FHIR Genomics Implementation Guide

Notice

Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.

StructureDefinition UKCore-Specimen

Used to capture information on Samples which will undergo or have undergone processing for genomic testing.

Within FHIR R4, there is no way to capture location against a sample to aid tracking, one of the key requirements of the Genomic Medicine Service. Investigation of a possible solution through backporting the container.location element within R5 is currently being investigated. Until this backport is adopted by UK Core, the location of samples, including interactions to manage and track samples, will be performed through changes to Task resources generated on submission of a ServiceRequest.

A diagram illustrating the links between resources is provided below (Duo Scenario)

Note: links from ServiceRequest.supportingInfo to samples collected after submission are pending further investigation

Profile url	FHIR Module	Normative Status
https://fhir.hl7.org.uk/StructureDefinition/UKCore-Specimen	UKCore	trial-use

UKCoreSpecimen (Specimen)	I		Specimen	Element id Specimen Short description Sample for analysis Definition A sample to be used for analysis. Data type Specimen Constraints dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources `contained.contained.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()` dom-3: 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-6: A resource should have narrative for robust management text.`div`.exists() dom-5: If a resource is contained in another resource, it SHALL NOT have a security label `contained.meta.security.empty()` ukcore-spec-001: There SHALL be only one reference between `collection.collector` and the extension `collectionCollectorR5` `collection.collector.reference.empty() or collection.collector.extension('http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.collector').empty()` Mappings rim: Entity. Role, or Act rim: Role[classCode=SPEC]
id	Σ	0..1	string	There are no (further) constraints on this element Element id Specimen.id Short description Logical id of this artifact Definition The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. 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. Data type string
meta	Σ	0..1	Meta	There are no (further) constraints on this element Element id Specimen.meta Short description Metadata about the resource Definition The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource. Data type Meta Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
implicitRules	Σ ?!	0..1	uri	There are no (further) constraints on this element Element id Specimen.implicitRules Short description A set of rules under which this content was created 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. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. 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. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc. Data type uri Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a
language		0..1	codeBinding	There are no (further) constraints on this element Element id Specimen.language Short description Language of the resource content Definition The base language in which the resource is written. 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). Data type code Binding A human language. CommonLanguages (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a
text		0..1	Narrative	There are no (further) constraints on this element Element id Specimen.text Short description Text summary of the resource, for human interpretation Alternate names narrative, html, xhtml, display Definition A human-readable narrative that contains a summary of the resource and can 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. 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 information is added later. Data type Narrative Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A rim: Act.text?
contained		0..*	Resource	There are no (further) constraints on this element Element id Specimen.contained Short description Contained, inline Resources Alternate names inline resources, anonymous resources, contained resources 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. 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. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels. Data type Resource Mappings rim: Entity. Role, or Act rim: N/A
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
sampleCategory	I	0..1	Extension(CodeableConcept)	Element id Specimen.extension:sampleCategory Short description An extension to record the category of a sample. Alternate names extensions, user content Definition This extension allows the recording of the category of a sample for use within Genomics, whether it is a tumour or germline sample. 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. Data type Extension(CodeableConcept) Extension URL https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	?! I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.modifierExtension Short description Extensions that cannot be ignored Alternate names extensions, user content 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 and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. 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. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
identifier	Σ	0..*	Identifier	There are no (further) constraints on this element Element id Specimen.identifier Short description External Identifier Definition Id for specimen. Data type Identifier Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CX / EI (occasionally, more often EI maps to a resource id or a URL) rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT] servd: Identifier w5: FiveWs.identifier v2: SPM-2 rim: .id
accessionIdentifier	Σ	0..1	Identifier	There are no (further) constraints on this element Element id Specimen.accessionIdentifier Short description Identifier assigned by the lab 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. Data type Identifier Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CX / EI (occasionally, more often EI maps to a resource id or a URL) rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT] servd: Identifier w5: FiveWs.identifier v2: SPM-30 (v2.7+) rim: .participation[typeCode=SBJ].act[classCode=ACSN, moodCode=EVN].id
status	S Σ ?!	0..1	codeBinding	Element id Specimen.status Short description The availability of the specimen sample. Definition The availability of the specimen. Comments This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid. Data type code Binding Codes providing the status/availability of a specimen. SpecimenStatus (required) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a w5: FiveWs.status v2: SPM-20 rim: status
type	S Σ	0..1	CodeableConceptBinding	Element id Specimen.type Short description The kind of material that forms the specimen. Definition The kind of material that forms the specimen. 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. Data type CodeableConcept Binding A code from the SNOMED CT UK Clinical Terminology coding system UKCoreSpecimenType (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD w5: FiveWs.what[x] v2: SPM-4 and possibly SPM-5 rim: .code
subject	S Σ I	0..1	Reference(Patient \| Group \| Device \| Substance \| Location)	Element id Specimen.subject Short description Where the specimen came from. Definition 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. Requirements Must know the subject context. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Patient \| Group \| Device \| Substance \| Location) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) w5: FiveWs.subject[x] rim: .scoper or .scoper.playsRole w5: FiveWs.subject
receivedTime	S Σ	0..1	dateTime	Element id Specimen.receivedTime Short description The time when specimen was received for processing. Definition Time when specimen was received for processing or testing. Data type dateTime Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a w5: FiveWs.done[x] v2: SPM-18 rim: .participation[typeCode=SBJ].act[code=SPCREC, moodCode=EVN].effectiveTime
parent	I	0..*	Reference(Specimen)	There are no (further) constraints on this element Element id Specimen.parent Short description Specimen from which this specimen originated Definition Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen. 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. Data type Reference(Specimen) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) rim: .scoper (if parent) .player.scopesRole[classCode=SPEC].player (if child)
request	I	0..*	Reference(ServiceRequest)	There are no (further) constraints on this element Element id Specimen.request Short description Why the specimen was collected Definition Details concerning a service request that required a specimen to be collected. Comments The request may be explicit or implied such with a ServiceRequest that requires a blood draw. Data type Reference(ServiceRequest) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) w5: FiveWs.why[x] v2: ORC? OBR-2/3? rim: outboundRelationship[typeCode=FLFS].target
collection		0..1	BackboneElement	There are no (further) constraints on this element Element id Specimen.collection Short description Collection details Definition Details concerning the specimen collection. Data type BackboneElement Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: SPM-14 rim: .participation[typeCode=SBJ].act[classCode=SPECCOLLECT, moodCode=EVN]
id		0..1	string	There are no (further) constraints on this element Element id Specimen.collection.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.collection.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
specialHandling	I	0..*	Extension(CodeableConcept)	Element id Specimen.collection.extension:specialHandling Short description This SHOULD be included if there is a high contamination risk reason for a sample / biopsy. Alternate names extensions, user content Definition Special handling during the collection, transport, or storage of the specimen. 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. Data type Extension(CodeableConcept) Extension URL http://hl7.org/fhir/StructureDefinition/specimen-specialHandling Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	Σ ?! I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.collection.modifierExtension Short description Extensions that cannot be ignored even if unrecognized Alternate names extensions, user content, modifiers 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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. 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. Data type Extension Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
collector	Σ I	0..1	Reference(Practitioner \| PractitionerRole)	There are no (further) constraints on this element Element id Specimen.collection.collector Short description Who collected the specimen Definition Person who collected the specimen. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Practitioner \| PractitionerRole) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) w5: FiveWs.actor v2: PRT rim: .participation[typeCode=PFM].role
id		0..1	string	There are no (further) constraints on this element Element id Specimen.collection.collector.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.collection.collector.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
collectionCollectorR5	I	0..1	Extension(Reference(Patient \| RelatedPerson))	Element id Specimen.collection.collector.extension:collectionCollectorR5 Short description The person who collected the specimen. This is an R5 backport. Alternate names extensions, user content Definition Person who collected the specimen. This is an R5 backport 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. Data type Extension(Reference(Patient \| RelatedPerson)) Extension URL http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.collector Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
id		0..1	string	There are no (further) constraints on this element Element id Specimen.collection.collector.extension:collectionCollectorR5.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.collection.collector.extension:collectionCollectorR5.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
url		1..1	uriFixed Value	There are no (further) constraints on this element Element id Specimen.collection.collector.extension:collectionCollectorR5.url Short description identifies the meaning of the extension Definition Source of the definition for the extension code - a logical name or a URL. Comments The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension. Data type uri Fixed value http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.collection.collector Mappings rim: N/A
value[x]		1..1		There are no (further) constraints on this element Element id Specimen.collection.collector.extension:collectionCollectorR5.value[x] Short description Person who collected the specimen. Definition Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
valueReference			Reference(Patient \| RelatedPerson)	There are no (further) constraints on this element Data type Reference(Patient \| RelatedPerson)
reference	Σ I	0..1	string	There are no (further) constraints on this element Element id Specimen.collection.collector.reference Short description Literal reference, Relative, internal or absolute URL Definition 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. Comments 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. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
type	Σ	0..1	uriBinding	There are no (further) constraints on this element Element id Specimen.collection.collector.type Short description Type the reference refers to (e.g. "Patient") Definition The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent. The type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. "Patient" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources). Comments This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified. Data type uri Binding Aa resource (or, for logical models, the URI of the logical model). ResourceType (extensible) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
identifier	Σ	0..1	Identifier	There are no (further) constraints on this element Element id Specimen.collection.collector.identifier Short description Logical reference, when literal reference is not known Definition An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents 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. Comments 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. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation\|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any). Data type Identifier Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CX / EI (occasionally, more often EI maps to a resource id or a URL) rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT] servd: Identifier rim: .identifier
display	Σ	0..1	string	There are no (further) constraints on this element Element id Specimen.collection.collector.display Short description Text alternative for the resource Definition Plain text narrative that identifies the resource in addition to the resource reference. Comments 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. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
collected[x]	Σ	0..1		There are no (further) constraints on this element Element id Specimen.collection.collected[x] Short description Collection time Definition Time when specimen was collected from subject - the physiologically relevant time. Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a w5: FiveWs.init v2: SPM-17 rim: .effectiveTime
collectedDateTime			dateTime	There are no (further) constraints on this element Data type dateTime
collectedPeriod			Period	There are no (further) constraints on this element Data type Period
duration	Σ I	0..1	Duration	There are no (further) constraints on this element Element id Specimen.collection.duration Short description How long it took to collect specimen Definition The span of time over which the collection of a specimen occurred. Comments The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator. Data type Duration Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` qty-3: If a code for the unit is present, the system SHALL also be present `code.empty() or system.exists()` drt-1: There SHALL be a code if there is a value and it SHALL be an expression of time. If system is present, it SHALL be UCUM. `code.exists() implies ((system = %ucum) and value.exists())` Mappings rim: n/a v2: SN (see also Range) or CQ rim: PQ, IVL<PQ>, MO, CO, depending on the values rim: PQ, IVL<PQ> depending on the values w5: FiveWs.init
quantity	I	0..1	SimpleQuantity	There are no (further) constraints on this element Element id Specimen.collection.quantity Short description The quantity of specimen collected Definition The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample. Comments The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator. Data type SimpleQuantity Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` qty-3: If a code for the unit is present, the system SHALL also be present `code.empty() or system.exists()` sqty-1: The comparator is not used on a SimpleQuantity `comparator.empty()` Mappings rim: n/a v2: SN (see also Range) or CQ rim: PQ, IVL<PQ>, MO, CO, depending on the values v2: SPM-12 rim: .participation[typeCode=SBJ].role[classCode=SPEC].player.quantity
method		0..1	CodeableConcept	There are no (further) constraints on this element Element id Specimen.collection.method Short description Technique used to perform collection Definition A coded value specifying the technique that is used to perform the procedure. Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding The technique that is used to perform the procedure. FHIRSpecimenCollectionMethod (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD v2: SPM-7 rim: .methodCode
bodySite		0..1	CodeableConceptBinding	Element id Specimen.collection.bodySite Short description Anatomical collection site 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. 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 bodySite. Data type CodeableConcept Binding Codes describing anatomical locations. May include laterality. UKCoreSpecimenBodySite (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD v2: SPM-8 and SPM-9 rim: .targetSiteCode
id		0..1	string	There are no (further) constraints on this element Element id Specimen.collection.bodySite.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.collection.bodySite.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
bodySiteReference	I	0..1	Extension(Reference(BodyStructure))	Element id Specimen.collection.bodySite.extension:bodySiteReference Short description An extension to allow referencing to a BodyStructure. Alternate names extensions, user content Definition An extension to replicate the changes within R5 altering the data type of Specimen.collection.bodySite from CodeableConcept to CodeableReference (bodyStructure). 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. Data type Extension(Reference(BodyStructure)) Extension URL https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BodySiteReference Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
id		0..1	string	There are no (further) constraints on this element Element id Specimen.collection.bodySite.extension:bodySiteReference.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.collection.bodySite.extension:bodySiteReference.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
url		1..1	uriFixed Value	There are no (further) constraints on this element Element id Specimen.collection.bodySite.extension:bodySiteReference.url Short description identifies the meaning of the extension Definition Source of the definition for the extension code - a logical name or a URL. Comments The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension. Data type uri Fixed value https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-BodySiteReference Mappings rim: N/A
value[x]		1..1		Element id Specimen.collection.bodySite.extension:bodySiteReference.value[x] Short description A reference to a BodyStructure Definition Value of extension - must be one of a constrained set of the data types (see Extensibility for a list). Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
valueReference			Reference(BodyStructure)	There are no (further) constraints on this element Data type Reference(BodyStructure)
coding	Σ	0..*	Coding	There are no (further) constraints on this element Element id Specimen.collection.bodySite.coding Short description Code defined by a terminology system Definition A reference to a code defined by a terminology system. Requirements Allows for alternative encodings within a code system, and translations to other code systems. Comments 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. Data type Coding Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE subset one of the sets of component 1-3 or 4-6 rim: CV orim: fhir:Coding rdfs:subClassOf dt:CDCoding v2: CE.1-8, CE.10-22 rim: union(., ./translation) orim: fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding
text	Σ	0..1	string	There are no (further) constraints on this element Element id Specimen.collection.bodySite.text Short description Plain text representation of the concept Definition 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. Requirements 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. Comments Very often the text is the same as a displayName of one of the codings. Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE.9. But note many systems use CE.2 for this rim: ./originalText[mediaType/code="text/plain"]/data orim: fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText
fastingStatus[x]	Σ	0..1	Binding	There are no (further) constraints on this element Element id Specimen.collection.fastingStatus[x] Short description Whether or how long patient abstained from food and/or drink Definition Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection. Requirements Many diagnostic tests require fasting to facilitate accurate interpretation. Comments 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). Binding Codes describing the fasting status of the patient. v2.0916 (extensible) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: OBR-
fastingStatusCodeableConcept			CodeableConcept	There are no (further) constraints on this element Data type CodeableConcept
fastingStatusDuration			Duration	There are no (further) constraints on this element Data type Duration
processing		0..*	BackboneElement	There are no (further) constraints on this element Element id Specimen.processing Short description Processing and processing step details Definition Details concerning processing and processing steps for the specimen. Data type BackboneElement Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: .participation[typeCode=SBJ].act[code=SPCTRT, moodCode=EVN]
id		0..1	string	There are no (further) constraints on this element Element id Specimen.processing.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.processing.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	Σ ?! I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.processing.modifierExtension Short description Extensions that cannot be ignored even if unrecognized Alternate names extensions, user content, modifiers 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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. 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. Data type Extension Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
description		0..1	string	There are no (further) constraints on this element Element id Specimen.processing.description Short description Textual description of procedure Definition Textual description of procedure. Comments Note that FHIR strings SHALL NOT exceed 1MB in size Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: .text
procedure		0..1	CodeableConcept	There are no (further) constraints on this element Element id Specimen.processing.procedure Short description Indicates the treatment step applied to the specimen Definition A coded value specifying the procedure used to process the specimen. Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding Type indicating the technique used to process the specimen. SpecimenProcessingProcedure (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD rim: .code
additive	I	0..*	Reference(Substance)	There are no (further) constraints on this element Element id Specimen.processing.additive Short description Material used in the processing step Definition Material used in the processing step. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Substance) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) v2: SPM-6 rim: .participation[typeCode=CSM].role[classCode=ADTV].code
time[x]		0..1		There are no (further) constraints on this element Element id Specimen.processing.time[x] Short description Date and time of specimen processing 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. Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: .effectiveTime
timeDateTime			dateTime	There are no (further) constraints on this element Data type dateTime
timePeriod			Period	There are no (further) constraints on this element Data type Period
container		0..*	BackboneElement	There are no (further) constraints on this element Element id Specimen.container Short description Direct container of specimen (tube/slide, etc.) Definition The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here. Data type BackboneElement Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: .player.scopingRole[classCode=CONT].scoper
id		0..1	string	There are no (further) constraints on this element Element id Specimen.container.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	Element id Specimen.container.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. 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. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
deviceR5	I	0..1	Extension(Reference(UKCoreDevice))	Element id Specimen.container.extension:deviceR5 Short description Device resource for the container. Alternate names extensions, user content Definition The device resource for the the container holding the specimen. If the container is in a holder then the referenced device will point to a parent device. 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. Data type Extension(Reference(UKCoreDevice)) Extension URL http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.container.device Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
locationR5	I	0..1	Extension(Reference(UKCoreLocation))	Element id Specimen.container.extension:locationR5 Short description Where the container is. Alternate names extensions, user content Definition The location of the container holding the specimen. 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. Data type Extension(Reference(UKCoreLocation)) Extension URL http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.container.location Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	Σ ?! I	0..*	Extension	There are no (further) constraints on this element Element id Specimen.container.modifierExtension Short description Extensions that cannot be ignored even if unrecognized Alternate names extensions, user content, modifiers 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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. 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. Data type Extension Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
identifier	Σ	0..*	Identifier	There are no (further) constraints on this element Element id Specimen.container.identifier Short description Id for the container 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. Data type Identifier Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CX / EI (occasionally, more often EI maps to a resource id or a URL) rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT] servd: Identifier v2: SAC-3 rim: .id
description		0..1	string	There are no (further) constraints on this element Element id Specimen.container.description Short description Textual description of the container Definition Textual description of the container. Comments Note that FHIR strings SHALL NOT exceed 1MB in size Data type string Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: .desc
type		0..1	CodeableConceptBinding	Element id Specimen.container.type Short description Kind of container directly associated with specimen Definition The type of container associated with the specimen (e.g. slide, aliquot, etc.). Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding Type of specimen container. SpecimenContainerType (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD v2: SPM-27 rim: .code
capacity	I	0..1	SimpleQuantity	There are no (further) constraints on this element Element id Specimen.container.capacity Short description Container volume or size Definition The capacity (volume or other measure) the container may contain. Comments The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator. Data type SimpleQuantity Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` qty-3: If a code for the unit is present, the system SHALL also be present `code.empty() or system.exists()` sqty-1: The comparator is not used on a SimpleQuantity `comparator.empty()` Mappings rim: n/a v2: SN (see also Range) or CQ rim: PQ, IVL<PQ>, MO, CO, depending on the values v2: one of: SAC 16, SAC17 and SAC 20, or SAC 21 and SAC 20 rim: .quantity
specimenQuantity	I	0..1	SimpleQuantity	There are no (further) constraints on this element Element id Specimen.container.specimenQuantity Short description Quantity of specimen within container Definition The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type. Comments The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator. Data type SimpleQuantity Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` qty-3: If a code for the unit is present, the system SHALL also be present `code.empty() or system.exists()` sqty-1: The comparator is not used on a SimpleQuantity `comparator.empty()` Mappings rim: n/a v2: SN (see also Range) or CQ rim: PQ, IVL<PQ>, MO, CO, depending on the values v2: SAC-23 (value) SAC-24 (units rim: .playedRole[classCode=CONT].quantity
additive[x]		0..1		There are no (further) constraints on this element Element id Specimen.container.additive[x] Short description Additive associated with container Definition Introduced substance to preserve, maintain or enhance the specimen. Examples: Formalin, Citrate, EDTA. Binding Substance added to specimen container. v2.0371 (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: SAC-27 rim: .scopesRole[classCode=ADTV].player
additiveCodeableConcept			CodeableConcept	There are no (further) constraints on this element Data type CodeableConcept
additiveReference			Reference(Substance)	There are no (further) constraints on this element Data type Reference(Substance)
condition	Σ	0..*	CodeableConceptBinding	Element id Specimen.condition Short description State of the specimen Definition A mode or state of being that describes the nature of the specimen. Requirements The specimen condition can be used to assess its quality or appropriateness for a specific test. Comments 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. Data type CodeableConcept Binding Codes describing the state of the specimen. UKCoreSampleState (extensible) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD v2: SPM-24
note		0..*	Annotation	There are no (further) constraints on this element Element id Specimen.note Short description Comments Definition To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen). Comments For systems that do not have structured annotations, they can simply communicate a single annotation with no author or time. This element may need to be included in narrative because of the potential for modifying information. Annotations SHOULD NOT be used to communicate "modifying" information that could be computable. (This is a SHOULD because enforcing user behavior is nearly impossible). Data type Annotation Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: N/A rim: Act v2: OBX rim: .inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code="annotation"].value

FHIR	MDS	HL7v2
Specimen	Sample/Biopsy inc germline, Extracted Specimen	SPM
Specimen.subject	Fetus - Is sample for fetal or unregistered neonate, Raw specimen/biopsy - Family member provided by	PID segment attached to SPM
Specimen.collection.quantity	PLCM activity - Sample volume, Raw specimen/biopsy - Volume	SPM-12
Specimen.type	PLCM activity - Sample category code	SPM-4
Specimen.identifier.assigner	Raw specimen/biopsy - Id assigning authority ODS code (many), Raw specimen/biopsy - Is assigning authority a histopathology laboratory (many), Extracted specimen - Id assigning authority ODS code (many)	SPM-2.1.2
Specimen.identifier.value	Raw specimen/biopsy - Id (many), Extracted specimen - Id (many)	SPM-2
Specimen.container.identifier	Raw specimen/biopsy - Sample well identifier	SAC-3
Specimen.note	Raw specimen/biopsy - Location details (will use backported R5 container.location once released), Extracted specimen - Location details, Raw specimen/biopsy - Sample to follow reason, Raw specimen/biopsy - Additional specimen/biopsy information, Extracted specimen - Additional specimen information	SAC-15, NTE segment attached to ORC, OBX segments attached to SPM
Specimen.extension:sampleCategory	Raw specimen/biopsy - WGS specimen type category	SPM-5
Specimen.type	Raw specimen/biopsy - Type, Raw specimen/biopsy - Blood component, Extracted specimen - Type	SPM-4
Specimen.condition	Raw specimen/biopsy - State	SPM-24
Specimen.processing	Raw specimen/biopsy - Sample preparation (submitted to GLH)	Combination of SPM-6/SPM-24 or NTE segments if other processing
Specimen.collection.collectedDateTime	Raw specimen/biopsy - Obtained date	SPM-17
Specimen.receivedTime	Raw specimen/biopsy - Received date	SPM-18
Specimen.collection.extension:specimen-specialHandling.valueCoding.code	Raw specimen/biopsy - High risk reason, Raw specimen/biopsy - Option for products of conception	SPM-16.2, SPM-15
Specimen.collection.bodySite	Raw specimen/biopsy - Biopsy site	SPM-8/SPM-9
Specimen.status	Raw specimen/biopsy - Sample to follow	N/A implied through absence of SPM segment in test order
Specimen.condition	Extracted specimen - State	SPM-24
Specimen.processing.timeDateTime	Extracted specimen - Extracted date	OBR-7 attached to processing procedure in SAC-30

Propose a change to UKCore-Specimen

extension:sampleCategory

Allows the categorisation of a sample into either tumour or germline. Additional terms may be added upon review though the valueCodeableConcept.text field MAY be used as a free text representation if needed.

"extension": [
        {
            "url": "https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-SampleCategory",
            "valueCodeableConcept": {
                "coding": [
                    {
                        "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-SampleCategory",
                        "code": "germline",
                        "display": "Germline"
                    }
                ]
            }
        }
    ]

identifier

Multiple identifiers MAY be assigned to a sample as it travels between labs. Each lab SHOULD append their local identifier to the identifier array if needed, ensuring either the system or assigner, is able to disambiguate any identifiers from possibly overlapping numbers from other organizations. Assigner is preferred in this case (see identifier example on the

Command 'pagelink' could not render: Page not found.

page for further guidance)

Note: accessionIdentifier is unused by the Genomic Medicine Service to facilitate movement of samples across organizational boundaries.

"identifier":  [
        {
            "system": "https://fhir.add.nhs.uk/Id/specimenId",
            "value": "RGT03135"
        }
    ],

status

If a Specimen has not been collected, the status SHOULD be marked as 'unavailable'. If the quality of the Specimen is such that it cannot be processed, the status SHOULD be 'unsatisfactory' (this is equivalent to a QC status of Failed). If the Specimen passes quality control, the status SHOULD be set as 'available

"status": "unsatisfactory",

type

The sample type, SNOMED CT preferred. Used to differentiate between raw and extracted (DNA) samples.

ConceptMaps for the allowed values for primary (raw) and final (extracted DNA) samples upon release of MDSv1.04, to aid identification of whether a sample is primary vs. final

"type": {
        "coding":  [
            {
                "system": "http://snomed.info/sct",
                "code": "445295009",
                "display": "Blood specimen with EDTA"
            }
        ]
    },

subject

SHALL be provided. This SHOULD be a reference to the Patient resource or the identifier, NHS number, for the patient.

Samples collected from a Fetus SHOULD reference a Patient resource for the Fetus. This should then be linked to relevant maternal/paternal resources through the RelatedPerson resource. Further information can be found on the Fetus Management clinical scenario. It is not envisaged that samples would need to be linked to more than one person e.g. both fetus and mother, though this assumption will be tested within the Alpha phase of the Genomic Medicine Service.

"subject": {
        "reference": "Patient/Patient-MeirLieberman-Example",
        "identifier": {
            "system": "https://fhir.nhs.uk/Id/nhs-number",
            "value": "9449307873"
        }
    },

receivedTime

SHOULD be updated upon receipt at a destination lab

"receivedTime": "2023-09-18T18:30:00Z"

parent

If a sample has been split into multiple parts, such as DNA being extracted from a primary sample, each SHOULD be represented using an additional Specimen resource, referencing the parent sample through the parent element.

The central Order Management broker will only create Tasks for Specimen resources which do not have a parent element, i.e. primary samples. If required, clients can create Tasks for processing of derivative samples manually.

"parent": [
        {
            "reference": "Specimen/Specimen-BloodEDTA-Example"
        }
    ],

request

SHALL be provided. This SHOULD be a reference to the request which initiated collection of the sample. SHALL NOT be updated if the sample is used for another test e.g. for re-analysis. In the case that a Specimen needs to be processed as part of a new request, e.g. using a sample in storage, the ServiceRequest SHALL reference the pre-existing sample via ServiceRequest.specimen.

"request":  [
        {
            "reference": "ServiceRequest/ServiceRequest-NonWGSTestOrderForm-Example"
        }
    ]

collection

Additional information which can be collected about the circumstances under which as sample was collected, if relevant. This include extensions for specialHandling of the sample, e.g. due to high risk of infection, as well as an extension to bodySite to extend the coding to a BodyStructure reference, for more detailed collection of structural information e.g. where tumour morphology and topography need to be collected.

Where the collector is an Organization, or where the individual is not known, ODS codes MAY be used as identifiers in place of SDS-User-IDs. However, if referencing a resource, the PractitionerRole resource SHOULD still be referenced. In this case the PractitionerRole.identifier and PractitionerRole.practitioner reference would not be filled, leaving only the reference to an Organization from PractitionerRole.organization.

Note on quanitities

The Specimen.collection.quantity is the amount of the sample collected at collection time. This quantity does not change as the sample is processed.

The Specimen.container.specimenQuantity is the amount of sample remaining in a container, this is equivalent to GEL 1001 banked volume. This value should be updated as the specimen is used.

If a specimen is split, additional specimen resources SHOULD be created (referencing the parent specimen), with individual container.specimenQuantity values.

"collection": {
        "collector": {
            "identifier": {
                "system": "https://fhir.nhs.uk/Id/sds-user-id",
                "value": "999999"
            }
        },
        "collectedDateTime": "2022-07-11T09:00:00Z",
        "quantity": {
            "system": "http://unitsofmeasure.org",
            "code": "mL",
            "value": 2.5
        },
        "method": {
            "coding":  [
                {
                    "system": "http://snomed.info/sct",
                    "code": "129300006",
                    "display": "Puncture - action"
                }
            ]
        },
        "bodySite": {
            "coding":  [
                {
                    "system": "http://snomed.info/sct",
                    "code": "14975008",
                    "display": "Forearm structure (body structure)"
                }
            ]
        }
    },

processing

SHOULD be updated if processing occurs on the sample which affects later use, e.g. additives added

"processing": [
    {
      "description": "Acidify to pH < 3.0 with 6 N HCl.",
      "procedure": {
        "coding": [
          {
            "system": "http://terminology.hl7.org/CodeSystem/v2-0373",
            "code": "ACID"
          }
        ]
      },
      "additive": [
        {
          "display": "6 N HCl"
        }
      ],
      "timeDateTime": "2015-08-18T08:10:00Z"
    }
  ],

container

The UK Core STU3 version of Specimen backports the R5 changes to the container BackboneElement to support capturing of storage location for a sample (through `container.location`) and recursive capture of device identifiers (e.g. tube, well, rack, freezer through `container.device`).

Additional examples/guidance will be provided within this IG once use of the fields has been appropriately tested.

Sample tracking information SHOULD be added to Tasks acting on Specimen resources, e.g. Tasks marked SamplePreparation or SampleProcessing, on either the output or input elements. This information MAY include consignment number, destination, date sent etc.

"container":  [
        {
            "extension":  [
                {
                    "url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-Specimen.container.location",
                    "valueReference": {
                            "reference": "Location/Location-NTGLHFridge-Example"
                    }
                }
            ]
        }
    ]

condition

Used to record the condition of a specimen. Within Genomics, SHOULD be used to record the fixed/frozen state, using the UK Core bound ValueSet.

"condition":  [
        {
            "coding":  [
                {
                    "system": "https://fhir.hl7.org.uk/CodeSystem/UKCore-BiopsyState",
                    "code": "fresh-frozen",
                    "display": "Fresh Frozen"
                }
            ]
        }
    ]