HL7 FHIR Implementation Guide: Breast Cancer Data, Release 1 - US Realm (Draft for Comment 2)

SpecimenProfile

Definitions for cimi-entity-Specimen.

1. Specimen:cimi-entity-Specimen
Definition

A specimen is a substance, physical object, or collection of objects, that the laboratory considers a single discrete, uniquely identified unit that is the subject of one or more steps in the laboratory workflow. A specimen may include multiple physical pieces as long as they are considered a single unit within the laboratory workflow. A specimen results from one to many specimen collection procedures, and may be contained in multiple specimen containers. Specimen may have one or more processing activities.

Control0..*
InvariantsDefined on this element
dom-1: If the resource is contained in another resource, it SHALL NOT contain any narrative (: contained.text.empty())
dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (: contained.contained.empty())
dom-3: 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())
dom-4: 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())
2. Specimen:cimi-entity-Specimen.id
Definition

The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.

Control0..1
Typeid
Comments

The only time that a resource does not have an id is when it is being submitted to the server using a create operation.

3. Specimen:cimi-entity-Specimen.meta
Definition

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.

Control0..1
TypeMeta
4. Specimen:cimi-entity-Specimen.implicitRules
Definition

A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content.

Control0..1
Typeuri
Is Modifiertrue
Comments

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.

5. Specimen:cimi-entity-Specimen.language
Definition

The base language in which the resource is written.

Control0..1
BindingA human language.
The codes SHALL be taken from Common Languages; other codes may be used where these codes are not suitable
Max Binding: All Languages
Typecode
Comments

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).

6. Specimen:cimi-entity-Specimen.text
Definition

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.

Control0..1 This element is affected by the following invariants: dom-1
TypeNarrative
Alternate Namesnarrative, html, xhtml, display
Comments

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.

7. Specimen:cimi-entity-Specimen.contained
Definition

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.

Control0..*
TypeResource
Alternate Namesinline resources, anonymous resources, contained resources
Comments

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.

8. Specimen:cimi-entity-Specimen.extension
Definition

May be used to represent additional information that is not part of the basic definition of the resource. 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.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

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.

9. Specimen:cimi-entity-Specimen.extension:collectiontime
Definition

When the sample was obtained, as a specific time or time period.

Control0..1
TypeExtension(CollectionTimeExtension) (Extension Type: Choice of: dateTime, Period)
10. Specimen:cimi-entity-Specimen.extension:specimentreatment
Definition

Treatment performed on the specimen.

Control0..*
TypeExtension(SpecimenTreatmentExtension) (Extension Type: Reference(SpecimenTreatmentProfile))
11. Specimen:cimi-entity-Specimen.extension:handlingrisk
Definition

Cautions on the handling of this specimen.

Control0..*
TypeExtension(HandlingRiskExtension) (Extension Type: CodeableConcept)
12. Specimen:cimi-entity-Specimen.extension:specialhandling
Definition

Information about the proper handling of the specimen.

Control0..*
TypeExtension(SpecialHandlingExtension) (Extension Type: CodeableConcept)
13. Specimen:cimi-entity-Specimen.modifierExtension
Definition

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.

Control0..*
TypeExtension
Is Modifiertrue
Alternate Namesextensions, user content
Comments

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.

14. Specimen:cimi-entity-Specimen.identifier
Definition

Id for specimen.

NoteThis is a business identifier, not a resource identifier (see discussion)
Control0..*
TypeIdentifier
15. Specimen:cimi-entity-Specimen.accessionIdentifier
Definition

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.

Control0..1
TypeIdentifier(AccessionIdentifierProfile)
16. Specimen:cimi-entity-Specimen.status
Definition

The availability of the specimen.

Control0..1
BindingCodes providing the status/availability of a specimen.
The codes SHALL be taken from SpecimenStatus
Typecode
Is Modifiertrue
Comments

This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.

17. Specimen:cimi-entity-Specimen.type
Definition

The kind of material that forms the specimen.

Control1..1
BindingThe type of the specimen.
The codes SHALL be taken from v2 Specimen Type
TypeCodeableConcept
Comments

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.

18. Specimen:cimi-entity-Specimen.subject
Definition

Where the specimen came from. This may be from the patient(s) or from the environment or a device.

Control1..1
TypeReference(US Core Patient Profile | GroupProfile | US Core Device Profile | SubstanceProfile)
Requirements

Must know the subject context.

19. Specimen:cimi-entity-Specimen.receivedTime
Definition

Time when specimen was received for processing or testing.

Control0..1
TypedateTime
20. Specimen:cimi-entity-Specimen.parent
Definition

Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen.

Control0..1
TypeReference(SpecimenProfile)
Comments

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.

21. Specimen:cimi-entity-Specimen.request
Definition

Details concerning a test or procedure request that required a specimen to be collected.

Control0..*
TypeReference(ProcedureRequest)
Comments

The request may be explicit or implied such with a ProcedureRequest that requires a blood draw.

22. Specimen:cimi-entity-Specimen.collection
Definition

Details concerning the specimen collection.

Control0..1
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() | (children().count() > id.count()))
23. Specimen:cimi-entity-Specimen.collection.id
Definition

unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
24. Specimen:cimi-entity-Specimen.collection.extension
Definition

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.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

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.

25. Specimen:cimi-entity-Specimen.collection.modifierExtension
Definition

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.

Control0..*
TypeExtension
Is Modifiertrue
Alternate Namesextensions, user content, modifiers
Comments

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.

26. Specimen:cimi-entity-Specimen.collection.collector
Definition

Person who collected the specimen.

Control0..1
TypeReference(Practitioner)
27. Specimen:cimi-entity-Specimen.collection.collected[x]
Definition

Time when specimen was collected from subject - the physiologically relevant time.

Control0..1
TypeChoice of: dateTime, Period
[x] NoteSee Choice of Data Types for further information about how to use [x]
28. Specimen:cimi-entity-Specimen.collection.quantity
Definition

The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample.

Control0..1
TypeQuantity(SimpleQuantity)
29. Specimen:cimi-entity-Specimen.collection.method
Definition

A coded value specifying the technique that is used to perform the procedure.

Control0..1
BindingThe technique that is used to perform the procedure
For example codes, see FHIR Specimen Collection Method
TypeCodeableConcept
30. Specimen:cimi-entity-Specimen.collection.bodySite
Definition

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.

Control0..1
BindingThe codes SHALL be taken from BC AnatomicalLocationVS ValueSet
TypeCodeableConcept
Comments

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.

31. Specimen:cimi-entity-Specimen.processing
Definition

Details concerning processing and processing steps for the specimen.

Control0..*
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() | (children().count() > id.count()))
32. Specimen:cimi-entity-Specimen.processing.id
Definition

unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
33. Specimen:cimi-entity-Specimen.processing.extension
Definition

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.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

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.

34. Specimen:cimi-entity-Specimen.processing.modifierExtension
Definition

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.

Control0..*
TypeExtension
Is Modifiertrue
Alternate Namesextensions, user content, modifiers
Comments

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.

35. Specimen:cimi-entity-Specimen.processing.description
Definition

Textual description of procedure.

Control0..1
Typestring
36. Specimen:cimi-entity-Specimen.processing.procedure
Definition

A coded value specifying the procedure used to process the specimen.

Control0..1
BindingType indicating the technique used to process the specimen
For example codes, see SpecimenProcessingProcedure
TypeCodeableConcept
37. Specimen:cimi-entity-Specimen.processing.additive
Definition

Material used in the processing step.

Control0..*
TypeReference(Substance)
38. Specimen:cimi-entity-Specimen.processing.time[x]
Definition

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.

Control0..1
TypeChoice of: dateTime, Period
[x] NoteSee Choice of Data Types for further information about how to use [x]
39. Specimen:cimi-entity-Specimen.container
Definition

The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here.

Control0..*
TypeBackboneElement
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() | (children().count() > id.count()))
40. Specimen:cimi-entity-Specimen.container.id
Definition

unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Control0..1
Typestring
41. Specimen:cimi-entity-Specimen.container.extension
Definition

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.

Control0..*
TypeExtension
Alternate Namesextensions, user content
Comments

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.

42. Specimen:cimi-entity-Specimen.container.modifierExtension
Definition

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.

Control0..*
TypeExtension
Is Modifiertrue
Alternate Namesextensions, user content, modifiers
Comments

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.

43. Specimen:cimi-entity-Specimen.container.identifier
Definition

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.

NoteThis is a business identifier, not a resource identifier (see discussion)
Control0..*
TypeIdentifier(IdentifierProfile)
44. Specimen:cimi-entity-Specimen.container.description
Definition

Textual description of the container.

Control0..1
Typestring
45. Specimen:cimi-entity-Specimen.container.type
Definition

The type of container associated with the specimen (e.g. slide, aliquot, etc.).

Control0..1
BindingType of specimen container
For example codes, see SpecimenContainer
TypeCodeableConcept
46. Specimen:cimi-entity-Specimen.container.capacity
Definition

The capacity (volume or other measure) the container may contain.

Control0..1
TypeQuantity(SimpleQuantity)
47. Specimen:cimi-entity-Specimen.container.specimenQuantity
Definition

The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type.

Control0..1
TypeQuantity(SimpleQuantity)
48. Specimen:cimi-entity-Specimen.container.additive[x]
Definition

Introduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA.

Control0..1
BindingSubstance added to specimen container
For example codes, see v2 Additive/Preservative
TypeChoice of: CodeableConcept, Reference(SubstanceProfile)
[x] NoteSee Choice of Data Types for further information about how to use [x]
49. Specimen:cimi-entity-Specimen.note
Definition

To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen).

Control0..*
TypeAnnotation