Resource type: specimen

Description

A sample to be used for analysis.

Elements

PathShortDefinitionComments
Sample for analysisA sample to be used for analysis.
identifierExternal IdentifierId for specimen.
accessionIdentifierIdentifier assigned by the labThe identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab procedures.
statusavailable | unavailable | unsatisfactory | entered-in-errorThe availability of the specimen.This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.
typeKind of material that forms the specimenThe kind of material that forms the specimen.The type can change the way that a specimen is handled and drives what kind of analyses can properly be performed on the specimen. It is frequently used in diagnostic work flow decision making systems.
subjectWhere 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 or a deviceWhere 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 or a device.
receivedTimeThe time when specimen was received for processingTime when specimen was received for processing or testing.
parentSpecimen from which this specimen originatedReference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen.The parent specimen could be the source from which the current specimen is derived by some processing step (e.g. an aliquot or isolate or extracted nucleic acids from clinical samples) or one of many specimens that were combined to create a pooled sample.
requestWhy the specimen was collectedDetails concerning a service request that required a specimen to be collected.The request may be explicit or implied such with a ServiceRequest that requires a blood draw.
collectionCollection detailsDetails concerning the specimen collection.
collection.idUnique id for inter-element referencingUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
collection.extensionAdditional content defined by implementationsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
collection.modifierExtensionExtensions that cannot be ignored even if unrecognizedMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
collection.collectorWho collected the specimenPerson who collected the specimen.
collection.collected[x]Collection timeTime when specimen was collected from subject - the physiologically relevant time.
collection.durationHow long it took to collect specimenThe span of time over which the collection of a specimen occurred.
collection.quantityThe quantity of specimen collectedThe quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample.
collection.methodTechnique used to perform collectionA coded value specifying the technique that is used to perform the procedure.
collection.bodySiteAnatomical collection siteAnatomical location from which the specimen was collected (if subject is a patient). This is the target site. This element is not used for environmental specimens.If the use case requires BodySite to be handled as a separate resource instead of an inline coded element (e.g. to identify and track separately) then use the standard extension [bodySite](extension-bodysite.html).
collection.fastingStatus[x]Whether or how long patient abstained from food and/or drinkAbstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection.Representing fasting status using this element is preferred to representing it with an observation using a 'precoordinated code' such as LOINC 2005-7 (Calcium [Moles/​time] in 2 hour Urine --12 hours fasting), or using a component observation ` such as `Observation.component code` = LOINC 49541-6 (Fasting status - Reported).
processingProcessing and processing step detailsDetails concerning processing and processing steps for the specimen.
processing.idUnique id for inter-element referencingUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
processing.extensionAdditional content defined by implementationsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
processing.modifierExtensionExtensions that cannot be ignored even if unrecognizedMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
processing.descriptionTextual description of procedureTextual description of procedure.
processing.procedureIndicates the treatment step applied to the specimenA coded value specifying the procedure used to process the specimen.
processing.additiveMaterial used in the processing stepMaterial used in the processing step.
processing.time[x]Date and time of specimen processingA record of the time or period when the specimen processing occurred. For example the time of sample fixation or the period of time the sample was in formalin.
containerDirect container of specimen (tube/slide, etc.)The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here.
container.idUnique id for inter-element referencingUnique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
container.extensionAdditional content defined by implementationsMay be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
container.modifierExtensionExtensions that cannot be ignored even if unrecognizedMay be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.
container.identifierId for the containerId for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The container ID may differ from the specimen id in some circumstances.
container.descriptionTextual description of the containerTextual description of the container.
container.typeKind of container directly associated with specimenThe type of container associated with the specimen (e.g. slide, aliquot, etc.).
container.capacityContainer volume or sizeThe capacity (volume or other measure) the container may contain.
container.specimenQuantityQuantity of specimen within containerThe quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type.
container.additive[x]Additive associated with containerIntroduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA.
conditionState of the specimenA mode or state of being that describes the nature of the specimen.Specimen condition is an observation made about the specimen. It's a point-in-time assessment. It can be used to assess it's quality or it's appropriateness for a specific test.
noteCommentsTo communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen).

Scope and Usage

Any material sample:

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, biobanking, etc. Comments from reviewers on the appropriate scope for this resource, and the need for tracking related specimen management attributes, are welcomed.

Search Parameters

accessionThe accession number associated with the specimenSpecimen.accessionIdentifier
bodysiteThe code for the body site from where the specimen originatedSpecimen.collection.bodySite
collectedThe date the specimen was collectedSpecimen.collection.collected
collectorWho collected the specimenSpecimen.collection.collector
containerThe kind of specimen containerSpecimen.container.type
container-idThe unique identifier associated with the specimen containerSpecimen.container.identifier
identifierThe unique identifier associated with the specimenSpecimen.identifier
parentThe parent of the specimenSpecimen.parent
patientThe patient the specimen comes fromSpecimen.subject.where(resolve() is Patient)
statusavailable | unavailable | unsatisfactory | entered-in-errorSpecimen.status
subjectThe subject of the specimenSpecimen.subject
typeThe specimen typeSpecimen.type

Extension Definitions

These are extension definitions for this resource defined by the spec