Generated Narrative: StructureDefinition profile-Specimen Name Flags Card. Type Description & Constraints Specimen 0..* Specimen Sample for analysis #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:combined 0..1 code R5: grouped | pooled (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.combined Binding: R5SpecimenCombinedForR3 (0.1.0) (required): Codes for the combined status of a specimen. #xD; extension:role 0..* CodeableConcept R5: The role the specimen serves (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.role Binding: R5SpecimenRoleForR3 (0.1.0) (preferred): Codes describing specimen role. #xD; extension:feature 0..* (Complex) R5: The physical feature of a specimen (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.feature #xD; extension:condition 0..* CodeableConcept R5: State of the specimen (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.condition Binding: v2 Specimen Condition (extensible): Codes describing the state of the specimen. #xD; subject #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:subject 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: 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 URL: http://hl7.org/fhir/StructureDefinition/alternate-reference #xD; parent #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:parent 0..* ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: parent additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference #xD; request #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:request 0..* ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: request additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference #xD; collection #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:duration 0..1 Duration R5: How long it took to collect specimen (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.duration #xD; extension:device 0..1 (Complex) R5: Device used to perform collection (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.device #xD; extension:procedure 0..1 Reference(Cross-version Profile for R5.Procedure for use in FHIR STU3(0.1.0) | Procedure) R5: The procedure that collects the specimen (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.procedure #xD; extension:fastingStatus 0..1 CodeableConcept, Duration R5: Whether or how long patient abstained from food and/or drink (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.fastingStatus Binding: v2 Relevant Clincial Information (extensible): Codes describing the fasting status of the patient. #xD; collector #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:collector 0..1 ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: collector URL: http://hl7.org/fhir/StructureDefinition/alternate-reference #xD; bodySite #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:bodySite 0..1 Reference(Cross-version Profile for R5.BodyStructure for use in FHIR STU3(0.1.0) | BodySite) R5: bodySite additional types URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.bodySite #xD; processing #xD; additive #xD; Slices for extension 0..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:additive 0..* ?gen-e1? [CanonicalType[http://hl7.org/fhir/StructureDefinition/alternate-reference]] R5: additive additional types URL: http://hl7.org/fhir/StructureDefinition/alternate-reference #xD; container #xD; Slices for extension 1..* Extension Extension Slice: Unordered, Open by value:url #xD; extension:device 1..1 Reference(Cross-version Profile for R5.Device for use in FHIR STU3(0.1.0) | Device) R5: Device resource for the container (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.container.device #xD; extension:location 0..1 Reference(Cross-version Profile for R5.Location for use in FHIR STU3(0.1.0) | Location) R5: Where the container is (new) URL: http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.container.location #xD; Documentation for this format
Cross-version Profile for R5.Specimen for use in FHIR STU3
This cross-version profile allows R5 Specimen content to be represented via FHIR STU3 Specimen resources.
If the resource is contained in another resource, it SHALL NOT contain nested Resources
not(parent::f:contained and f:contained)
If the resource is contained in another resource, it SHALL NOT contain any narrative
If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))
If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource
contained.where(('#'+id in %resource.descendants().reference).not()).empty()
not(exists(for $id in f:contained/*/@id return $id[not(ancestor::f:contained/parent::*/descendant::f:reference/@value=concat('#', $id))]))
The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
The only time that a resource does not have an id is when it is being submitted to the server using a create operation.
The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content may not always be associated with version changes to the resource.
A set of rules under which this content was created
A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content.
Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. This element is labelled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation.
The base language in which the resource is written.
Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute).
Text summary of the resource, for human interpretation
A human-readable narrative that contains a summary of the resource, and may be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.
Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded in formation is added later.
These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.
This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again.
Element `Specimen.combined` has a context of Specimen based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.combined` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).
All FHIR elements must have a @value or children
hasValue() | (children().count() > id.count())
Must have either extensions or value[x], not both
exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])
R5: `Specimen.role` (new:CodeableConcept)
Element `Specimen.role` has a context of Specimen based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.role` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).
R5: The physical feature of a specimen (new)
R5: `Specimen.feature` (new:BackboneElement)
Element `Specimen.feature` has a context of Specimen based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.feature` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).
R5: `Specimen.condition` (new:CodeableConcept)
Element `Specimen.condition` has a context of Specimen based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.condition` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element). Specimen condition is an observation made about the specimen. It's a point-in-time assessment. It can be used to assess its quality or appropriateness for a specific test.
May be used to represent additional information that is not part of the basic definition of the resource, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order 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 is allowed to 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.
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.
The identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab procedures.
.participation[typeCode=SBJ].act[classCode=ACSN, moodCode=EVN].id
available | unavailable | unsatisfactory | entered-in-error
This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.
Codes providing the status/availability of a specimen.
Kind of material that forms the specimen
The 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.
Where the specimen came from. This may be from the patient(s) or from the environment or a device
Where the specimen came from. This may be from the patient(s) or from the environment or a device.
unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.
Extensions are always sliced by (at least) url
R5: 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
Element `Specimen.subject` is mapped to FHIR STU3 element `Specimen.subject` as `SourceIsBroaderThanTarget`. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `Specimen.subject` with unmapped reference targets: BiologicallyDerivedProduct, Device, Group, Location, Patient, Substance.
Literal reference, Relative, internal or absolute URL
A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources.
Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure "/[type]/[id]" then it should be assumed that the reference is to a FHIR RESTful server.
Logical reference, when literal reference is not known
An identifier for the other resource. This is used when there is no way to reference the other resource directly, either because the entity is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference.
When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it.
Plain text narrative that identifies the resource in addition to the resource reference.
This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it.
The time when specimen was received for processing
Time when specimen was received for processing or testing.
.participation[typeCode=SBJ].act[code=SPCREC, moodCode=EVN].effectiveTime
Specimen from which this specimen originated
Reference 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.
.scoper (if parent) .player.scopesRole[classCode=SPEC].player (if child)
R5: `Specimen.parent` additional types from child elements (display, identifier, reference, type)
Element `Specimen.parent` is mapped to FHIR STU3 element `Specimen.parent` as `SourceIsBroaderThanTarget`. The mappings for `Specimen.parent` do not cover the following types based on type expansion: display, identifier, reference, type. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `Specimen.parent` with unmapped reference targets: 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.
Details concerning a test or procedure request that required a specimen to be collected.
The request may be explicit or implied such with a ProcedureRequest that requires a blood draw.
R5: `Specimen.request` additional types from child elements (display, identifier, reference, type)
Element `Specimen.request` is mapped to FHIR STU3 element `Specimen.request` as `SourceIsBroaderThanTarget`. The mappings for `Specimen.request` do not cover the following types based on type expansion: display, identifier, reference, type. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `Specimen.request` with unmapped reference targets: ServiceRequest. The request may be explicit or implied such with a ServiceRequest that requires a blood draw.
Details concerning the specimen collection.
.participation[typeCode=SBJ].act[classCode=SPECCOLLECT, moodCode=EVN]
R5: How long it took to collect specimen (new)
R5: `Specimen.collection.duration` (new:Duration)
Element `Specimen.collection.duration` has a context of Specimen.collection based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.collection.duration` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).
R5: Device used to perform collection (new)
R5: `Specimen.collection.device` (new:CodeableReference(Device))
Element `Specimen.collection.device` has a context of Specimen.collection based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.collection.device` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).
R5: The procedure that collects the specimen (new)
R5: `Specimen.collection.procedure` (new:Reference(Procedure))
Element `Specimen.collection.procedure` has a context of Specimen.collection based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.collection.procedure` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).
R5: Whether or how long patient abstained from food and/or drink (new)
R5: `Specimen.collection.fastingStatus[x]` (new:CodeableConcept, Duration)
Element `Specimen.collection.fastingStatus[x]` has a context of Specimen.collection based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.collection.fastingStatus[x]` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element). Representing fasting status using this element is preferred to representing it with an observation using a 'pre-coordinated 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).
May 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 that contains it. Usually modifier elements provide negation or qualification. In order 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 is allowed to 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.
Element `Specimen.collection.collector` is mapped to FHIR STU3 element `Specimen.collection.collector` as `SourceIsBroaderThanTarget`. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `Specimen.collection.collector` with unmapped reference targets: Patient, Practitioner, PractitionerRole, RelatedPerson.
Time when specimen was collected from subject - the physiologically relevant time.
The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample.
A coded value specifying the technique that is used to perform the procedure.
The technique that is used to perform the procedure
Anatomical 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 [body-site-instance](http://hl7.org/fhir/STU3/extension-body-site-instance.html).
Codes describing anatomical locations. May include laterality.
R5: `Specimen.collection.bodySite` additional types (CodeableReference(http://hl7.org/fhir/StructureDefinition/BodyStructure)) additional types from child elements (reference)
Element `Specimen.collection.bodySite` is mapped to FHIR STU3 element `Specimen.collection.bodySite` as `SourceIsBroaderThanTarget`. The mappings for `Specimen.collection.bodySite` do not cover the following types: CodeableReference. The mappings for `Specimen.collection.bodySite` do not cover the following types based on type expansion: reference. Reasons for using BodyStructure reference include: 1.) Need to identify a specific site instance (e.g. a specific mole), 2.) a single pre-coordinated coded concept for the body site does not exist, 3.) a desire to represent bodySite using multiple attributes (e.g. modifiers).
A reference to a code defined by a terminology system.
Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.
Allows for translations and alternate encodings within a code system. Also supports communication of the same instance to systems requiring different encodings.
fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding
Plain text representation of the concept
A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.
Very often the text is the same as a displayName of one of the codings.
The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.
C*E.9. But note many systems use C*E.2 for this
fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText
Details concerning processing and processing steps for the specimen.
.participation[typeCode=SBJ].act[code=SPCTRT, moodCode=EVN]
Additional Content defined by implementations
May be used to represent additional information that is not part of the basic definition of the element. In order 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 is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.
Indicates the treatment step applied to the specimen
A coded value specifying the procedure used to process the specimen.
Type indicating the technique used to process the specimen
R5: `Specimen.processing.additive` additional types from child elements (display, identifier, reference, type)
Element `Specimen.processing.additive` is mapped to FHIR STU3 element `Specimen.processing.additive` as `SourceIsBroaderThanTarget`. The mappings for `Specimen.processing.additive` do not cover the following types based on type expansion: display, identifier, reference, type. The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `Specimen.processing.additive` with unmapped reference targets: Substance.
A 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.
Direct 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.
R5: Device resource for the container (new)
R5: `Specimen.container.device` (new:Reference(Device))
Element `Specimen.container.device` has a context of Specimen.container based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.container.device` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).
R5: `Specimen.container.location` (new:Reference(Location))
Element `Specimen.container.location` has a context of Specimen.container based on following the parent source element upwards and mapping to `Specimen`. Element `Specimen.container.location` has no mapping targets in FHIR STU3. Typically, this is because the element has been added (is a new element).
Id 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.
Kind of container directly associated with specimen
The type of container associated with the specimen (e.g. slide, aliquot, etc.).
The capacity (volume or other measure) the container may contain.
one of: SAC 16, SAC17 and SAC 20, or SAC 21 and SAC 20
The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type.
Introduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA.
To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen).
.inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code="annotation"].value