HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE), v0.9.0

- Local Development build (v0.9.0). See the Directory of published versions

GenomicsReport

 

The official URL for this profile is:

http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-GenomicsReport

Genetic analysis summary report. The report may include one or more tests, with two distinct test types. The first type is a targeted mutation test, where a specific mutation on a specific gene is tested for. The result is either positive or negative for that mutation. The second type is a more general test for variants. This type of test returns the identity of variants found in a certain region of the genome.

The identity of laboratory tests is typically represented by a LOINC code. However, many genetic tests and panels do not have LOINC codes, although some might have an identifier in NCBI Genetic Testing Registry (GTR), a central location for voluntary submission of genetic test information by providers. To identify the diagnostic report, the name of the report must be in the text sub-field of the code structure. If there is a coded identifier from GTR, LOINC, or other source, then it should be included into the the code sub-field of the code structure. If there is no suitable code, the code can be omitted.

The performer of the test (organization or practitioner) should be included in the FHIR profile as the performer.actor.

FHIR implementation note: The category for this profile is set to GE (Genetics), a code from http://hl7.org/fhir/ValueSet/diagnostic-service-sections. This may be contrary to the Argonaut specification, which assigns the category LAB to any diagnostic report containing a laboratory result.

This profile builds on DiagnosticReport.

This profile was published on Wed Apr 17 00:00:00 EDT 2019 as a draft by The MITRE Corporation.

Summary

Mandatory: 0 element (3 nested mandatory elements)
Must-Support: 7 elements
Fixed Value: 2 elements

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

  • The element DiagnosticReport.category.coding is sliced based on the value of value:code
  • The element DiagnosticReport.result is sliced based on the value of profile:target.reference

Mapping Source

This structure represents the following mapping definition:

onco.core.GenomicsReport maps to DiagnosticReport:
  _Entry.EntryId maps to id
  Language maps to language
  Narrative maps to text
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Identifier maps to identifier
  Status maps to status
  Code maps to code
  Category maps to category
  PatientSubjectOfRecord maps to subject
  CareContext maps to encounter
  RelevantTime maps to effective[x]
  StatementDateTime maps to issued
  Participation.ParticipationType maps to performer.extension
  Participation.Participant maps to performer
  MedicationStatementRelatedRequest maps to request
  Specimen maps to specimen
  Observation maps to result (slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes)
  Media maps to image.link
  Conclusion maps to conclusion
  DiagnosisCode maps to codedDiagnosis
  OriginalReport maps to presentedForm

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport onco-core-GenomicsReport
... extension Slice: Unordered, Open by value:url
... shr-core-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-SpecimenType-extension
Binding: v2 Specimen Type (example)
.... valueCodeableConcept Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-RegionStudied-extension
... category 1..1
.... coding Slice: Unordered, Open by value:code
.... coding Σ1..1Coding
..... system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... code Fixed Value: GE
... code SBinding: https://www.ncbi.nlm.nih.gov/gtr (preferred)
... subject Reference(shr-core-Patient)
... encounter Reference(shr-core-Encounter)
... effective[x] S
... performer SReference(shr-core-Practitioner | shr-core-Organization)
... request Reference(shr-core-ProcedureRequest | shr-core-ReferralRequest)
... specimen Reference(shr-core-Specimen)
... result SReference(shr-core-Observation)Slice: Unordered, Open by profile:target.reference
... result S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound
... result S0..*Reference(onco-core-GeneticMutationTestResult)GeneticMutationTestResult
... image
.... link Reference(shr-core-Media)

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..*onco-core-GenomicsReport
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: http://tools.ietf.org/html/bcp47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
... shr-core-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-SpecimenType-extension
Binding: v2 Specimen Type (example)
.... id 0..1stringxml:id (or equivalent in JSON)
.... url 1..1uri"http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-SpecimenType-extension"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-RegionStudied-extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierId for external references to this report
... status ?!Σ1..1coderegistered | partial | final | corrected | appended | cancelled | entered-in-error
Binding: DiagnosticReportStatus (required)
... category Σ1..1CodeableConceptService category
Binding: Diagnostic Service Section Codes (example)
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
.... coding Σ1..1Coding
..... id 0..1idxml:id (or equivalent in JSON)
..... extension 0..*ExtensionAdditional Content defined by implementations
..... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: GE
..... display Σ0..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConceptName/Code for this diagnostic report
Binding: https://www.ncbi.nlm.nih.gov/gtr (preferred)
... subject Σ1..1Reference(shr-core-Patient)The subject of the report, usually, but not always, the patient
... encounter Σ0..1Reference(shr-core-Encounter)Health care event when test ordered
... effective[x] SΣ1..1dateTime, PeriodClinically Relevant time/time-period for report
... issued Σ1..1instantDateTime this version was released
... performer SΣ1..1Reference(shr-core-Practitioner | shr-core-Organization)Responsible Diagnostic Service
... request 0..*Reference(shr-core-ProcedureRequest | shr-core-ReferralRequest)What was requested
... specimen 0..*Reference(shr-core-Specimen)Specimens this report is based on
... result SReference(shr-core-Observation)Observations - simple, or complex nested groups
Slice: Unordered, Open by profile:target.reference
... result S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound
... result S0..*Reference(onco-core-GeneticMutationTestResult)GeneticMutationTestResult
... imagingStudy 0..*Reference(ImagingStudy | ImagingObjectSelection)Reference to full details of imaging associated with the diagnostic report
... image Σ0..*BackboneElementKey images associated with this report
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... comment 0..1stringComment about the image (e.g. explanation)
.... link Σ1..1Reference(shr-core-Media)Reference to the image source
... conclusion 0..1stringClinical Interpretation of test results
... codedDiagnosis 0..*CodeableConceptCodes for the conclusion
Binding: SNOMED CT Clinical Findings (example)
... presentedForm 0..*AttachmentEntire report as issued

doco Documentation for this format

Summary

Mandatory: 0 element (3 nested mandatory elements)
Must-Support: 7 elements
Fixed Value: 2 elements

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

  • The element DiagnosticReport.category.coding is sliced based on the value of value:code
  • The element DiagnosticReport.result is sliced based on the value of profile:target.reference

Mapping Source

This structure represents the following mapping definition:

onco.core.GenomicsReport maps to DiagnosticReport:
  _Entry.EntryId maps to id
  Language maps to language
  Narrative maps to text
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Identifier maps to identifier
  Status maps to status
  Code maps to code
  Category maps to category
  PatientSubjectOfRecord maps to subject
  CareContext maps to encounter
  RelevantTime maps to effective[x]
  StatementDateTime maps to issued
  Participation.ParticipationType maps to performer.extension
  Participation.Participant maps to performer
  MedicationStatementRelatedRequest maps to request
  Specimen maps to specimen
  Observation maps to result (slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes)
  Media maps to image.link
  Conclusion maps to conclusion
  DiagnosisCode maps to codedDiagnosis
  OriginalReport maps to presentedForm

Differential View

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport onco-core-GenomicsReport
... extension Slice: Unordered, Open by value:url
... shr-core-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-SpecimenType-extension
Binding: v2 Specimen Type (example)
.... valueCodeableConcept Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-RegionStudied-extension
... category 1..1
.... coding Slice: Unordered, Open by value:code
.... coding Σ1..1Coding
..... system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... code Fixed Value: GE
... code SBinding: https://www.ncbi.nlm.nih.gov/gtr (preferred)
... subject Reference(shr-core-Patient)
... encounter Reference(shr-core-Encounter)
... effective[x] S
... performer SReference(shr-core-Practitioner | shr-core-Organization)
... request Reference(shr-core-ProcedureRequest | shr-core-ReferralRequest)
... specimen Reference(shr-core-Specimen)
... result SReference(shr-core-Observation)Slice: Unordered, Open by profile:target.reference
... result S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound
... result S0..*Reference(onco-core-GeneticMutationTestResult)GeneticMutationTestResult
... image
.... link Reference(shr-core-Media)

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport 0..*onco-core-GenomicsReport
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: http://tools.ietf.org/html/bcp47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
... shr-core-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-SpecimenType-extension
Binding: v2 Specimen Type (example)
.... id 0..1stringxml:id (or equivalent in JSON)
.... url 1..1uri"http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-SpecimenType-extension"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-RegionStudied-extension
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierId for external references to this report
... status ?!Σ1..1coderegistered | partial | final | corrected | appended | cancelled | entered-in-error
Binding: DiagnosticReportStatus (required)
... category Σ1..1CodeableConceptService category
Binding: Diagnostic Service Section Codes (example)
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
.... coding Σ1..1Coding
..... id 0..1idxml:id (or equivalent in JSON)
..... extension 0..*ExtensionAdditional Content defined by implementations
..... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: GE
..... display Σ0..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConceptName/Code for this diagnostic report
Binding: https://www.ncbi.nlm.nih.gov/gtr (preferred)
... subject Σ1..1Reference(shr-core-Patient)The subject of the report, usually, but not always, the patient
... encounter Σ0..1Reference(shr-core-Encounter)Health care event when test ordered
... effective[x] SΣ1..1dateTime, PeriodClinically Relevant time/time-period for report
... issued Σ1..1instantDateTime this version was released
... performer SΣ1..1Reference(shr-core-Practitioner | shr-core-Organization)Responsible Diagnostic Service
... request 0..*Reference(shr-core-ProcedureRequest | shr-core-ReferralRequest)What was requested
... specimen 0..*Reference(shr-core-Specimen)Specimens this report is based on
... result SReference(shr-core-Observation)Observations - simple, or complex nested groups
Slice: Unordered, Open by profile:target.reference
... result S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound
... result S0..*Reference(onco-core-GeneticMutationTestResult)GeneticMutationTestResult
... imagingStudy 0..*Reference(ImagingStudy | ImagingObjectSelection)Reference to full details of imaging associated with the diagnostic report
... image Σ0..*BackboneElementKey images associated with this report
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
.... comment 0..1stringComment about the image (e.g. explanation)
.... link Σ1..1Reference(shr-core-Media)Reference to the image source
... conclusion 0..1stringClinical Interpretation of test results
... codedDiagnosis 0..*CodeableConceptCodes for the conclusion
Binding: SNOMED CT Clinical Findings (example)
... presentedForm 0..*AttachmentEntire report as issued

doco Documentation for this format

Downloads: StructureDefinition: (XML, JSON, TTL), Schema: XML Schematron

 

Terminology Bindings

PathConformanceValueSet
DiagnosticReport-GenomicsReport.codepreferredhttps://www.ncbi.nlm.nih.gov/gtr

 

Constraints

IdPathDetailsRequirements