Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication | Version: 3.0.0-ballot | |||
| Active as of 2023-12-18 | Computable Name: DiagnosticImplication | |||
Copyright/Legal: This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc. |
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Observation stating a linkage between one or more genotype/haplotype/variation Observations and evidence for or against a particular disease, condition, or cancer diagnosis.
The content in this section may be significantly revised prior to the next ballot after initial use and feedback.
This section provides guidance for genomic reporting of patient genetic implications regarding specific conditions (sometimes referred to as phenotypes). This portion of the implementation guide relies on the content in the General Genomic Reporting and Variant Reporting portions of this implementation guide.
At times, external terminology development organizations develop codes that don't fit neatly into a particular field in an HL7 specification. For implications, we have identified two codes lists that conflate clinical significance and level of evidence, which we recommend not being used. These include:
See Genomic Implication for guidance. Implication fields affected by this guidance include: derivedFrom, evidence-level, predicted-phenotype, genomic-risk-assessment.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from GenomicImplication
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Observation | 0..* | GenomicImplication | Diagnostic Implication | |
  genomic-risk-assessment | 0..* | Reference(RiskAssessment) | Genomic Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment | |
  code | 1..1 | CodeableConcept | diagnostic-implication Required Pattern: At least the following | |
   coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
 system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
 code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: diagnostic-implication | |
| component:predicted-phenotype | 0..* | BackboneElement | Predicted phenotype | |
 extension:related-artifact | 0..* | RelatedArtifactComponent | Related Artifact for Observation component | |
 code | 1..1 | CodeableConcept | 81259-4 Required Pattern: At least the following | |
 coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81259-4 | |
  value[x] | 1..1 | CodeableConcept | Phenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO Binding: (unbound) (example): Multiple bindings accepted | |
| component:mode-of-inheritance | 0..1 | BackboneElement | Mode of Inheritance | |
| extension:related-artifact | 0..* | RelatedArtifactComponent | Related Artifact for Observation component | |
| code | 1..1 | CodeableConcept | condition-inheritance Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: condition-inheritance | |
| value[x] | 1..1 | CodeableConcept | Autosomal dominant | Autosomal recessive | X-linked | ... (more) Binding: Condition Inheritance Patterns (preferred) | |
| component:clinical-significance | 0..1 | BackboneElement | Clinical significance | |
| extension:related-artifact | 0..* | RelatedArtifactComponent | Related Artifact for Observation component | |
| code | 1..1 | CodeableConcept | 53037-8 Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8 | |
| value[x] | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (extensible) | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet |
| Observation.component:predicted-phenotype.value[x] | example | |
| Observation.component:mode-of-inheritance.value[x] | preferred | ConditionInheritanceModeVS |
| Observation.component:clinical-significance.value[x] | extensible | LOINC LL4034-6 |
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | GenomicImplication | Diagnostic Implication |
 implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding. | |
| body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
| workflow-relatedArtifact | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact | |
| genomic-risk-assessment | 0..* | Reference(RiskAssessment) | Genomic Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment | |
 modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
 Slices for category | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
 category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
  coding | Σ | 1..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/observation-category | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
 category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding | Σ | 1..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 | diagnostic-implication Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: diagnostic-implication | |
| Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() |
 derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant the implication is derived from |
| derivedFrom:genotype | Σ | 0..* | Reference(Genotype) | Genotype the implication is derived from |
| derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype the implication is derived from |
 derivedFrom:biomarker | Σ | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from |
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code |
| component:All Slices | Content/Rules for all slices | |||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
| component:evidence-level | Σ | 0..* | BackboneElement | Level of Evidence |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93044-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar |
| component:predicted-phenotype | Σ | 0..* | BackboneElement | Predicted phenotype |
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 81259-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81259-4 | |
| value[x] | Σ | 1..1 | CodeableConcept | Phenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO Binding: (unbound) (example): Multiple bindings accepted |
| component:mode-of-inheritance | Σ | 0..1 | BackboneElement | Mode of Inheritance |
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | condition-inheritance Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: condition-inheritance | |
| value[x] | Σ | 1..1 | CodeableConcept | Autosomal dominant | Autosomal recessive | X-linked | ... (more) Binding: Condition Inheritance Patterns (preferred) |
| component:clinical-significance | Σ | 0..1 | BackboneElement | Clinical significance |
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8 | |
| value[x] | Σ | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (extensible) |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code |
| Observation.status | required | ObservationStatus |
| Observation.category | preferred | ObservationCategoryCodes |
| Observation.category:labCategory | preferred | ObservationCategoryCodes |
| Observation.category:geCategory | preferred | ObservationCategoryCodes |
| Observation.code | example | Pattern: diagnostic-implication |
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) |
| Observation.component:conclusion-string.code | example | Pattern: conclusion-string |
| Observation.component:evidence-level.code | example | Pattern: LOINC code 93044-6 |
| Observation.component:evidence-level.value[x] | example | EvidenceLevelExampleVS |
| Observation.component:predicted-phenotype.code | example | Pattern: LOINC code 81259-4 |
| Observation.component:predicted-phenotype.value[x] | example | |
| Observation.component:mode-of-inheritance.code | example | Pattern: condition-inheritance |
| Observation.component:mode-of-inheritance.value[x] | preferred | ConditionInheritanceModeVS |
| Observation.component:clinical-significance.code | example | Pattern: LOINC code 53037-8 |
| Observation.component:clinical-significance.value[x] | extensible | LOINC LL4034-6 |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Observation | 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 | Observation | 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 | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Observation | 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() | |
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
| obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | GenomicImplication | Diagnostic Implication | ||||
| 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 pattern:url | |||||
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding. | |||||
| body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
| workflow-relatedArtifact | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact | |||||
| genomic-risk-assessment | 0..* | Reference(RiskAssessment) | Genomic Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment | |||||
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
 basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) | Part of referenced event | ||||
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| Slices for category | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| 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..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/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| 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 | ||||
| category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| 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..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 | diagnostic-implication Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: diagnostic-implication | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| subject | Σ | 0..1 | Reference(Patient | Group | Device | Location) | Who and/or what the observation is about | ||||
| focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
 effective[x] | Σ | 0..1 | Clinically relevant time/time-period for observation | |||||
| effectiveDateTime | dateTime | |||||||
| effectivePeriod | Period | |||||||
| effectiveTiming | Timing | |||||||
| effectiveInstant | instant | |||||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note | 0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |||||
| bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |||||
| method | 0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen | 0..1 | Reference(Specimen) | Specimen used for this observation | |||||
| device | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
| referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation | ||||
| 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 | ||||
| low | C | 0..1 | SimpleQuantity | Low Range, if relevant | ||||
| high | C | 0..1 | SimpleQuantity | High Range, if relevant | ||||
| type | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
| appliesTo | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
| age | 0..1 | Range | Applicable age range, if relevant | |||||
| text | 0..1 | string | Text based reference range in an observation | |||||
| hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() | ||||
| derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant the implication is derived from | ||||
| derivedFrom:genotype | Σ | 0..* | Reference(Genotype) | Genotype the implication is derived from | ||||
| derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype the implication is derived from | ||||
| derivedFrom:biomarker | Σ | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from | ||||
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
| component:All Slices | Content/Rules for all slices | |||||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] | Σ | 0..1 | Actual component result | |||||
| valueQuantity | Quantity | |||||||
| valueCodeableConcept | CodeableConcept | |||||||
| valueString | string | |||||||
| valueBoolean | boolean | |||||||
| valueInteger | integer | |||||||
| valueRange | Range | |||||||
| valueRatio | Ratio | |||||||
| valueSampledData | SampledData | |||||||
| valueTime | time | |||||||
| valueDateTime | dateTime | |||||||
| valuePeriod | Period | |||||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion | ||||
| 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 | ||||
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:evidence-level | Σ | 0..* | BackboneElement | Level of Evidence | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93044-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:predicted-phenotype | Σ | 0..* | BackboneElement | Predicted phenotype | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 81259-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81259-4 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Phenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO Binding: (unbound) (example): Multiple bindings accepted | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:mode-of-inheritance | Σ | 0..1 | BackboneElement | Mode of Inheritance | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | condition-inheritance Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: condition-inheritance | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Autosomal dominant | Autosomal recessive | X-linked | ... (more) Binding: Condition Inheritance Patterns (preferred) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:clinical-significance | Σ | 0..1 | BackboneElement | Clinical significance | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | ||||
| Observation.language | preferred | CommonLanguages
| ||||
| Observation.status | required | ObservationStatus | ||||
| Observation.category | preferred | ObservationCategoryCodes | ||||
| Observation.category:labCategory | preferred | ObservationCategoryCodes | ||||
| Observation.category:geCategory | preferred | ObservationCategoryCodes | ||||
| Observation.code | example | Pattern: diagnostic-implication | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructures | ||||
| Observation.method | example | ObservationMethods | ||||
| Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodes | ||||
| Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodes | ||||
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) | ||||
| Observation.component.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:conclusion-string.code | example | Pattern: conclusion-string | ||||
| Observation.component:conclusion-string.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:conclusion-string.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:evidence-level.code | example | Pattern: LOINC code 93044-6 | ||||
| Observation.component:evidence-level.value[x] | example | EvidenceLevelExampleVS | ||||
| Observation.component:evidence-level.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:evidence-level.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:predicted-phenotype.code | example | Pattern: LOINC code 81259-4 | ||||
| Observation.component:predicted-phenotype.value[x] | example | |||||
| Observation.component:predicted-phenotype.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:predicted-phenotype.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:mode-of-inheritance.code | example | Pattern: condition-inheritance | ||||
| Observation.component:mode-of-inheritance.value[x] | preferred | ConditionInheritanceModeVS | ||||
| Observation.component:mode-of-inheritance.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:mode-of-inheritance.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:clinical-significance.code | example | Pattern: LOINC code 53037-8 | ||||
| Observation.component:clinical-significance.value[x] | extensible | LOINC LL4034-6 | ||||
| Observation.component:clinical-significance.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:clinical-significance.interpretation | extensible | ObservationInterpretationCodes |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Observation | 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 | Observation | 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 | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Observation | 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() | |
| obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text : low.exists() or high.exists() or text.exists() | |
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
| obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
This structure is derived from GenomicImplication
Differential View
This structure is derived from GenomicImplication
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | 0..* | GenomicImplication | Diagnostic Implication | |
| genomic-risk-assessment | 0..* | Reference(RiskAssessment) | Genomic Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment | |
| code | 1..1 | CodeableConcept | diagnostic-implication Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: diagnostic-implication | |
| component:predicted-phenotype | 0..* | BackboneElement | Predicted phenotype | |
| extension:related-artifact | 0..* | RelatedArtifactComponent | Related Artifact for Observation component | |
| code | 1..1 | CodeableConcept | 81259-4 Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81259-4 | |
| value[x] | 1..1 | CodeableConcept | Phenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO Binding: (unbound) (example): Multiple bindings accepted | |
| component:mode-of-inheritance | 0..1 | BackboneElement | Mode of Inheritance | |
| extension:related-artifact | 0..* | RelatedArtifactComponent | Related Artifact for Observation component | |
| code | 1..1 | CodeableConcept | condition-inheritance Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: condition-inheritance | |
| value[x] | 1..1 | CodeableConcept | Autosomal dominant | Autosomal recessive | X-linked | ... (more) Binding: Condition Inheritance Patterns (preferred) | |
| component:clinical-significance | 0..1 | BackboneElement | Clinical significance | |
| extension:related-artifact | 0..* | RelatedArtifactComponent | Related Artifact for Observation component | |
| code | 1..1 | CodeableConcept | 53037-8 Required Pattern: At least the following | |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8 | |
| value[x] | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (extensible) | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet |
| Observation.component:predicted-phenotype.value[x] | example | |
| Observation.component:mode-of-inheritance.value[x] | preferred | ConditionInheritanceModeVS |
| Observation.component:clinical-significance.value[x] | extensible | LOINC LL4034-6 |
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | GenomicImplication | Diagnostic Implication |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding. | |
| body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
| workflow-relatedArtifact | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact | |
| genomic-risk-assessment | 0..* | Reference(RiskAssessment) | Genomic Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment | |
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
| Slices for category | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding | Σ | 1..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/observation-category | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding | Σ | 1..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 | diagnostic-implication Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: diagnostic-implication | |
| Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() |
| derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant the implication is derived from |
| derivedFrom:genotype | Σ | 0..* | Reference(Genotype) | Genotype the implication is derived from |
| derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype the implication is derived from |
| derivedFrom:biomarker | Σ | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from |
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code |
| component:All Slices | Content/Rules for all slices | |||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
| component:evidence-level | Σ | 0..* | BackboneElement | Level of Evidence |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93044-6 | |
| value[x] | Σ | 1..1 | CodeableConcept | 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar |
| component:predicted-phenotype | Σ | 0..* | BackboneElement | Predicted phenotype |
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 81259-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81259-4 | |
| value[x] | Σ | 1..1 | CodeableConcept | Phenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO Binding: (unbound) (example): Multiple bindings accepted |
| component:mode-of-inheritance | Σ | 0..1 | BackboneElement | Mode of Inheritance |
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | condition-inheritance Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: condition-inheritance | |
| value[x] | Σ | 1..1 | CodeableConcept | Autosomal dominant | Autosomal recessive | X-linked | ... (more) Binding: Condition Inheritance Patterns (preferred) |
| component:clinical-significance | Σ | 0..1 | BackboneElement | Clinical significance |
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8 | |
| value[x] | Σ | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (extensible) |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code |
| Observation.status | required | ObservationStatus |
| Observation.category | preferred | ObservationCategoryCodes |
| Observation.category:labCategory | preferred | ObservationCategoryCodes |
| Observation.category:geCategory | preferred | ObservationCategoryCodes |
| Observation.code | example | Pattern: diagnostic-implication |
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) |
| Observation.component:conclusion-string.code | example | Pattern: conclusion-string |
| Observation.component:evidence-level.code | example | Pattern: LOINC code 93044-6 |
| Observation.component:evidence-level.value[x] | example | EvidenceLevelExampleVS |
| Observation.component:predicted-phenotype.code | example | Pattern: LOINC code 81259-4 |
| Observation.component:predicted-phenotype.value[x] | example | |
| Observation.component:mode-of-inheritance.code | example | Pattern: condition-inheritance |
| Observation.component:mode-of-inheritance.value[x] | preferred | ConditionInheritanceModeVS |
| Observation.component:clinical-significance.code | example | Pattern: LOINC code 53037-8 |
| Observation.component:clinical-significance.value[x] | extensible | LOINC LL4034-6 |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Observation | 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 | Observation | 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 | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Observation | 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() | |
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
| obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | GenomicImplication | Diagnostic Implication | ||||
| 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 pattern:url | |||||
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding. | |||||
| body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
| workflow-relatedArtifact | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact | |||||
| genomic-risk-assessment | 0..* | Reference(RiskAssessment) | Genomic Risk Assessment URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-risk-assessment | |||||
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
| basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) | Part of referenced event | ||||
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| Slices for category | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| 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..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/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| 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 | ||||
| category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| 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..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 | diagnostic-implication Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: diagnostic-implication | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| subject | Σ | 0..1 | Reference(Patient | Group | Device | Location) | Who and/or what the observation is about | ||||
| focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
| effective[x] | Σ | 0..1 | Clinically relevant time/time-period for observation | |||||
| effectiveDateTime | dateTime | |||||||
| effectivePeriod | Period | |||||||
| effectiveTiming | Timing | |||||||
| effectiveInstant | instant | |||||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note | 0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |||||
| bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |||||
| method | 0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen | 0..1 | Reference(Specimen) | Specimen used for this observation | |||||
| device | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
| referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation | ||||
| 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 | ||||
| low | C | 0..1 | SimpleQuantity | Low Range, if relevant | ||||
| high | C | 0..1 | SimpleQuantity | High Range, if relevant | ||||
| type | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
| appliesTo | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
| age | 0..1 | Range | Applicable age range, if relevant | |||||
| text | 0..1 | string | Text based reference range in an observation | |||||
| hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() | ||||
| derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant the implication is derived from | ||||
| derivedFrom:genotype | Σ | 0..* | Reference(Genotype) | Genotype the implication is derived from | ||||
| derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype the implication is derived from | ||||
| derivedFrom:biomarker | Σ | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from | ||||
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
| component:All Slices | Content/Rules for all slices | |||||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] | Σ | 0..1 | Actual component result | |||||
| valueQuantity | Quantity | |||||||
| valueCodeableConcept | CodeableConcept | |||||||
| valueString | string | |||||||
| valueBoolean | boolean | |||||||
| valueInteger | integer | |||||||
| valueRange | Range | |||||||
| valueRatio | Ratio | |||||||
| valueSampledData | SampledData | |||||||
| valueTime | time | |||||||
| valueDateTime | dateTime | |||||||
| valuePeriod | Period | |||||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion | ||||
| 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 | ||||
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:evidence-level | Σ | 0..* | BackboneElement | Level of Evidence | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93044-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:predicted-phenotype | Σ | 0..* | BackboneElement | Predicted phenotype | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 81259-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81259-4 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Phenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO Binding: (unbound) (example): Multiple bindings accepted | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:mode-of-inheritance | Σ | 0..1 | BackboneElement | Mode of Inheritance | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | condition-inheritance Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: condition-inheritance | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Autosomal dominant | Autosomal recessive | X-linked | ... (more) Binding: Condition Inheritance Patterns (preferred) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:clinical-significance | Σ | 0..1 | BackboneElement | Clinical significance | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| related-artifact | 0..* | RelatedArtifact | Related Artifact for Observation component URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| 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://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | ||||
| Observation.language | preferred | CommonLanguages
| ||||
| Observation.status | required | ObservationStatus | ||||
| Observation.category | preferred | ObservationCategoryCodes | ||||
| Observation.category:labCategory | preferred | ObservationCategoryCodes | ||||
| Observation.category:geCategory | preferred | ObservationCategoryCodes | ||||
| Observation.code | example | Pattern: diagnostic-implication | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructures | ||||
| Observation.method | example | ObservationMethods | ||||
| Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodes | ||||
| Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodes | ||||
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) | ||||
| Observation.component.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:conclusion-string.code | example | Pattern: conclusion-string | ||||
| Observation.component:conclusion-string.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:conclusion-string.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:evidence-level.code | example | Pattern: LOINC code 93044-6 | ||||
| Observation.component:evidence-level.value[x] | example | EvidenceLevelExampleVS | ||||
| Observation.component:evidence-level.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:evidence-level.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:predicted-phenotype.code | example | Pattern: LOINC code 81259-4 | ||||
| Observation.component:predicted-phenotype.value[x] | example | |||||
| Observation.component:predicted-phenotype.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:predicted-phenotype.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:mode-of-inheritance.code | example | Pattern: condition-inheritance | ||||
| Observation.component:mode-of-inheritance.value[x] | preferred | ConditionInheritanceModeVS | ||||
| Observation.component:mode-of-inheritance.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:mode-of-inheritance.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:clinical-significance.code | example | Pattern: LOINC code 53037-8 | ||||
| Observation.component:clinical-significance.value[x] | extensible | LOINC LL4034-6 | ||||
| Observation.component:clinical-significance.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:clinical-significance.interpretation | extensible | ObservationInterpretationCodes |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Observation | 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 | Observation | 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 | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Observation | 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() | |
| obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text : low.exists() or high.exists() or text.exists() | |
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
| obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
This structure is derived from GenomicImplication
Other representations of profile: CSV, Excel, Schematron
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
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