Genomic Base - Genomics Reporting Implementation Guide v4.0.0-cibuild

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-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Resource Profile: Genomic Base ( Abstract )

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-base				Version: 4.0.0-cibuild
Standards status: Trial-use			Maturity Level: 2	Computable Name: GenomicBase

Base profile that defines characteristics shared by all genetic observations.

Scope and Usage

This profile is the base profile for all other profiles in this guide, defining a set of constraints that are applicable across all observations.

Common Elements

secondary-finding (extension) can flag an observation as a secondary finding, a finding that is unrelated to the primary purpose for the test
partOf is limited to references which are applicable to genomic observations
category slices required two categories for all genomic observations in order to facilitate more efficient queries
note is a CodedAnnotation that allow all comments to also contain coded type
derivedFrom is limited to references which are applicable to genomic observations
conclusion-string (component) represents a summary conclusion to provide interpretation or impression guidance

Usages:

Derived from this Profile: Genomic Finding and Genomic Implication

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

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

Key Elements Table
Differential Table
Snapshot Table
Statistics/References
All

Name	Flags	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	C	0..*	Observation	This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions Constraints: obs-6, obs-7
Observation.implicitRules	This element is a modifier element. This element is included in summaries.	0..1	uri	A set of rules under which this content was created
Observation.Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
Observation.Slices for extension.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: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension	This element is a modifier element.	0..*	Extension	Extensions that cannot be ignored
Observation.partOf	This element is included in summaries.	0..*	Reference(MedicationAdministration \| MedicationDispense \| MedicationStatement \| Procedure \| Immunization \| ImagingStudy \| Genomic Study)	Part of referenced event
Observation.status	This element is a modifier element. This element is included in summaries.	1..1	code	registered \| preliminary \| final \| amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
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.
Observation.Slices for category.category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.coding	This element is included in summaries.	1..1	Coding	Code defined by a terminology system Required Pattern: `{ "system" : "http://terminology.hl7.org/CodeSystem/observation-category", "code" : "laboratory" }`
Observation.Slices for category.category:geCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.coding	This element is included in summaries.	1..1	Coding	Code defined by a terminology system Required Pattern: `{ "system" : "http://terminology.hl7.org/CodeSystem/v2-0074", "code" : "GE" }`
Observation.code	This element is included in summaries.	1..1	CodeableConcept	Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.note		0..*	CodedAnnotation	Comments about the Observation that also contain a coded type
Observation.derivedFrom	This element is included in summaries.	0..*	Reference(DocumentReference \| ImagingStudy \| Media \| QuestionnaireResponse \| Observation \| MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
Observation.Slices for component	This element is included in summaries.	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices				Content/Rules for all slices
Observation.Slices for component.component:All Slices.modifierExtension	This element is a modifier element. This element is included in summaries.	0..*	Extension	Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code	This element is included in summaries.	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:conclusion-string	This element is included in summaries.	0..1	BackboneElement	Clinical Conclusion
Observation.Slices for component.component:conclusion-string.modifierExtension	This element is a modifier element. This element is included in summaries.	0..*	Extension	Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code	This element is included in summaries.	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: `{ "coding" : [ { "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code" : "conclusion-string" } ] }`
Observation.Slices for component.component:conclusion-string.value[x]	This element is included in summaries.	0..1	string	Summary conclusion (interpretation/impression)
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.status	Base	required	ObservationStatus	📍4.0.1	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📍4.0.1	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📍4.0.1	FHIR Std.
Observation.category:geCategory	Base	preferred	Observation Category Codes	📍4.0.1	FHIR Std.
Observation.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:conclusion-string.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.

Constraints

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 in (%resource.descendants().reference \| %resource.descendants().as(canonical) \| %resource.descendants().as(uri) \| %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()`
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	`contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()`
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label	`contained.meta.security.empty()`
dom-6	best practice	Observation	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	ALL elements	All FHIR elements must have a @value or children	`hasValue() or (children().count() > id.count())`
ext-1	error	ALL extensions	Must have either extensions or value[x], not both	`extension.exists() != value.exists()`
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present	`dataAbsentReason.empty() or value.empty()`
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present	`value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()`

This structure is derived from Observation

Name	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	0..*	Observation	This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions
Observation.Slices for extension	0..*	Extension	Extension Slice: Unordered, Open by value:url
Observation.Slices for extension.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: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure	0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.partOf	0..*	Reference(MedicationAdministration \| MedicationDispense \| MedicationStatement \| Procedure \| Immunization \| ImagingStudy \| Genomic Study)	Part of referenced event
Observation.Slices for category	2..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding
Observation.Slices for category.category:labCategory	1..1	CodeableConcept	Classification of type of observation
Observation.Slices for category.category:labCategory.coding	1..1	Coding	Code defined by a terminology system Required Pattern: `{ "system" : "http://terminology.hl7.org/CodeSystem/observation-category", "code" : "laboratory" }`
Observation.Slices for category.category:geCategory	1..1	CodeableConcept	Classification of type of observation
Observation.Slices for category.category:geCategory.coding	1..1	Coding	Code defined by a terminology system Required Pattern: `{ "system" : "http://terminology.hl7.org/CodeSystem/v2-0074", "code" : "GE" }`
Observation.note	0..*	CodedAnnotation	Comments about the Observation that also contain a coded type
Observation.derivedFrom	0..*	Reference(DocumentReference \| ImagingStudy \| Media \| QuestionnaireResponse \| Observation \| MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
Observation.Slices for component	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code
Observation.Slices for component.component:conclusion-string	0..1	BackboneElement	Clinical Conclusion
Observation.Slices for component.component:conclusion-string.code	1..1	CodeableConcept	conclusion-string Required Pattern: `{ "coding" : [ { "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code" : "conclusion-string" } ] }`
Observation.Slices for component.component:conclusion-string.value[x]	0..1	string	Summary conclusion (interpretation/impression)
Documentation for this format

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

Observation.id This element is included in summaries. 0..1 id Logical id of this artifact

Observation.meta This element is included in summaries. 0..1 Meta Metadata about the resource

Observation.implicitRules This element is a modifier element. This element is included in summaries. 0..1 uri A set of rules under which this content was created

language

0..1

code

Language of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional Bindings

Purpose

AllLanguages

Max Binding

Observation.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

Observation.contained 0..* Resource Contained, inline Resources

Observation.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url

Observation.Slices for extension.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: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.

Observation.Slices for extension.extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite

Observation.modifierExtension This element is a modifier element. 0..* Extension Extensions that cannot be ignored

Observation.identifier This element is included in summaries. 0..* Identifier Business Identifier for observation

Observation.status This element is a modifier element. This element is included in summaries. 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

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.

Observation.Slices for category.category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.

Observation.Slices for category.category:labCategory.id 0..1 string Unique id for inter-element referencing

Observation.Slices for category.category:labCategory.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:

{
  "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
  "code" : "laboratory"
}

Observation.Slices for category.category:labCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept

Observation.Slices for category.category:geCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.

Observation.Slices for category.category:geCategory.id 0..1 string Unique id for inter-element referencing

Observation.Slices for category.category:geCategory.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:

{
  "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
  "code" : "GE"
}

Observation.Slices for category.category:geCategory.text This element is included in summaries. 0..1 string Plain text representation of the concept

Observation.code This element is included in summaries. 1..1 CodeableConcept Type of observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

Observation.subject This element is included in summaries. 0..1 Reference(Patient | Group | Device | Location) Who and/or what the observation is about

Observation.focus This element is included in summaries. 0..* Reference(Resource) What the observation is about, when it is not about the subject of record

Observation.encounter This element is included in summaries. 0..1 Reference(Encounter) Healthcare event during which this observation is made

Observation.effective[x] This element is included in summaries. 0..1 Clinically relevant time/time-period for observation

Observation.effective[x].effectiveDateTime dateTime

Observation.effective[x].effectivePeriod Period

Observation.effective[x].effectiveTiming Timing

Observation.effective[x].effectiveInstant instant

Observation.issued This element is included in summaries. 0..1 instant Date/Time this version was made available

Observation.value[x] This element is included in summaries. C 0..1 Actual result

Observation.value[x].valueQuantity Quantity

Observation.value[x].valueCodeableConcept CodeableConcept

Observation.value[x].valueString string

Observation.value[x].valueBoolean boolean

Observation.value[x].valueInteger integer

Observation.value[x].valueRange Range

Observation.value[x].valueRatio Ratio

Observation.value[x].valueSampledData SampledData

Observation.value[x].valueTime time

Observation.value[x].valueDateTime dateTime

Observation.value[x].valuePeriod Period

Observation.dataAbsentReason C 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

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

Observation.note 0..* CodedAnnotation Comments about the Observation that also contain a coded type

Observation.bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

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

Observation.specimen 0..1 Reference(Specimen) Specimen used for this observation

Observation.device 0..1 Reference(Device | DeviceMetric) (Measurement) Device

Observation.referenceRange C 0..* BackboneElement Provides guide for interpretation
Constraints: obs-3

Observation.referenceRange.id 0..1 string Unique id for inter-element referencing

Observation.referenceRange.extension 0..* Extension Additional content defined by implementations

Observation.referenceRange.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized

Observation.referenceRange.low C 0..1 SimpleQuantity(4.0.1) Low Range, if relevant
Constraints: sqty-1

Observation.referenceRange.high C 0..1 SimpleQuantity(4.0.1) High Range, if relevant
Constraints: sqty-1

Observation.referenceRange.type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

Observation.referenceRange.appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.

Observation.referenceRange.age 0..1 Range Applicable age range, if relevant

Observation.referenceRange.text 0..1 string Text based reference range in an observation

Observation.hasMember This element is included in summaries. 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group

Observation.derivedFrom This element is included in summaries. 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()

Observation.Slices for component This element is included in summaries. 0..* BackboneElement Component results
Slice: Unordered, Open by value:code

Observation.Slices for component.component:All Slices Content/Rules for all slices

Observation.Slices for component.component:All Slices.id 0..1 string Unique id for inter-element referencing

Observation.Slices for component.component:All Slices.extension 0..* Extension Additional content defined by implementations

Observation.Slices for component.component:All Slices.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized

Observation.Slices for component.component:All Slices.code This element is included in summaries. 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

Observation.Slices for component.component:All Slices.value[x] This element is included in summaries. 0..1 Actual component result

Observation.Slices for component.component:All Slices.value[x].valueQuantity Quantity

Observation.Slices for component.component:All Slices.value[x].valueCodeableConcept CodeableConcept

Observation.Slices for component.component:All Slices.value[x].valueString string

Observation.Slices for component.component:All Slices.value[x].valueBoolean boolean

Observation.Slices for component.component:All Slices.value[x].valueInteger integer

Observation.Slices for component.component:All Slices.value[x].valueRange Range

Observation.Slices for component.component:All Slices.value[x].valueRatio Ratio

Observation.Slices for component.component:All Slices.value[x].valueSampledData SampledData

Observation.Slices for component.component:All Slices.value[x].valueTime time

Observation.Slices for component.component:All Slices.value[x].valueDateTime dateTime

Observation.Slices for component.component:All Slices.value[x].valuePeriod Period

Observation.Slices for component.component:All Slices.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

Observation.Slices for component.component:All Slices.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.

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

Observation.Slices for component.component:conclusion-string This element is included in summaries. 0..1 BackboneElement Clinical Conclusion

Observation.Slices for component.component:conclusion-string.id 0..1 string Unique id for inter-element referencing

Observation.Slices for component.component:conclusion-string.extension 0..* Extension Additional content defined by implementations

Observation.Slices for component.component:conclusion-string.modifierExtension This element is a modifier element. This element is included in summaries. 0..* Extension Extensions that cannot be ignored even if unrecognized

code

1..1

CodeableConcept

conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern:

{
  "coding" : [
    {
      "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code" : "conclusion-string"
    }
  ]
}

Observation.Slices for component.component:conclusion-string.value[x] This element is included in summaries. 0..1 string Summary conclusion (interpretation/impression)

Observation.Slices for component.component:conclusion-string.dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

Observation.Slices for component.component:conclusion-string.interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.

Observation.Slices for component.component:conclusion-string.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.language	Base	preferred	Common Languages	📍4.0.1	FHIR Std.
Observation.status	Base	required	ObservationStatus	📍4.0.1	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📍4.0.1	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📍4.0.1	FHIR Std.
Observation.category:geCategory	Base	preferred	Observation Category Codes	📍4.0.1	FHIR Std.
Observation.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.dataAbsentReason	Base	extensible	DataAbsentReason	📍4.0.1	FHIR Std.
Observation.interpretation	Base	extensible	Observation Interpretation Codes	📍4.0.1	FHIR Std.
Observation.bodySite	Base	example	SNOMED CT Body Structures	📍4.0.1	FHIR Std.
Observation.method	Base	example	Observation Methods	📍4.0.1	FHIR Std.
Observation.referenceRange.type	Base	preferred	Observation Reference Range Meaning Codes	📍4.0.1	FHIR Std.
Observation.referenceRange.appliesTo	Base	example	Observation Reference Range Applies To Codes	📍4.0.1	FHIR Std.
Observation.component.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component.dataAbsentReason	Base	extensible	DataAbsentReason	📍4.0.1	FHIR Std.
Observation.component.interpretation	Base	extensible	Observation Interpretation Codes	📍4.0.1	FHIR Std.
Observation.component:conclusion-string.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:conclusion-string.dataAbsentReason	Base	extensible	DataAbsentReason	📍4.0.1	FHIR Std.
Observation.component:conclusion-string.interpretation	Base	extensible	Observation Interpretation Codes	📍4.0.1	FHIR Std.

Constraints

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 in (%resource.descendants().reference \| %resource.descendants().as(canonical) \| %resource.descendants().as(uri) \| %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()`
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	`contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()`
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label	`contained.meta.security.empty()`
dom-6	best practice	Observation	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	ALL elements	All FHIR elements must have a @value or children	`hasValue() or (children().count() > id.count())`
ext-1	error	ALL extensions	Must have either extensions or value[x], not both	`extension.exists() != value.exists()`
obs-3	error	Observation.referenceRange	Must have at least a low or a high or text	`low.exists() or high.exists() or text.exists()`
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present	`dataAbsentReason.empty() or value.empty()`
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present	`value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()`
sqty-1	error	Observation.referenceRange.low, Observation.referenceRange.high	The comparator is not used on a SimpleQuantity	`comparator.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:

The element 1 is sliced based on the value of Observation.category
The element 1 is sliced based on the value of Observation.derivedFrom
The element 1 is sliced based on the value of Observation.component

Maturity: 2

Key Elements View

Name	Flags	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	C	0..*	Observation	This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions Constraints: obs-6, obs-7
Observation.implicitRules	This element is a modifier element. This element is included in summaries.	0..1	uri	A set of rules under which this content was created
Observation.Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
Observation.Slices for extension.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: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.modifierExtension	This element is a modifier element.	0..*	Extension	Extensions that cannot be ignored
Observation.partOf	This element is included in summaries.	0..*	Reference(MedicationAdministration \| MedicationDispense \| MedicationStatement \| Procedure \| Immunization \| ImagingStudy \| Genomic Study)	Part of referenced event
Observation.status	This element is a modifier element. This element is included in summaries.	1..1	code	registered \| preliminary \| final \| amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
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.
Observation.Slices for category.category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:labCategory.coding	This element is included in summaries.	1..1	Coding	Code defined by a terminology system Required Pattern: `{ "system" : "http://terminology.hl7.org/CodeSystem/observation-category", "code" : "laboratory" }`
Observation.Slices for category.category:geCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
Observation.Slices for category.category:geCategory.coding	This element is included in summaries.	1..1	Coding	Code defined by a terminology system Required Pattern: `{ "system" : "http://terminology.hl7.org/CodeSystem/v2-0074", "code" : "GE" }`
Observation.code	This element is included in summaries.	1..1	CodeableConcept	Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.note		0..*	CodedAnnotation	Comments about the Observation that also contain a coded type
Observation.derivedFrom	This element is included in summaries.	0..*	Reference(DocumentReference \| ImagingStudy \| Media \| QuestionnaireResponse \| Observation \| MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
Observation.Slices for component	This element is included in summaries.	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code
Observation.Slices for component.component:All Slices				Content/Rules for all slices
Observation.Slices for component.component:All Slices.modifierExtension	This element is a modifier element. This element is included in summaries.	0..*	Extension	Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:All Slices.code	This element is included in summaries.	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
Observation.Slices for component.component:conclusion-string	This element is included in summaries.	0..1	BackboneElement	Clinical Conclusion
Observation.Slices for component.component:conclusion-string.modifierExtension	This element is a modifier element. This element is included in summaries.	0..*	Extension	Extensions that cannot be ignored even if unrecognized
Observation.Slices for component.component:conclusion-string.code	This element is included in summaries.	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: `{ "coding" : [ { "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code" : "conclusion-string" } ] }`
Observation.Slices for component.component:conclusion-string.value[x]	This element is included in summaries.	0..1	string	Summary conclusion (interpretation/impression)
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.status	Base	required	ObservationStatus	📍4.0.1	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📍4.0.1	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📍4.0.1	FHIR Std.
Observation.category:geCategory	Base	preferred	Observation Category Codes	📍4.0.1	FHIR Std.
Observation.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:conclusion-string.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.

Constraints

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 in (%resource.descendants().reference \| %resource.descendants().as(canonical) \| %resource.descendants().as(uri) \| %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()`
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	`contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()`
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label	`contained.meta.security.empty()`
dom-6	best practice	Observation	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	ALL elements	All FHIR elements must have a @value or children	`hasValue() or (children().count() > id.count())`
ext-1	error	ALL extensions	Must have either extensions or value[x], not both	`extension.exists() != value.exists()`
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present	`dataAbsentReason.empty() or value.empty()`
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present	`value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()`

Differential View

This structure is derived from Observation

Name	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	0..*	Observation	This is an abstract profile. Child profiles: GenomicFinding, GenomicImplication Measurements and simple assertions
Observation.Slices for extension	0..*	Extension	Extension Slice: Unordered, Open by value:url
Observation.Slices for extension.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: ObservationCategoryCodes (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
Observation.Slices for extension.extension:body-structure	0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
Observation.partOf	0..*	Reference(MedicationAdministration \| MedicationDispense \| MedicationStatement \| Procedure \| Immunization \| ImagingStudy \| Genomic Study)	Part of referenced event
Observation.Slices for category	2..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding
Observation.Slices for category.category:labCategory	1..1	CodeableConcept	Classification of type of observation
Observation.Slices for category.category:labCategory.coding	1..1	Coding	Code defined by a terminology system Required Pattern: `{ "system" : "http://terminology.hl7.org/CodeSystem/observation-category", "code" : "laboratory" }`
Observation.Slices for category.category:geCategory	1..1	CodeableConcept	Classification of type of observation
Observation.Slices for category.category:geCategory.coding	1..1	Coding	Code defined by a terminology system Required Pattern: `{ "system" : "http://terminology.hl7.org/CodeSystem/v2-0074", "code" : "GE" }`
Observation.note	0..*	CodedAnnotation	Comments about the Observation that also contain a coded type
Observation.derivedFrom	0..*	Reference(DocumentReference \| ImagingStudy \| Media \| QuestionnaireResponse \| Observation \| MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
Observation.Slices for component	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code
Observation.Slices for component.component:conclusion-string	0..1	BackboneElement	Clinical Conclusion
Observation.Slices for component.component:conclusion-string.code	1..1	CodeableConcept	conclusion-string Required Pattern: `{ "coding" : [ { "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code" : "conclusion-string" } ] }`
Observation.Slices for component.component:conclusion-string.value[x]	0..1	string	Summary conclusion (interpretation/impression)
Documentation for this format

Snapshot View