Specimen

Introduction

Scope and Usage

Any material sample:

• taken from a biological entity, living or dead
• taken from a physical object or the environment

Some specimens are biological and can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products (source: NCI Thesaurus, modified).

The specimen resource covers substances used for diagnostic and environmental testing. The focus of the specimen resource is the process for gathering, maintaining and processing the specimen as well as where the specimen originated. This is distinct from the use of Substance which is only used when these other aspects are not relevant.

Background and Context

The current definition of the specimen resource contains only basic information about specimen containers. It does not address the recursive nature of containers or the tracking of the location of a container within its parent container (for instance: a tube in a tray in a rack in a freezer). The frequency with which these elements are tracked may depend on the context of use; general lab, bio-banking, etc. Comments from reviewers on the appropriate scope for this resource, and the need for tracking related specimen management attributes, are welcomed.

Notes

Notes:

Specimen Grouping

Specimens can be grouped at the Observation level via two ways:

• A group at Observation.specimen with a reference to a group
• By creating a group of specimens independent of observations

Additionally, a parent specimen can have multiple child specimens.

Specimen Searching

Specimens can be searched by parent, as described here. Additionally, a recursive, child-based search could be performed, using the instructions here. Note that recursive or reverse searching is highly dependent on the configuration of the local system(s) involved.

StructureDefinition

Elements (Simplified)

• Specimen [0..*]: - Sample for analysis
• Specimen.identifier [0..*]: Identifier Primary specimen identifier
• Specimen.status [0..1]: code required:specimen-status available | unavailable | unsatisfactory | entered-in-error
• Specimen.type [0..1]: CodeableConcept example:v2-0487 Kind of material that forms the specimen
• Specimen.subject [0..1]: [Reference(Patient](/Reference(Patient), Group, Device, BiologicallyDerivedProduct, Substance, Location, NutritionProduct)) Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance, a biologically-derived product, or a device
• Specimen.receivedTime [0..1]: dateTime The time when specimen is received by the testing laboratory
• Specimen.parent [0..*]: Reference(Specimen) Specimen from which this specimen originated
• Specimen.request [0..*]: Reference(ServiceRequest) Why the specimen was collected
• Specimen.combined [0..1]: code required:specimen-combined grouped | pooled
• Specimen.role [0..*]: CodeableConcept preferred:specimen-role The role the specimen serves
• Specimen.feature [0..*]: BackboneElement The physical feature of a specimen
• Specimen.feature.type [1..1]: CodeableConcept example:body-site Highlighted feature
• Specimen.feature.description [1..1]: string Information about the feature
• Specimen.collection [0..1]: BackboneElement Collection details
• Specimen.collection.collector [0..1]: [Reference(Organization](/Reference(Organization), Practitioner, PractitionerRole, Patient, RelatedPerson)) Who collected the specimen
• Specimen.collection.collected[x] [0..1]: dateTime, Period Collection time
• Specimen.collection.duration [0..1]: Duration How long it took to collect specimen
• Specimen.collection.quantity [0..1]: Quantity(SimpleQuantity) The quantity of specimen collected
• Specimen.collection.method [0..1]: CodeableConcept example:specimen-collection-method Technique used to perform collection
• Specimen.collection.device[x] [0..1]: CodeableConcept, Reference(Device), canonical example:specimen-container-type Device used to perform collection
• Specimen.collection.procedure [0..1]: Reference(Procedure) The procedure that collects the specimen
• Specimen.collection.bodySite [0..1]: CodeableReference example:body-site Anatomical collection site
• Specimen.collection.fastingStatus[x] [0..1]: CodeableConcept, Duration extensible:v2-0916 Whether or how long patient abstained from food and/or drink
• Specimen.processing [0..*]: BackboneElement Processing and processing step details
• Specimen.processing.description [0..1]: string Textual description of procedure
• Specimen.processing.method [0..1]: CodeableConcept example:specimen-processing-method Indicates the treatment step applied to the specimen
• Specimen.processing.performer [0..1]: [Reference(Practitioner](/Reference(Practitioner), PractitionerRole, Patient, RelatedPerson)) Entity processing specimen
• Specimen.processing.device[x] [0..1]: CodeableConcept, Reference(Device), canonical example:processingdevice-code Device used to process the specimen
• Specimen.processing.additive [0..*]: CodeableReference Material used in the processing step
• Specimen.processing.time[x] [0..1]: dateTime, Period, Duration Date and time of specimen processing
• Specimen.container [0..*]: BackboneElement Direct container of specimen (tube/slide, etc.)
• Specimen.container.device[x] [1..1]: CodeableConcept, Reference(Device), canonical example:containerdevice-code Device resource for the container
• Specimen.container.specimenQuantity [0..1]: Quantity(SimpleQuantity) Quantity of specimen within container
• Specimen.condition [0..*]: CodeableConcept example:v2-0493 State of the specimen
• Specimen.note [0..*]: Annotation Comments

Mappings

• Specimen Mappings — 60 mapping entries

Implementation Guide

implementationguide-Specimen-core.xml

<?xml version="1.0" encoding="UTF-8"?>

<ImplementationGuide xmlns="http://hl7.org/fhir">
  <id value="Specimen-core"/>
  <version value="0.1"/>
  <name value="SpecimenHL7Extensions"/>
  <title value="Specimen  H L7  Extensions"/>
  <status value="draft"/>
  <date value="2015-02-19T00:00:00.000"/>
  <publisher value="Health Level Seven, Inc. - FHIR WG"/>
  <description value="Defines common extensions used with or related to the Specimen resource"/>
</ImplementationGuide>

Resource Packs

list-Specimen-packs.xml

<?xml version="1.0" encoding="UTF-8"?>

<List xmlns="http://hl7.org/fhir">
  <id value="Specimen-packs"/>
  <status value="current"/>
  <mode value="working"/>
  <entry>
    <item>
      <reference value="ImplementationGuide/Specimen-core"/>
    </item>
  </entry>
</List>

Search Parameters

• bodysite — reference — Reference to a resource (by instance) — Specimen.collection.bodySite.reference
• collected — date — The date the specimen was collected — Specimen.collection.collected.ofType(dateTime) | Specimen.collection.collected.ofType(Period)
• collector — reference — Who collected the specimen — Specimen.collection.collector
• procedure — reference — The procedure that collected the specimen — Specimen.collection.procedure
• container-device-code — token — The code associated with the specimen container — Specimen.container.device.ofType(CodeableConcept)
• identifier — token — The unique identifier associated with the specimen — Specimen.identifier
• parent — reference — The parent of the specimen — Specimen.parent
• patient — reference — The patient the specimen comes from — Specimen.subject.where(resolve() is Patient)
• status — token — available | unavailable | unsatisfactory | entered-in-error — Specimen.status
• subject — reference — The subject of the specimen — Specimen.subject
• type — token — The specimen type — Specimen.type
• request — reference — The request/order associated with the specimen — Specimen.request
• processing-device-code — token — The code associated with the processing device — Specimen.processing.device.ofType(CodeableConcept)
• collection-device-code — token — The code associated with the collection device — Specimen.collection.device.ofType(CodeableConcept)

Full Search Parameters

Examples

• 101 — specimen-example — General Specimen Example
• isolate — specimen-example-isolate — Bacterial Isolate from Stool sample
• liver-biopsy — specimen-example-liver-biopsy — Liver biopsy specimen
• pooled-serum — specimen-example-pooled-serum — Pooled serum sample
• specimen-example — specimen-example
• specimen-example-isolate — specimen-example-isolate
• specimen-example-liver-biopsy — specimen-example-liver-biopsy
• specimen-example-pooled-serum — specimen-example-pooled-serum
• specimen-example-serum — specimen-example-serum
• specimen-example-serum-control — specimen-example-serum-control
• specimen-example-urine — specimen-example-urine
• specimen-examples-header — specimen-examples-header
• sst — specimen-example-serum — Serum Sample
• vma-urine — specimen-example-urine — VMA, Random Urine Sample

Full Examples

Mapping Exceptions

specimen-fivews-mapping-exceptions.xml

Unmapped Elements

• FiveWs.recorded — Unknown
• FiveWs.author — Unknown
• FiveWs.cause — Unknown
• FiveWs.version — Unknown
• FiveWs.witness — Unknown
• FiveWs.class — Unknown
• FiveWs.where — Unknown
• FiveWs.context — Unknown
• FiveWs.source — Unknown
• FiveWs.who — Unknown
• FiveWs.grade — Unknown
• FiveWs.planned — Unknown