Specimen
A biological specimen collected from a patient for diagnostic testing. Tracks collection details, container type, laboratory receipt, and sample condition for quality control and laboratory workflow management.
Overview
Specimen documents the biological sample collected from a patient for laboratory analysis. It tracks the complete specimen lifecycle: collection (who, when, where, how), transport to laboratory, receipt and accessioning, quality assessment, and processing. Specimen quality directly affects result reliability, making this entity critical for laboratory quality management.
Key Concepts
Specimen Status
The status field tracks availability:
| Status | Description | Testing Allowed |
|---|---|---|
available | Ready for testing | Yes |
unavailable | Not currently available | No |
unsatisfactory | Quality issues | Limited/No |
entered-in-error | Record invalid | No |
Specimen Type
The type field uses Coding to classify:
- Blood (venous, arterial, capillary)
- Serum, Plasma
- Urine (random, timed, catheterized)
- CSF (cerebrospinal fluid)
- Tissue (biopsy, surgical specimen)
- Swabs (throat, wound, nasal)
- Other body fluids
Collection Information
Details about specimen collection:
collectedDateTime- When collectedcollector- Who collected (Practitioner)collectionMethod- How collected (venipuncture, swab)collectionSite- Body location (left arm, wound)
Specimen Quantity
Physical amount collected:
quantity- Numeric amountquantityUnit- ml, g, cm- Affects available testing
- Minimum volumes required
Container Type
The container field describes storage:
- Red top tube (clot for serum)
- Lavender top (EDTA for CBC)
- Blue top (citrate for coagulation)
- Sterile cup (urine)
- Tissue cassette (biopsy)
Laboratory Receipt
Accessioning information:
accessionIdentifier- Lab's tracking numberreceivedDateTime- When lab received specimenturnaroundHours(calculated) - Transport time- Starts specimen chain of custody
Specimen Condition
Quality assessment upon receipt:
| Condition | Description | Impact |
|---|---|---|
adequate | Good quality | Full testing |
hemolyzed | Red blood cell breakdown | Some tests affected |
lipemic | High lipid content | Some tests affected |
clotted | Improper coagulation | Hematology affected |
insufficient | Not enough volume | Limited testing |
contaminated | Foreign material present | Testing compromised |
Processing Notes
The processingNote field captures:
- Special handling requirements
- Centrifugation specifications
- Storage temperature
- Time-sensitive instructions
Derived Specimens
The parentSpecimen field links to source:
- Serum derived from whole blood
- Aliquots from original specimen
- Tissue sections from biopsy
- Enables specimen genealogy
Use Cases
Blood Collection
For routine phlebotomy:
- Verify patient identity
- Select appropriate tubes
- Perform venipuncture
- Label specimens at bedside
- Document collection time and site
- Transport to laboratory
Specimen Receipt
When lab receives specimen:
- Assign accession number
- Record received time
- Assess specimen condition
- Flag quality issues
- Enter into LIS
- Route for processing
Quality Assessment
For specimen evaluation:
- Visual inspection
- Check for hemolysis/lipemia
- Verify adequate volume
- Note any concerns in
conditionNote - Determine suitability for requested tests
- Set status appropriately
Specimen Rejection
When specimen is unsatisfactory:
- Set
status: "unsatisfactory" - Document
conditionandconditionNote - Notify ordering provider
- Request recollection if needed
- Document communication
- Maintain rejected specimen record
Specimen Processing
Preparing specimen for analysis:
- Follow
processingNoteinstructions - Centrifuge if required
- Separate serum/plasma
- Create aliquots if multiple tests
- Link derived specimens via
parentSpecimen - Store at appropriate temperature
Related Entities
| Entity | Relationship | Description |
|---|---|---|
| Patient | References | Whose specimen |
| Practitioner | References | Who collected |
| HealthReferenceBodySite | References | Collection site |
| Coding | Contains | Specimen type and method |
| ClinicalIdentifier | Contains | Specimen identifiers |
| Specimen | References | Parent specimen if derived |
| LaboratoryOrder | Referenced by | Orders requiring this specimen |
| LaboratoryResult | Referenced by | Results from this specimen |
| LaboratoryPanel | Referenced by | Panels using this specimen |
Calculated Fields
| Field | Type | Description |
|---|---|---|
isAdequate | boolean | True when condition is adequate |
turnaroundHours | number | Hours from collection to receipt |
Enums
status
| Value | Description |
|---|---|
available | Specimen is available for laboratory testing |
unavailable | Specimen is not currently available |
unsatisfactory | Specimen has quality issues affecting testing |
entered-in-error | Specimen record was created in error |
condition
| Value | Description |
|---|---|
adequate | Specimen is of acceptable quality for testing |
hemolyzed | Red blood cells have ruptured, releasing hemoglobin |
lipemic | High lipid content causing turbidity |
clotted | Specimen has clotted when it should not have |
insufficient | Specimen volume is insufficient for requested tests |
contaminated | Specimen contains foreign material or contamination |
Properties
| Property | Type | Mode | Description | Required |
|---|---|---|---|---|
| identifier | ClinicalIdentifier[] | stored | Unique identifiers assigned to this specimen, including barcode labels, specimen numbers, and tracking codes used throughout the collection, transport, and analysis process Example: | Optional |
| accessionIdentifier | string | stored | Laboratory accession number assigned when the specimen is received and entered into the laboratory information system, serving as the primary tracking identifier for the specimen throughout its lifecycle | Optional |
| status | string | stored | Current availability status of the specimen indicating whether it is available for testing, has been used/consumed, is unsuitable for analysis, or was recorded in error Values: | Required |
| type | Coding | stored | Coded classification of the specimen material such as whole blood, serum, plasma, urine, tissue biopsy, cerebrospinal fluid, or other biological sample types following standard specimen type terminologies Example: | Required |
| patient | Patient | stored | Reference to the patient from whom this specimen was collected, establishing the critical link between the sample and the individual for proper identification and result reporting Example: | Required |
| collectedDateTime | DateTime | stored | Date and time when the specimen was collected from the patient, critical for determining specimen stability, interpreting time-dependent test results, and calculating turnaround times | Required |
| collector | Practitioner | stored | Reference to the healthcare practitioner who performed the specimen collection, important for accountability, quality assurance, and addressing collection-related questions Example: | Optional |
| collectionMethod | Coding | stored | Coded technique or procedure used to collect the specimen such as venipuncture, capillary puncture, clean catch void, needle biopsy, or swab, which may impact specimen quality and result interpretation Example: | Optional |
| collectionSite | HealthReferenceBodySite | stored | Anatomical location on the patient's body from which the specimen was collected, particularly important for specimens where collection site affects interpretation such as biopsies, wound cultures, or site-specific samples Example: | Optional |
| quantity | number | stored | Numerical amount of specimen collected, indicating the volume or mass available for testing and determining whether sufficient material exists for all requested analyses | Optional |
| quantityUnit | string | stored | Unit of measurement for the specimen quantity such as milliliters, grams, or other standard units appropriate to the specimen type and laboratory practice | Optional |
| container | string | stored | Type of container or tube in which the specimen is stored, such as red top tube, lavender top tube with EDTA, sterile urine cup, or tissue cassette, which determines appropriate handling and testing | Optional |
| receivedDateTime | DateTime | stored | Date and time when the specimen was received at the laboratory, used to calculate transport time, assess specimen stability, and track pre-analytical workflow metrics | Optional |
| condition | string | stored | Quality assessment of the specimen upon receipt indicating whether it is adequate for testing or has issues such as hemolysis, lipemia, clotting, insufficient quantity, or contamination that may affect results Values: | Optional |
| conditionNote | string | stored | Detailed notes about the specimen condition including severity of hemolysis, degree of lipemia, presence of clots, or other quality issues observed during visual inspection or processing | Optional |
| processingNote | string | stored | Special instructions or notes about specimen processing requirements such as centrifugation speed, storage temperature, time-sensitive handling, or specific preparation needed before analysis | Optional |
| parentSpecimen | Specimen | stored | Reference to the original or parent specimen from which this specimen was derived through processing such as serum separated from whole blood, aliquots created for different tests, or tissue sections cut from a biopsy Example: | Optional |
| isAdequate | boolean | calculated | Computed indicator that is true when the specimen condition is adequate for testing, providing a quick quality check flag for laboratory workflows and result validation processes | Optional |
| turnaroundHours | number | calculated | Calculated number of hours elapsed between specimen collection and laboratory receipt, used to monitor pre-analytical turnaround time metrics and identify specimens that may have exceeded stability limits | Optional |
Examples
Example 1
{
"@type": "Specimen",
"identifier": [
{
"system": "http://hospital.example.org/specimens",
"value": "SPEC-2024-VB-00123"
}
],
"accessionIdentifier": "LAB2024-A-005678",
"status": "available",
"type": {
"system": "http://snomed.info/sct",
"code": "122555007",
"display": "Venous blood specimen"
},
"patient": {
"reference": "Patient/patient-45678",
"display": "Robert Anderson"
},
"collectedDateTime": "2024-01-20T07:15:00Z",
"collector": {
"reference": "Practitioner/practitioner-234",
"display": "Maria Garcia, RN"
},
"collectionMethod": {
"system": "http://snomed.info/sct",
"code": "278450005",
"display": "Venipuncture"
},
"collectionSite": {
"reference": "HealthReferenceBodySite/left-antecubital-fossa",
"display": "Left antecubital fossa"
},
"quantity": 10,
"quantityUnit": "mL",
"container": "Red top tube (no additive)",
"receivedDateTime": "2024-01-20T08:30:00Z",
"condition": "adequate",
"conditionNote": "Specimen in good condition, no hemolysis or clotting observed",
"processingNote": "Allow to clot for 30 minutes before centrifugation",
"_comment": "isAdequate: true, turnaroundHours: 1.25"
}Example 2
{
"@type": "Specimen",
"identifier": [
{
"system": "http://hospital.example.org/specimens",
"value": "SPEC-2024-UR-00456"
}
],
"accessionIdentifier": "LAB2024-A-005679",
"status": "available",
"type": {
"system": "http://snomed.info/sct",
"code": "122575003",
"display": "Urine specimen"
},
"patient": {
"reference": "Patient/patient-78901",
"display": "Emily Chen"
},
"collectedDateTime": "2024-01-20T09:00:00Z",
"collector": {
"reference": "Practitioner/practitioner-567",
"display": "James Wilson, CNA"
},
"collectionMethod": {
"system": "http://snomed.info/sct",
"code": "258574006",
"display": "Clean catch urine collection"
},
"quantity": 50,
"quantityUnit": "mL",
"container": "Sterile urine collection cup",
"receivedDateTime": "2024-01-20T09:45:00Z",
"condition": "adequate",
"conditionNote": "Clear, amber-colored specimen with no visible contamination",
"processingNote": "Refrigerate if not processed within 2 hours. Perform culture within 24 hours.",
"_comment": "isAdequate: true, turnaroundHours: 0.75"
}Example 3
{
"@type": "Specimen",
"identifier": [
{
"system": "http://pathology.example.org/specimens",
"value": "SPEC-2024-BX-00789"
}
],
"accessionIdentifier": "PATH2024-S-001234",
"status": "available",
"type": {
"system": "http://snomed.info/sct",
"code": "309226005",
"display": "Tissue specimen from biopsy"
},
"patient": {
"reference": "Patient/patient-23456",
"display": "Michael Thompson"
},
"collectedDateTime": "2024-01-19T14:30:00Z",
"collector": {
"reference": "Practitioner/practitioner-890",
"display": "Dr. Patricia Lee, MD"
},
"collectionMethod": {
"system": "http://snomed.info/sct",
"code": "129314006",
"display": "Needle biopsy"
},
"collectionSite": {
"reference": "HealthReferenceBodySite/right-upper-lobe-lung",
"display": "Right upper lobe of lung"
},
"quantity": 0.5,
"quantityUnit": "cm",
"container": "Tissue cassette in 10% formalin",
"receivedDateTime": "2024-01-19T16:00:00Z",
"condition": "adequate",
"conditionNote": "Tissue core measuring approximately 0.5 cm in length, fixed in formalin",
"processingNote": "Process for routine histology with H&E staining. Consider IHC panel based on preliminary morphology.",
"_comment": "isAdequate: true, turnaroundHours: 1.5"
}