Specimen

Overview

The Specimen resource represents a sample to be used for analysis. It tracks specimen collection, processing, and container information. Specimens are commonly referenced by DiagnosticReport and Observation resources.

FHIR R4 Specification

See the official HL7 specification: https://hl7.org/fhir/R4/specimen.html

Supported Fields

Field	Type	Description
id	string	Logical ID of the resource
meta	Meta	Resource metadata
identifier	Identifier[]	Specimen identifiers
accessionIdentifier	Identifier	Lab accession number
status	code	available, unavailable, unsatisfactory, entered-in-error
type	CodeableConcept	Type of specimen (SNOMED CT)
subject	Reference(Patient)	Patient the specimen is from
receivedTime	dateTime	When specimen was received
collection	BackboneElement	Collection details
processing	BackboneElement[]	Processing steps
container	BackboneElement[]	Container information

Search Parameters

Parameter	Type	Description	Example
_id	token	Resource ID	_id=specimen-001
patient	reference	Patient	patient=Patient/123
subject	reference	Subject (alias)	subject=Patient/123
status	token	Specimen status	status=available
type	token	Specimen type	type=http://snomed.info/sct\|119297000
collector	reference	Who collected	collector=Practitioner/nurse-1
accession	token	Accession identifier	accession=ACC-2024-001
collected	date	Collection date	collected=2024-01-15

Examples

Create a Specimen

curl -X POST http://localhost:8080/baseR4/Specimen \
  -H "Content-Type: application/fhir+json" \
  -d '{
    "resourceType": "Specimen",
    "identifier": [{
      "system": "http://lab.example.org/specimens",
      "value": "SPEC-2024-001234"
    }],
    "accessionIdentifier": {
      "system": "http://lab.example.org/accession",
      "value": "ACC-2024-5678"
    },
    "status": "available",
    "type": {
      "coding": [{
        "system": "http://snomed.info/sct",
        "code": "119297000",
        "display": "Blood specimen"
      }]
    },
    "subject": {"reference": "Patient/patient-1"},
    "receivedTime": "2024-01-15T07:30:00Z",
    "collection": {
      "collector": {"reference": "Practitioner/nurse-1"},
      "collectedDateTime": "2024-01-15T07:15:00Z",
      "quantity": {
        "value": 10,
        "unit": "mL"
      },
      "bodySite": {
        "coding": [{
          "system": "http://snomed.info/sct",
          "code": "49852007",
          "display": "Median cubital vein"
        }]
      }
    },
    "container": [{
      "type": {
        "text": "Purple top EDTA tube"
      },
      "specimenQuantity": {
        "value": 8,
        "unit": "mL"
      }
    }]
  }'

Search Specimens

# By patient
curl "http://localhost:8080/baseR4/Specimen?patient=Patient/patient-1"

# By type
curl "http://localhost:8080/baseR4/Specimen?type=http://snomed.info/sct|119297000"

# By status
curl "http://localhost:8080/baseR4/Specimen?status=available"

Specimen Types (SNOMED CT)

Code	Display
119297000	Blood specimen
122555007	Venous blood specimen
119339001	Serum specimen
119361006	Plasma specimen
122575003	Urine specimen
119376003	Tissue specimen
119295008	Aspirate
258580003	Whole blood

Status Codes

Code	Description
available	Specimen is available for processing
unavailable	Specimen is not available
unsatisfactory	Specimen quality is not acceptable
entered-in-error	Entry was made in error