Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build
Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build
Phenomics Exchange for Research and Diagnostics, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/phenomics-exchange-ig/ and changes regularly. See the Directory of published versions
| Official URL: http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-genomic-interpretation | Version: 0.1.0 | |||
| Draft as of 2021-10-18 | Computable Name: PhenopacketsGenomicInterpretation | |||
Copyright/Legal: Global Alliance for Genomics and Health |
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A profile of Genomics Reporting Genomics Report profile that represents relevant phenopackets building blocks.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from GenomicsReport
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  DiagnosticReport |
GenomicsReport | |||
  Slices for modifierExtension |
1..* | Extension | Extension Slice: Unordered, Open by value:url | |
   modifierExtension:interpretationStatus |
1..1 | InterpretationStatus | Phenopackets GenomicInterpretation.interpretation_status: status of the interpretation. | |
  status |
1..1 | code | registered | partial | preliminary | final + Required Pattern: unknown | |
| subject |
SC | 0..1 | Reference(Patient | Group | Device | Location) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check specimen element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present |
| specimen |
C | 0..1 | Reference(Specimen) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check subject element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present |
| result |
1..* | Reference(Observation) | Observations | |
  Slices for result |
Content/Rules for all slices | |||
 result:variant |
S | 1..1 | Reference(Phenopackets Variant) | Phenopackets GenomicInterpretation.call: Represents the interpretation, i.e., oneof {GeneDescriptor|VariantInterpretation}. |
| Documentation for this format | ||||
| Id | Grade | Path(s) | Details | Requirements |
| phenopackets-subject-or-specimen-id | error | DiagnosticReport.subject, DiagnosticReport.specimen | subject.id and/or specimen.id SHALL be present : |
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport |
0..* | GenomicsReport | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
 implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created |
| Slices for extension |
Content/Rules for all slices | |||
 genomics-artifact |
0..* | RelatedArtifact | Genomics Artifact URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact | |
| genomics-file |
0..* | Reference(Genomics DocumentReference) | Genomics File URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-file | |
| recommended-action |
0..* | Reference(Medication Recommendation | Followup Recommendation) | Recommended Action URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action | |
| genomics-risk-assessment |
0..* | Reference(RiskAssessment) | Genomics Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment | |
| coded-note |
0..* | CodedAnnotation | Comments about the report that also contain a coded type URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note | |
| supporting-info |
0..* | Reference(Resource) | Other information that may be relevant to this event. URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo | |
| Slices for modifierExtension |
?! | 1..* | Extension | Extension Slice: Unordered, Open by value:url |
| modifierExtension:interpretationStatus |
?! | 1..1 | InterpretationStatus | Phenopackets GenomicInterpretation.interpretation_status: status of the interpretation. |
| status |
?!Σ | 1..1 | code | registered | partial | preliminary | final + Binding: DiagnosticReportStatus (required): The status of the diagnostic report. Required Pattern: unknown |
| Slices for category |
Σ | 1..* | CodeableConcept | Service category Slice: Unordered, Open by pattern:coding Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
 category:Genetics |
Σ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
  coding |
Σ | 1..* | Coding | Code defined by a terminology system Required Pattern: At least the following |
 system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
 code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| code |
Σ | 1..1 | CodeableConcept | Name/Code for this diagnostic report Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports. |
 subject |
SΣC | 0..1 | Reference(Patient | Group | Device | Location) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check specimen element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present |
| specimen |
C | 0..1 | Reference(Specimen) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check subject element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present |
| Slices for result |
1..* | Reference(Observation) | Observations Slice: Unordered, Open by profile:resolve() | |
| result:overall |
0..1 | Reference(Overall Interpretation) | Assessment of overall results | |
| result:diagnostic-implication |
0..* | Reference(Diagnostic Implication) | Diagnostic Implication | |
| result:therapeutic-implication |
0..* | Reference(Therapeutic Implication) | Therapeutic Implication | |
| result:variant |
S | 1..1 | Reference(Phenopackets Variant) | Phenopackets GenomicInterpretation.call: Represents the interpretation,
i.e., oneof {GeneDescriptor|VariantInterpretation}. |
| result:sequence-phase-relation |
0..* | Reference(Sequence Phase Relationship) | Sequence Phase Relationship | |
| result:region-studied |
0..* | Reference(Region Studied) | Region Studied | |
| result:genotype |
0..* | Reference(Genotype) | Genotype | |
| result:haplotype |
0..* | Reference(Haplotype) | Haplotype | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code | URI |
| DiagnosticReport.status | required | Pattern: unknownhttp://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1from the FHIR Standard | |
| DiagnosticReport.category | example | DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sectionsfrom the FHIR Standard | |
| DiagnosticReport.category:Genetics | example | DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sectionsfrom the FHIR Standard | |
| DiagnosticReport.code | preferred | LOINCDiagnosticReportCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/report-codesfrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | DiagnosticReport | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | DiagnosticReport | 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 | error | DiagnosticReport | 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 | error | DiagnosticReport | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | DiagnosticReport | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| phenopackets-subject-or-specimen-id | error | DiagnosticReport.subject, DiagnosticReport.specimen | subject.id and/or specimen.id SHALL be present : |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| DiagnosticReport |
0..* | GenomicsReport | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |||||
| 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 | |||||
| genomics-artifact |
0..* | RelatedArtifact | Genomics Artifact URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact | |||||
| genomics-file |
0..* | Reference(Genomics DocumentReference) | Genomics File URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-file | |||||
| recommended-action |
0..* | Reference(Medication Recommendation | Followup Recommendation) | Recommended Action URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action | |||||
| genomics-risk-assessment |
0..* | Reference(RiskAssessment) | Genomics Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment | |||||
| coded-note |
0..* | CodedAnnotation | Comments about the report that also contain a coded type URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note | |||||
| supporting-info |
0..* | Reference(Resource) | Other information that may be relevant to this event. URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo | |||||
| Slices for modifierExtension |
?! | 1..* | Extension | Extension Slice: Unordered, Open by value:url | ||||
| modifierExtension:interpretationStatus |
?! | 1..1 | InterpretationStatus | Phenopackets GenomicInterpretation.interpretation_status: status of the interpretation. | ||||
| identifier |
Σ | 0..* | Identifier | Business identifier for report | ||||
| basedOn |
0..* | Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | What was requested | |||||
| status |
?!Σ | 1..1 | code | registered | partial | preliminary | final + Binding: DiagnosticReportStatus (required): The status of the diagnostic report. Required Pattern: unknown | ||||
| Slices for category |
Σ | 1..* | CodeableConcept | Service category Slice: Unordered, Open by pattern:coding Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. | ||||
| category:Genetics |
Σ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. | ||||
 id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
 coding |
Σ | 1..* | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
 id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |||||
| display |
0..1 | string | Representation defined by the system | |||||
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |||||
 text |
Σ | 0..1 | string | Plain text representation of the concept | ||||
| code |
Σ | 1..1 | CodeableConcept | Name/Code for this diagnostic report Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports. | ||||
| subject |
SΣC | 0..1 | Reference(Patient | Group | Device | Location) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check specimen element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present | ||||
| encounter |
Σ | 0..1 | Reference(Encounter) | Health care event when test ordered | ||||
| effective[x] |
Σ | 0..1 | dateTime | Clinically relevant time/time-period for report | ||||
| issued |
Σ | 0..1 | instant | DateTime this version was made | ||||
| performer |
Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Responsible Diagnostic Service | ||||
| resultsInterpreter |
Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Primary result interpreter | ||||
| specimen |
C | 0..1 | Reference(Specimen) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check subject element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present | ||||
| Slices for result |
1..* | Reference(Observation) | Observations Slice: Unordered, Open by profile:resolve() | |||||
| result:overall |
0..1 | Reference(Overall Interpretation) | Assessment of overall results | |||||
| result:diagnostic-implication |
0..* | Reference(Diagnostic Implication) | Diagnostic Implication | |||||
| result:therapeutic-implication |
0..* | Reference(Therapeutic Implication) | Therapeutic Implication | |||||
| result:variant |
S | 1..1 | Reference(Phenopackets Variant) | Phenopackets GenomicInterpretation.call: Represents the interpretation,
i.e., oneof {GeneDescriptor|VariantInterpretation}. | ||||
| result:sequence-phase-relation |
0..* | Reference(Sequence Phase Relationship) | Sequence Phase Relationship | |||||
| result:region-studied |
0..* | Reference(Region Studied) | Region Studied | |||||
| result:genotype |
0..* | Reference(Genotype) | Genotype | |||||
| result:haplotype |
0..* | Reference(Haplotype) | Haplotype | |||||
| imagingStudy |
0..* | Reference(ImagingStudy) | Reference to full details of imaging associated with the diagnostic report | |||||
| media |
Σ | 0..* | BackboneElement | Key images associated with this report | ||||
| 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 | ||||
| comment |
0..1 | string | Comment about the image (e.g. explanation) | |||||
| link |
Σ | 1..1 | Reference(Media) | Reference to the image source | ||||
| conclusion |
0..1 | string | Clinical conclusion (interpretation) of test results | |||||
| conclusionCode |
0..* | CodeableConcept | Codes for the clinical conclusion of test results Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report. | |||||
| presentedForm |
0..* | Attachment | Entire report as issued | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | URI | |||
| DiagnosticReport.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| DiagnosticReport.status | required | Pattern: unknownhttp://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1from the FHIR Standard | ||||
| DiagnosticReport.category | example | DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sectionsfrom the FHIR Standard | ||||
| DiagnosticReport.category:Genetics | example | DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sectionsfrom the FHIR Standard | ||||
| DiagnosticReport.code | preferred | LOINCDiagnosticReportCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/report-codesfrom the FHIR Standard | ||||
| DiagnosticReport.conclusionCode | example | SNOMEDCTClinicalFindingshttp://hl7.org/fhir/ValueSet/clinical-findingsfrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | DiagnosticReport | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | DiagnosticReport | 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 | error | DiagnosticReport | 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 | error | DiagnosticReport | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | DiagnosticReport | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| phenopackets-subject-or-specimen-id | error | DiagnosticReport.subject, DiagnosticReport.specimen | subject.id and/or specimen.id SHALL be present : |
This structure is derived from GenomicsReport
Differential View
This structure is derived from GenomicsReport
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport |
GenomicsReport | |||
| Slices for modifierExtension |
1..* | Extension | Extension Slice: Unordered, Open by value:url | |
| modifierExtension:interpretationStatus |
1..1 | InterpretationStatus | Phenopackets GenomicInterpretation.interpretation_status: status of the interpretation. | |
| status |
1..1 | code | registered | partial | preliminary | final + Required Pattern: unknown | |
| subject |
SC | 0..1 | Reference(Patient | Group | Device | Location) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check specimen element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present |
| specimen |
C | 0..1 | Reference(Specimen) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check subject element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present |
| result |
1..* | Reference(Observation) | Observations | |
| Slices for result |
Content/Rules for all slices | |||
| result:variant |
S | 1..1 | Reference(Phenopackets Variant) | Phenopackets GenomicInterpretation.call: Represents the interpretation, i.e., oneof {GeneDescriptor|VariantInterpretation}. |
| Documentation for this format | ||||
| Id | Grade | Path(s) | Details | Requirements |
| phenopackets-subject-or-specimen-id | error | DiagnosticReport.subject, DiagnosticReport.specimen | subject.id and/or specimen.id SHALL be present : |
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport |
0..* | GenomicsReport | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
| implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created |
| Slices for extension |
Content/Rules for all slices | |||
| genomics-artifact |
0..* | RelatedArtifact | Genomics Artifact URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact | |
| genomics-file |
0..* | Reference(Genomics DocumentReference) | Genomics File URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-file | |
| recommended-action |
0..* | Reference(Medication Recommendation | Followup Recommendation) | Recommended Action URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action | |
| genomics-risk-assessment |
0..* | Reference(RiskAssessment) | Genomics Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment | |
| coded-note |
0..* | CodedAnnotation | Comments about the report that also contain a coded type URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note | |
| supporting-info |
0..* | Reference(Resource) | Other information that may be relevant to this event. URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo | |
| Slices for modifierExtension |
?! | 1..* | Extension | Extension Slice: Unordered, Open by value:url |
| modifierExtension:interpretationStatus |
?! | 1..1 | InterpretationStatus | Phenopackets GenomicInterpretation.interpretation_status: status of the interpretation. |
| status |
?!Σ | 1..1 | code | registered | partial | preliminary | final + Binding: DiagnosticReportStatus (required): The status of the diagnostic report. Required Pattern: unknown |
| Slices for category |
Σ | 1..* | CodeableConcept | Service category Slice: Unordered, Open by pattern:coding Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
| category:Genetics |
Σ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
| coding |
Σ | 1..* | Coding | Code defined by a terminology system Required Pattern: At least the following |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| code |
Σ | 1..1 | CodeableConcept | Name/Code for this diagnostic report Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports. |
| subject |
SΣC | 0..1 | Reference(Patient | Group | Device | Location) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check specimen element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present |
| specimen |
C | 0..1 | Reference(Specimen) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check subject element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present |
| Slices for result |
1..* | Reference(Observation) | Observations Slice: Unordered, Open by profile:resolve() | |
| result:overall |
0..1 | Reference(Overall Interpretation) | Assessment of overall results | |
| result:diagnostic-implication |
0..* | Reference(Diagnostic Implication) | Diagnostic Implication | |
| result:therapeutic-implication |
0..* | Reference(Therapeutic Implication) | Therapeutic Implication | |
| result:variant |
S | 1..1 | Reference(Phenopackets Variant) | Phenopackets GenomicInterpretation.call: Represents the interpretation,
i.e., oneof {GeneDescriptor|VariantInterpretation}. |
| result:sequence-phase-relation |
0..* | Reference(Sequence Phase Relationship) | Sequence Phase Relationship | |
| result:region-studied |
0..* | Reference(Region Studied) | Region Studied | |
| result:genotype |
0..* | Reference(Genotype) | Genotype | |
| result:haplotype |
0..* | Reference(Haplotype) | Haplotype | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code | URI |
| DiagnosticReport.status | required | Pattern: unknownhttp://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1from the FHIR Standard | |
| DiagnosticReport.category | example | DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sectionsfrom the FHIR Standard | |
| DiagnosticReport.category:Genetics | example | DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sectionsfrom the FHIR Standard | |
| DiagnosticReport.code | preferred | LOINCDiagnosticReportCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/report-codesfrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | DiagnosticReport | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | DiagnosticReport | 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 | error | DiagnosticReport | 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 | error | DiagnosticReport | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | DiagnosticReport | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| phenopackets-subject-or-specimen-id | error | DiagnosticReport.subject, DiagnosticReport.specimen | subject.id and/or specimen.id SHALL be present : |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| DiagnosticReport |
0..* | GenomicsReport | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |||||
| 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 | |||||
| genomics-artifact |
0..* | RelatedArtifact | Genomics Artifact URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact | |||||
| genomics-file |
0..* | Reference(Genomics DocumentReference) | Genomics File URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-file | |||||
| recommended-action |
0..* | Reference(Medication Recommendation | Followup Recommendation) | Recommended Action URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action | |||||
| genomics-risk-assessment |
0..* | Reference(RiskAssessment) | Genomics Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment | |||||
| coded-note |
0..* | CodedAnnotation | Comments about the report that also contain a coded type URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note | |||||
| supporting-info |
0..* | Reference(Resource) | Other information that may be relevant to this event. URL: http://hl7.org/fhir/StructureDefinition/workflow-supportingInfo | |||||
| Slices for modifierExtension |
?! | 1..* | Extension | Extension Slice: Unordered, Open by value:url | ||||
| modifierExtension:interpretationStatus |
?! | 1..1 | InterpretationStatus | Phenopackets GenomicInterpretation.interpretation_status: status of the interpretation. | ||||
| identifier |
Σ | 0..* | Identifier | Business identifier for report | ||||
| basedOn |
0..* | Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | What was requested | |||||
| status |
?!Σ | 1..1 | code | registered | partial | preliminary | final + Binding: DiagnosticReportStatus (required): The status of the diagnostic report. Required Pattern: unknown | ||||
| Slices for category |
Σ | 1..* | CodeableConcept | Service category Slice: Unordered, Open by pattern:coding Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. | ||||
| category:Genetics |
Σ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
Σ | 1..* | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |||||
| display |
0..1 | string | Representation defined by the system | |||||
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |||||
| text |
Σ | 0..1 | string | Plain text representation of the concept | ||||
| code |
Σ | 1..1 | CodeableConcept | Name/Code for this diagnostic report Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports. | ||||
| subject |
SΣC | 0..1 | Reference(Patient | Group | Device | Location) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check specimen element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present | ||||
| encounter |
Σ | 0..1 | Reference(Encounter) | Health care event when test ordered | ||||
| effective[x] |
Σ | 0..1 | dateTime | Clinically relevant time/time-period for report | ||||
| issued |
Σ | 0..1 | instant | DateTime this version was made | ||||
| performer |
Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Responsible Diagnostic Service | ||||
| resultsInterpreter |
Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Primary result interpreter | ||||
| specimen |
C | 0..1 | Reference(Specimen) | Phenopackets GenomicInterpretation.subject_or_biosample_id: The id of the patient
or biosample that is the subject being interpreted.
Check subject element. phenopackets-subject-or-specimen-id: subject.id and/or specimen.id SHALL be present | ||||
| Slices for result |
1..* | Reference(Observation) | Observations Slice: Unordered, Open by profile:resolve() | |||||
| result:overall |
0..1 | Reference(Overall Interpretation) | Assessment of overall results | |||||
| result:diagnostic-implication |
0..* | Reference(Diagnostic Implication) | Diagnostic Implication | |||||
| result:therapeutic-implication |
0..* | Reference(Therapeutic Implication) | Therapeutic Implication | |||||
| result:variant |
S | 1..1 | Reference(Phenopackets Variant) | Phenopackets GenomicInterpretation.call: Represents the interpretation,
i.e., oneof {GeneDescriptor|VariantInterpretation}. | ||||
| result:sequence-phase-relation |
0..* | Reference(Sequence Phase Relationship) | Sequence Phase Relationship | |||||
| result:region-studied |
0..* | Reference(Region Studied) | Region Studied | |||||
| result:genotype |
0..* | Reference(Genotype) | Genotype | |||||
| result:haplotype |
0..* | Reference(Haplotype) | Haplotype | |||||
| imagingStudy |
0..* | Reference(ImagingStudy) | Reference to full details of imaging associated with the diagnostic report | |||||
| media |
Σ | 0..* | BackboneElement | Key images associated with this report | ||||
| 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 | ||||
| comment |
0..1 | string | Comment about the image (e.g. explanation) | |||||
| link |
Σ | 1..1 | Reference(Media) | Reference to the image source | ||||
| conclusion |
0..1 | string | Clinical conclusion (interpretation) of test results | |||||
| conclusionCode |
0..* | CodeableConcept | Codes for the clinical conclusion of test results Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report. | |||||
| presentedForm |
0..* | Attachment | Entire report as issued | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | URI | |||
| DiagnosticReport.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| DiagnosticReport.status | required | Pattern: unknownhttp://hl7.org/fhir/ValueSet/diagnostic-report-status|4.0.1from the FHIR Standard | ||||
| DiagnosticReport.category | example | DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sectionsfrom the FHIR Standard | ||||
| DiagnosticReport.category:Genetics | example | DiagnosticServiceSectionCodeshttp://hl7.org/fhir/ValueSet/diagnostic-service-sectionsfrom the FHIR Standard | ||||
| DiagnosticReport.code | preferred | LOINCDiagnosticReportCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/report-codesfrom the FHIR Standard | ||||
| DiagnosticReport.conclusionCode | example | SNOMEDCTClinicalFindingshttp://hl7.org/fhir/ValueSet/clinical-findingsfrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | DiagnosticReport | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | DiagnosticReport | 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 | error | DiagnosticReport | 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 | error | DiagnosticReport | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | DiagnosticReport | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| phenopackets-subject-or-specimen-id | error | DiagnosticReport.subject, DiagnosticReport.specimen | subject.id and/or specimen.id SHALL be present : |
This structure is derived from GenomicsReport
Other representations of profile: CSV, Excel, Schematron
IG © 2021+ HL7 International / Clinical Interoperability Council. Package hl7.fhir.uv.phenomics-exchange#0.1.0 based on FHIR 4.0.1. Generated 2024-06-18
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