HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE), v0.9.1

HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE), v0.9.1 FHIR Profiles - Local Development build (v0.9.1). See the Directory of published versions

GenomicsReport

 

The official URL for this profile is:

http://mcodeinitiative.org/us/mcode/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 non-genomic 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.

Conformance note: To be conformant to US Core, the code attribute must be a LOINC code, if available. If there is no suitable code in LOINC, then a code from an alternative code system (such as GTR) can be used.

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

Conformance note: The category for this profile is set to GE (Genetics), a code from http://hl7.org/fhir/ValueSet/diagnostic-service-sections. This is contrary to the Argonaut and US Core specifications, which require the category 'LAB' in diagnostic reports containing laboratory results. This is assumed to be an oversight in the US Core and Argonaut specifications.

This profile builds on DiagnosticReport.

This profile was published on Wed Oct 23 00:00:00 EDT 2019 as a draft by The MITRE Corporation.

Summary

Mandatory: 0 element (1 nested mandatory element)
Must-Support: 7 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.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:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.extension
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier
  Status maps to status
  Code maps to code
  Category maps to category
  ObservationSubjectOfRecord maps to subject
  CareContext maps to encounter
  RelevantTime maps to effective[x]
  StatementDateTime maps to issued
  DiagnosticReportPerformer maps to performer
  ResultsInterpreter maps to extension
  Specimen maps to specimen
  Observation maps to result (slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes)
  MediaIncluded.CommentOrDescription maps to image.comment
  MediaIncluded.Media maps to image.link
  ConclusionText maps to conclusion
  ConclusionCode maps to codedDiagnosis
  PresentedForm maps to presentedForm

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport onco-core-GenomicsReport
... meta
.... extension Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SourceSystem-extension
... extension Slice: Unordered, Open by value:url
... obf-ResultsInterpreter-extension 0..1Reference(Practitioner | Organization)ResultsInterpreter
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ResultsInterpreter-extension
... obf-BasedOn-extension 0..*Reference(Basic | ReferralRequest | obf-ProcedureRequest | obf-MedicationRequest | obf-CarePlan)BasedOn
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-BasedOn-extension
... obf-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SpecimenType-extension
Binding: http://terminology.hl7.org/ValueSet/v2-0487 (example)
.... valueCodeableConcept Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-RegionStudied-extension
... category 1..1
... code SBinding: GeneticTestVS (extensible)
... subject Reference(obf-Patient)The subject of an observation
... effective[x] S
... performer S
... result S(Slice Definition)Slice: Unordered, Open by profile:target.reference
.... result:onco-core-GeneticVariantFound S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound: Records an alteration in the most common DNA nucleotide sequence
.... result:onco-core-GeneticVariantTested S0..*Reference(onco-core-GeneticVariantTested)GeneticVariantTested: A test for a specific mutation on a particular gene

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
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SourceSystem-extension
.... versionId Σ0..1idVersion specific identifier
.... lastUpdated Σ0..1instantWhen the resource version last changed
.... profile Σ0..*uriProfiles this resource claims to conform to
.... security Σ0..*CodingSecurity Labels applied to this resource
Binding: All Security Labels (extensible)
.... tag Σ0..*CodingTags applied to this resource
Binding: (unbound) (example)
... 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
... obf-ResultsInterpreter-extension 0..1Reference(Practitioner | Organization)ResultsInterpreter
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ResultsInterpreter-extension
... obf-BasedOn-extension 0..*Reference(Basic | ReferralRequest | obf-ProcedureRequest | obf-MedicationRequest | obf-CarePlan)BasedOn
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-BasedOn-extension
... obf-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SpecimenType-extension
Binding: http://terminology.hl7.org/ValueSet/v2-0487 (example)
.... id 0..1idxml:id (or equivalent in JSON)
.... url 1..1uri"http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SpecimenType-extension"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://mcodeinitiative.org/us/mcode/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)
... code SΣ1..1CodeableConceptName/Code for this diagnostic report
Binding: GeneticTestVS (extensible)
... subject Σ1..1Reference(obf-Patient)The subject of an observation
... encounter Σ0..1Reference(Encounter)Health care event when test ordered
... effective[x] SΣ1..1Clinically Relevant time/time-period for report
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
... issued Σ1..1instantDateTime this version was released
... performer SΣ1..1Reference(Practitioner | Organization)Responsible Diagnostic Service
... request 0..*Reference(DiagnosticOrder | ProcedureRequest | ReferralRequest)What was requested
... specimen 0..*Reference(Specimen)Specimens this report is based on
... result S0..*(Slice Definition)Observations - simple, or complex nested groups
Slice: Unordered, Open by profile:target.reference
.... result:onco-core-GeneticVariantFound S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound: Records an alteration in the most common DNA nucleotide sequence
.... result:onco-core-GeneticVariantTested S0..*Reference(onco-core-GeneticVariantTested)GeneticVariantTested: A test for a specific mutation on a particular gene
... 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(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 (1 nested mandatory element)
Must-Support: 7 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.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:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.extension
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier
  Status maps to status
  Code maps to code
  Category maps to category
  ObservationSubjectOfRecord maps to subject
  CareContext maps to encounter
  RelevantTime maps to effective[x]
  StatementDateTime maps to issued
  DiagnosticReportPerformer maps to performer
  ResultsInterpreter maps to extension
  Specimen maps to specimen
  Observation maps to result (slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes)
  MediaIncluded.CommentOrDescription maps to image.comment
  MediaIncluded.Media maps to image.link
  ConclusionText maps to conclusion
  ConclusionCode maps to codedDiagnosis
  PresentedForm maps to presentedForm

Differential View

NameFlagsCard.TypeDescription & Constraintsdoco
.. DiagnosticReport onco-core-GenomicsReport
... meta
.... extension Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SourceSystem-extension
... extension Slice: Unordered, Open by value:url
... obf-ResultsInterpreter-extension 0..1Reference(Practitioner | Organization)ResultsInterpreter
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ResultsInterpreter-extension
... obf-BasedOn-extension 0..*Reference(Basic | ReferralRequest | obf-ProcedureRequest | obf-MedicationRequest | obf-CarePlan)BasedOn
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-BasedOn-extension
... obf-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SpecimenType-extension
Binding: http://terminology.hl7.org/ValueSet/v2-0487 (example)
.... valueCodeableConcept Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-RegionStudied-extension
... category 1..1
... code SBinding: GeneticTestVS (extensible)
... subject Reference(obf-Patient)The subject of an observation
... effective[x] S
... performer S
... result S(Slice Definition)Slice: Unordered, Open by profile:target.reference
.... result:onco-core-GeneticVariantFound S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound: Records an alteration in the most common DNA nucleotide sequence
.... result:onco-core-GeneticVariantTested S0..*Reference(onco-core-GeneticVariantTested)GeneticVariantTested: A test for a specific mutation on a particular gene

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
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SourceSystem-extension
.... versionId Σ0..1idVersion specific identifier
.... lastUpdated Σ0..1instantWhen the resource version last changed
.... profile Σ0..*uriProfiles this resource claims to conform to
.... security Σ0..*CodingSecurity Labels applied to this resource
Binding: All Security Labels (extensible)
.... tag Σ0..*CodingTags applied to this resource
Binding: (unbound) (example)
... 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
... obf-ResultsInterpreter-extension 0..1Reference(Practitioner | Organization)ResultsInterpreter
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ResultsInterpreter-extension
... obf-BasedOn-extension 0..*Reference(Basic | ReferralRequest | obf-ProcedureRequest | obf-MedicationRequest | obf-CarePlan)BasedOn
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-BasedOn-extension
... obf-SpecimenType-extension S0..1CodeableConceptSpecimenType
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SpecimenType-extension
Binding: http://terminology.hl7.org/ValueSet/v2-0487 (example)
.... id 0..1idxml:id (or equivalent in JSON)
.... url 1..1uri"http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SpecimenType-extension"
.... valueCodeableConcept 1..1CodeableConceptValue of extension
Binding: GeneticSpecimenTypeVS (extensible)
... onco-core-RegionStudied-extension 0..*stringRegionStudied
URL: http://mcodeinitiative.org/us/mcode/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)
... code SΣ1..1CodeableConceptName/Code for this diagnostic report
Binding: GeneticTestVS (extensible)
... subject Σ1..1Reference(obf-Patient)The subject of an observation
... encounter Σ0..1Reference(Encounter)Health care event when test ordered
... effective[x] SΣ1..1Clinically Relevant time/time-period for report
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
... issued Σ1..1instantDateTime this version was released
... performer SΣ1..1Reference(Practitioner | Organization)Responsible Diagnostic Service
... request 0..*Reference(DiagnosticOrder | ProcedureRequest | ReferralRequest)What was requested
... specimen 0..*Reference(Specimen)Specimens this report is based on
... result S0..*(Slice Definition)Observations - simple, or complex nested groups
Slice: Unordered, Open by profile:target.reference
.... result:onco-core-GeneticVariantFound S0..*Reference(onco-core-GeneticVariantFound)GeneticVariantFound: Records an alteration in the most common DNA nucleotide sequence
.... result:onco-core-GeneticVariantTested S0..*Reference(onco-core-GeneticVariantTested)GeneticVariantTested: A test for a specific mutation on a particular gene
... 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(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.meta.securityextensibleAll Security Labels
DiagnosticReport.meta.tagexample
DiagnosticReport.languagerequiredhttp://tools.ietf.org/html/bcp47
DiagnosticReport.extension-specimentype.valueCodeableConceptextensibleGeneticSpecimenTypeVS
DiagnosticReport.statusrequiredDiagnosticReportStatus
DiagnosticReport.categoryexampleDiagnostic Service Section Codes
DiagnosticReport.codeextensibleGeneticTestVS
DiagnosticReport.codedDiagnosisexampleSNOMED CT Clinical Findings

 

Constraints

IdPathDetailsRequirements