OMOP/Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/SPECIMEN.md

2.3 KiB

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

Field Required Type Description
specimen_id Yes integer A unique identifier for each specimen.
person_id Yes integer A foreign key identifier to the Person for whom the Specimen is recorded.
specimen_concept_id Yes integer A foreign key referring to a Standard Concept identifier in the Standardized Vocabularies for the Specimen.
specimen_type_concept_id Yes integer A 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_date No date The date the specimen was obtained from the Person.
specimen_datetime Yes datetime The date and time on the date when the Specimen was obtained from the person.
quantity No float The amount of specimen collection from the person during the sampling procedure.
unit_concept_id No integer A foreign key to a Standard Concept identifier for the Unit associated with the numeric quantity of the Specimen collection.
anatomic_site_concept_id Yes integer A foreign key to a Standard Concept identifier for the anatomic location of specimen collection.
disease_status_concept_id Yes integer A foreign key to a Standard Concept identifier for the Disease Status of specimen collection.
specimen_source_id No varchar(50) The Specimen identifier as it appears in the source data.
specimen_source_value No varchar(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_value No varchar(50) The information about the Unit as detailed in the source.
anatomic_site_source_value No varchar(50) The information about the anatomic site as detailed in the source.
disease_status_source_value No varchar(50) The information about the disease status as detailed in the source.

Conventions

No. Convention Description
1 Anatomic site is coded at the most specific level of granularity possible, such that higher level classifications can be derived using the Standardized Vocabularies.