Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Resource Profile: Genomic Implication ( Abstract )

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/implication Version: 3.0.1-SNAPSHOT
Active as of 2024-03-12 Computable Name: GenomicImplication

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.

Properties common to genomic implications expressed as computable discrete elements.

The content in this section may be significantly revised prior to the next ballot after initial use and feedback.

The Genomic Implication profile is an abstract profile for Therapeutic and Diagnostic implications. Implications are relevant information which are derived from the presence of a haplotype, genotype, variant or other observed genetic change. This portion of the implementation guide relies on the content in the General Genomic Reporting and Variant Reporting portions of this implementation guide.

This profile defines a common set of elements for other Implications:

  • Related Artifact (base extension) supports conveying references to citations, supporting documentation and other information relevant to the asserted implication
  • evidence-level (component) indicates the strength of the evidence behind the asserted implication

Here are some examples of how the evidence-level component can be used (NOTE - they would be used in the appropriate, use case specific profile):

  • Coded ACMG (see ACMG)
    {
      "valueCodeableConcept": {
        "coding": [{
          "system": "https://www.acmg.org",
          "code": "PS1",
        },
        {
          "system": "https://www.acmg.org",
          "code": "PM2"
        }
        ]
      }
    }
    			
  • Coded PGx (see PharmGKB)
    {
      "valueCodeableConcept": {
        "coding": [{
          "system": "https://www.pharmgkb.org/",
          "code": "Level 1A",
        }
        ]
      }
    }
    			
  • Coded Somatic (see MVLD)
    {
      "valueCodeableConcept": {
        "coding": [{
          "system": "https://www.clinicalgenome.org/mvld/",
          "code": "Tier1 LevelA",
        }
        ]
      }
    }
    			

Differentiating AND vs OR

There are several cases where it is necessary to differentiate 'AND' conditions (e.g. both drug X AND drug Y, in combination, are indicated in the presence of a variant) vs. 'OR' conditions (e.g., either drug X OR drug Y are indicated in the presence of a variant). This situation is not unique to genomic implications, and arises elsewhere within FHIR (e.g. FHIR Search) and outside of FHIR (e.g., ClinVar submission API condition set). To be consistent with other precedents:

Where Diagnostic and Therapeutic implications have fields with cardinality > 1, the inclusion of multiple values within a field SHALL indicate an 'AND' condition. An 'OR' condition SHALL be represented by multiple observation instances.

Implication fields affected by this guidance include:

Molecular consequences: derivedFrom, evidence-level, feature-consequence.

Therapeutic implications: derivedFrom, evidence-level, therapeutic-implication, phenotypic-treatment-context, medication-assessed, therapy-assessed.

Diagnostic implications: derivedFrom, evidence-level, predicted-phenotype, genomic-risk-assessment.

As an example, assume Variant X is pathogenic for Disease Y AND Disease Z in combination. This would be a single diagnostic implication, where predicted-phenotype is a list containing both Disease Y and Disease Z. If on the other hand, Variant X might be pathogenic for Disease Y alone, or Disease Z alone, this would be two diagnostic implications, one containing a predicted-phenotype of Disease Y, and the other containing a predicted-phenotype of Disease Z.

Usage:

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

This structure is derived from GenomicBase

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*GenomicBaseThis is an abstract profile. Child profiles: DiagnosticImplication, MolecularConsequence, TherapeuticImplication
Measurements and simple assertions
... workflow-relatedArtifact 0..*RelatedArtifactDocumentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... value[x] 0..0
... derivedFrom 1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... derivedFrom:genotype 0..*Reference(Genotype)Genotype the implication is derived from
... derivedFrom:haplotype 0..*Reference(Haplotype)Haplotype the implication is derived from
... derivedFrom:biomarker 0..*Reference(Molecular Biomarker)MolecularBiomarker the implication is derived from
... component 0..*BackboneElementComponent results
.... related-artifact 0..*RelatedArtifactRelated Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
... component:evidence-level 0..*BackboneElementLevel of Evidence
.... code 1..1CodeableConcept93044-6
Required Pattern: At least the following
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93044-6
.... value[x] 1..1CodeableConcept1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar


doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Observation.component:evidence-level.value[x]exampleEvidenceLevelExampleVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/evidence-level-example-vs
from this IG
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*GenomicBaseThis is an abstract profile. Child profiles: DiagnosticImplication, MolecularConsequence, TherapeuticImplication
Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... secondary-finding 0..1CodeableConceptSecondary 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..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category 2..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
.... category:geCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: GE
... code Σ1..1CodeableConceptType of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

... Slices for derivedFrom Σ1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
.... derivedFrom:variant Σ0..*Reference(Variant)Variant the implication is derived from
.... derivedFrom:genotype Σ0..*Reference(Genotype)Genotype the implication is derived from
.... derivedFrom:haplotype Σ0..*Reference(Haplotype)Haplotype the implication is derived from
.... derivedFrom:biomarker Σ0..*Reference(Molecular Biomarker)MolecularBiomarker the implication is derived from
... Slices for component Σ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... related-artifact 0..*RelatedArtifactRelated Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... component:conclusion-string Σ0..1BackboneElementClinical Conclusion
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
.... component:evidence-level Σ0..*BackboneElementLevel of Evidence
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93044-6
..... value[x] Σ1..1CodeableConcept1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar


doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:evidence-level.codeexamplePattern: LOINC code 93044-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:evidence-level.value[x]exampleEvidenceLevelExampleVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/evidence-level-example-vs
from this IG

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*GenomicBaseThis is an abstract profile. Child profiles: DiagnosticImplication, MolecularConsequence, TherapeuticImplication
Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by pattern:url
.... secondary-finding 0..1CodeableConceptSecondary 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..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
.... workflow-relatedArtifact 0..*RelatedArtifactDocumentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study)Part of referenced event
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category 2..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... category:geCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: GE
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
... code Σ1..1CodeableConceptType of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

... subject Σ0..1Reference(Patient | Group | Device | Location)Who and/or what the observation is about
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] Σ0..1Clinically relevant time/time-period for observation
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... dataAbsentReason C0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note 0..*CodedAnnotationComments about the Observation that also contain a coded type
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method 0..1CodeableConceptHow it was done
Binding: ObservationMethods (example): Methods for simple observations.

... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange C0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low C0..1SimpleQuantityLow Range, if relevant
.... high C0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... Slices for derivedFrom Σ1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
.... derivedFrom:variant Σ0..*Reference(Variant)Variant the implication is derived from
.... derivedFrom:genotype Σ0..*Reference(Genotype)Genotype the implication is derived from
.... derivedFrom:haplotype Σ0..*Reference(Haplotype)Haplotype the implication is derived from
.... derivedFrom:biomarker Σ0..*Reference(Molecular Biomarker)MolecularBiomarker the implication is derived from
... Slices for component Σ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
..... related-artifact 0..*RelatedArtifactRelated Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

..... value[x] Σ0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, 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 Σ0..1BackboneElementClinical Conclusion
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1stringSummary conclusion (interpretation/impression)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, 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 Σ0..*BackboneElementLevel of Evidence
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionExtension
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93044-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConcept1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
from the FHIR Standard
Observation.methodexampleObservationMethods
http://hl7.org/fhir/ValueSet/observation-methods
from the FHIR Standard
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
http://hl7.org/fhir/ValueSet/referencerange-meaning
from the FHIR Standard
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
http://hl7.org/fhir/ValueSet/referencerange-appliesto
from the FHIR Standard
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:conclusion-string.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:evidence-level.codeexamplePattern: LOINC code 93044-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:evidence-level.value[x]exampleEvidenceLevelExampleVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/evidence-level-example-vs
from this IG
Observation.component:evidence-level.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:evidence-level.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-3errorObservation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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()

Differential View

This structure is derived from GenomicBase

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*GenomicBaseThis is an abstract profile. Child profiles: DiagnosticImplication, MolecularConsequence, TherapeuticImplication
Measurements and simple assertions
... workflow-relatedArtifact 0..*RelatedArtifactDocumentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... value[x] 0..0
... derivedFrom 1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... derivedFrom:genotype 0..*Reference(Genotype)Genotype the implication is derived from
... derivedFrom:haplotype 0..*Reference(Haplotype)Haplotype the implication is derived from
... derivedFrom:biomarker 0..*Reference(Molecular Biomarker)MolecularBiomarker the implication is derived from
... component 0..*BackboneElementComponent results
.... related-artifact 0..*RelatedArtifactRelated Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
... component:evidence-level 0..*BackboneElementLevel of Evidence
.... code 1..1CodeableConcept93044-6
Required Pattern: At least the following
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93044-6
.... value[x] 1..1CodeableConcept1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar


doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Observation.component:evidence-level.value[x]exampleEvidenceLevelExampleVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/evidence-level-example-vs
from this IG

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*GenomicBaseThis is an abstract profile. Child profiles: DiagnosticImplication, MolecularConsequence, TherapeuticImplication
Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... secondary-finding 0..1CodeableConceptSecondary 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..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category 2..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
.... category:geCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: GE
... code Σ1..1CodeableConceptType of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

... Slices for derivedFrom Σ1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
.... derivedFrom:variant Σ0..*Reference(Variant)Variant the implication is derived from
.... derivedFrom:genotype Σ0..*Reference(Genotype)Genotype the implication is derived from
.... derivedFrom:haplotype Σ0..*Reference(Haplotype)Haplotype the implication is derived from
.... derivedFrom:biomarker Σ0..*Reference(Molecular Biomarker)MolecularBiomarker the implication is derived from
... Slices for component Σ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... related-artifact 0..*RelatedArtifactRelated Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... component:conclusion-string Σ0..1BackboneElementClinical Conclusion
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
.... component:evidence-level Σ0..*BackboneElementLevel of Evidence
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93044-6
..... value[x] Σ1..1CodeableConcept1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar


doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:evidence-level.codeexamplePattern: LOINC code 93044-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:evidence-level.value[x]exampleEvidenceLevelExampleVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/evidence-level-example-vs
from this IG

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*GenomicBaseThis is an abstract profile. Child profiles: DiagnosticImplication, MolecularConsequence, TherapeuticImplication
Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by pattern:url
.... secondary-finding 0..1CodeableConceptSecondary 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..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
.... workflow-relatedArtifact 0..*RelatedArtifactDocumentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study)Part of referenced event
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category 2..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... category:geCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: GE
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
... code Σ1..1CodeableConceptType of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

... subject Σ0..1Reference(Patient | Group | Device | Location)Who and/or what the observation is about
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] Σ0..1Clinically relevant time/time-period for observation
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... dataAbsentReason C0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note 0..*CodedAnnotationComments about the Observation that also contain a coded type
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method 0..1CodeableConceptHow it was done
Binding: ObservationMethods (example): Methods for simple observations.

... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange C0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low C0..1SimpleQuantityLow Range, if relevant
.... high C0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... Slices for derivedFrom Σ1..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
.... derivedFrom:variant Σ0..*Reference(Variant)Variant the implication is derived from
.... derivedFrom:genotype Σ0..*Reference(Genotype)Genotype the implication is derived from
.... derivedFrom:haplotype Σ0..*Reference(Haplotype)Haplotype the implication is derived from
.... derivedFrom:biomarker Σ0..*Reference(Molecular Biomarker)MolecularBiomarker the implication is derived from
... Slices for component Σ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
..... related-artifact 0..*RelatedArtifactRelated Artifact for Observation component
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/related-artifact-component
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

..... value[x] Σ0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, 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 Σ0..1BackboneElementClinical Conclusion
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1stringSummary conclusion (interpretation/impression)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, 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 Σ0..*BackboneElementLevel of Evidence
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionExtension
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93044-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConcept1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
from the FHIR Standard
Observation.methodexampleObservationMethods
http://hl7.org/fhir/ValueSet/observation-methods
from the FHIR Standard
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
http://hl7.org/fhir/ValueSet/referencerange-meaning
from the FHIR Standard
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
http://hl7.org/fhir/ValueSet/referencerange-appliesto
from the FHIR Standard
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:conclusion-string.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:evidence-level.codeexamplePattern: LOINC code 93044-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:evidence-level.value[x]exampleEvidenceLevelExampleVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/evidence-level-example-vs
from this IG
Observation.component:evidence-level.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:evidence-level.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-3errorObservation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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()

 

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