ID

19489

Description

OMOP Common Data Model (CDM) Specimen The SPECIMEN table contains the records identifying each biological sample from a person. 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.

Link

http://omop.fnih.org/publiclicense

Keywords

Versions (3)
  1. 1/4/17 1/4/17 -
  2. 2/18/19 2/18/19 -
  3. 2/26/19 2/26/19 -
Uploaded on

January 4, 2017

DOI

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License

Creative Commons BY-NC 3.0
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OMOP Common Data Model (CDM) Specimen

English

OMOP Common Data Model (CDM) Specimen

1 forms  
Specimen
Description

Specimen

Alias
UMLS CUI-1
C0370003
Specimen ID
Description

A unique identifier for each specimen.

Data type

integer

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C1300638
Person ID
Description

A foreign key identifier to the person for whom the specimen is recorded.

Data type

integer

Alias
UMLS CUI [1]
C2348585
Specimen concept ID
Description

A foreign key referring to a standard concept identifier in the Standardized Vocabularies for the specimen.

Data type

integer

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C0178566
UMLS CUI [1,3]
C1300638
Specimen type concept ID
Description

A foreign key referring to the predefined concept identifier in the Standardized Vocabularies reflecting the system of record from which the specimen was represented in the source data.

Data type

integer

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C0332307
UMLS CUI [1,3]
C0178566
UMLS CUI [1,4]
C1300638
Specimen date
Description

The date the specimen was obtained from the person.

Data type

date

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C0011008
Specimen time
Description

The time on the date when the specimen was obtained from the person.

Data type

time

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C0040223
Specimen quantity
Description

The amount of specimen collection from the person during the sampling procedure

Data type

float

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C1265611
Unit concept ID
Description

A foreign key to a standard concept identifier for the unit associated with the numeric quantity of the specimen collection.

Data type

integer

Alias
UMLS CUI [1,1]
C1519795
UMLS CUI [1,2]
C0178566
UMLS CUI [1,3]
C1300638
Anatomic site concept ID
Description

A foreign key to a standard concept identifier for the anatomic location of specimen collection.

Data type

integer

Alias
UMLS CUI [1,1]
C1515974
UMLS CUI [1,2]
C0178566
UMLS CUI [1,3]
C1300638
Disease status concept ID
Description

A foreign key to a standard concept identifier for the disease status of specimen collection.

Data type

integer

Alias
UMLS CUI [1,1]
C0012634
UMLS CUI [1,2]
C0449438
UMLS CUI [1,3]
C0178566
UMLS CUI [1,4]
C1300638
Specimen source ID
Description

disease status concept ID

Data type

text

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C0449416
UMLS CUI [1,3]
C1300638
Specimen source value
Description

The specimen value as it appears in the source data. This value is mapped to a standard concept in the Standardized Vocabularies and the original code is, stored here for reference.

Data type

text

Alias
UMLS CUI [1,1]
C0370003
UMLS CUI [1,2]
C0449416
UMLS CUI [1,3]
C1522609
Unit source value
Description

The information about the unit as detailed in the source.

Data type

text

Alias
UMLS CUI [1,1]
C1519795
UMLS CUI [1,2]
C0449416
UMLS CUI [1,3]
C1522609
Anatomic site source value
Description

The information about the anatomic site as detailed in the source.

Data type

text

Alias
UMLS CUI [1,1]
C1515974
UMLS CUI [1,2]
C0449416
UMLS CUI [1,3]
C1522609
Disease status source value
Description

The information about the disease status as detailed in the source.

Data type

text

Alias
UMLS CUI [1,1]
C0012634
UMLS CUI [1,2]
C0449438
UMLS CUI [1,3]
C0449416
UMLS CUI [1,4]
C1522609
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Similar models

OMOP Common Data Model (CDM) Specimen

1 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Specimen
C0370003 (UMLS CUI-1)
Specimen ID
Item
Specimen ID
integer
C0370003 (UMLS CUI [1,1])
C1300638 (UMLS CUI [1,2])
Person ID
Item
Person ID
integer
C2348585 (UMLS CUI [1])
Specimen concept ID
Item
Specimen concept ID
integer
C0370003 (UMLS CUI [1,1])
C0178566 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
Specimen type concept ID
Item
Specimen type concept ID
integer
C0370003 (UMLS CUI [1,1])
C0332307 (UMLS CUI [1,2])
C0178566 (UMLS CUI [1,3])
C1300638 (UMLS CUI [1,4])
Specimen date
Item
Specimen date
date
C0370003 (UMLS CUI [1,1])
C0011008 (UMLS CUI [1,2])
Specimen time
Item
Specimen time
time
C0370003 (UMLS CUI [1,1])
C0040223 (UMLS CUI [1,2])
Specimen quantity
Item
Specimen quantity
float
C0370003 (UMLS CUI [1,1])
C1265611 (UMLS CUI [1,2])
Unit concept ID
Item
Unit concept ID
integer
C1519795 (UMLS CUI [1,1])
C0178566 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
Anatomic site concept ID
Item
Anatomic site concept ID
integer
C1515974 (UMLS CUI [1,1])
C0178566 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
disease status concept ID
Item
Disease status concept ID
integer
C0012634 (UMLS CUI [1,1])
C0449438 (UMLS CUI [1,2])
C0178566 (UMLS CUI [1,3])
C1300638 (UMLS CUI [1,4])
Specimen source ID
Item
Specimen source ID
text
C0370003 (UMLS CUI [1,1])
C0449416 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
Specimen source value
Item
Specimen source value
text
C0370003 (UMLS CUI [1,1])
C0449416 (UMLS CUI [1,2])
C1522609 (UMLS CUI [1,3])
Unit source value
Item
Unit source value
text
C1519795 (UMLS CUI [1,1])
C0449416 (UMLS CUI [1,2])
C1522609 (UMLS CUI [1,3])
Anatomic site source value
Item
Anatomic site source value
text
C1515974 (UMLS CUI [1,1])
C0449416 (UMLS CUI [1,2])
C1522609 (UMLS CUI [1,3])
Disease status source value
Item
Disease status source value
text
C0012634 (UMLS CUI [1,1])
C0449438 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,3])
C1522609 (UMLS CUI [1,4])
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