Example Usage Scenarios:

The following are example usage scenarios for the US Core Specimen profile:

• Query for a patient’s specimen
• Record or update a specimen for a patient

Mandatory and Must Support Data Elements

The following data elements must always be present (Mandatory definition) or must be supported if the data is present in the sending system (Must Support definition). They are presented below in a simple human-readable explanation. Profile specific guidance and examples are provided as well. The Formal Views below provides the formal summary, definitions, and terminology requirements.

Each Specimen Must Have:

1. a specimen code

Each Specimen Must Support:

1. a patient

Profile Specific Implementation Guidance:

• Since the binding is extensible when a code is unavailable, just text is allowed.
• in addition to Specimen search criteria, clients may request Specimen resources be included with Observation or DiagnosticReport resource query. An example query is provided in the Notes section below.

• Differential Table
• Key Elements Table
• Snapshot Table
• Statistics/References
• All

This structure is derived from Specimen

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
type	S	1..1	CodeableConcept	(USCDI) Kind of material that forms the specimen Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)
subject	S	0..1	Reference(US Core Patient Profile)	(USCDI) The patient where the specimen came from.
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet
Specimen.type	extensible	http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	SΣ	1..1	CodeableConcept	(USCDI) Kind of material that forms the specimen Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)
subject	SΣ	0..1	Reference(US Core Patient Profile)	(USCDI) The patient where the specimen came from.
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Specimen.status	required	SpecimenStatus
Specimen.type	extensible	http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Specimen	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Specimen	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Specimen	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()
dom-5	error	Specimen	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Specimen	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	External Identifier
accessionIdentifier	Σ	0..1	Identifier	Identifier assigned by the lab
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	SΣ	1..1	CodeableConcept	(USCDI) Kind of material that forms the specimen Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)
subject	SΣ	0..1	Reference(US Core Patient Profile)	(USCDI) The patient where the specimen came from.
receivedTime	Σ	0..1	dateTime	The time when specimen was received for processing
parent		0..*	Reference(Specimen)	Specimen from which this specimen originated
request		0..*	Reference(ServiceRequest)	Why the specimen was collected
collection		0..1	BackboneElement	Collection details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
collector	Σ	0..1	Reference(Practitioner | PractitionerRole)	Who collected the specimen
collected[x]	Σ	0..1		Collection time
collectedDateTime			dateTime
collectedPeriod			Period
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity		0..1	SimpleQuantity	The quantity of specimen collected
method		0..1	CodeableConcept	Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
fastingStatus[x]	Σ	0..1		Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.
fastingStatusCodeableConcept			CodeableConcept
fastingStatusDuration			Duration
processing		0..*	BackboneElement	Processing and processing step details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
description		0..1	string	Textual description of procedure
procedure		0..1	CodeableConcept	Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.
additive		0..*	Reference(Substance)	Material used in the processing step
time[x]		0..1		Date and time of specimen processing
timeDateTime			dateTime
timePeriod			Period
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
identifier	Σ	0..*	Identifier	Id for the container
description		0..1	string	Textual description of the container
type		0..1	CodeableConcept	Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container.
capacity		0..1	SimpleQuantity	Container volume or size
specimenQuantity		0..1	SimpleQuantity	Quantity of specimen within container
additive[x]		0..1		Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container.
additiveCodeableConcept			CodeableConcept
additiveReference			Reference(Substance)
condition	Σ	0..*	CodeableConcept	State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
note		0..*	Annotation	Comments
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Specimen.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding
Specimen.status	required	SpecimenStatus
Specimen.type	extensible	http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54
Specimen.collection.method	example	FHIRSpecimenCollectionMethod
Specimen.collection.bodySite	example	SNOMEDCTBodyStructures
Specimen.collection.fastingStatus[x]	extensible	Hl7VSRelevantClincialInformation
Specimen.processing.procedure	example	SpecimenProcessingProcedure
Specimen.container.type	example	SpecimenContainerType
Specimen.container.additive[x]	example	Hl7VSAdditivePreservative
Specimen.condition	extensible	Hl7VSSpecimenCondition

Constraints

Id	Grade	Path(s)	Details	Requirements
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Differential View

This structure is derived from Specimen

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
type	S	1..1	CodeableConcept	(USCDI) Kind of material that forms the specimen Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)
subject	S	0..1	Reference(US Core Patient Profile)	(USCDI) The patient where the specimen came from.
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet
Specimen.type	extensible	http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	SΣ	1..1	CodeableConcept	(USCDI) Kind of material that forms the specimen Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)
subject	SΣ	0..1	Reference(US Core Patient Profile)	(USCDI) The patient where the specimen came from.
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Specimen.status	required	SpecimenStatus
Specimen.type	extensible	http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Specimen	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Specimen	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Specimen	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()
dom-5	error	Specimen	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Specimen	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Snapshot View

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	External Identifier
accessionIdentifier	Σ	0..1	Identifier	Identifier assigned by the lab
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	SΣ	1..1	CodeableConcept	(USCDI) Kind of material that forms the specimen Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)
subject	SΣ	0..1	Reference(US Core Patient Profile)	(USCDI) The patient where the specimen came from.
receivedTime	Σ	0..1	dateTime	The time when specimen was received for processing
parent		0..*	Reference(Specimen)	Specimen from which this specimen originated
request		0..*	Reference(ServiceRequest)	Why the specimen was collected
collection		0..1	BackboneElement	Collection details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
collector	Σ	0..1	Reference(Practitioner | PractitionerRole)	Who collected the specimen
collected[x]	Σ	0..1		Collection time
collectedDateTime			dateTime
collectedPeriod			Period
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity		0..1	SimpleQuantity	The quantity of specimen collected
method		0..1	CodeableConcept	Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
fastingStatus[x]	Σ	0..1		Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.
fastingStatusCodeableConcept			CodeableConcept
fastingStatusDuration			Duration
processing		0..*	BackboneElement	Processing and processing step details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
description		0..1	string	Textual description of procedure
procedure		0..1	CodeableConcept	Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.
additive		0..*	Reference(Substance)	Material used in the processing step
time[x]		0..1		Date and time of specimen processing
timeDateTime			dateTime
timePeriod			Period
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
identifier	Σ	0..*	Identifier	Id for the container
description		0..1	string	Textual description of the container
type		0..1	CodeableConcept	Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container.
capacity		0..1	SimpleQuantity	Container volume or size
specimenQuantity		0..1	SimpleQuantity	Quantity of specimen within container
additive[x]		0..1		Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container.
additiveCodeableConcept			CodeableConcept
additiveReference			Reference(Substance)
condition	Σ	0..*	CodeableConcept	State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
note		0..*	Annotation	Comments
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Specimen.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding
Specimen.status	required	SpecimenStatus
Specimen.type	extensible	http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54
Specimen.collection.method	example	FHIRSpecimenCollectionMethod
Specimen.collection.bodySite	example	SNOMEDCTBodyStructures
Specimen.collection.fastingStatus[x]	extensible	Hl7VSRelevantClincialInformation
Specimen.processing.procedure	example	SpecimenProcessingProcedure
Specimen.container.type	example	SpecimenContainerType
Specimen.container.additive[x]	example	Hl7VSAdditivePreservative
Specimen.condition	extensible	Hl7VSSpecimenCondition

Constraints

Id	Grade	Path(s)	Details	Requirements
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

This structure is derived from Specimen

Summary

Mandatory: 1 element
Must-Support: 2 elements

Structures

This structure refers to these other structures:

• US Core Patient Profile (http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient)

Quick Start

Below is an overview of the required Server RESTful FHIR interactions for this profile - for example, search and read operations - when supporting the US Core interactions to access this profile’s information (Profile Support + Interaction Support). Note that systems that support only US Core Profiles (Profile Only Support) are not required to support these interactions. See the US Core Server CapabilityStatement for a complete list of supported RESTful interactions for this IG.

• The syntax used to describe the interactions is described here.

• Servers providing access to specimen data can use US Core SMART Scopes for:
  • resource level scopes (for example, patient/Specimen.rs).
• See the General Requirements section for additional rules and expectations when a server requires status parameters.
• See the General Guidance section for additional guidance on searching for multiple patients.

Mandatory Search Parameters:

The following search parameters and search parameter combinations SHALL be supported:

1. SHALL support both read Specimen by id AND Specimen search using the _id search parameter:

   GET [base]/Specimen/[id] or GET [base]/Specimen?_id=[id]

   Example:

   1. GET [base]/Specimen?_id=123

   Implementation Notes: (how to search by the logical id of the resource)

Optional Search Parameters:

The following search parameter combinations SHOULD be supported:

1. SHOULD support searching for all specimens for a patient using the patient search parameter:

   GET [base]/Specimen?patient={Type/}[id]

   Example:

   1. GET [base]/Specimen?patient=1137192

   Implementation Notes: Fetches a bundle of all Specimen resources for the specified patient (how to search by reference)

Including Specimen when searching for an Observation or DiagnosticReport

Servers MAY support the _include parameter to request that additional resources be included in the response of a search query. For example, when searching for an Observation or DiagnosticReport that references Specimen, the client can use the _include parameter to retrieve information about a specimen associated with the search results. The syntax for querying an Observation and the associated Specimen is:

GET [base]/[Resource-type]?[parameter1]=[value1]{&...}&_include=Observation:specimen

Example:

GET [base]/Observation?_id=9163726&_include=Observation:specimen