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:

StatusDescriptionTesting Allowed
availableReady for testingYes
unavailableNot currently availableNo
unsatisfactoryQuality issuesLimited/No
entered-in-errorRecord invalidNo

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 collected
  • collector - Who collected (Practitioner)
  • collectionMethod - How collected (venipuncture, swab)
  • collectionSite - Body location (left arm, wound)

Specimen Quantity

Physical amount collected:

  • quantity - Numeric amount
  • quantityUnit - 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 number
  • receivedDateTime - When lab received specimen
  • turnaroundHours (calculated) - Transport time
  • Starts specimen chain of custody

Specimen Condition

Quality assessment upon receipt:

ConditionDescriptionImpact
adequateGood qualityFull testing
hemolyzedRed blood cell breakdownSome tests affected
lipemicHigh lipid contentSome tests affected
clottedImproper coagulationHematology affected
insufficientNot enough volumeLimited testing
contaminatedForeign material presentTesting 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:

  1. Verify patient identity
  2. Select appropriate tubes
  3. Perform venipuncture
  4. Label specimens at bedside
  5. Document collection time and site
  6. Transport to laboratory

Specimen Receipt

When lab receives specimen:

  1. Assign accession number
  2. Record received time
  3. Assess specimen condition
  4. Flag quality issues
  5. Enter into LIS
  6. Route for processing

Quality Assessment

For specimen evaluation:

  1. Visual inspection
  2. Check for hemolysis/lipemia
  3. Verify adequate volume
  4. Note any concerns in conditionNote
  5. Determine suitability for requested tests
  6. Set status appropriately

Specimen Rejection

When specimen is unsatisfactory:

  1. Set status: "unsatisfactory"
  2. Document condition and conditionNote
  3. Notify ordering provider
  4. Request recollection if needed
  5. Document communication
  6. Maintain rejected specimen record

Specimen Processing

Preparing specimen for analysis:

  1. Follow processingNote instructions
  2. Centrifuge if required
  3. Separate serum/plasma
  4. Create aliquots if multiple tests
  5. Link derived specimens via parentSpecimen
  6. Store at appropriate temperature

Related Entities

EntityRelationshipDescription
PatientReferencesWhose specimen
PractitionerReferencesWho collected
HealthReferenceBodySiteReferencesCollection site
CodingContainsSpecimen type and method
ClinicalIdentifierContainsSpecimen identifiers
SpecimenReferencesParent specimen if derived
LaboratoryOrderReferenced byOrders requiring this specimen
LaboratoryResultReferenced byResults from this specimen
LaboratoryPanelReferenced byPanels using this specimen

Calculated Fields

FieldTypeDescription
isAdequatebooleanTrue when condition is adequate
turnaroundHoursnumberHours from collection to receipt

Enums

status

ValueDescription
availableSpecimen is available for laboratory testing
unavailableSpecimen is not currently available
unsatisfactorySpecimen has quality issues affecting testing
entered-in-errorSpecimen record was created in error

condition

ValueDescription
adequateSpecimen is of acceptable quality for testing
hemolyzedRed blood cells have ruptured, releasing hemoglobin
lipemicHigh lipid content causing turbidity
clottedSpecimen has clotted when it should not have
insufficientSpecimen volume is insufficient for requested tests
contaminatedSpecimen contains foreign material or contamination
19 properties
Schema

Properties

PropertyTypeModeDescriptionRequired
identifierClinicalIdentifier[]
stored

Unique identifiers assigned to this specimen, including barcode labels, specimen numbers, and tracking codes used throughout the collection, transport, and analysis process

Example: [{"system":"http://lab.example.org/specimens","value":"SPEC-2024-0012345"}]

Optional
accessionIdentifierstring
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
statusstring
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: available, unavailable, unsatisfactory, entered-in-error

Required
typeCoding
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: {"system":"http://snomed.info/sct","code":"122555007","display":"Venous blood specimen"}

Required
patientPatient
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: {"reference":"Patient/patient-12345","display":"Jane Smith"}

Required
collectedDateTimeDateTime
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
collectorPractitioner
stored

Reference to the healthcare practitioner who performed the specimen collection, important for accountability, quality assurance, and addressing collection-related questions

Example: {"reference":"Practitioner/practitioner-789","display":"Sarah Johnson, RN"}

Optional
collectionMethodCoding
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: {"system":"http://snomed.info/sct","code":"278450005","display":"Venipuncture"}

Optional
collectionSiteHealthReferenceBodySite
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: {"reference":"HealthReferenceBodySite/left-antecubital-fossa","display":"Left antecubital fossa"}

Optional
quantitynumber
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
quantityUnitstring
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
containerstring
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
receivedDateTimeDateTime
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
conditionstring
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: adequate, hemolyzed, lipemic, clotted, insufficient, contaminated

Optional
conditionNotestring
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
processingNotestring
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
parentSpecimenSpecimen
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: {"reference":"Specimen/specimen-parent-001","display":"Whole blood specimen"}

Optional
isAdequateboolean
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
turnaroundHoursnumber
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"
}