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 | Yes | bigint | CONCEPT | The source of the specimen record, as in an EHR system. Accepted Concepts |
| 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 | The amount of specimen collected from the person. | |
| unit_concept_id | No | bigint | CONCEPT | The unit for the quantity of the specimen. |
| 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) | The identifier for the specimen from the source system. | |
| specimen_source_value | No | varchar(50) | ||
| unit_source_value | No | varchar(50) | Unit for the quantity of the specimen, as represented in the source. | |
| anatomic_site_source_value | No | varchar(50) | The site on the body where the specimen was taken from, as represented in the source. | |
| disease_status_source_value | No | varchar(50) |
Conventions
- Values for
specimen_concept_idshould come from the Specimen domain and class in Athena. 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 in Athena.
- Any sample (blood, sputum, urine, tissue etc.) is stored here with datetimes referencing the time the sample was taken.
-
Samples here should be linked via the FACT_RELATIONSHIP table to the OBSERVATION or MEASUREMENT tables, where results of the sample are reported. In this case we should expect at least 2 types of linking:
- Organisms: there may be none, one or many, and each organism linking to its own Sensitivity profile.
- Sensitivity profile: there may be none, one or many.
- Samples that are used to link physiological measurements (for example a
vital sign panel) should use the concept
4001345|Specimen from patient. - Specimens may not have an accompanying row in the MEASUREMENT table if that specimen has yet to be reported (for example, a COVID swab that does not yet have a result).