This profile sets minimum expectations for the [Specimen] resource to represent data requested as part of the U.S. Public Health Case Based Surveillance messaging guides. It identifies which core elements, extensions, vocabularies and value sets SHALL be present in the resource when using this profile.

Example Usage Scenarios:

The following are example usage scenarios for the US CBS Patient profile:

• Represent a specimen tested as part of a diagnostic lab report.

Relationship to CDC Message Mapping Guides

The Center for Disease Control’s (CDC) Message Mapping Guides (MMGs) provide guidance on the transmission of records from jurisdictions to case based surveillance programs. MMG documents are publicly available through the CDC’s website. In addition to generic information captured by the Gen V2 guide, there are program specific guides tied to specific conditions or groups of condition.

The US CBS Condition of Interest profile represents the core reported condition of interest (as defined by the Nationally Notifiable Disease Surveillance System & Other Conditions of Public Health Importance valueset) which is reported in the Gen V2 message mapping guide. It should be considered the resource which determines the recipient case surveillance program which oversees surveillance for the specified condition of interest.

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 Profile Definition below provides the formal summary, definitions, and terminology requirements.

Each Specimen must have:

1. a subject reference

Each Specimen must support:

1. an extension capturing specimen role
2. a placer assigned identifier
3. a filler assigned identifier
4. a specimen type
5. a received time for when the specimen was received by the performing laboratory
6. a collected date time or period
7. a collected quantity
8. a collection body site
9. a note

• Text Summary
• Differential Table
• Snapshot Table
• Snapshot Table (Must Support)
• All

This structure is derived from Specimen

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
cbs-specimen-role	S	0..1	CodeableConcept	Case Based Surveillance Specimen Role Extension URL: http://cbsig.chai.gatech.edu/StructureDefinition/cbs-specimen-role Binding: Specimen Role (required): Code for Specimen Role Value Set
Slices for identifier		0..*	Identifier	External Identifier Slice: Unordered, Open by pattern:type
identifier:placerAssignedId	S	0..1	Identifier	External Identifier
type		1..1	CodeableConcept	Description of identifier Binding: hl7VS-identifierType (required) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
code		1..1	code	Symbol in syntax defined by the system Fixed Value: PLAC
system	S	0..1	uri	The namespace for the identifier value
value	S	1..1	string	The value that is unique
identifier:fillerAssignedId	S	0..1	Identifier	External Identifier
type		1..1	CodeableConcept	Description of identifier Binding: hl7VS-identifierType (required) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
code		1..1	code	Symbol in syntax defined by the system Fixed Value: FILL
system	S	0..1	uri	The namespace for the identifier value
value	S	1..1	string	The value that is unique
type	S	0..1	CodeableConcept	Kind of material that forms the specimen Binding: Specimen (extensible)
subject	S	1..1	Reference(US Case Based Surveillance Patient Profile)	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 or a device
receivedTime	S	0..1	dateTime	The time when specimen was received for processing
collection
collected[x]	S	0..1	dateTime, Period	Collection time
quantity	S	0..1	SimpleQuantity	The quantity of specimen collected
bodySite	S	0..1	CodeableConcept	Anatomical collection site Binding: Body site (extensible)
note	S	0..*	Annotation	Comments
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
id	Σ	0..1	string	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) Max Binding: AllLanguages: A human language.
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
cbs-specimen-role	S	0..1	CodeableConcept	Case Based Surveillance Specimen Role Extension URL: http://cbsig.chai.gatech.edu/StructureDefinition/cbs-specimen-role Binding: Specimen Role (required): Code for Specimen Role Value Set
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
Slices for identifier	Σ	0..*	Identifier	External Identifier Slice: Unordered, Open by pattern:type
identifier:placerAssignedId	SΣ	0..1	Identifier	External Identifier
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
use	?!Σ	0..1	code	usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
type	Σ	1..1	CodeableConcept	Description of identifier Binding: hl7VS-identifierType (required) Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: PLAC
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
system	SΣ	0..1	uri	The namespace for the identifier value Example General: http://www.acme.com/identifiers/patient
value	SΣ	1..1	string	The value that is unique Example General: 123456
period	Σ	0..1	Period	Time period when id is/was valid for use
assigner	Σ	0..1	Reference(Organization)	Organization that issued id (may be just text)
identifier:fillerAssignedId	SΣ	0..1	Identifier	External Identifier
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
use	?!Σ	0..1	code	usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
type	Σ	1..1	CodeableConcept	Description of identifier Binding: hl7VS-identifierType (required) Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: FILL
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
system	SΣ	0..1	uri	The namespace for the identifier value Example General: http://www.acme.com/identifiers/patient
value	SΣ	1..1	string	The value that is unique Example General: 123456
period	Σ	0..1	Period	Time period when id is/was valid for use
assigner	Σ	0..1	Reference(Organization)	Organization that issued id (may be just text)
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	0..1	CodeableConcept	Kind of material that forms the specimen Binding: Specimen (extensible)
subject	SΣ	1..1	Reference(US Case Based Surveillance Patient Profile)	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 or a device
receivedTime	SΣ	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]	SΣ	0..1		Collection time
collectedDateTime			dateTime
collectedPeriod			Period
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity	S	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	S	0..1	CodeableConcept	Anatomical collection site Binding: Body site (extensible)
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	S	0..*	Annotation	Comments
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
cbs-specimen-role		0..1	CodeableConcept	Case Based Surveillance Specimen Role Extension URL: http://cbsig.chai.gatech.edu/StructureDefinition/cbs-specimen-role Binding: Specimen Role (required): Code for Specimen Role Value Set
identifier:placerAssignedId	Σ	0..1	Identifier	External Identifier
system	Σ	0..1	uri	The namespace for the identifier value
value	Σ	1..1	string	The value that is unique
identifier:fillerAssignedId	Σ	0..1	Identifier	External Identifier
system	Σ	0..1	uri	The namespace for the identifier value
value	Σ	1..1	string	The value that is unique
type	Σ	0..1	CodeableConcept	Kind of material that forms the specimen Binding: Specimen (extensible)
subject	Σ	1..1	Reference(US Case Based Surveillance Patient Profile)	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 or a device
receivedTime	Σ	0..1	dateTime	The time when specimen was received for processing
collection		0..1	BackboneElement	Collection details
collected[x]	Σ	0..1		Collection time
collectedDateTime			dateTime
collectedPeriod			Period
quantity		0..1	SimpleQuantity	The quantity of specimen collected
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: Body site (extensible)
note		0..*	Annotation	Comments
Documentation for this format

This structure is derived from Specimen

Summary

Mandatory: 1 element (4 nested mandatory elements)
Must-Support: 14 elements

Structures

This structure refers to these other structures:

• US Case Based Surveillance Patient Profile (http://cbsig.chai.gatech.edu/StructureDefinition/us-cbs-patient)

Extensions

This structure refers to these extensions:

• http://cbsig.chai.gatech.edu/StructureDefinition/cbs-specimen-role

Slices

This structure defines the following Slices:

• The element Specimen.identifier is sliced based on the value of pattern:type

Differential View

This structure is derived from Specimen

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
cbs-specimen-role	S	0..1	CodeableConcept	Case Based Surveillance Specimen Role Extension URL: http://cbsig.chai.gatech.edu/StructureDefinition/cbs-specimen-role Binding: Specimen Role (required): Code for Specimen Role Value Set
Slices for identifier		0..*	Identifier	External Identifier Slice: Unordered, Open by pattern:type
identifier:placerAssignedId	S	0..1	Identifier	External Identifier
type		1..1	CodeableConcept	Description of identifier Binding: hl7VS-identifierType (required) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
code		1..1	code	Symbol in syntax defined by the system Fixed Value: PLAC
system	S	0..1	uri	The namespace for the identifier value
value	S	1..1	string	The value that is unique
identifier:fillerAssignedId	S	0..1	Identifier	External Identifier
type		1..1	CodeableConcept	Description of identifier Binding: hl7VS-identifierType (required) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
code		1..1	code	Symbol in syntax defined by the system Fixed Value: FILL
system	S	0..1	uri	The namespace for the identifier value
value	S	1..1	string	The value that is unique
type	S	0..1	CodeableConcept	Kind of material that forms the specimen Binding: Specimen (extensible)
subject	S	1..1	Reference(US Case Based Surveillance Patient Profile)	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 or a device
receivedTime	S	0..1	dateTime	The time when specimen was received for processing
collection
collected[x]	S	0..1	dateTime, Period	Collection time
quantity	S	0..1	SimpleQuantity	The quantity of specimen collected
bodySite	S	0..1	CodeableConcept	Anatomical collection site Binding: Body site (extensible)
note	S	0..*	Annotation	Comments
Documentation for this format

Snapshot View

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
id	Σ	0..1	string	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) Max Binding: AllLanguages: A human language.
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
cbs-specimen-role	S	0..1	CodeableConcept	Case Based Surveillance Specimen Role Extension URL: http://cbsig.chai.gatech.edu/StructureDefinition/cbs-specimen-role Binding: Specimen Role (required): Code for Specimen Role Value Set
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
Slices for identifier	Σ	0..*	Identifier	External Identifier Slice: Unordered, Open by pattern:type
identifier:placerAssignedId	SΣ	0..1	Identifier	External Identifier
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
use	?!Σ	0..1	code	usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
type	Σ	1..1	CodeableConcept	Description of identifier Binding: hl7VS-identifierType (required) Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: PLAC
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
system	SΣ	0..1	uri	The namespace for the identifier value Example General: http://www.acme.com/identifiers/patient
value	SΣ	1..1	string	The value that is unique Example General: 123456
period	Σ	0..1	Period	Time period when id is/was valid for use
assigner	Σ	0..1	Reference(Organization)	Organization that issued id (may be just text)
identifier:fillerAssignedId	SΣ	0..1	Identifier	External Identifier
id		0..1	string	Unique id for inter-element referencing
Slices for extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
use	?!Σ	0..1	code	usual | official | temp | secondary | old (If known) Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
type	Σ	1..1	CodeableConcept	Description of identifier Binding: hl7VS-identifierType (required) Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0203
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: FILL
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
system	SΣ	0..1	uri	The namespace for the identifier value Example General: http://www.acme.com/identifiers/patient
value	SΣ	1..1	string	The value that is unique Example General: 123456
period	Σ	0..1	Period	Time period when id is/was valid for use
assigner	Σ	0..1	Reference(Organization)	Organization that issued id (may be just text)
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	0..1	CodeableConcept	Kind of material that forms the specimen Binding: Specimen (extensible)
subject	SΣ	1..1	Reference(US Case Based Surveillance Patient Profile)	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 or a device
receivedTime	SΣ	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]	SΣ	0..1		Collection time
collectedDateTime			dateTime
collectedPeriod			Period
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity	S	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	S	0..1	CodeableConcept	Anatomical collection site Binding: Body site (extensible)
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	S	0..*	Annotation	Comments
Documentation for this format