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documentation:cdm:specimen

SPECIMEN

THIS IS OUTDATED. All documentation is now on the github wiki. Please refer there or to the CDM working group for more information

This table changed in version 5.1 of the OMOP CDM. The field specimen_datetime was added.


The specimen domain contains the records identifying biological samples from a person.

FieldRequiredTypeDescription
specimen_idYesintegerA unique identifier for each specimen.
person_idYesintegerA foreign key identifier to the Person for whom the Specimen is recorded.
specimen_concept_idYesintegerA foreign key referring to a Standard Concept identifier in the Standardized Vocabularies for the Specimen.
specimen_type_concept_idYesintegerA foreign key referring to the Concept identifier in the Standardized Vocabularies reflecting the system of record from which the Specimen was represented in the source data.
specimen_dateYesdateThe date the specimen was obtained from the Person.
specimen_datetimeNodatetimeThe date and time on the date when the Specimen was obtained from the person.
quantityNofloatThe amount of specimen collection from the person during the sampling procedure.
unit_concept_idNointegerA foreign key to a Standard Concept identifier for the Unit associated with the numeric quantity of the Specimen collection.
anatomic_site_concept_idNointegerA foreign key to a Standard Concept identifier for the anatomic location of specimen collection.
disease_status_concept_idNointegerA foreign key to a Standard Concept identifier for the Disease Status of specimen collection.
specimen_source_idNovarchar(50)The Specimen identifier as it appears in the source data.
specimen_source_valueNovarchar(50)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.
unit_source_valueNovarchar(50)The information about the Unit as detailed in the source.
anatomic_site_source_valueNovarchar(50)The information about the anatomic site as detailed in the source.
disease_status_source_valueNovarchar(50)The information about the disease status as detailed in the source.

Conventions

  • Anatomic site is coded at the most specific level of granularity possible, such that higher level classifications can be derived using the Standardized Vocabularies.
documentation/cdm/specimen.txt · Last modified: 2017/09/25 15:00 by clairblacketer