Genomics Reporting Implementation Guide
2.0.0 - trial-use

This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions

Resource Profile: Diagnostic Implication

Defining URL:http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication
Version:2.0.0
Name:DiagnosticImplication
Title:Diagnostic Implication
Status:Active as of 2022-05-09 04:59:16+0000
Definition:

Observation stating a linkage between one or more genotype/haplotype/variation Observations and evidence for or against a particular disease, condition, or cancer diagnosis.

Publisher:HL7 Clinical Genomics Working Group
Copyright:

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.

Source Resource:XML / JSON / Turtle

The official URL for this profile is: 

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication

Contents:

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.

Non-conflated semantics

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:

  • LOINC list LL5356 https://loinc.org/LL5356-2/
  • Oncokb levels https://www.oncokb.org/levels#version=V2

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 is represented by multiple observation instances.

see Genomic Implication for additional information.

Implication fields affected by this guidance include:

derivedFrom, evidence-level, predicted-phenotype, functional-effect, genomics-risk-assessment.

Formal Views of Profile Content

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

This structure is derived from GenomicImplication

Summary

Mandatory: 0 element (4 nested mandatory elements)

Extensions

This structure refers to these extensions:

This structure is derived from GenomicImplication

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*GenomicImplicationDiagnostic Implication
... genomics-risk-assessment 0..*Reference(RiskAssessment)Genomics Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
... code 1..1CodeableConceptdiagnostic-implication
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: diagnostic-implication
... component:predicted-phenotype 0..*BackboneElementPredicted phenotype
.... code 1..1CodeableConcept81259-4
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: 81259-4
.... value[x] 1..1CodeableConceptPhenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO
Binding: (unbound) (example): Multiple bindings accepted

.... code 1..1CodeableConceptcondition-inheritance
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: condition-inheritance
.... value[x] 1..1CodeableConceptAutosomal dominant | Autosomal recessive | X-linked | ... (more)
Binding: Condition Inheritance Patterns (preferred)
... component:clinical-significance 0..1BackboneElementClinical significance
.... code 1..1CodeableConcept53037-8
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: 53037-8
.... value[x] 1..1CodeableConceptPathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (extensible)
... component:functional-effect 0..*BackboneElementFunctional Effect
.... code 1..1CodeableConceptfunctional-effect
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: functional-effect
.... value[x] 1..1CodeableConceptgain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect (extensible): Sequence Ontology terms under SO:0001536


doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*GenomicImplicationDiagnostic Implication
... id Σ0..1stringLogical 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 value:url
... observation-secondaryFinding 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.


... bodySite 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... genomics-artifact 0..1RelatedArtifactAttachments and/or related metadata or citations
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact
... genomics-risk-assessment 0..*Reference(RiskAssessment)Genomics Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
... 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)Part of referenced event
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category 1..*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
..... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ1..*CodingCode 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
... code Σ1..1CodeableConceptdiagnostic-implication
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: diagnostic-implication
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... 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 I0..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 I0..*BackboneElementProvides guide for interpretation
.... 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 I0..1SimpleQuantityLow Range, if relevant
.... high I0..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:$this.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
... 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
..... extension 0..*ExtensionAdditional content defined by implementations
..... 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 I0..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 I0..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..*ExtensionAdditional content defined by implementations
..... 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 I0..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:prognosis Σ0..1BackboneElementPrognosis
..... 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..1CodeableConceptprognostic-implication
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: prognostic-implication
....... 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..1CodeableConceptBetter outcome | poorer outcome
..... dataAbsentReason I0..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:predicted-phenotype Σ0..*BackboneElementPredicted phenotype
..... 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..1CodeableConcept81259-4
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: 81259-4
....... 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..1CodeableConceptPhenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO
Binding: (unbound) (example): Multiple bindings accepted

..... dataAbsentReason I0..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:mode-of-inheritance Σ0..1BackboneElementMode of Inheritance
..... 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..1CodeableConceptcondition-inheritance
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: condition-inheritance
....... 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..1CodeableConceptAutosomal dominant | Autosomal recessive | X-linked | ... (more)
Binding: Condition Inheritance Patterns (preferred)
..... dataAbsentReason I0..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:clinical-significance Σ0..1BackboneElementClinical significance
..... 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..1CodeableConcept53037-8
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: 53037-8
....... 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..1CodeableConceptPathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (extensible)
..... dataAbsentReason I0..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:functional-effect Σ0..*BackboneElementFunctional Effect
..... 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..1CodeableConceptfunctional-effect
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: functional-effect
....... 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..1CodeableConceptgain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect (extensible): Sequence Ontology terms under SO:0001536

..... dataAbsentReason I0..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

This structure is derived from GenomicImplication

Summary

Mandatory: 0 element (4 nested mandatory elements)

Extensions

This structure refers to these extensions:

Differential View

This structure is derived from GenomicImplication

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*GenomicImplicationDiagnostic Implication
... genomics-risk-assessment 0..*Reference(RiskAssessment)Genomics Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
... code 1..1CodeableConceptdiagnostic-implication
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: diagnostic-implication
... component:predicted-phenotype 0..*BackboneElementPredicted phenotype
.... code 1..1CodeableConcept81259-4
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: 81259-4
.... value[x] 1..1CodeableConceptPhenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO
Binding: (unbound) (example): Multiple bindings accepted

.... code 1..1CodeableConceptcondition-inheritance
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: condition-inheritance
.... value[x] 1..1CodeableConceptAutosomal dominant | Autosomal recessive | X-linked | ... (more)
Binding: Condition Inheritance Patterns (preferred)
... component:clinical-significance 0..1BackboneElementClinical significance
.... code 1..1CodeableConcept53037-8
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: 53037-8
.... value[x] 1..1CodeableConceptPathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (extensible)
... component:functional-effect 0..*BackboneElementFunctional Effect
.... code 1..1CodeableConceptfunctional-effect
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: functional-effect
.... value[x] 1..1CodeableConceptgain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect (extensible): Sequence Ontology terms under SO:0001536


doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*GenomicImplicationDiagnostic Implication
... id Σ0..1stringLogical 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 value:url
... observation-secondaryFinding 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.


... bodySite 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... genomics-artifact 0..1RelatedArtifactAttachments and/or related metadata or citations
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-artifact
... genomics-risk-assessment 0..*Reference(RiskAssessment)Genomics Risk Assessment
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
... 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)Part of referenced event
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category 1..*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
..... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ1..*CodingCode 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
... code Σ1..1CodeableConceptdiagnostic-implication
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: diagnostic-implication
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... 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 I0..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 I0..*BackboneElementProvides guide for interpretation
.... 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 I0..1SimpleQuantityLow Range, if relevant
.... high I0..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:$this.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
... 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
..... extension 0..*ExtensionAdditional content defined by implementations
..... 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 I0..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 I0..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..*ExtensionAdditional content defined by implementations
..... 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 I0..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:prognosis Σ0..1BackboneElementPrognosis
..... 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..1CodeableConceptprognostic-implication
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: prognostic-implication
....... 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..1CodeableConceptBetter outcome | poorer outcome
..... dataAbsentReason I0..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:predicted-phenotype Σ0..*BackboneElementPredicted phenotype
..... 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..1CodeableConcept81259-4
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: 81259-4
....... 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..1CodeableConceptPhenotype code, e.g. from SNOMED CT Clinical finding, ICD-10-CM chapters 1-18, or HPO
Binding: (unbound) (example): Multiple bindings accepted

..... dataAbsentReason I0..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:mode-of-inheritance Σ0..1BackboneElementMode of Inheritance
..... 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..1CodeableConceptcondition-inheritance
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: condition-inheritance
....... 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..1CodeableConceptAutosomal dominant | Autosomal recessive | X-linked | ... (more)
Binding: Condition Inheritance Patterns (preferred)
..... dataAbsentReason I0..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:clinical-significance Σ0..1BackboneElementClinical significance
..... 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..1CodeableConcept53037-8
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: 53037-8
....... 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..1CodeableConceptPathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (extensible)
..... dataAbsentReason I0..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:functional-effect Σ0..*BackboneElementFunctional Effect
..... 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..1CodeableConceptfunctional-effect
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: functional-effect
....... 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..1CodeableConceptgain of function | loss of function | loss of heterozygosity | decreased transcript level | increased transcipt level | dominant negative variant | ... (more)
Binding: Functional Effect (extensible): Sequence Ontology terms under SO:0001536

..... dataAbsentReason I0..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

 

Other representations of profile: CSV, Excel, Schematron

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Max Binding: AllLanguages
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.category:labCategorypreferredObservationCategoryCodes
Observation.codeexamplePattern: diagnostic-implication
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.interpretationextensibleObservationInterpretationCodes
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodexampleObservationMethods
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationextensibleObservationInterpretationCodes
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
Observation.component:conclusion-string.dataAbsentReasonextensibleDataAbsentReason
Observation.component:conclusion-string.interpretationextensibleObservationInterpretationCodes
Observation.component:evidence-level.codeexamplePattern: LOINC code 93044-6
Observation.component:evidence-level.value[x]exampleEvidenceLevelExampleVS
Observation.component:evidence-level.dataAbsentReasonextensibleDataAbsentReason
Observation.component:evidence-level.interpretationextensibleObservationInterpretationCodes
Observation.component:prognosis.codeexamplePattern: prognostic-implication
Observation.component:prognosis.dataAbsentReasonextensibleDataAbsentReason
Observation.component:prognosis.interpretationextensibleObservationInterpretationCodes
Observation.component:predicted-phenotype.codeexamplePattern: LOINC code 81259-4
Observation.component:predicted-phenotype.value[x]example
Observation.component:predicted-phenotype.dataAbsentReasonextensibleDataAbsentReason
Observation.component:predicted-phenotype.interpretationextensibleObservationInterpretationCodes
Observation.component:mode-of-inheritance.codeexamplePattern: condition-inheritance
Observation.component:mode-of-inheritance.value[x]preferredConditionInheritanceModeVS
Observation.component:mode-of-inheritance.dataAbsentReasonextensibleDataAbsentReason
Observation.component:mode-of-inheritance.interpretationextensibleObservationInterpretationCodes
Observation.component:clinical-significance.codeexamplePattern: LOINC code 53037-8
Observation.component:clinical-significance.value[x]extensibleLOINC LL4034-6
Observation.component:clinical-significance.dataAbsentReasonextensibleDataAbsentReason
Observation.component:clinical-significance.interpretationextensibleObservationInterpretationCodes
Observation.component:functional-effect.codeexamplePattern: functional-effect
Observation.component:functional-effect.value[x]extensibleFunctionalEffectVS
Observation.component:functional-effect.dataAbsentReasonextensibleDataAbsentReason
Observation.component:functional-effect.interpretationextensibleObservationInterpretationCodes

Constraints

IdGradePathDetailsRequirements
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()
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()
ele-1errorObservation.metaAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.implicitRulesAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.languageAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.extension:secondary-findingAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.extension:secondary-findingMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.extension:body-structureAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.extension:body-structureMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.extension:related-artifactAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.extension:related-artifactMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.extension:genomics-risk-assessmentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.extension:genomics-risk-assessmentMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.identifierAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.basedOnAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.partOfAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.statusAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.categoryAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.category:labCategoryAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.category:labCategory.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.category:labCategory.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.category:labCategory.codingAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.category:labCategory.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.subjectAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.focusAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.encounterAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.effective[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.issuedAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.performerAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.noteAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.bodySiteAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.methodAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.specimenAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.deviceAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
obs-3errorObservation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
ele-1errorObservation.referenceRange.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.referenceRange.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.referenceRange.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.referenceRange.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.referenceRange.lowAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.highAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.typeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.appliesToAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.ageAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.referenceRange.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.hasMemberAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.derivedFromAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.derivedFrom:variantAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.derivedFrom:genotypeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.derivedFrom:haplotypeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:conclusion-stringAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:conclusion-string.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:conclusion-string.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:conclusion-string.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:conclusion-string.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:conclusion-string.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:conclusion-string.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:conclusion-string.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:conclusion-string.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:conclusion-string.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:evidence-levelAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:evidence-level.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:evidence-level.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:evidence-level.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:evidence-level.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:evidence-level.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:evidence-level.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:evidence-level.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:evidence-level.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:evidence-level.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:prognosisAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:prognosis.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:prognosis.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:prognosis.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:prognosis.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:prognosis.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:prognosis.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:prognosis.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:prognosis.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:prognosis.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:predicted-phenotypeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:predicted-phenotype.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:predicted-phenotype.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:predicted-phenotype.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:predicted-phenotype.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:predicted-phenotype.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:predicted-phenotype.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:predicted-phenotype.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:predicted-phenotype.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:predicted-phenotype.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:mode-of-inheritanceAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:mode-of-inheritance.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:mode-of-inheritance.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:mode-of-inheritance.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:mode-of-inheritance.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:mode-of-inheritance.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:mode-of-inheritance.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:mode-of-inheritance.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:mode-of-inheritance.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:mode-of-inheritance.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:clinical-significanceAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:clinical-significance.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:clinical-significance.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:clinical-significance.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:clinical-significance.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:clinical-significance.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:clinical-significance.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:clinical-significance.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:clinical-significance.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:clinical-significance.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:functional-effectAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:functional-effect.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:functional-effect.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:functional-effect.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorObservation.component:functional-effect.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorObservation.component:functional-effect.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:functional-effect.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:functional-effect.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:functional-effect.interpretationAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorObservation.component:functional-effect.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())