved to . Come join us over there!

documentation:cdm_members

Anonymous (anonymous@undisclosed.example.com) — 2016-06-13T15:47:15+0000

CDM Workgroup Members * Charlie Bailey * Rimma Belenkaya * Clair/Margret Blacketer * Zahid Butt * Mark Danese * Jennifer Duryea * Ryan Duryea * Fern Fitzhenry * Rob Follet * Voijtech Huser * Mark Khayter * Tara Knight * Chris Knoll * Michael Matheny * Daniella Meeker * Robert Miller * Toan Ong * Laura Pearlman * Christian Reich * Patrick Ryan * Lisa Schilling * William Stephens * Don Torok * King Wah Fung * Nicole Weisko…

documentation:cdm_workgroup_documents

Anonymous (anonymous@undisclosed.example.com) — 2016-04-05T18:05:19+0000

CDM and Vocabulary Working Group Documents * Process for adopting CDM/Vocabulary changes * next_cdm

documentation:etl_best_practices

Anonymous (anonymous@undisclosed.example.com) — 2017-06-28T20:35:26+0000

ETL creation best practices * CDM Conversion Best Practices This document describes some of the best practices we have developed over the years when trying to create an ETL (Extract, Transform, Load) process to convert data into the OMOP Common Data Model (CDM). We have found it best to split the process into four distinct activities:

documentation:example_etls

Anonymous (anonymous@undisclosed.example.com) — 2016-11-04T17:46:24+0000

Example ETLs Janssen Research & Development CDM v5.0 * All manuals can be found in GitHub: * Currently there are manuals for: * Clinical Practice Research Datalink (CPRD) * Japan Medical Data Center (JMDC) * Optum Extended Socio-Economic Status (SES) and Date of Death (DOD)

documentation:getting_started

Anonymous (anonymous@undisclosed.example.com) — 2015-04-06T22:54:30+0000

Getting Started with OHDSI Fundamentally, getting started with OHDSI involves three steps: 1) Converting your data to the OMOP Common Data Model. 2) Utilizing OHDSI tools to learn more from your data 3) Joining the OHDSI research network to collaborate on studies involving over 650 million patients from around the world

documentation:international_drugs

Anonymous (anonymous@undisclosed.example.com) — 2024-09-02T12:35:47+0000

RxNorm Extension - an OHDSI resource to represent international drugs Thank you for visiting the wiki! This page has moved to .

documentation:laertes_etl

Anonymous (anonymous@undisclosed.example.com) — 2015-06-23T10:58:53+0000

Background LAERTES: Large scale Adverse Effects Related to Treatment Evidence Standardization LAERTES provides an evidence base of a wide variety of sources with information relevant for assessing associations between drugs and health outcomes of interest. Please see the following publication for a description of the goal and use cases driving the system:

documentation:next_cdm

Anonymous (anonymous@undisclosed.example.com) — 2018-01-31T17:51:40+0000

CDM and Vocabulary Working Group Running List Process for adopting CDM and Vocabulary changes Running Meeting Agendas Google Doc Agenda Workgroups * Oncology Subgroup - Christian Reich, Rimma Belenkaya * Drug benefit indicator- Don Torok * Genomics Subgroup - Clair Blacketer Face-To-Face Notes Notes: Need preparation Proposals are now being housed as github issues. Please use this

documentation:observational_health_data

Anonymous (anonymous@undisclosed.example.com) — 2014-11-09T18:22:33+0000

Observational Health Data This part That part

documentation:overview

Anonymous (anonymous@undisclosed.example.com) — 2022-11-04T12:32:56+0000

Documentation Getting Started with OHDSI Common Data Model (CDM) * CDM Specifications * CDM Vocabulary v5 * CDM Vocabulary v4.5 (outdated) * Sample CDM Data Convert Database to CDM (ETL) * ETL creation best practices * Example ETLs * ETL Tools * ETL Support ETL Processes * Vocabulary ETL * Laertes ETL Tool Specific Documentation * ATLAS * ACHILLES * WhiteRabbit * Usagi * Methods Library * WebAPI * OHDSI-In-A-Box OHDSI Cloud * Deployed Demo Techn…

documentation:r_setup

Anonymous (anonymous@undisclosed.example.com) — 2016-07-06T21:37:49+0000

How to set up your R environment Many of the OHDSI tools need to be executed from within R, and it is not always that easy to configure it correctly. Below are our recommendations for various use cases. Tool users Here are instructions for when you just want to run the OHDSI tools.

documentation:sidebar

Anonymous (anonymous@undisclosed.example.com) — 2018-03-28T14:06:32+0000

Documentation Getting Started with OHDSI Common Data Model (CDM) * CDM Specifications * CDM Vocabulary Convert Database to CDM (ETL) * ETL creation best practices * Example ETLs * ETL Tools * ETL Support Tool Specific Documentation * ATLAS * ACHILLES * White Rabbit * Usagi * Methods Library * WebAPI * Common Evidence Model

documentation:sidebar2

Anonymous (anonymous@undisclosed.example.com) — 2014-11-11T03:29:35+0000

Common Data Model * Model * Vocabulary * ETLs Applications * Data Summarization (ACHILLES) * Cohort Creation & Analysis (HERACLES) * Drug Outcome Evidence (HOMER) * Drug Knowledgebase (LAERTES) Research Network * Submitting a Research Question

documentation:support_for_database_platforms

Anonymous (anonymous@undisclosed.example.com) — 2025-02-14T12:46:02+0000

Support for database platforms The OHDSI tools interact directly with the data in the OMOP Common Data Model (CDM). As such, they need to connect with the database server, and perform advanced analytics, both on the server and the client. The OHDSI tools currently support a wide range of DataBase Management Systems (DBMS), to varying degrees. Many have expressed interest in expanding the list of DBMSs even further.

documentation:vocabulary

Anonymous (anonymous@undisclosed.example.com) — 2024-09-10T08:28:56+0000

OMOP Standardized Vocabulary V5.0 Thank you for visiting the Vocabulary wiki! All documentation for the vocabulary has now moved to theOHDSI GitHub wiki. Come join us over there!

documentation:vocabulary4.5

Anonymous (anonymous@undisclosed.example.com) — 2016-08-03T21:33:42+0000

Standardized Vocabulary V4.5 For a consolidated one-document version click here Standardized Vocabularies * 1. Introduction * 1.1. Background * 1.2. Definition of Terms * 1.3. Vocabulary Representation in the CDM1.3. Vocabulary Representation in the CDM * 2. Changes from Vocabulary Version V4 * 2.1. Fundamental Changes * 2.1.1. Introduction of a Record Lifecycle * 2.1.2. Handling of Unambiguous Mapping * 2.1.3. Handling of Hierarchical Relationships between Concep…

documentation:vocabulary_etl

Anonymous (anonymous@undisclosed.example.com) — 2024-09-04T12:01:45+0000

!! This cookbook is outdated - do not follow these instructions !! Vocabulary Users download vocabularies from Athena: