Specimen
The Specimen domain contains the records identifying biological samples from a Person.
| Field | Required | Type | FK Table | Description |
|---|---|---|---|---|
| specimen_id | Yes | bigint | A unique identifier for each specimen. | |
| person_id | Yes | bigint | PERSON | A foreign key identifier to the Person for whom the Specimen is recorded. |
| specimen_concept_id | Yes | bigint | CONCEPT | A foreign key referring to a Standard Concept identifier in the Standardized Vocabularies for the Specimen (arterial blood, urine, etc). |
| specimen_type_concept_id | No | bigint | CONCEPT | Not used. |
| specimen_date | Yes | date | The UTC date the specimen was obtained from the Person. | |
| specimen_datetime | No | datetime | The UTC date and time when the Specimen was obtained from the Person. | |
| quantity | No | numeric | Not used. | |
| unit_concept_id | No | bigint | CONCEPT | Not used. |
| anatomic_site_concept_id | No | bigint | CONCEPT | A foreign key to a Standard Concept identifier for the anatomic location of specimen collection. |
| disease_status_concept_id | No | bigint | CONCEPT | Not used. |
| specimen_source_id | No | varchar(50) | Not used. | |
| specimen_source_value | No | varchar(50) | Not used. | |
| unit_source_value | No | varchar(50) | Not used. | |
| anatomic_site_source_value | No | varchar(50) | Not used. | |
| disease_status_source_value | No | varchar(50) | Not used. | |
| last_updated_datetime | Yes | datetime | Initially this is the time the row was written to OMOP. If the row is subsequently updated, it then becomes the most recent update time. | |
| deleted_datetime | No | datetime | NULL
initially. Set to the time when the row was marked for deletion. A value in this column sent to the central data source will result in this row being deleted (by person_id
) from the combined dataset. Deletions only need to be sent once. |
Conventions
- Values for
specimen_concept_idshould come from the Specimen domain. These describe what the specimen was (blood, urine, etc). - Anatomic site is coded at the most specific level of granularity possible, such that higher level classifications can be derived using the Standardized Vocabularies. These should come from the “Spec Anatomic Site” domain.
- Any sample (blood, sputum, urine, tissue etc.) is stored here with datetimes referencing the time the sample was taken.