documentation:vocabulary:introduction
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| - | ====== Background ====== | + | ====== Introduction ====== |
| - | The Standardized Vocabularies are part of the OMOP Common Data Model (CDM). They contain all of the code sets, terminologies, vocabularies, nomenclatures, lexicons, thesauri, ontologies, taxonomies, classifications, abstractions, and other such data that are required for: | + | This document reflects the requirements and implementation for the Standardized Vocabularies which are part of the OMOP Common Data Model (CDM), version 5.x. They are maintained by the Observational Health Data Science and Informatics [[http://ohdsi.org|(OHDSI]], pronounced "Odyssey") collaborative. |
| - | * Creating the transformed data in CDM format from the raw data sets, | + | |
| - | * Searching and querying the data, and browsing and navigating the hierarchies of classes and abstractions inherent in the transformed data, and | + | The Standardized Vocabularies contain all of the code sets, terminologies, vocabularies, nomenclatures, lexicons, thesauri, ontologies, taxonomies, classifications, abstractions, and other such data that are required for: |
| + | * Generation of the transformed (i.e., standardized) data from the raw dataset into CDM , | ||
| + | * Searching, querying and extraction of the transformed data, and browsing and navigating the hierarchies of classes and abstractions inherent in the transformed data, and | ||
| * Interpreting the meanings of the data. | * Interpreting the meanings of the data. | ||
| - | The Standardized Vocabularies are now released in Version 5.0. There have been changes to the previous versions, without violating any of the design principles. In particular, all concepts in previous versions are still available and identified using the same Concept IDs. New data domains were added to the concept list (Device, Measurement, Specimen) and all concepts are now formally assigned a Domain. | + | |
| + | Patient-level data available in OMOP CDM explicitly require the representation of all clinical facts and events using Concepts from the Standardized Vocabularies. With few exceptions, there are no verbatim pieces of information in the CDM tables. Therefore, the Standardized Vocabularies are an integral part of the OMOP CDM. It is available for free to anyone and can be downloaded from the [[http://www.ohdsi.org/web/athena|Download]] page. Generally, all parts and components are Open Source - unless otherwise specified for a very few commercial vocabularies. Please see [[documentation:vocabulary:license|Apache License V2.0]] for details. | ||
| + | |||
| + | The Standardized Vocabularies provide a standardized representation of data in the following clinical domains: | ||
| + | * Demographics: [[documentation:vocabulary:gender|Gender]], [[documentation:vocabulary:ethnicity| Ethnicity]], [[documentation:vocabulary:race |Race]] | ||
| + | * [[documentation:vocabulary:condition|Condition]] | ||
| + | * [[documentation:vocabulary:drug|Drug]] | ||
| + | * [[documentation:vocabulary:procedure|Procedure]] | ||
| + | * [[documentation:vocabulary:measurement|Measurement]] | ||
| + | * [[documentation:vocabulary:observation|Observation]] | ||
| + | * [[documentation:vocabulary:note|Note]] | ||
| + | * [[documentation:vocabulary:device|Device]] | ||
| + | * [[documentation:vocabulary:specimen|Specimen]] | ||
| + | * [[documentation:vocabulary:unit|Unit]] | ||
| + | * [[documentation:vocabulary:visit|Visit]] | ||
| + | * [[documentation:vocabulary:death|Death]] | ||
| + | * [[documentation:vocabulary:provider|Provider]] | ||
| + | * [[documentation:vocabulary:cost|Cost]] | ||
| + | |||
| + | Currently, 81 vocabularies are part of the Standardized Vocabularies. Many of them are adopted from 3rd party sources, which develop and maintain them for specific purposes, such as ICD9CM, ICD10 or SNOMEDCT. Consolidation of the vocabularies into a standardized form requires a number of decisions and conventions. This document discusses both the organization of vocabularies within the clinical domains, the specific implementation of each vocabulary into the Standardized Vocabularies, and the mapping of Concepts within and between vocabularies. It also provides guidance of how to apply them for transformation of source data into the CDM and about the querying of data once they are established in CDM format. | ||
| + | |||
| + | The Standardized Vocabularies are now released in Version 5.x. There have been changes to the previous versions, without violating any of the design principles. In particular, all concepts in previous versions are still available and identified using the same Concept IDs. All changes to the CDM from the previous version is described below. | ||
documentation/vocabulary/introduction.1418494876.txt.gz · Last modified: 2014/12/13 18:21 by cgreich
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