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Added VOCABULARY.md

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clairblacketer 2017-06-14 13:53:16 -04:00
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Documentation/StandardizedVocabularies/CONCEPT.md
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@ -35,7 +35,7 @@ Concepts in the Common Data Model are derived from a number of public or proprie
* For all Concepts, whether they are custom generated or adopted from published terminologies, a unique numeric identifier concept_id is assigned and used as the key to link all observational data to the corresponding Concept reference data. * For all Concepts, whether they are custom generated or adopted from published terminologies, a unique numeric identifier concept_id is assigned and used as the key to link all observational data to the corresponding Concept reference data.
* The concept_id of a Concept is persistent, i.e. stays the same for the same Concept between releases of the Standardized Vocabularies. * The concept_id of a Concept is persistent, i.e. stays the same for the same Concept between releases of the Standardized Vocabularies.
* A descriptive name for each Concept is stored as the Concept Name as part of the CONCEPT table. Additional names and descriptions for the Concept are stored as Synonyms in the [CONCEPT_SYNONYM](CONCEPT_SYNONYM.md) table. * A descriptive name for each Concept is stored as the Concept Name as part of the CONCEPT table. Additional names and descriptions for the Concept are stored as Synonyms in the [CONCEPT_SYNONYM](CONCEPT_SYNONYM.md) table.
* Each Concept is assigned to a Domain. For Standard Concepts, these is always a single Domain. Source Concepts can be composite or coordinated entities, and therefore can belong to more than one Domain. The domain_id field of the record contains the abbreviation of the Domain, or Domain combination. Please refer to the Standardized Vocabularies [[documentation:vocabulary:domains|Specification]] for details of the Domain Assignment. * Each Concept is assigned to a Domain. For Standard Concepts, these is always a single Domain. Source Concepts can be composite or coordinated entities, and therefore can belong to more than one Domain. The domain_id field of the record contains the abbreviation of the Domain, or Domain combination. Please refer to the Standardized Vocabularies [specification](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary) for details of the Domain Assignment.
* For details of the Vocabularies adopted for use in the OMOP CDM refer to the Standardized Vocabularies specification. * For details of the Vocabularies adopted for use in the OMOP CDM refer to the Standardized Vocabularies specification.
* Concept Class designation are attributes of Concepts. Each Vocabulary has its own set of permissible Concept Classes, although the same Concept Class can be used by more than one Vocabulary. Depending on the Vocabulary, the Concept Class may categorize Concepts vertically (parallel) or horizontally (hierarchically). See the specification of each vocabulary for details. * Concept Class designation are attributes of Concepts. Each Vocabulary has its own set of permissible Concept Classes, although the same Concept Class can be used by more than one Vocabulary. Depending on the Vocabulary, the Concept Class may categorize Concepts vertically (parallel) or horizontally (hierarchically). See the specification of each vocabulary for details.
* Concept Class attributes should not be confused with Classification Concepts. These are separate Concepts that have a hierarchical relationship to Standard Concepts or each other, while Concept Classes are unique Vocabulary-specific attributes for each Concept. * Concept Class attributes should not be confused with Classification Concepts. These are separate Concepts that have a hierarchical relationship to Standard Concepts or each other, while Concept Classes are unique Vocabulary-specific attributes for each Concept.

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Documentation/StandardizedVocabularies/StandardizedVocabularies.md
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# 3 Standardized Vocabularies # 3 Standardized Vocabularies
<br>[3.1 CONCEPT](CONCEPT.md) <br>[3.1 CONCEPT](CONCEPT.md)
<br>3.2 VOCABULARY <br>[3.2 VOCABULARY](VOCABULARY.md)
<br>3.3 DOMAIN <br>3.3 DOMAIN
<br>3.4 CONCEPT_CLASS <br>3.4 CONCEPT_CLASS
<br>3.5 CONCEPT_RELATIONSHIP <br>3.5 CONCEPT_RELATIONSHIP

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Documentation/StandardizedVocabularies/VOCABULARY.md Normal file
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*OMOP Common Data Model v5.1 Specifications*
<br>*Authors: Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan, Clair Blacketer*
<br>***Release date needed***
[Back to Table of Contents](https://github.com/OHDSI/CommonDataModel/blob/master/Documentation/TableofContents.md)
<br>[Back to Standardized Vocabularies](StandardizedVocabularies.md)
---
# 3.2 VOCABULARY
The VOCABULARY table includes a list of the Vocabularies collected from various sources or created de novo by the OMOP community. This reference table is populated with a single record for each Vocabulary source and includes a descriptive name and other associated attributes for the Vocabulary.
Field|Required|Type|Description
:----|:----|:----|:-----
|vocabulary_id|Yes|varchar(20)|A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit.|
|vocabulary_name|Yes|varchar(255)|The name describing the vocabulary, for example "International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)" etc.|
|vocabulary_reference|Yes|varchar(255)|External reference to documentation or available download of the about the vocabulary.|
|vocabulary_version|Yes|varchar(255)|Version of the Vocabulary as indicated in the source.|
|vocabulary_concept_id|Yes|integer|A foreign key that refers to a standard concept identifier in the CONCEPT table for the Vocabulary the VOCABULARY record belongs to.|
## Conventions
* There is one record for each Vocabulary. One Vocabulary source or vendor can issue several Vocabularies, each of them creating their own record in the VOCABULARY table. However, the choice of whether a Vocabulary contains Concepts of different Concept Classes, or when these different classes constitute separate Vocabularies cannot precisely be decided based on the definition of what constitutes a Vocabulary. For example, the ICD-9 Volume 1 and 2 codes (ICD9CM, containing predominantly conditions and some procedures and observations) and the ICD-9 Volume 3 codes (ICD9Proc, containing predominantly procedures) are realized as two different Vocabularies. On the other hand, SNOMED-CT codes of the class Condition and those of the class Procedure are part of one and the same Vocabulary. Please refer to the Standardized Vocabularies [specifications](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary) for details of each Vocabulary.
* The vocabulary_id field contains an alphanumerical identifier, that can also be used as the abbreviation of the Vocabulary name.
* The record with vocabulary_id = 'None' is reserved to contain information regarding the current version of the Entire Standardized Vocabularies.
* The vocabulary_name field contains the full official name of the Vocabulary, as well as the source or vendor in parenthesis.
* Each Vocabulary has an entry in the CONCEPT table, which is recorded in the vocabulary_concept_id field. This is for purposes of creating a closed Information Model, where all entities in the OMOP CDM are covered by a unique Concept.
* In past versions of the VOCABULARY table, the vocabulary_id used to be a numerical value. A conversion table between these old and new IDs is given below:
vocabulary_id previously|vocabulary_id Version 5
-----|-----
|0|None|
|1|[SNOMED](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:snomed)|
|2|[ICD9CM](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:icd9cm)|
|3|ICD9Proc|
|4|[CPT4](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:cpt4)|
|5|HCPCS|
|6|[LOINC](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:loinc)|
|7|NDFRT|
|8|[RxNorm](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:rxnorm)|
|9|[NDC](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:ndc)|
|10|GPI|
|11|[UCUM](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:ucum)|
|12|[Gender](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:gender)|
|13|Race|
|14|Place of Service|
|15|MedDRA|
|16|Multum|
|17|Read|
|18|OXMIS|
|19|Indication|
|20|ETC|
|21|[ATC](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:atc)|
|22|Multilex|
|24|Visit|
|28|VA Product|
|31|SMQ|
|32|VA Class|
|33|Cohort|
|34|[ICD10](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:icd10)|
|35|[ICD10PCS](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:icd10pcs)|
|36|Drug Type|
|37|Condition Type|
|38|Procedure Type|
|39|Observation Type|
|40|DRG|
|41|MDC|
|42|APC|
|43|Revenue Code|
|44|[Ethnicity](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:ethnicity)|
|45|Death Type|
|46|[Mesh](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:mesh)|
|47|NUCC|
|48|Specialty|
|49|[LOINC](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:loinc)|
|50|SPL|
|53|Genseqno|
|54|CCS|
|55|OPCS4|
|56|Gemscript|
|57|HES Specialty|
|58|Note Type|
|59|Domain|
|60|PCORNet|
|61|Obs Period Type|
|62|Visit Type|
|63|Device Type|
|64|Meas Type|
|65|[Currency](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:currency)|
|66|Relationship|
|67|Vocabulary|
|68|Concept Class|
|69|Cohort Type|
|70|[ICD10CM](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:icd10cm)|

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Documentation/TableofContents.md
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<br> <br>
<br>**[3 Standardized Vocabularies](StandardizedVocabularies/StandardizedVocabularies.md)** <br>**[3 Standardized Vocabularies](StandardizedVocabularies/StandardizedVocabularies.md)**
<br>[3.1 CONCEPT](StandardizedVocabularies/CONCEPT.md) <br>[3.1 CONCEPT](StandardizedVocabularies/CONCEPT.md)
<br>3.2 VOCABULARY <br>[3.2 VOCABULARY](StandardizedVocabularies/VOCABULARY.md)
<br>3.3 DOMAIN <br>3.3 DOMAIN
<br>3.4 CONCEPT_CLASS <br>3.4 CONCEPT_CLASS
<br>3.5 CONCEPT_RELATIONSHIP <br>3.5 CONCEPT_RELATIONSHIP