Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot
Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot 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
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-base | Version: 4.0.0-ballot | |||
| Standards status: Trial-use | Maturity Level: 2 | Computable Name: GenomicBase | ||
Base profile that defines characteristics shared by all genetic observations.
This profile is the base profile for all other profiles in this guide, defining a set of constraints that are applicable across all observations.
secondary-finding (extension) can flag an observation as a secondary finding, a finding that is unrelated to the primary purpose for the testpartOf is limited to references which are applicable to genomic observationscategory slices required two categories for all genomic observations in order to facilitate more efficient queriesnote is a CodedAnnotation that allow all comments to also contain coded typederivedFrom is limited to references which are applicable to genomic observationsconclusion-string (component) represents a summary conclusion to provide interpretation or impression guidanceUsages:
You can also check for usages in the FHIR IG Statistics
Description of Profiles, Differentials, Snapshots and how the different presentations work.
| Name | Flags | Card. | Type | Description & Constraints Filter:   |
|---|---|---|---|---|
  Observation |
C | 0..* | Observation | This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions Constraints: obs-6, obs-7, obs-8, obs-10, obs-11 |
  implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created |
| contained |
0..* | Resource | Contained, inline Resources | |
  Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |
   extension:secondary-finding |
0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |
 extension:body-structure |
0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
 modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| status |
?!Σ | 1..1 | code | registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained Binding: ObservationStatus (required): Codes providing the status of an observation. |
 Slices for category |
2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
 category:labCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
   coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |
 id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
 system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
| version |
0..1 | string | Version of the system - if relevant | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| display |
0..1 | string | Representation defined by the system | |
 userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |
 category:geCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
| version |
0..1 | string | Version of the system - if relevant | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| display |
0..1 | string | Representation defined by the system | |
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |
| code |
ΣC | 1..1 | CodeableConcept | Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
 focus |
?!Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record |
 value[x] |
ΣC | 0..1 | Actual result | |
| valueQuantity |
Quantity | |||
| valueCodeableConcept |
CodeableConcept | |||
| valueString |
string | |||
| valueBoolean |
boolean | |||
| valueInteger |
integer | |||
| valueRange |
Range | |||
| valueRatio |
Ratio | |||
| valueSampledData |
SampledData | |||
| valueTime |
time | |||
| valueDateTime |
dateTime | |||
| valuePeriod |
Period | |||
| valueAttachment |
Attachment | |||
| valueReference |
Reference(MolecularSequence) | |||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| note |
0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |
| derivedFrom |
Σ | 0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() |
 Slices for component |
ΣC | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code |
 component:All Slices |
Content/Rules for all slices | |||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| component:conclusion-string |
ΣC | 0..1 | BackboneElement | Clinical Conclusion |
 modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
 code |
ΣC | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
 id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| version |
0..1 | string | Version of the system - if relevant | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
| display |
0..1 | string | Representation defined by the system | |
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |
| text |
0..1 | string | Plain text representation of the concept | |
 value[x] |
ΣC | 0..1 | string | Summary conclusion (interpretation/impression) |
| Documentation for this format | ||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.status | Base | required | Observation Status | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:conclusion-string.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource |
contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()
|
| dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated |
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
|
| dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | Observation | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
| obs-6 | error | Observation | Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). |
value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
|
| obs-8 | error | Observation | bodyStructure SHALL only be present if Observation.bodySite is not present |
bodySite.exists() implies bodyStructure.empty()
|
| obs-10 | error | Observation | Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present |
component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
|
| obs-11 | error | Observation | if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present |
(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())
|
This structure is derived from Observation
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| Observation |
0..* | Observation | This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions | |
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:secondary-finding |
0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |
| extension:body-structure |
0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
| Slices for category |
2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding | |
| category:labCategory |
1..1 | CodeableConcept | Classification of type of observation | |
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| category:geCategory |
1..1 | CodeableConcept | Classification of type of observation | |
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| note |
0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |
| derivedFrom |
0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() | |
| Slices for component |
0..* | BackboneElement | Component results Slice: Unordered, Open by value:code | |
| component:conclusion-string |
0..1 | BackboneElement | Clinical Conclusion | |
| code |
1..1 | CodeableConcept | conclusion-string Required Pattern: At least the following | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
| value[x] |
0..1 | string | Summary conclusion (interpretation/impression) | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| Observation |
C | 0..* | Observation | This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions Constraints: obs-6, obs-7, obs-8, obs-10, obs-11 | ||||
| id |
Σ | 0..1 | id | Logical id of this artifact | ||||
| meta |
Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language |
0..1 | code | Language of the resource content Binding: AllLanguages (required): IETF language tag for a human language
| |||||
| text |
0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| extension:secondary-finding |
0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |||||
| extension:body-structure |
0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
Σ | 0..* | Identifier | Business Identifier for observation | ||||
| instantiates[x] |
Σ | 0..1 | canonical(ObservationDefinition), Reference(ObservationDefinition) | Instantiates FHIR ObservationDefinition | ||||
| basedOn |
Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| triggeredBy |
0..* | BackboneElement | Triggering observation(s) | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| observation |
Σ | 1..1 | Reference(Observation) | Triggering observation | ||||
| type |
Σ | 1..1 | code | reflex | repeat | re-run Binding: TriggeredBytype (required): The type of TriggeredBy Observation. | ||||
| reason |
0..1 | string | Reason that the observation was triggered | |||||
| partOf |
Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | GenomicStudy) | Part of referenced event | ||||
| status |
?!Σ | 1..1 | code | registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| Slices for category |
2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| category:labCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id |
0..1 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display |
0..1 | string | Representation defined by the system | |||||
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |||||
| text |
0..1 | string | Plain text representation of the concept | |||||
| category:geCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id |
0..1 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |||||
| display |
0..1 | string | Representation defined by the system | |||||
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |||||
| text |
0..1 | string | Plain text representation of the concept | |||||
| code |
ΣC | 1..1 | CodeableConcept | Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| subject |
Σ | 0..1 | Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct) | Who and/or what the observation is about | ||||
| focus |
?!Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| organizer |
ΣC | 0..1 | boolean | This observation organizes/groups a set of sub-observations | ||||
| encounter |
Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
| effective[x] |
Σ | 0..1 | Clinically relevant time/time-period for observation | |||||
| effectiveDateTime |
dateTime | |||||||
| effectivePeriod |
Period | |||||||
| effectiveTiming |
Timing | |||||||
| effectiveInstant |
instant | |||||||
| issued |
Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer |
Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson | HealthcareService) | Who is responsible for the observation | ||||
| value[x] |
ΣC | 0..1 | Actual result | |||||
| valueQuantity |
Quantity | |||||||
| valueCodeableConcept |
CodeableConcept | |||||||
| valueString |
string | |||||||
| valueBoolean |
boolean | |||||||
| valueInteger |
integer | |||||||
| valueRange |
Range | |||||||
| valueRatio |
Ratio | |||||||
| valueSampledData |
SampledData | |||||||
| valueTime |
time | |||||||
| valueDateTime |
dateTime | |||||||
| valuePeriod |
Period | |||||||
| valueAttachment |
Attachment | |||||||
| valueReference |
Reference(MolecularSequence) | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note |
0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |||||
| bodySite |
C | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts | ||||
| bodyStructure |
C | 0..1 | Reference(BodyStructure) | Observed body structure | ||||
| method |
0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen |
C | 0..1 | Reference(Specimen | Group) | Specimen used for this observation Constraints: obs-9 | ||||
| device |
0..1 | Reference(Device | DeviceMetric) | A reference to the device that generates the measurements or the device settings for the device | |||||
| referenceRange |
C | 0..* | BackboneElement | Provides guide for interpretation Constraints: obs-3 | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| low |
C | 0..1 | SimpleQuantity(6.0.0-ballot3) | Low Range, if relevant | ||||
| high |
C | 0..1 | SimpleQuantity(6.0.0-ballot3) | High Range, if relevant | ||||
| normalValue |
0..1 | CodeableConcept | Normal value, if relevant Binding: ObservationReferenceRangeNormalValueCodes (extensible): Codes identifying the normal value of the observation. | |||||
| type |
0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
| appliesTo |
0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
| age |
0..1 | Range | Applicable age range, if relevant | |||||
| text |
C | 0..1 | markdown | Text based reference range in an observation | ||||
| hasMember |
Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| derivedFrom |
Σ | 0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() | ||||
| Slices for component |
ΣC | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code | ||||
| component:All Slices |
Content/Rules for all slices | |||||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] |
ΣC | 0..1 | Actual component result | |||||
| valueQuantity |
Quantity | |||||||
| valueCodeableConcept |
CodeableConcept | |||||||
| valueString |
string | |||||||
| valueBoolean |
boolean | |||||||
| valueInteger |
integer | |||||||
| valueRange |
Range | |||||||
| valueRatio |
Ratio | |||||||
| valueSampledData |
SampledData | |||||||
| valueTime |
time | |||||||
| valueDateTime |
dateTime | |||||||
| valuePeriod |
Period | |||||||
| valueAttachment |
Attachment | |||||||
| valueReference |
Reference(MolecularSequence) | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange |
0..* | See referenceRange (Observation) | Provides guide for interpretation of component result value | |||||
| component:conclusion-string |
ΣC | 0..1 | BackboneElement | Clinical Conclusion | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code |
ΣC | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
| display |
0..1 | string | Representation defined by the system | |||||
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |||||
| text |
0..1 | string | Plain text representation of the concept | |||||
| value[x] |
ΣC | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange |
0..* | See referenceRange (Observation) | Provides guide for interpretation of component result value | |||||
| Documentation for this format | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.language | Base | required | All Languages | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.triggeredBy.type | Base | required | triggered Bytype | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.status | Base | required | Observation Status | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.bodySite | Base | example | SNOMED CT Body Structures | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.method | Base | example | Observation Methods | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.normalValue | Base | extensible | Observation Reference Range Normal Value Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.type | Base | preferred | Observation Reference Range Meaning Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.appliesTo | Base | example | Observation Reference Range Applies To Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:conclusion-string.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:conclusion-string.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:conclusion-string.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource |
contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()
|
| dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated |
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
|
| dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | Observation | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
| obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text |
low.exists() or high.exists() or text.exists()
|
| obs-6 | error | Observation | Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). |
value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
|
| obs-8 | error | Observation | bodyStructure SHALL only be present if Observation.bodySite is not present |
bodySite.exists() implies bodyStructure.empty()
|
| obs-9 | error | Observation.specimen | If Observation.specimen is a reference to Group, the group can only have specimens |
(reference.resolve().exists() and reference.resolve() is Group) implies reference.resolve().member.entity.resolve().all($this is Specimen)
|
| obs-10 | error | Observation | Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present |
component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
|
| obs-11 | error | Observation | if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present |
(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())
|
This structure is derived from Observation
Summary
Mandatory: 4 elements
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Slices
This structure defines the following Slices:
Maturity: 2
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| Observation |
C | 0..* | Observation | This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions Constraints: obs-6, obs-7, obs-8, obs-10, obs-11 |
| implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created |
| contained |
0..* | Resource | Contained, inline Resources | |
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:secondary-finding |
0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |
| extension:body-structure |
0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| status |
?!Σ | 1..1 | code | registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained Binding: ObservationStatus (required): Codes providing the status of an observation. |
| Slices for category |
2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| category:labCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
| version |
0..1 | string | Version of the system - if relevant | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| display |
0..1 | string | Representation defined by the system | |
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |
| category:geCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
| version |
0..1 | string | Version of the system - if relevant | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| display |
0..1 | string | Representation defined by the system | |
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |
| code |
ΣC | 1..1 | CodeableConcept | Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| focus |
?!Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record |
| value[x] |
ΣC | 0..1 | Actual result | |
| valueQuantity |
Quantity | |||
| valueCodeableConcept |
CodeableConcept | |||
| valueString |
string | |||
| valueBoolean |
boolean | |||
| valueInteger |
integer | |||
| valueRange |
Range | |||
| valueRatio |
Ratio | |||
| valueSampledData |
SampledData | |||
| valueTime |
time | |||
| valueDateTime |
dateTime | |||
| valuePeriod |
Period | |||
| valueAttachment |
Attachment | |||
| valueReference |
Reference(MolecularSequence) | |||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| note |
0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |
| derivedFrom |
Σ | 0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() |
| Slices for component |
ΣC | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code |
| component:All Slices |
Content/Rules for all slices | |||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| component:conclusion-string |
ΣC | 0..1 | BackboneElement | Clinical Conclusion |
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code |
ΣC | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| version |
0..1 | string | Version of the system - if relevant | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
| display |
0..1 | string | Representation defined by the system | |
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |
| text |
0..1 | string | Plain text representation of the concept | |
| value[x] |
ΣC | 0..1 | string | Summary conclusion (interpretation/impression) |
| Documentation for this format | ||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.status | Base | required | Observation Status | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:conclusion-string.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource |
contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()
|
| dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated |
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
|
| dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | Observation | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
| obs-6 | error | Observation | Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). |
value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
|
| obs-8 | error | Observation | bodyStructure SHALL only be present if Observation.bodySite is not present |
bodySite.exists() implies bodyStructure.empty()
|
| obs-10 | error | Observation | Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present |
component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
|
| obs-11 | error | Observation | if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present |
(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())
|
Differential View
This structure is derived from Observation
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| Observation |
0..* | Observation | This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions | |
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:secondary-finding |
0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |
| extension:body-structure |
0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
| Slices for category |
2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding | |
| category:labCategory |
1..1 | CodeableConcept | Classification of type of observation | |
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| category:geCategory |
1..1 | CodeableConcept | Classification of type of observation | |
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| note |
0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |
| derivedFrom |
0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() | |
| Slices for component |
0..* | BackboneElement | Component results Slice: Unordered, Open by value:code | |
| component:conclusion-string |
0..1 | BackboneElement | Clinical Conclusion | |
| code |
1..1 | CodeableConcept | conclusion-string Required Pattern: At least the following | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
| value[x] |
0..1 | string | Summary conclusion (interpretation/impression) | |
| Documentation for this format | ||||
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| Observation |
C | 0..* | Observation | This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions Constraints: obs-6, obs-7, obs-8, obs-10, obs-11 | ||||
| id |
Σ | 0..1 | id | Logical id of this artifact | ||||
| meta |
Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language |
0..1 | code | Language of the resource content Binding: AllLanguages (required): IETF language tag for a human language
| |||||
| text |
0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| extension:secondary-finding |
0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |||||
| extension:body-structure |
0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
Σ | 0..* | Identifier | Business Identifier for observation | ||||
| instantiates[x] |
Σ | 0..1 | canonical(ObservationDefinition), Reference(ObservationDefinition) | Instantiates FHIR ObservationDefinition | ||||
| basedOn |
Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| triggeredBy |
0..* | BackboneElement | Triggering observation(s) | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| observation |
Σ | 1..1 | Reference(Observation) | Triggering observation | ||||
| type |
Σ | 1..1 | code | reflex | repeat | re-run Binding: TriggeredBytype (required): The type of TriggeredBy Observation. | ||||
| reason |
0..1 | string | Reason that the observation was triggered | |||||
| partOf |
Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | GenomicStudy) | Part of referenced event | ||||
| status |
?!Σ | 1..1 | code | registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| Slices for category |
2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| category:labCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id |
0..1 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display |
0..1 | string | Representation defined by the system | |||||
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |||||
| text |
0..1 | string | Plain text representation of the concept | |||||
| category:geCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id |
0..1 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |||||
| display |
0..1 | string | Representation defined by the system | |||||
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |||||
| text |
0..1 | string | Plain text representation of the concept | |||||
| code |
ΣC | 1..1 | CodeableConcept | Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| subject |
Σ | 0..1 | Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct) | Who and/or what the observation is about | ||||
| focus |
?!Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| organizer |
ΣC | 0..1 | boolean | This observation organizes/groups a set of sub-observations | ||||
| encounter |
Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
| effective[x] |
Σ | 0..1 | Clinically relevant time/time-period for observation | |||||
| effectiveDateTime |
dateTime | |||||||
| effectivePeriod |
Period | |||||||
| effectiveTiming |
Timing | |||||||
| effectiveInstant |
instant | |||||||
| issued |
Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer |
Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson | HealthcareService) | Who is responsible for the observation | ||||
| value[x] |
ΣC | 0..1 | Actual result | |||||
| valueQuantity |
Quantity | |||||||
| valueCodeableConcept |
CodeableConcept | |||||||
| valueString |
string | |||||||
| valueBoolean |
boolean | |||||||
| valueInteger |
integer | |||||||
| valueRange |
Range | |||||||
| valueRatio |
Ratio | |||||||
| valueSampledData |
SampledData | |||||||
| valueTime |
time | |||||||
| valueDateTime |
dateTime | |||||||
| valuePeriod |
Period | |||||||
| valueAttachment |
Attachment | |||||||
| valueReference |
Reference(MolecularSequence) | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note |
0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |||||
| bodySite |
C | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts | ||||
| bodyStructure |
C | 0..1 | Reference(BodyStructure) | Observed body structure | ||||
| method |
0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen |
C | 0..1 | Reference(Specimen | Group) | Specimen used for this observation Constraints: obs-9 | ||||
| device |
0..1 | Reference(Device | DeviceMetric) | A reference to the device that generates the measurements or the device settings for the device | |||||
| referenceRange |
C | 0..* | BackboneElement | Provides guide for interpretation Constraints: obs-3 | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| low |
C | 0..1 | SimpleQuantity(6.0.0-ballot3) | Low Range, if relevant | ||||
| high |
C | 0..1 | SimpleQuantity(6.0.0-ballot3) | High Range, if relevant | ||||
| normalValue |
0..1 | CodeableConcept | Normal value, if relevant Binding: ObservationReferenceRangeNormalValueCodes (extensible): Codes identifying the normal value of the observation. | |||||
| type |
0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
| appliesTo |
0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
| age |
0..1 | Range | Applicable age range, if relevant | |||||
| text |
C | 0..1 | markdown | Text based reference range in an observation | ||||
| hasMember |
Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| derivedFrom |
Σ | 0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() | ||||
| Slices for component |
ΣC | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code | ||||
| component:All Slices |
Content/Rules for all slices | |||||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] |
ΣC | 0..1 | Actual component result | |||||
| valueQuantity |
Quantity | |||||||
| valueCodeableConcept |
CodeableConcept | |||||||
| valueString |
string | |||||||
| valueBoolean |
boolean | |||||||
| valueInteger |
integer | |||||||
| valueRange |
Range | |||||||
| valueRatio |
Ratio | |||||||
| valueSampledData |
SampledData | |||||||
| valueTime |
time | |||||||
| valueDateTime |
dateTime | |||||||
| valuePeriod |
Period | |||||||
| valueAttachment |
Attachment | |||||||
| valueReference |
Reference(MolecularSequence) | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange |
0..* | See referenceRange (Observation) | Provides guide for interpretation of component result value | |||||
| component:conclusion-string |
ΣC | 0..1 | BackboneElement | Clinical Conclusion | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code |
ΣC | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
| display |
0..1 | string | Representation defined by the system | |||||
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |||||
| text |
0..1 | string | Plain text representation of the concept | |||||
| value[x] |
ΣC | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange |
0..* | See referenceRange (Observation) | Provides guide for interpretation of component result value | |||||
| Documentation for this format | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.language | Base | required | All Languages | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.triggeredBy.type | Base | required | triggered Bytype | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.status | Base | required | Observation Status | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.bodySite | Base | example | SNOMED CT Body Structures | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.method | Base | example | Observation Methods | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.normalValue | Base | extensible | Observation Reference Range Normal Value Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.type | Base | preferred | Observation Reference Range Meaning Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.appliesTo | Base | example | Observation Reference Range Applies To Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:conclusion-string.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:conclusion-string.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:conclusion-string.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource |
contained.where((('#'+id.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').exists()).not()).trace('unmatched', id).empty()
|
| dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated |
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
|
| dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | Observation | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
| obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text |
low.exists() or high.exists() or text.exists()
|
| obs-6 | error | Observation | Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). |
value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
|
| obs-8 | error | Observation | bodyStructure SHALL only be present if Observation.bodySite is not present |
bodySite.exists() implies bodyStructure.empty()
|
| obs-9 | error | Observation.specimen | If Observation.specimen is a reference to Group, the group can only have specimens |
(reference.resolve().exists() and reference.resolve() is Group) implies reference.resolve().member.entity.resolve().all($this is Specimen)
|
| obs-10 | error | Observation | Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present |
component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
|
| obs-11 | error | Observation | if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present |
(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())
|
This structure is derived from Observation
Summary
Mandatory: 4 elements
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Slices
This structure defines the following Slices:
Maturity: 2
Other representations of profile: CSV, Excel, Schematron
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-ballot based on FHIR 6.0.0-ballot3. Generated 2025-10-16
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