SPECIMEN

Table Description

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

ETL 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.

CDM Field	User Guide	ETL Conventions	Datatype	Required	Primary Key	Foreign Key	FK Table	FK Domain
specimen_id	Unique identifier for each specimen.		integer	Yes	Yes	No
person_id	The person from whom the specimen is collected.		integer	Yes	No	Yes	PERSON
specimen_concept_id		The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the specimen domain. Accepted Concepts	integer	Yes	No	Yes	CONCEPT
specimen_type_concept_id		Put the source of the specimen record, as in an EHR system. Accepted Concepts. A more detailed explanation of each Type Concept can be found on the vocabulary wiki.	integer	Yes	No	Yes	CONCEPT	Type Concept
specimen_date	The date the specimen was collected.		date	Yes	No	No
specimen_datetime			datetime	No	No	No
quantity	The amount of specimen collected from the person.		float	No	No	No
unit_concept_id	The unit for the quantity of the specimen.	Map the UNIT_SOURCE_VALUE to a Standard Concept in the Unit domain. Accepted Concepts	integer	No	No	Yes	CONCEPT
anatomic_site_concept_id	This is the site on the body where the specimen is from.	Map the ANATOMIC_SITE_SOURCE_VALUE to a Standard Concept in the Spec Anatomic Site domain. This should be coded at the lowest level of granularity Accepted Concepts	integer	No	No	Yes	CONCEPT
disease_status_concept_id			integer	No	No	Yes	CONCEPT
specimen_source_id	This is the identifier for the specimen from the source system.		varchar(50)	No	No	No
specimen_source_value			varchar(50)	No	No	No
unit_source_value		This unit for the quantity of the specimen, as represented in the source.	varchar(50)	No	No	No
anatomic_site_source_value		This is the site on the body where the specimen was taken from, as represented in the source.	varchar(50)	No	No	No
disease_status_source_value			varchar(50)	No	No	No