ID

35275

Beschreibung

OMOP Common Data Model (CDM) Source to Concept Map The source to concept map table is a legacy data structure within the OMOP Common Data Model, recommended for use in ETL processes to maintain local source codes which are not available as Concepts in the Standardized Vocabularies, and to establish mappings for each source code into a Standard Concept as target_concept_ids that can be used to populate the Common Data Model tables. The SOURCE_TO_CONCEPT_MAP table is no longer populated with content within the Standardized Vocabularies published to the OMOP community. This table is no longer used to distribute mapping information between source codes and Standard Concepts for the Standard Vocabularies. Instead, the CONCEPT_RELATIONSHIP table is used for this purpose, using the relationship_id='Maps to'. However, this table can still be used for the translation of local source codes into Standard Concepts. Note: This table should not be used to translate source codes to Source Concepts. The source code of a Source Concept is captured in its concept_code field. If the source codes used in a given database do not follow correct formatting the ETL will have to perform this translation. For example, if ICD-9-CM codes are recorded without a dot the ETL will have to perform a lookup function that allows identifying the correct ICD-9-CM Source Concept (with the dot in the concept_code field). OMOP Common Data Model Specifications Version 6.0 Specifications 11October2018 The Observational Medical Outcomes Partnership (OMOP) was a public-private partnership established to inform the appropriate use of observational healthcare databases for studying the effects of medical products. © 2014 Observational Health Data Sciences and Informatics This work is based on work by the Observational Medical Outcomes Partnership (OMOP) and used under license from the FNIH at http://omop.fnih.org/publiclicense. Version updated on 26.02.2019, from https://github.com/OHDSI/CommonDataModel/wiki/SOURCE_TO_CONCEPT_MAP

Link

http://omop.fnih.org/publiclicense

Stichworte

Versionen (2)
  1. 04.01.17 04.01.17 -
  2. 26.02.19 26.02.19 -
Rechteinhaber

Observational Medical Outcomes Partnership (OMOP)

Hochgeladen am

26. Februar 2019

DOI

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Lizenz

Creative Commons BY-NC 3.0
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OMOP Common Data Model (CDM) Source to Concept Map

Englisch

OMOP Common Data Model (CDM) Source to Concept Map

1 Formulare  
Source to Concept Map
Beschreibung

Source to Concept Map

Alias
UMLS CUI-1
C0449416
UMLS CUI-2
C0178566
UMLS CUI-3
C0034925
UMLS CUI-4
C0178566
UMLS CUI-5
C0024779
Source code
Beschreibung

The source code being translated into a standard concept. (Type varchar(50))

Datentyp

text

Alias
UMLS CUI [1]
C1710131
Source concept ID
Beschreibung

A foreign key to the Source Concept that is being translated into a Standard Concept. If there is no SOURCE_CONCEPT_ID available because the source codes are local and not supported by the Standard Vocabulary, the content of the field is 0 (zero, not null) encoding an undefined concept. However, local Source Concepts are established (concept_id values above 2,000,000,000).

Datentyp

integer

Alias
UMLS CUI [1,1]
C0449416
UMLS CUI [1,2]
C0178566
UMLS CUI [1,3]
C1300638
Source vocabulary ID
Beschreibung

A foreign key to the VOCABULARY table defining the vocabulary of the source code that is being translated to a Standard Concept. (Type varchar(20))

Datentyp

text

Alias
UMLS CUI [1,1]
C0449416
UMLS CUI [1,2]
C0042926
UMLS CUI [1,3]
C1300638
Source code description
Beschreibung

An optional description for the source code. This is included as a convenience to compare the description of the source code to the name of the concept. (Type varchar(255))

Datentyp

text

Alias
UMLS CUI [1,1]
C0449416
UMLS CUI [1,2]
C0678257
Target concept ID
Beschreibung

A foreign key to the target concept to which the source code is being mapped. It is equivalent to the concept_id_2 in the CONCEPT_RELATIONSHIP table.

Datentyp

integer

Alias
UMLS CUI [1,1]
C1521840
UMLS CUI [1,2]
C0178566
UMLS CUI [1,3]
C1300638
Target vocabulary ID
Beschreibung

A foreign key to the vocabulary table defining the vocabulary of the target concept. The TARGET_VOCABULARY_ID field contains the VOCABULARY_ID of the target concept. It is a duplication of the same information in the CONCEPT record of the Target Concept. (Type varchar(20))

Datentyp

text

Alias
UMLS CUI [1,1]
C1521840
UMLS CUI [1,2]
C0042926
UMLS CUI [1,3]
C1300638
valid start date
Beschreibung

The date when the mapping instance was first recorded.

Datentyp

date

Alias
UMLS CUI [1,1]
C0808070
UMLS CUI [1,2]
C0449416
UMLS CUI [1,3]
C0178566
UMLS CUI [1,4]
C0034925
UMLS CUI [1,5]
C0178566
UMLS CUI [1,6]
C0024779
valid end date
Beschreibung

The date when the mapping instance became invalid because it was deleted or superseded (updated) by a new relationship. Default value is 31- Dec-2099.

Datentyp

date

Alias
UMLS CUI [1,1]
C0806020
UMLS CUI [1,2]
C0449416
UMLS CUI [1,3]
C0178566
UMLS CUI [1,4]
C0034925
UMLS CUI [1,5]
C0178566
UMLS CUI [1,6]
C0024779
Invalid reason
Beschreibung

Reason the mapping instance was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value. (Type varchar(1))

Datentyp

text

Alias
UMLS CUI [1,1]
C0024779
UMLS CUI [1,2]
C0596404
UMLS CUI [1,3]
C3245471
UMLS CUI [1,4]
C0566251
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Ähnliche Modelle

OMOP Common Data Model (CDM) Source to Concept Map

1 Formulare
Name
Typ
Description | Question | Decode (Coded Value)
Datentyp
Alias
Item Group
Source to Concept Map
C0449416 (UMLS CUI-1)
C0178566 (UMLS CUI-2)
C0034925 (UMLS CUI-3)
C0178566 (UMLS CUI-4)
C0024779 (UMLS CUI-5)
Source code
Item
Source code
text
C1710131 (UMLS CUI [1])
Source concept ID
Item
Source concept ID
integer
C0449416 (UMLS CUI [1,1])
C0178566 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
Source vocabulary ID
Item
Source vocabulary ID
text
C0449416 (UMLS CUI [1,1])
C0042926 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
Source code description
Item
Source code description
text
C0449416 (UMLS CUI [1,1])
C0678257 (UMLS CUI [1,2])
Target concept ID
Item
Target concept ID
integer
C1521840 (UMLS CUI [1,1])
C0178566 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
Target vocabulary ID
Item
Target vocabulary ID
text
C1521840 (UMLS CUI [1,1])
C0042926 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
valid start date
Item
valid start date
date
C0808070 (UMLS CUI [1,1])
C0449416 (UMLS CUI [1,2])
C0178566 (UMLS CUI [1,3])
C0034925 (UMLS CUI [1,4])
C0178566 (UMLS CUI [1,5])
C0024779 (UMLS CUI [1,6])
valid end date
Item
valid end date
date
C0806020 (UMLS CUI [1,1])
C0449416 (UMLS CUI [1,2])
C0178566 (UMLS CUI [1,3])
C0034925 (UMLS CUI [1,4])
C0178566 (UMLS CUI [1,5])
C0024779 (UMLS CUI [1,6])
Item
Invalid reason
text
C0024779 (UMLS CUI [1,1])
C0596404 (UMLS CUI [1,2])
C3245471 (UMLS CUI [1,3])
C0566251 (UMLS CUI [1,4])
invalid reason
Code List
Invalid reason
CL Item
Deleted (D)
CL Item
Replaced with an update (U)
CL Item
valid end date has the default value (NULL)
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