User Tools

Site Tools


documentation:cdm:specimen

SPECIMEN

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: 2017/02/07 18:36 by cgreich