minimal Common Oncology Data Elements (mCODE) Implementation Guide
3.0.0-ballot - 2023May United States of America flag

minimal Common Oncology Data Elements (mCODE) Implementation Guide, published by HL7 International Clinical Interoperability Council. This is not an authorized publication; it is the continuous build for version 3.0.0-ballot). This version is based on the current content of https://github.com/HL7/fhir-mCODE-ig/ and changes regularly. See the Directory of published versions

Resource Profile: HumanSpecimen - Detailed Descriptions

Active as of 2023-03-23 Maturity Level: 1

Definitions for the mcode-human-specimen resource profile.

Guidance on how to interpret the contents of this table can be found here.

1. Specimen
2. Specimen.identifier
NoteThis is a business identifier, not a resource identifier (see discussion)
Must Supporttrue
SlicingThis element introduces a set of slices on Specimen.identifier. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • pattern @ type
3. Specimen.identifier:bodyStructureIdentifier
SliceNamebodyStructureIdentifier
NoteThis is a business identifier, not a resource identifier (see discussion)
Control0..*
TypeIdentifier(BodyStructureIdentifier)
Must Supporttrue
4. Specimen.identifier:bodyStructureIdentifier.type
Control0..?
Must Supporttrue
5. Specimen.identifier:bodyStructureIdentifier.value
Control0..?
Must Supporttrue
6. Specimen.status
Must Supporttrue
7. Specimen.type
BindingThe codes SHALL be taken from Human Specimen Type Value Set; other codes may be used where these codes are not suitableFor example codes, see hl7VS-specimenType
Must Supporttrue
8. Specimen.subject
Definition

The patient associated with this specimen.

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.

TypeReference(CancerPatient|Patient|Group|Device|Substance|Location)
Must Supporttrue
9. Specimen.collection
Must Supporttrue
10. Specimen.collection.bodySite
Must Supporttrue
11. Specimen.collection.bodySite.extension
Control0..?
Must Supporttrue
12. Specimen.collection.bodySite.extension:locationQualifier
SliceNamelocationQualifier
Definition

General location qualifier (excluding laterality) for this bodySite

Control0..*
TypeExtension(BodyLocationQualifier) (Extension Type: CodeableConcept)
Must Supporttrue
13. Specimen.collection.bodySite.extension:lateralityQualifier
SliceNamelateralityQualifier
Definition

Laterality qualifier for this bodySite

Control0..1
TypeExtension(LateralityQualifier) (Extension Type: CodeableConcept)
Must Supporttrue

Guidance on how to interpret the contents of this table can be found here.

1. Specimen
Definition

A sample to be used for analysis.

Control0..*
Summaryfalse
InvariantsDefined on this element
dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources (: contained.contained.empty())
dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource (: contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty())
dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated (: contained.meta.versionId.empty() and contained.meta.lastUpdated.empty())
dom-5: If a resource is contained in another resource, it SHALL NOT have a security label (: contained.meta.security.empty())
dom-6: A resource should have narrative for robust management (: text.`div`.exists())
2. Specimen.implicitRules
Definition

A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.

Control0..1
Typeuri
Is Modifiertrue
Summarytrue
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.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
3. Specimen.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it 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).

Control0..*
TypeExtension
Is Modifiertrue
Summaryfalse
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.

Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
4. Specimen.identifier
Definition

Id for specimen.

NoteThis is a business identifier, not a resource identifier (see discussion)
Control0..*
TypeIdentifier
Must Supporttrue
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
SlicingThis element introduces a set of slices on Specimen.identifier. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • pattern @ type
5. Specimen.identifier:bodyStructureIdentifier
SliceNamebodyStructureIdentifier
Definition

An identifier - identifies some entity uniquely and unambiguously. Typically this is used for business identifiers.

Id for specimen.

NoteThis is a business identifier, not a resource identifier (see discussion)
Control0..* This element is affected by the following invariants: ele-1
TypeIdentifier(BodyStructureIdentifier)
Must Supporttrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
6. Specimen.identifier:bodyStructureIdentifier.use
Definition

The purpose of this identifier.

Control0..1
BindingThe codes SHALL be taken from IdentifierUse

Identifies the purpose for this identifier, if known .

Typecode
Is Modifiertrue
Summarytrue
Requirements

Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.

Comments

Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.

Pattern Valueusual
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
7. Specimen.identifier:bodyStructureIdentifier.type
Definition

A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.

Control0..1
BindingThe codes SHALL be taken from Identifier Type Codes; other codes may be used where these codes are not suitable

A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.

TypeCodeableConcept
Must Supporttrue
Summarytrue
Requirements

Allows users to make use of identifiers when the identifier system is not known.

Comments

This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. Where the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.

Pattern Value<valueCodeableConcept xmlns="http://hl7.org/fhir">
  <coding>
    <system value="http://hl7.org/fhir/resource-types"/>
    <code value="BodyStructure"/>
  </coding>
</valueCodeableConcept>
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
8. Specimen.identifier:bodyStructureIdentifier.value
Definition

The portion of the identifier typically relevant to the user and which is unique within the context of the system.

Control10..1
Typestring
Must Supporttrue
Summarytrue
Comments

If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the Rendered Value extension. Identifier.value is to be treated as case sensitive unless knowledge of the Identifier.system allows the processer to be confident that non-case-sensitive processing is safe.

Example
General:123456
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
9. Specimen.status
Definition

The availability of the specimen.

Control0..1
BindingThe codes SHALL be taken from SpecimenStatus

Codes providing the status/availability of a specimen.

Typecode
Is Modifiertrue
Must Supporttrue
Summarytrue
Comments

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

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
10. Specimen.type
Definition

The kind of material that forms the specimen.

Control0..1
BindingThe codes SHALL be taken from Human Specimen Type Value Set; other codes may be used where these codes are not suitableFor example codes, see hl7VS-specimenType
TypeCodeableConcept
Must Supporttrue
Summarytrue
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.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
11. Specimen.subject
Definition

The patient associated with this specimen.

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.

Control0..1
TypeReference(CancerPatient|Patient|Group|Device|Substance|Location)
Must Supporttrue
Summarytrue
Requirements

Must know the subject context.

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

Details concerning the specimen collection.

Control0..1
TypeBackboneElement
Must Supporttrue
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
13. Specimen.collection.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element 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).

Control0..*
TypeExtension
Is Modifiertrue
Summarytrue
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.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
14. Specimen.collection.bodySite
Definition

Anatomical location from which the specimen was collected (if subject is a patient). This is the target site. This element is not used for environmental specimens.

Control0..1
BindingFor example codes, see SNOMEDCTBodyStructures

Codes describing anatomical locations. May include laterality.

TypeCodeableConcept
Must Supporttrue
Summaryfalse
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.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
15. Specimen.collection.bodySite.extension
Definition

An Extension

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.

Control0..*
TypeExtension
Must Supporttrue
Summaryfalse
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
SlicingThis element introduces a set of slices on Specimen.collection.bodySite.extension. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • value @ url
16. Specimen.collection.bodySite.extension:locationQualifier
SliceNamelocationQualifier
Definition

General location qualifier (excluding laterality) for this bodySite

Control0..*
TypeExtension(BodyLocationQualifier) (Extension Type: CodeableConcept)
Must Supporttrue
Summaryfalse
InvariantsDefined on this element
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())
17. Specimen.collection.bodySite.extension:lateralityQualifier
SliceNamelateralityQualifier
Definition

Laterality qualifier for this bodySite

Control0..1
TypeExtension(LateralityQualifier) (Extension Type: CodeableConcept)
Must Supporttrue
Summaryfalse
InvariantsDefined on this element
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())

Guidance on how to interpret the contents of this table can be found here.

1. Specimen
Definition

A sample to be used for analysis.

Control0..*
Summaryfalse
2. Specimen.id
Definition

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

Control0..1
Typeid
Summarytrue
Comments

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

3. Specimen.meta
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.

Control0..1
TypeMeta
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
4. Specimen.implicitRules
Definition

A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.

Control0..1
Typeuri
Is Modifiertrue
Summarytrue
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.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
5. Specimen.language
Definition

The base language in which the resource is written.

Control0..1
BindingThe codes SHOULD be taken from CommonLanguages A human language
Additional BindingsPurpose
AllLanguagesMax Binding
Typecode
Summaryfalse
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).

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
6. Specimen.text
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.

Control0..1
TypeNarrative
Summaryfalse
Alternate Namesnarrative, html, xhtml, display
Comments

Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
7. Specimen.contained
Definition

These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.

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

This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels.

8. Specimen.extension
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.

Control0..*
TypeExtension
Summaryfalse
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
9. Specimen.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it 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).

Control0..*
TypeExtension
Is Modifiertrue
Summaryfalse
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.

Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
10. Specimen.identifier
Definition

Id for specimen.

NoteThis is a business identifier, not a resource identifier (see discussion)
Control0..*
TypeIdentifier
Must Supporttrue
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
SlicingThis element introduces a set of slices on Specimen.identifier. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • pattern @ type
11. Specimen.identifier:bodyStructureIdentifier
SliceNamebodyStructureIdentifier
Definition

An identifier - identifies some entity uniquely and unambiguously. Typically this is used for business identifiers.

NoteThis is a business identifier, not a resource identifier (see discussion)
Control0..* This element is affected by the following invariants: ele-1
TypeIdentifier(BodyStructureIdentifier)
Must Supporttrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
12. Specimen.identifier:bodyStructureIdentifier.id
Definition

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

Control0..1
Typestring
XML RepresentationIn the XML format, this property is represented as an attribute.
Summaryfalse
13. Specimen.identifier:bodyStructureIdentifier.extension
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.

Control0..*
TypeExtension
Summaryfalse
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
SlicingThis element introduces a set of slices on Specimen.identifier.extension. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • value @ url
14. Specimen.identifier:bodyStructureIdentifier.use
Definition

The purpose of this identifier.

Control0..1
BindingThe codes SHALL be taken from IdentifierUse Identifies the purpose for this identifier, if known
Typecode
Is Modifiertrue
Summarytrue
Requirements

Allows the appropriate identifier for a particular context of use to be selected from among a set of identifiers.

Comments

Applications can assume that an identifier is permanent unless it explicitly says that it is temporary.

Pattern Valueusual
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
15. Specimen.identifier:bodyStructureIdentifier.type
Definition

A coded type for the identifier that can be used to determine which identifier to use for a specific purpose.

Control0..1
BindingThe codes SHALL be taken from Identifier Type Codes; other codes may be used where these codes are not suitable A coded type for an identifier that can be used to determine which identifier to use for a specific purpose
TypeCodeableConcept
Must Supporttrue
Summarytrue
Requirements

Allows users to make use of identifiers when the identifier system is not known.

Comments

This element deals only with general categories of identifiers. It SHOULD not be used for codes that correspond 1..1 with the Identifier.system. Some identifiers may fall into multiple categories due to common usage. Where the system is known, a type is unnecessary because the type is always part of the system definition. However systems often need to handle identifiers where the system is not known. There is not a 1:1 relationship between type and system, since many different systems have the same type.

Pattern Value<valueCodeableConcept xmlns="http://hl7.org/fhir">
  <coding>
    <system value="http://hl7.org/fhir/resource-types"/>
    <code value="BodyStructure"/>
  </coding>
</valueCodeableConcept>
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
16. Specimen.identifier:bodyStructureIdentifier.system
Definition

Establishes the namespace for the value - that is, a URL that describes a set values that are unique.

Control0..1
Typeuri
Summarytrue
Requirements

There are many sets of identifiers. To perform matching of two identifiers, we need to know what set we're dealing with. The system identifies a particular set of unique identifiers.

Comments

Identifier.system is always case sensitive.

Example
General:http://www.acme.com/identifiers/patient
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
17. Specimen.identifier:bodyStructureIdentifier.value
Definition

The portion of the identifier typically relevant to the user and which is unique within the context of the system.

Control1..1
Typestring
Must Supporttrue
Summarytrue
Comments

If the value is a full URI, then the system SHALL be urn:ietf:rfc:3986. The value's primary purpose is computational mapping. As a result, it may be normalized for comparison purposes (e.g. removing non-significant whitespace, dashes, etc.) A value formatted for human display can be conveyed using the Rendered Value extension. Identifier.value is to be treated as case sensitive unless knowledge of the Identifier.system allows the processer to be confident that non-case-sensitive processing is safe.

Example
General:123456
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
18. Specimen.identifier:bodyStructureIdentifier.period
Definition

Time period during which identifier is/was valid for use.

Control0..1
TypePeriod
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
19. Specimen.identifier:bodyStructureIdentifier.assigner
Definition

Organization that issued/manages the identifier.

Control0..1
TypeReference(Organization)
Summarytrue
Comments

The Identifier.assigner may omit the .reference element and only contain a .display element reflecting the name or other textual information about the assigning organization.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
20. Specimen.accessionIdentifier
Definition

The identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab procedures.

Control0..1
TypeIdentifier
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
21. Specimen.status
Definition

The availability of the specimen.

Control0..1
BindingThe codes SHALL be taken from SpecimenStatus Codes providing the status/availability of a specimen
Typecode
Is Modifiertrue
Must Supporttrue
Summarytrue
Comments

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

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
22. Specimen.type
Definition

The kind of material that forms the specimen.

Control0..1
BindingThe codes SHALL be taken from Human Specimen Type Value Set; other codes may be used where these codes are not suitable
TypeCodeableConcept
Must Supporttrue
Summarytrue
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.

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

The patient associated with this specimen.

Control0..1
TypeReference(CancerPatient)
Must Supporttrue
Summarytrue
Requirements

Must know the subject context.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
24. Specimen.receivedTime
Definition

Time when specimen was received for processing or testing.

Control0..1
TypedateTime
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
25. Specimen.parent
Definition

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

Control0..*
TypeReference(Specimen)
Summaryfalse
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.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
26. Specimen.request
Definition

Details concerning a service request that required a specimen to be collected.

Control0..*
TypeReference(ServiceRequest)
Summaryfalse
Comments

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

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

Details concerning the specimen collection.

Control0..1
TypeBackboneElement
Must Supporttrue
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
28. Specimen.collection.id
Definition

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

Control0..1
Typestring
XML RepresentationIn the XML format, this property is represented as an attribute.
Summaryfalse
29. Specimen.collection.extension
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.

Control0..*
TypeExtension
Summaryfalse
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
30. Specimen.collection.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element 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).

Control0..*
TypeExtension
Is Modifiertrue
Summarytrue
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.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
31. Specimen.collection.collector
Definition

Person who collected the specimen.

Control0..1
TypeReference(Practitioner|PractitionerRole)
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
32. Specimen.collection.collected[x]
Definition

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

Control0..1
TypeChoice of: dateTime, Period
[x] NoteSee Choice of Data Types for further information about how to use [x]
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
33. Specimen.collection.duration
Definition

The span of time over which the collection of a specimen occurred.

Control0..1
TypeDuration
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
34. Specimen.collection.quantity
Definition

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

Control0..1
TypeQuantity(SimpleQuantity)
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
35. Specimen.collection.method
Definition

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

Control0..1
BindingFor example codes, see FHIRSpecimenCollectionMethod The technique that is used to perform the procedure
TypeCodeableConcept
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
36. Specimen.collection.bodySite
Definition

Anatomical location from which the specimen was collected (if subject is a patient). This is the target site. This element is not used for environmental specimens.

Control0..1
BindingFor example codes, see SNOMEDCTBodyStructures Codes describing anatomical locations. May include laterality
TypeCodeableConcept
Must Supporttrue
Summaryfalse
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.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
37. Specimen.collection.bodySite.id
Definition

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

Control0..1
Typestring
XML RepresentationIn the XML format, this property is represented as an attribute.
Summaryfalse
38. Specimen.collection.bodySite.extension
Definition

An Extension

Control0..*
TypeExtension
Must Supporttrue
Summaryfalse
InvariantsDefined on this element
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())
SlicingThis element introduces a set of slices on Specimen.collection.bodySite.extension. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • value @ url
39. Specimen.collection.bodySite.extension:locationQualifier
SliceNamelocationQualifier
Definition

General location qualifier (excluding laterality) for this bodySite

Control0..*
TypeExtension(BodyLocationQualifier) (Extension Type: CodeableConcept)
Must Supporttrue
Summaryfalse
InvariantsDefined on this element
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())
40. Specimen.collection.bodySite.extension:lateralityQualifier
SliceNamelateralityQualifier
Definition

Laterality qualifier for this bodySite

Control0..1
TypeExtension(LateralityQualifier) (Extension Type: CodeableConcept)
Must Supporttrue
Summaryfalse
InvariantsDefined on this element
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())
41. Specimen.collection.bodySite.coding
Definition

A reference to a code defined by a terminology system.

Control0..*
TypeCoding
Summarytrue
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.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
42. Specimen.collection.bodySite.text
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.

Control0..1
Typestring
Summarytrue
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.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
43. Specimen.collection.fastingStatus[x]
Definition

Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection.

Control0..1
BindingThe codes SHALL be taken from hl7VS-relevantClincialInformation; other codes may be used where these codes are not suitable Codes describing the fasting status of the patient
TypeChoice of: CodeableConcept, Duration
[x] NoteSee Choice of Data Types for further information about how to use [x]
Summarytrue
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/‚Äčtime] in 2 hour Urine --12 hours fasting), or using a component observation such asObservation.component code` = LOINC 49541-6 (Fasting status - Reported).

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
44. Specimen.processing
Definition

Details concerning processing and processing steps for the specimen.

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

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

Control0..1
Typestring
XML RepresentationIn the XML format, this property is represented as an attribute.
Summaryfalse
46. Specimen.processing.extension
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.

Control0..*
TypeExtension
Summaryfalse
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
47. Specimen.processing.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element 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).

Control0..*
TypeExtension
Is Modifiertrue
Summarytrue
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.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
48. Specimen.processing.description
Definition

Textual description of procedure.

Control0..1
Typestring
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
49. Specimen.processing.procedure
Definition

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

Control0..1
BindingFor example codes, see SpecimenProcessingProcedure Type indicating the technique used to process the specimen
TypeCodeableConcept
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
50. Specimen.processing.additive
Definition

Material used in the processing step.

Control0..*
TypeReference(Substance)
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
51. Specimen.processing.time[x]
Definition

A record of the time or period when the specimen processing occurred. For example the time of sample fixation or the period of time the sample was in formalin.

Control0..1
TypeChoice of: dateTime, Period
[x] NoteSee Choice of Data Types for further information about how to use [x]
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
52. Specimen.container
Definition

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

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

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

Control0..1
Typestring
XML RepresentationIn the XML format, this property is represented as an attribute.
Summaryfalse
54. Specimen.container.extension
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.

Control0..*
TypeExtension
Summaryfalse
Alternate Namesextensions, user content
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
55. Specimen.container.modifierExtension
Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element 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).

Control0..*
TypeExtension
Is Modifiertrue
Summarytrue
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.

Alternate Namesextensions, user content, modifiers
Comments

There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone.

InvariantsDefined on this element
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())
56. Specimen.container.identifier
Definition

Id for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The container ID may differ from the specimen id in some circumstances.

NoteThis is a business identifier, not a resource identifier (see discussion)
Control0..*
TypeIdentifier
Summarytrue
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
57. Specimen.container.description
Definition

Textual description of the container.

Control0..1
Typestring
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
58. Specimen.container.type
Definition

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

Control0..1
BindingFor example codes, see SpecimenContainerType Type of specimen container
TypeCodeableConcept
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
59. Specimen.container.capacity
Definition

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

Control0..1
TypeQuantity(SimpleQuantity)
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
60. Specimen.container.specimenQuantity
Definition

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

Control0..1
TypeQuantity(SimpleQuantity)
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
61. Specimen.container.additive[x]
Definition

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

Control0..1
BindingFor example codes, see hl7VS-additivePreservative Substance added to specimen container
TypeChoice of: CodeableConcept, Reference(Substance)
[x] NoteSee Choice of Data Types for further information about how to use [x]
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
62. Specimen.condition
Definition

A mode or state of being that describes the nature of the specimen.

Control0..*
BindingThe codes SHALL be taken from hl7VS-specimenCondition; other codes may be used where these codes are not suitable Codes describing the state of the specimen
TypeCodeableConcept
Summarytrue
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.

InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
63. Specimen.note
Definition

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

Control0..*
TypeAnnotation
Summaryfalse
InvariantsDefined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))