minimal Common Oncology Data Elements (mCODE) Implementation Guide
2.1.0 - STU 2.1
minimal Common Oncology Data Elements (mCODE) Implementation Guide
2.1.0 - STU 2.1
This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v2.1.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions 
| Official URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-specimen | Version: 2.1.0 | |||
| Active as of 2023-03-21 | Computable Name: GenomicSpecimen | |||
A small sample of blood, hair, skin, amniotic fluid (the fluid that surrounds a fetus during pregnancy), or other tissue which is excised from a subject for the purposes of genomics testing or analysis.
The specimen SHOULD be referenced by GenomicsReport. Multiple specimens are possible in the case of a tumor normal test where the variants found in a tumor specimen are compared with the variants in a normal specimen.
Specimen resources associated with an in-scope patient with a Specimen.code in the value set GenomicSpecimenTypeVS MUST conform to this profile. Beyond this requirement, a producer of resources SHOULD ensure that any resource instance associated with an in-scope patient that would reasonably be expected to conform to this profile SHOULD be published in this form.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Specimen
| Path | Conformance | ValueSet |
| Specimen.type | extensible | GenomicSpecimenTypeVS |
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Specimen | 0..* | Specimen | Sample for analysis | |
  implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
 Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
  relatedCondition | S | 0..1 | Reference(Condition) | Cancer condition associated with this specimen. URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition |
  extension | 0..0 | |||
| url | 1..1 | uri | "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition" | |
  value[x] | 1..1 | Reference(Primary Cancer Condition Profile | Secondary Cancer Condition Profile) | Value of extension | |
 modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| status | ?!SΣ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. |
 type | SΣ | 1..1 | CodeableConcept | Kind of material that forms the specimen Binding: Genomic Specimen Type Value Set (extensible) |
| subject | SΣ | 0..1 | Reference(Cancer Patient Profile) | Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device |
 collection | S | 0..1 | BackboneElement | Collection details |
 modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| bodySite | S | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. |
| Slices for extension | S | 0..* | Extension | Extension Slice: Unordered, Open by value:url |
| locationQualifier | S | 0..* | CodeableConcept | Body Location Qualifier Extension URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier Binding: Body Location Qualifier Value Set (required) |
 lateralityQualifier | S | 0..1 | CodeableConcept | Laterality Qualifier Extension URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier Binding: Laterality Qualifier Value Set (required) |
| Documentation for this format | ||||
| Path | Conformance | ValueSet |
| Specimen.status | required | SpecimenStatus |
| Specimen.type | extensible | GenomicSpecimenTypeVS |
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructures |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Specimen | 0..* | Specimen | Sample for analysis | |||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| relatedCondition | S | 0..1 | Reference(Condition) | Cancer condition associated with this specimen. URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..0 | |||||||
| url | 1..1 | uri | "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition" | |||||
| value[x] | 1..1 | Reference(Primary Cancer Condition Profile | Secondary Cancer Condition Profile) | Value of extension | |||||
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier | Σ | 0..* | Identifier | External Identifier | ||||
| accessionIdentifier | Σ | 0..1 | Identifier | Identifier assigned by the lab | ||||
| status | ?!SΣ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. | ||||
| type | SΣ | 1..1 | CodeableConcept | Kind of material that forms the specimen Binding: Genomic Specimen Type Value Set (extensible) | ||||
| subject | SΣ | 0..1 | Reference(Cancer Patient Profile) | Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device | ||||
| receivedTime | Σ | 0..1 | dateTime | The time when specimen was received for processing | ||||
| parent | 0..* | Reference(Specimen) | Specimen from which this specimen originated | |||||
| request | 0..* | Reference(ServiceRequest) | Why the specimen was collected | |||||
| collection | S | 0..1 | BackboneElement | Collection details | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| collector | Σ | 0..1 | Reference(Practitioner | PractitionerRole) | Who collected the specimen | ||||
 collected[x] | Σ | 0..1 | Collection time | |||||
| collectedDateTime | dateTime | |||||||
| collectedPeriod | Period | |||||||
| duration | Σ | 0..1 | Duration | How long it took to collect specimen | ||||
| quantity | 0..1 | SimpleQuantity | The quantity of specimen collected | |||||
| method | 0..1 | CodeableConcept | Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure. | |||||
| bodySite | S | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | S | 0..* | Extension | Extension Slice: Unordered, Open by value:url | ||||
| locationQualifier | S | 0..* | CodeableConcept | Body Location Qualifier Extension URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier Binding: Body Location Qualifier Value Set (required) | ||||
| lateralityQualifier | S | 0..1 | CodeableConcept | Laterality Qualifier Extension URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier Binding: Laterality Qualifier Value Set (required) | ||||
| coding | Σ | 0..* | Coding | Code defined by a terminology system | ||||
| text | Σ | 0..1 | string | Plain text representation of the concept | ||||
| fastingStatus[x] | Σ | 0..1 | Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient. | |||||
| fastingStatusCodeableConcept | CodeableConcept | |||||||
| fastingStatusDuration | Duration | |||||||
| processing | 0..* | BackboneElement | Processing and processing step details | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| description | 0..1 | string | Textual description of procedure | |||||
| procedure | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen. | |||||
| additive | 0..* | Reference(Substance) | Material used in the processing step | |||||
| time[x] | 0..1 | Date and time of specimen processing | ||||||
| timeDateTime | dateTime | |||||||
| timePeriod | Period | |||||||
| container | 0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| identifier | Σ | 0..* | Identifier | Id for the container | ||||
| description | 0..1 | string | Textual description of the container | |||||
| type | 0..1 | CodeableConcept | Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container. | |||||
| capacity | 0..1 | SimpleQuantity | Container volume or size | |||||
| specimenQuantity | 0..1 | SimpleQuantity | Quantity of specimen within container | |||||
| additive[x] | 0..1 | Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container. | ||||||
| additiveCodeableConcept | CodeableConcept | |||||||
| additiveReference | Reference(Substance) | |||||||
| condition | Σ | 0..* | CodeableConcept | State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen. | ||||
| note | 0..* | Annotation | Comments | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet | ||||
| Specimen.language | preferred | CommonLanguages
| ||||
| Specimen.status | required | SpecimenStatus | ||||
| Specimen.type | extensible | GenomicSpecimenTypeVS | ||||
| Specimen.collection.method | example | FHIRSpecimenCollectionMethod | ||||
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructures | ||||
| Specimen.collection.fastingStatus[x] | extensible | Hl7VSRelevantClincialInformation | ||||
| Specimen.processing.procedure | example | SpecimenProcessingProcedure | ||||
| Specimen.container.type | example | SpecimenContainerType | ||||
| Specimen.container.additive[x] | example | Hl7VSAdditivePreservative | ||||
| Specimen.condition | extensible | Hl7VSSpecimenCondition |
This structure is derived from Specimen
Summary
Mandatory: 1 element
Must-Support: 9 elements
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Differential View
This structure is derived from Specimen
| Path | Conformance | ValueSet |
| Specimen.type | extensible | GenomicSpecimenTypeVS |
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Specimen | 0..* | Specimen | Sample for analysis | |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| relatedCondition | S | 0..1 | Reference(Condition) | Cancer condition associated with this specimen. URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition |
| extension | 0..0 | |||
| url | 1..1 | uri | "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition" | |
| value[x] | 1..1 | Reference(Primary Cancer Condition Profile | Secondary Cancer Condition Profile) | Value of extension | |
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| status | ?!SΣ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. |
| type | SΣ | 1..1 | CodeableConcept | Kind of material that forms the specimen Binding: Genomic Specimen Type Value Set (extensible) |
| subject | SΣ | 0..1 | Reference(Cancer Patient Profile) | Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device |
| collection | S | 0..1 | BackboneElement | Collection details |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| bodySite | S | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. |
| Slices for extension | S | 0..* | Extension | Extension Slice: Unordered, Open by value:url |
| locationQualifier | S | 0..* | CodeableConcept | Body Location Qualifier Extension URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier Binding: Body Location Qualifier Value Set (required) |
| lateralityQualifier | S | 0..1 | CodeableConcept | Laterality Qualifier Extension URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier Binding: Laterality Qualifier Value Set (required) |
| Documentation for this format | ||||
| Path | Conformance | ValueSet |
| Specimen.status | required | SpecimenStatus |
| Specimen.type | extensible | GenomicSpecimenTypeVS |
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructures |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Specimen | 0..* | Specimen | Sample for analysis | |||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| relatedCondition | S | 0..1 | Reference(Condition) | Cancer condition associated with this specimen. URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..0 | |||||||
| url | 1..1 | uri | "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-related-condition" | |||||
| value[x] | 1..1 | Reference(Primary Cancer Condition Profile | Secondary Cancer Condition Profile) | Value of extension | |||||
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier | Σ | 0..* | Identifier | External Identifier | ||||
| accessionIdentifier | Σ | 0..1 | Identifier | Identifier assigned by the lab | ||||
| status | ?!SΣ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. | ||||
| type | SΣ | 1..1 | CodeableConcept | Kind of material that forms the specimen Binding: Genomic Specimen Type Value Set (extensible) | ||||
| subject | SΣ | 0..1 | Reference(Cancer Patient Profile) | Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device | ||||
| receivedTime | Σ | 0..1 | dateTime | The time when specimen was received for processing | ||||
| parent | 0..* | Reference(Specimen) | Specimen from which this specimen originated | |||||
| request | 0..* | Reference(ServiceRequest) | Why the specimen was collected | |||||
| collection | S | 0..1 | BackboneElement | Collection details | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| collector | Σ | 0..1 | Reference(Practitioner | PractitionerRole) | Who collected the specimen | ||||
| collected[x] | Σ | 0..1 | Collection time | |||||
| collectedDateTime | dateTime | |||||||
| collectedPeriod | Period | |||||||
| duration | Σ | 0..1 | Duration | How long it took to collect specimen | ||||
| quantity | 0..1 | SimpleQuantity | The quantity of specimen collected | |||||
| method | 0..1 | CodeableConcept | Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure. | |||||
| bodySite | S | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | S | 0..* | Extension | Extension Slice: Unordered, Open by value:url | ||||
| locationQualifier | S | 0..* | CodeableConcept | Body Location Qualifier Extension URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier Binding: Body Location Qualifier Value Set (required) | ||||
| lateralityQualifier | S | 0..1 | CodeableConcept | Laterality Qualifier Extension URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier Binding: Laterality Qualifier Value Set (required) | ||||
| coding | Σ | 0..* | Coding | Code defined by a terminology system | ||||
| text | Σ | 0..1 | string | Plain text representation of the concept | ||||
| fastingStatus[x] | Σ | 0..1 | Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient. | |||||
| fastingStatusCodeableConcept | CodeableConcept | |||||||
| fastingStatusDuration | Duration | |||||||
| processing | 0..* | BackboneElement | Processing and processing step details | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| description | 0..1 | string | Textual description of procedure | |||||
| procedure | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen. | |||||
| additive | 0..* | Reference(Substance) | Material used in the processing step | |||||
| time[x] | 0..1 | Date and time of specimen processing | ||||||
| timeDateTime | dateTime | |||||||
| timePeriod | Period | |||||||
| container | 0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| identifier | Σ | 0..* | Identifier | Id for the container | ||||
| description | 0..1 | string | Textual description of the container | |||||
| type | 0..1 | CodeableConcept | Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container. | |||||
| capacity | 0..1 | SimpleQuantity | Container volume or size | |||||
| specimenQuantity | 0..1 | SimpleQuantity | Quantity of specimen within container | |||||
| additive[x] | 0..1 | Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container. | ||||||
| additiveCodeableConcept | CodeableConcept | |||||||
| additiveReference | Reference(Substance) | |||||||
| condition | Σ | 0..* | CodeableConcept | State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen. | ||||
| note | 0..* | Annotation | Comments | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet | ||||
| Specimen.language | preferred | CommonLanguages
| ||||
| Specimen.status | required | SpecimenStatus | ||||
| Specimen.type | extensible | GenomicSpecimenTypeVS | ||||
| Specimen.collection.method | example | FHIRSpecimenCollectionMethod | ||||
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructures | ||||
| Specimen.collection.fastingStatus[x] | extensible | Hl7VSRelevantClincialInformation | ||||
| Specimen.processing.procedure | example | SpecimenProcessingProcedure | ||||
| Specimen.container.type | example | SpecimenContainerType | ||||
| Specimen.container.additive[x] | example | Hl7VSAdditivePreservative | ||||
| Specimen.condition | extensible | Hl7VSSpecimenCondition |
This structure is derived from Specimen
Summary
Mandatory: 1 element
Must-Support: 9 elements
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Other representations of profile: CSV, Excel, Schematron
IG © 2022+ HL7 International Clinical Interoperability Council. Package hl7.fhir.us.mcode#2.1.0 based on FHIR 4.0.1. Generated 2023-03-21
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