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

Definitions for onco-core-GenomicsReport.

1. DiagnosticReport
Definition

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.

Control0..*
Alternate NamesReport, Test, Result, Results, Labs, Laboratory
Comments

This is intended to capture a single report, and is not suitable for use in displaying summary information that covers multiple reports. For example, this resource has not been designed for laboratory cumulative reporting formats nor detailed structured reports for sequencing.

2. DiagnosticReport.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
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. Bundles always have an id, though it is usually a generated UUID.

3. DiagnosticReport.meta
Definition

The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content may not always be associated with version changes to the resource.

Control0..1
TypeMeta
4. DiagnosticReport.meta.id
Definition

unique id for the element within a resource (for internal references).

Control0..1
Typeid
5. DiagnosticReport.meta.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. In order 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.

Control0..*
TypeExtension
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.

SlicingThis element introduces a set of slices on DiagnosticReport.meta.extension. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • value @ url
6. sourcesystem
SliceNamesourcesystem
Definition

FHIR: This provides a minimal amount of Provenance information that can be used to track or differentiate the source of information in the resource. The source may identify another FHIR server, document, message, database, etc. FHIM: Identifies the computer system that created the medical record. This optional field may also be used to indicate that the medical record was originally created by a different organization from the one that is currently storing or utilizing the record in that the assigning authority of the Id could be set to that originating organization. This property is optional, as some systems will assume that all records that it contains originated in that system, however it is anticipated that it will become increasingly commonplace for records from multiple systems and organizations will be comingled in order to provide a complete picture of the patient's health record.

Control0..1
TypeExtension(SourceSystem) (Extension Type: uri)
7. DiagnosticReport.meta.versionId
Definition

The version specific identifier, as it appears in the version portion of the URL. This values changes when the resource is created, updated, or deleted.

Control0..1
Typeid
Comments

The server assigns this value, and ignores what the client specifies, except in the case that the server is imposing version integrity on updates/deletes.

8. DiagnosticReport.meta.lastUpdated
Definition

When the resource last changed - e.g. when the version changed.

Control0..1
Typeinstant
Comments

This value is always populated except when the resource is first being created. The server / resource manager sets this value; what a client provides is irrelevant.

9. DiagnosticReport.meta.profile
Definition

A list of profiles StructureDefinitions that this resource claims to conform to. The URL is a reference to StructureDefinition.url.

Control0..*
Typeuri
Comments

It is up to the server and/or other infrastructure of policy to determine whether/how these claims are verified and/or updated over time. The list of profile URLs is a set.

10. DiagnosticReport.meta.security
Definition

Security labels applied to this resource. These tags connect specific resources to the overall security policy and infrastructure.

Control0..*
BindingSecurity Labels from the Healthcare Privacy and Security Classification System.
The codes SHALL be taken from All Security Labels; other codes may be used where these codes are not suitable
TypeCoding
Comments

The security labels can be updated without changing the stated version of the resource The list of security labels is a set. Uniqueness is based the system/code, and version and display are ignored.

11. DiagnosticReport.meta.tag
Definition

Tags applied to this resource. Tags are intended to be used to identify and relate resources to process and workflow, and applications are not required to consider the tags when interpreting the meaning of a resource.

Control0..*
BindingCodes that represent various types of tags, commonly workflow-related; e.g. "Needs review by Dr. Jones"
TypeCoding
Comments

The tags can be updated without changing the stated version of the resource. The list of tags is a set. Uniqueness is based the system/code, and version and display are ignored.

12. DiagnosticReport.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.

Control0..1
Typeuri
Is Modifiertrue
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 as much as possible.

13. DiagnosticReport.language
Definition

The base language in which the resource is written.

Control0..1
BindingA human language.
The codes SHALL be taken from http://tools.ietf.org/html/bcp47
Typecode
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).

14. DiagnosticReport.text
Definition

A human-readable narrative that contains a summary of the resource, and may 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 This element is affected by the following invariants: dom-1
TypeNarrative
Alternate Namesnarrative, html, xhtml, display
Comments

Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative.

15. DiagnosticReport.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
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.

16. DiagnosticReport.extension
Definition

May be used to represent additional information that is not part of the basic definition of the resource. In order 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.

Control0..*
TypeExtension
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.

SlicingThis element introduces a set of slices on DiagnosticReport.extension. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • value @ url
17. resultsinterpreter
SliceNameresultsinterpreter
Definition

The practitioner or organization that is responsible for the report's conclusions and interpretations.

Control0..1
TypeExtension(ResultsInterpreter) (Extension Type: Reference(Practitioner | Organization))
18. basedon
SliceNamebasedon
Definition

The proposal, order, or plan that is partly or wholly fulfilled by this item.

Control0..*
TypeExtension(BasedOn) (Extension Type: Reference(Basic | ReferralRequest | ProcedureRequest | MedicationRequest | CarePlan))
19. specimentype
SliceNamespecimentype
Definition

The type of material the specimen contains or consists of.

Control0..1
TypeExtension(SpecimenType) (Extension Type: CodeableConcept)
Must Supporttrue
20. DiagnosticReport.extension-specimentype.id
Definition

unique id for the element within a resource (for internal references).

Control0..1
Typeid
21. DiagnosticReport.extension-specimentype.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. In order 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.

Control0..0
TypeExtension
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.

22. DiagnosticReport.extension-specimentype.url
Definition

Source of the definition for the extension code - a logical name or a URL.

Control1..1
Typeuri
Comments

The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition should be version specific. This will ideally be the URI for the Resource Profile defining the extension, with the code for the extension after a #.

Fixed Valuehttp://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SpecimenType-extension
23. DiagnosticReport.extension-specimentype.valueCodeableConcept
Definition

Value of extension - may be a resource or one of a constrained set of the data types (see Extensibility in the spec for list).

Control1..1
BindingThe codes SHALL be taken from GeneticSpecimenTypeVS; other codes may be used where these codes are not suitable
TypeCodeableConcept
24. regionstudied
SliceNameregionstudied
Definition

A description of the coverage of the genome that was tested for variants.

Control0..*
TypeExtension(RegionStudied) (Extension Type: string)
25. DiagnosticReport.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. Usually modifier elements provide negation or qualification. In order 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.

Control0..*
TypeExtension
Is Modifiertrue
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.

26. DiagnosticReport.identifier
Definition

The local ID assigned to the report by the order filler, usually by the Information System of the diagnostic service provider.

NoteThis is a business identifier, not a resource identifier (see discussion)
Control0..*
TypeIdentifier
Requirements

Need to know what identifier to use when making queries about this report from the source laboratory, and for linking to the report outside FHIR context.

Alternate NamesReportID
27. DiagnosticReport.status
Definition

The status of the diagnostic report as a whole.

Control1..1
BindingThe status of the diagnostic report as a whole.
The codes SHALL be taken from DiagnosticReportStatus
Typecode
Is Modifiertrue
Requirements

Diagnostic services routinely issue provisional/incomplete reports, and sometimes withdraw previously released reports.

Comments

This is labeled as "Is Modifier" because applications need to take appropriate action if a report is withdrawn.

28. DiagnosticReport.category
Definition

A code that classifies the clinical discipline, department or diagnostic service that created the report (e.g. cardiology, biochemistry, hematology, MRI). This is used for searching, sorting and display purposes.

Control1..1
BindingCodes for diagnostic service sections.
For example codes, see Diagnostic Service Section Codes
TypeCodeableConcept
Alternate NamesDepartment, Sub-department, service, discipline
Comments

The level of granularity is defined by the category concepts in the value set. More fine-grained filtering can be performed using the metadata and/or terminology hierarchy in DiagnosticReport.code.

29. DiagnosticReport.code
Definition

A code or name that describes this diagnostic report.

Control1..1
BindingThe codes SHALL be taken from GeneticTestVS; other codes may be used where these codes are not suitable
TypeCodeableConcept
Must Supporttrue
30. DiagnosticReport.subject
Definition

The subject of an observation.

Control1..1
TypeReference(Patient)
Requirements

SHALL know the subject context.

Alternate NamesPatient
31. DiagnosticReport.encounter
Definition

The link to the health care event (encounter) when the order was made.

Control0..1
TypeReference(Encounter)
32. DiagnosticReport.effectivex
Definition

The time or time-period the observed values are related to. When the subject of the report is a patient, this is usually either the time of the procedure or of specimen collection(s), but very often the source of the date/time is not known, only the date/time itself.

Control1..1
TypeChoice of: dateTime, Period
[x] NoteSee Choice of Data Types for further information about how to use [x]
Must Supporttrue
Requirements

Need to know where in the patient history to file/present this report.

Alternate NamesObservation time, Effective Time
Comments

If the diagnostic procedure was performed on the patient, this is the time it was performed. If there are specimens, the diagnostically relevant time can be derived from the specimen collection times, but the specimen information is not always available, and the exact relationship between the specimens and the diagnostically relevant time is not always automatic.

33. DiagnosticReport.issued
Definition

The date and time that this version of the report was released from the source diagnostic service.

Control1..1
Typeinstant
Requirements

Clinicians need to be able to check the date that the report was released.

Alternate NamesDate Created, Date published, Date Issued
Comments

May be different from the update time of the resource itself, because that is the status of the record (potentially a secondary copy), not the actual release time of the report.

34. DiagnosticReport.performer
Definition

The diagnostic service that is responsible for issuing the report.

Control1..1
TypeReference(Practitioner | Organization)
Must Supporttrue
Requirements

Need to know whom to contact if there are queries about the results. Also may need to track the source of reports for secondary data analysis.

Alternate NamesLaboratory, Service, Practitioner, Department, Company
Comments

This is not necessarily the source of the atomic data items. It is the entity that takes responsibility for the clinical report.

35. DiagnosticReport.request
Definition

Details concerning a test or procedure requested.

Control0..*
TypeReference(DiagnosticOrder | ProcedureRequest | ReferralRequest)
Requirements

Need to be able to track completion of requests based on reports issued and also to report what diagnostic tests were requested (not always the same as what is delivered).

Comments

Note: Usually there is one test request for each result, however in some circumstances multiple test requests may be represented using a single test result resource. Note that there are also cases where one request leads to multiple reports.

36. DiagnosticReport.specimen
Definition

Details about the specimens on which this diagnostic report is based.

Control0..*
TypeReference(Specimen)
Requirements

Need to be able to report information about the collected specimens on which the report is based.

Comments

If the specimen is sufficiently specified with a code in the test result name, then this additional data may be redundant. If there are multiple specimens, these may be represented per Observation or group.

37. DiagnosticReport.result
Definition

Observations that are part of this diagnostic report. Observations can be simple name/value pairs (e.g. "atomic" results), or they can be grouping observations that include references to other members of the group (e.g. "panels").

Control0..*
TypeReference(Observation)
Must Supporttrue
Requirements

Need to support individual results, or report groups of results, where the result grouping is arbitrary, but meaningful. This structure is recursive - observations can contain observations.

Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
SlicingThis element introduces a set of slices on DiagnosticReport.result. The slices are unordered and Open, and can be differentiated using the following discriminators:
  • profile @ target.reference
38. onco-core-GeneticVariantFound
SliceNameonco-core-GeneticVariantFound
Definition

Records an alteration in the most common DNA nucleotide sequence. The term variant can be used to describe an alteration that may be benign, pathogenic, or of unknown significance. The term variant is increasingly being used in place of the term mutation. When reporting 'Genetic Variant Found', at least one element out of the following must be reported: 'Variant Found Identifier', 'Variant Found HGVS Name', and 'Variant Found Description'.

Control0..*
TypeReference(GeneticVariantFound)
Must Supporttrue
Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
39. onco-core-GeneticVariantTested
SliceNameonco-core-GeneticVariantTested
Definition

A test for a specific mutation on a particular gene. This profile is used to record whether a single discrete variant tested is present or absent (denoted as positive or negative respectively).

Control0..*
TypeReference(GeneticVariantTested)
Must Supporttrue
Alternate NamesData, Atomic Value, Result, Atomic result, Data, Test, Analyte, Battery, Organizer
40. DiagnosticReport.imagingStudy
Definition

One or more links to full details of any imaging performed during the diagnostic investigation. Typically, this is imaging performed by DICOM enabled modalities, but this is not required. A fully enabled PACS viewer can use this information to provide views of the source images.

Control0..*
TypeReference(ImagingStudy | ImagingObjectSelection)
Comments

ImagingStudy and ImageObjectStudy and the image element are somewhat overlapping - typically, the list of image references in the image element will also be found in one of the imaging study resources. However each caters to different types of displays for different types of purposes. Neither, either, or both may be provided.

41. DiagnosticReport.image
Definition

A list of key images associated with this report. The images are generally created during the diagnostic process, and may be directly of the patient, or of treated specimens (i.e. slides of interest).

Control0..*
TypeBackboneElement
Requirements

Many diagnostic services include images in the report as part of their service.

Alternate NamesDICOM, Slides, Scans
42. DiagnosticReport.image.id
Definition

unique id for the element within a resource (for internal references).

Control0..1
Typeid
43. DiagnosticReport.image.extension
Definition

May be used to represent additional information that is not part of the basic definition of the element. In order 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.

Control0..*
TypeExtension
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.

44. DiagnosticReport.image.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 that contains it. Usually modifier elements provide negation or qualification. In order 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.

Control0..*
TypeExtension
Is Modifiertrue
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.

45. DiagnosticReport.image.comment
Definition

A comment about the image. Typically, this is used to provide an explanation for why the image is included, or to draw the viewer's attention to important features.

Control0..1
Typestring
Requirements

The provider of the report should make a comment about each image included in the report.

Comments

The comment should be displayed with the image. It would be common for the report to include additional discussion of the image contents in other sections such as the conclusion.

46. DiagnosticReport.image.link
Definition

Reference to the image source.

Control1..1
TypeReference(Media)
47. DiagnosticReport.conclusion
Definition

Concise and clinically contextualized narrative interpretation of the diagnostic report.

Control0..1
Typestring
Requirements

Need to be able to provide a conclusion that is not lost among the basic result data.

Alternate NamesReport
Comments

Typically, a report is either [all data, no narrative (e.g. Core lab)] or [a mix of data with some concluding narrative (e.g. Structured Pathology Report, Bone Density)], or [all narrative (e.g. typical imaging report, histopathology)]. In all of these cases, the narrative goes in "text".

48. DiagnosticReport.codedDiagnosis
Definition

Codes for the conclusion.

Control0..*
BindingDiagnoses codes provided as adjuncts to the report.
For example codes, see SNOMED CT Clinical Findings
TypeCodeableConcept
49. DiagnosticReport.presentedForm
Definition

Rich text representation of the entire result as issued by the diagnostic service. Multiple formats are allowed but they SHALL be semantically equivalent.

Control0..*
TypeAttachment
Requirements

Gives Laboratory the ability to provide its own fully formatted report for clinical fidelity.

Comments

"application/pdf" is recommended as the most reliable and interoperable in this context.