Genomic Annotation - 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 Annotation

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-annotation		Version: 4.0.0-cibuild
Standards status: Trial-use	Maturity Level: 2	Computable Name: GenomicAnnotation
Copyright/Legal: This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.

Profile for communicating miscellaneous genomic annotations that are neither Diagnostic Implications, Therapeutic Implications, nor Molecular Consequences.

This section provides guidance for reporting of miscellaneous genomic annotations. Several types of annotations (e.g. population allele frequency) are important for clinical decision making, but are neither Therapeutic Implications, Diagnostic Implications, nor Molecular Consequences. The intent of this profile is to provide a 'catch-all' mechanism for communicating existing or evolving annotations that don't fit nicely into other specific implication profiles.

Where the HL7 Clinical Genomics committee has identified specific use cases (e.g. for population allele frequency), this profile contains elements and/or extensions, along with examples, that enable a semantically consistent representation. For other use cases, one can apply new observation components and/or extensions as needed. In no case should one use this profile for use cases met by the DxImplication, TxImplication, or MolecularConsequence profiles.

General usage notes

The genomic annotation profile can be used to annotate variants, haplotypes, genotypes, or molecular biomarkers with miscellaneous associations. For example, this profile can be used to assert the population allele frequency of a given variant.

Useful components include those that are broadly applicable to a number of annotations (e.g. component:knowledge-base), and those that are specific to a given type of annotation (e.g. component:population-allele-frequency):

component:evidence-level: The amount of observed support for the association between an implication and a variant / haplotype / genotype / biomarker. (See the discussion of evidence-level vs. clinical significance for additional guidance).
component:knowledge-base: indicates the database from which the annotation is derived. Annotations are obtained from different knowledge bases (e.g. Clinvar, gnomAD, 1000 Genomes). Knowledge bases continue to evolve, with new ones being developed, and existing ones being updated/revised.
component:annotation-pipeline: indicates the name of the data pipeline that processed the genomic data file.
component:population-allele-frequency: a specific type of annotation that indicates the prevalence of an allele in a population. This component can use the knowledgebase-ancestry-group extension to further characterize the applicable population.
component:conservation-score: a specific type of annotation that indicates how much a specific DNA sequence or protein residue has remained unchanged across the evolutionary history of different species. High conservation scores indicate that a region is likely under strong selective pressure, meaning mutations in that region are detrimental to the organism's survival and reproduction. This component can use the knowledgebase-ancestry-group extension to further characterize the applicable population.
extension:knowledgebase-ancestry-group: The knowledgebase-ancestry-group extension can be used to characterize the ancestry of the population from which a given annotation was derived. The extension is optional, and is considered unknown if not included. To indicate that an annotation is based on all assessed individuals, one can populate the extension with "ALL".

As with all implications, the explicit reference to the variant(s)/haplotype(s)/genotype(s)/molecular biomarker(s) being annotated must be provided in the Observation.derivedFrom field.

evidence-level versus clinical-significance

See Genomic Implication for guidance.

Differentiating AND vs OR

See Genomic Implication for guidance. Implication fields affected by this guidance include: derivedFrom, evidence-level, predicted-phenotype, genomic-risk-assessment.

Usages:

Examples for this Profile: Observation/pop-allele-freq

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..*	GenomicImplication	Genomic Annotation 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				Content/Rules for all slices
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.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.modifierExtension	This element is a modifier element.	0..*	Extension	Extensions that cannot be ignored
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	genomic-annotation 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" : "genomic-annotation" } ] }`
Observation.Slices for derivedFrom	This element is included in summaries.	1..*	Reference(DocumentReference \| ImagingStudy \| Media \| QuestionnaireResponse \| Observation \| MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
Observation.Slices for derivedFrom.derivedFrom:variant	This element is included in summaries.	0..*	Reference(Variant)	Variant the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:genotype	This element is included in summaries.	0..*	Reference(Genotype)	Genotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:haplotype	This element is included in summaries.	0..*	Reference(Haplotype)	Haplotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:biomarker	This element is included in summaries.	0..*	Reference(Molecular Biomarker)	MolecularBiomarker the implication is derived from
Observation.Slices for component	This element is included in summaries.	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code Slicing Note: The rules on this element (including its children) apply to all the slices, but are not repeated in them
Observation.Slices for component.component:All Slices				Content/Rules for all slices
Observation.Slices for component.component:All Slices.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:All Slices.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:All Slices.Slices for extension.extension:knowledgebase-ancestry-group		0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
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:evidence-level	This element is included in summaries.	0..*	BackboneElement	Level of Evidence
Observation.Slices for component.component:evidence-level.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:evidence-level.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:evidence-level.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:evidence-level.code	This element is included in summaries.	1..1	CodeableConcept	93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "93044-6" } ] }`
Observation.Slices for component.component:evidence-level.value[x]	This element is included in summaries.	1..1	CodeableConcept	1A \| 1B \| 2A \| 2B \| 3 \| 4 \| 4-star \| 3-star \| 2-star \| 1-star \| no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar
Observation.Slices for component.component:clinical-significance	This element is included in summaries.	0..1	BackboneElement	Clinical significance
Observation.Slices for component.component:clinical-significance.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:clinical-significance.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:clinical-significance.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:clinical-significance.code	This element is included in summaries.	1..1	CodeableConcept	53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "53037-8" } ] }`
Observation.Slices for component.component:clinical-significance.value[x]	This element is included in summaries.	1..1	CodeableConcept	Pathogenic \| Likely pathogenic \| Uncertain significance \| Likely benign \| Benign Binding: LOINC Answer List LL4034-6 (example)
Observation.Slices for component.component:knowledge-base	This element is included in summaries.	0..1	BackboneElement	Knowledge Base
Observation.Slices for component.component:knowledge-base.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:knowledge-base.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:knowledge-base.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:knowledge-base.code	This element is included in summaries.	1..1	CodeableConcept	knowledge-base 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" : "knowledge-base" } ] }`
Observation.Slices for component.component:knowledge-base.value[x]	This element is included in summaries.	1..1	CodeableConcept	Actual component result Binding: Knowledge Base Version Codes (example)
Observation.Slices for component.component:annotation-pipeline	This element is included in summaries.	0..1	BackboneElement	Annotation Pipeline
Observation.Slices for component.component:annotation-pipeline.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:annotation-pipeline.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:annotation-pipeline.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:annotation-pipeline.code	This element is included in summaries.	1..1	CodeableConcept	annotation-pipeline 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" : "annotation-pipeline" } ] }`
Observation.Slices for component.component:annotation-pipeline.value[x]	This element is included in summaries.	1..1	CodeableConcept	Actual component result
Observation.Slices for component.component:population-allele-frequency	This element is included in summaries.	0..*	BackboneElement	Population Allele Frequency
Observation.Slices for component.component:population-allele-frequency.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:population-allele-frequency.Slices for extension.extension:knowledgebase-ancestry-group		0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component.component:population-allele-frequency.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:population-allele-frequency.code	This element is included in summaries.	1..1	CodeableConcept	population-allele-frequency Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "92821-8" } ] }`
Observation.Slices for component.component:population-allele-frequency.value[x]	This element is included in summaries.	1..1	Quantity	Actual component result
Observation.Slices for component.component:conservation-score	This element is included in summaries.	0..*	BackboneElement	conservation score
Observation.Slices for component.component:conservation-score.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:conservation-score.Slices for extension.extension:knowledgebase-ancestry-group		0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component.component:conservation-score.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:conservation-score.code	This element is included in summaries.	1..1	CodeableConcept	conservation-score 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" : "conservation-score" } ] }`
Observation.Slices for component.component:conservation-score.value[x]	This element is included in summaries.	1..1	Quantity	Actual component result
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.
Observation.component:evidence-level.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:evidence-level.value[x]	Base	example	Evidence Level Examples	📦4.0.0-cibuild	This IG
Observation.component:clinical-significance.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:clinical-significance.value[x]	Base	example	LOINC Answer Codes for LL4034-6	∅	unknown?
Observation.component:knowledge-base.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:knowledge-base.value[x]	Base	example	Knowledge Base Version Codes	📦4.0.0-cibuild	This IG
Observation.component:annotation-pipeline.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:population-allele-frequency.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:conservation-score.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 GenomicImplication

Name	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	0..*	GenomicImplication	Genomic Annotation
Observation.code	1..1	CodeableConcept	genomic-annotation Required Pattern: `{ "coding" : [ { "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code" : "genomic-annotation" } ] }`
Observation.component	0..*	BackboneElement	Component results
Observation.component.Slices for extension			Content/Rules for all slices
Observation.component.Slices for extension.extension:knowledgebase-ancestry-group	0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component			Content/Rules for all slices
Observation.Slices for component.component:population-allele-frequency	0..*	BackboneElement	Population Allele Frequency
Observation.Slices for component.component:population-allele-frequency.Slices for extension			Content/Rules for all slices
Observation.Slices for component.component:population-allele-frequency.Slices for extension.extension:knowledgebase-ancestry-group	0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component.component:population-allele-frequency.code	1..1	CodeableConcept	population-allele-frequency Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "92821-8" } ] }`
Observation.Slices for component.component:population-allele-frequency.value[x]	1..1	Quantity	Actual component result
Observation.Slices for component.component:conservation-score	0..*	BackboneElement	conservation score
Observation.Slices for component.component:conservation-score.Slices for extension			Content/Rules for all slices
Observation.Slices for component.component:conservation-score.Slices for extension.extension:knowledgebase-ancestry-group	0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component.component:conservation-score.code	1..1	CodeableConcept	conservation-score Required Pattern: `{ "coding" : [ { "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code" : "conservation-score" } ] }`
Observation.Slices for component.component:conservation-score.value[x]	1..1	Quantity	Actual component result
Documentation for this format

Description & Constraints Filter:

Observation C 0..* GenomicImplication Genomic Annotation
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.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact

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

code

1..1

CodeableConcept

genomic-annotation
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" : "genomic-annotation"
    }
  ]
}

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.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.Slices for derivedFrom This element is included in summaries. 1..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()

Observation.Slices for derivedFrom.derivedFrom:variant This element is included in summaries. 0..* Reference(Variant) Variant the implication is derived from

Observation.Slices for derivedFrom.derivedFrom:genotype This element is included in summaries. 0..* Reference(Genotype) Genotype the implication is derived from

Observation.Slices for derivedFrom.derivedFrom:haplotype This element is included in summaries. 0..* Reference(Haplotype) Haplotype the implication is derived from

Observation.Slices for derivedFrom.derivedFrom:biomarker This element is included in summaries. 0..* Reference(Molecular Biomarker) MolecularBiomarker the implication is derived from

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

Slicing Note: The rules on this element (including its children) apply to all the slices, but are not repeated in them

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

Observation.Slices for component.component:All Slices.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact

Observation.Slices for component.component:All Slices.Slices for extension.extension:knowledgebase-ancestry-group 0..1 CodeableConcept Knowledgebase Ancestry Group
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group

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

Observation.Slices for component.component:evidence-level This element is included in summaries. 0..* BackboneElement Level of Evidence

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

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

Observation.Slices for component.component:evidence-level.Slices for extension Content/Rules for all slices

Observation.Slices for component.component:evidence-level.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact

Observation.Slices for component.component:evidence-level.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

93044-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern:

{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "93044-6"
    }
  ]
}

Observation.Slices for component.component:evidence-level.value[x] This element is included in summaries. 1..1 CodeableConcept 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star
Binding: Evidence Level Examples (example): PharmGKB or ClinVar

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

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

Observation.Slices for component.component:clinical-significance This element is included in summaries. 0..1 BackboneElement Clinical significance

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

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

Observation.Slices for component.component:clinical-significance.Slices for extension Content/Rules for all slices

Observation.Slices for component.component:clinical-significance.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact

Observation.Slices for component.component:clinical-significance.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

53037-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern:

{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "53037-8"
    }
  ]
}

Observation.Slices for component.component:clinical-significance.value[x] This element is included in summaries. 1..1 CodeableConcept Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (example)

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

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

Observation.Slices for component.component:knowledge-base This element is included in summaries. 0..1 BackboneElement Knowledge Base

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

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

Observation.Slices for component.component:knowledge-base.Slices for extension Content/Rules for all slices

Observation.Slices for component.component:knowledge-base.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact

Observation.Slices for component.component:knowledge-base.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

knowledge-base
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" : "knowledge-base"
    }
  ]
}

Observation.Slices for component.component:knowledge-base.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result
Binding: Knowledge Base Version Codes (example)

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

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

Observation.Slices for component.component:annotation-pipeline This element is included in summaries. 0..1 BackboneElement Annotation Pipeline

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

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

Observation.Slices for component.component:annotation-pipeline.Slices for extension Content/Rules for all slices

Observation.Slices for component.component:annotation-pipeline.Slices for extension.extension:workflow-relatedArtifact 0..* RelatedArtifact Documentation relevant to the 'parent' resource
URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact

Observation.Slices for component.component:annotation-pipeline.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

annotation-pipeline
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" : "annotation-pipeline"
    }
  ]
}

Observation.Slices for component.component:annotation-pipeline.value[x] This element is included in summaries. 1..1 CodeableConcept Actual component result

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

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

Observation.Slices for component.component:population-allele-frequency This element is included in summaries. 0..* BackboneElement Population Allele Frequency

Observation.Slices for component.component:population-allele-frequency.id 0..1 string Unique id for inter-element referencing

Observation.Slices for component.component:population-allele-frequency.Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url

Observation.Slices for component.component:population-allele-frequency.Slices for extension Content/Rules for all slices

Observation.Slices for component.component:population-allele-frequency.Slices for extension.extension:knowledgebase-ancestry-group 0..1 CodeableConcept Knowledgebase Ancestry Group
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group

Observation.Slices for component.component:population-allele-frequency.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

population-allele-frequency
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern:

{
  "coding" : [
    {
      "system" : "http://loinc.org",
      "code" : "92821-8"
    }
  ]
}

Observation.Slices for component.component:population-allele-frequency.value[x] This element is included in summaries. 1..1 Quantity Actual component result

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

Observation.Slices for component.component:population-allele-frequency.referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

Observation.Slices for component.component:conservation-score This element is included in summaries. 0..* BackboneElement conservation score

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

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

Observation.Slices for component.component:conservation-score.Slices for extension Content/Rules for all slices

Observation.Slices for component.component:conservation-score.Slices for extension.extension:knowledgebase-ancestry-group 0..1 CodeableConcept Knowledgebase Ancestry Group
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group

Observation.Slices for component.component:conservation-score.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

conservation-score
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" : "conservation-score"
    }
  ]
}

Observation.Slices for component.component:conservation-score.value[x] This element is included in summaries. 1..1 Quantity Actual component result

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

Observation.Slices for component.component:conservation-score.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.
Observation.component:evidence-level.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:evidence-level.value[x]	Base	example	Evidence Level Examples	📦4.0.0-cibuild	This IG
Observation.component:evidence-level.dataAbsentReason	Base	extensible	DataAbsentReason	📍4.0.1	FHIR Std.
Observation.component:evidence-level.interpretation	Base	extensible	Observation Interpretation Codes	📍4.0.1	FHIR Std.
Observation.component:clinical-significance.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:clinical-significance.value[x]	Base	example	LOINC Answer Codes for LL4034-6	∅	unknown?
Observation.component:clinical-significance.dataAbsentReason	Base	extensible	DataAbsentReason	📍4.0.1	FHIR Std.
Observation.component:clinical-significance.interpretation	Base	extensible	Observation Interpretation Codes	📍4.0.1	FHIR Std.
Observation.component:knowledge-base.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:knowledge-base.value[x]	Base	example	Knowledge Base Version Codes	📦4.0.0-cibuild	This IG
Observation.component:knowledge-base.dataAbsentReason	Base	extensible	DataAbsentReason	📍4.0.1	FHIR Std.
Observation.component:knowledge-base.interpretation	Base	extensible	Observation Interpretation Codes	📍4.0.1	FHIR Std.
Observation.component:annotation-pipeline.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:annotation-pipeline.dataAbsentReason	Base	extensible	DataAbsentReason	📍4.0.1	FHIR Std.
Observation.component:annotation-pipeline.interpretation	Base	extensible	Observation Interpretation Codes	📍4.0.1	FHIR Std.
Observation.component:population-allele-frequency.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:population-allele-frequency.dataAbsentReason	Base	extensible	DataAbsentReason	📍4.0.1	FHIR Std.
Observation.component:population-allele-frequency.interpretation	Base	extensible	Observation Interpretation Codes	📍4.0.1	FHIR Std.
Observation.component:conservation-score.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:conservation-score.dataAbsentReason	Base	extensible	DataAbsentReason	📍4.0.1	FHIR Std.
Observation.component:conservation-score.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 GenomicImplication

Summary

Mandatory: 0 element(2 nested mandatory elements)

Extensions

This structure refers to these extensions:

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group

Maturity: 2

Key Elements View

Name	Flags	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicImplication	Genomic Annotation 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				Content/Rules for all slices
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.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.modifierExtension	This element is a modifier element.	0..*	Extension	Extensions that cannot be ignored
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	genomic-annotation 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" : "genomic-annotation" } ] }`
Observation.Slices for derivedFrom	This element is included in summaries.	1..*	Reference(DocumentReference \| ImagingStudy \| Media \| QuestionnaireResponse \| Observation \| MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
Observation.Slices for derivedFrom.derivedFrom:variant	This element is included in summaries.	0..*	Reference(Variant)	Variant the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:genotype	This element is included in summaries.	0..*	Reference(Genotype)	Genotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:haplotype	This element is included in summaries.	0..*	Reference(Haplotype)	Haplotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:biomarker	This element is included in summaries.	0..*	Reference(Molecular Biomarker)	MolecularBiomarker the implication is derived from
Observation.Slices for component	This element is included in summaries.	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code Slicing Note: The rules on this element (including its children) apply to all the slices, but are not repeated in them
Observation.Slices for component.component:All Slices				Content/Rules for all slices
Observation.Slices for component.component:All Slices.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:All Slices.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:All Slices.Slices for extension.extension:knowledgebase-ancestry-group		0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
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:evidence-level	This element is included in summaries.	0..*	BackboneElement	Level of Evidence
Observation.Slices for component.component:evidence-level.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:evidence-level.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:evidence-level.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:evidence-level.code	This element is included in summaries.	1..1	CodeableConcept	93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "93044-6" } ] }`
Observation.Slices for component.component:evidence-level.value[x]	This element is included in summaries.	1..1	CodeableConcept	1A \| 1B \| 2A \| 2B \| 3 \| 4 \| 4-star \| 3-star \| 2-star \| 1-star \| no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar
Observation.Slices for component.component:clinical-significance	This element is included in summaries.	0..1	BackboneElement	Clinical significance
Observation.Slices for component.component:clinical-significance.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:clinical-significance.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:clinical-significance.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:clinical-significance.code	This element is included in summaries.	1..1	CodeableConcept	53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "53037-8" } ] }`
Observation.Slices for component.component:clinical-significance.value[x]	This element is included in summaries.	1..1	CodeableConcept	Pathogenic \| Likely pathogenic \| Uncertain significance \| Likely benign \| Benign Binding: LOINC Answer List LL4034-6 (example)
Observation.Slices for component.component:knowledge-base	This element is included in summaries.	0..1	BackboneElement	Knowledge Base
Observation.Slices for component.component:knowledge-base.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:knowledge-base.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:knowledge-base.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:knowledge-base.code	This element is included in summaries.	1..1	CodeableConcept	knowledge-base 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" : "knowledge-base" } ] }`
Observation.Slices for component.component:knowledge-base.value[x]	This element is included in summaries.	1..1	CodeableConcept	Actual component result Binding: Knowledge Base Version Codes (example)
Observation.Slices for component.component:annotation-pipeline	This element is included in summaries.	0..1	BackboneElement	Annotation Pipeline
Observation.Slices for component.component:annotation-pipeline.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:annotation-pipeline.Slices for extension.extension:workflow-relatedArtifact		0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.Slices for component.component:annotation-pipeline.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:annotation-pipeline.code	This element is included in summaries.	1..1	CodeableConcept	annotation-pipeline 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" : "annotation-pipeline" } ] }`
Observation.Slices for component.component:annotation-pipeline.value[x]	This element is included in summaries.	1..1	CodeableConcept	Actual component result
Observation.Slices for component.component:population-allele-frequency	This element is included in summaries.	0..*	BackboneElement	Population Allele Frequency
Observation.Slices for component.component:population-allele-frequency.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:population-allele-frequency.Slices for extension.extension:knowledgebase-ancestry-group		0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component.component:population-allele-frequency.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:population-allele-frequency.code	This element is included in summaries.	1..1	CodeableConcept	population-allele-frequency Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "92821-8" } ] }`
Observation.Slices for component.component:population-allele-frequency.value[x]	This element is included in summaries.	1..1	Quantity	Actual component result
Observation.Slices for component.component:conservation-score	This element is included in summaries.	0..*	BackboneElement	conservation score
Observation.Slices for component.component:conservation-score.Slices for extension				Content/Rules for all slices
Observation.Slices for component.component:conservation-score.Slices for extension.extension:knowledgebase-ancestry-group		0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component.component:conservation-score.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:conservation-score.code	This element is included in summaries.	1..1	CodeableConcept	conservation-score 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" : "conservation-score" } ] }`
Observation.Slices for component.component:conservation-score.value[x]	This element is included in summaries.	1..1	Quantity	Actual component result
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.
Observation.component:evidence-level.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:evidence-level.value[x]	Base	example	Evidence Level Examples	📦4.0.0-cibuild	This IG
Observation.component:clinical-significance.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:clinical-significance.value[x]	Base	example	LOINC Answer Codes for LL4034-6	∅	unknown?
Observation.component:knowledge-base.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:knowledge-base.value[x]	Base	example	Knowledge Base Version Codes	📦4.0.0-cibuild	This IG
Observation.component:annotation-pipeline.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:population-allele-frequency.code	Base	example	LOINC Codes	📍4.0.1	FHIR Std.
Observation.component:conservation-score.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 GenomicImplication

Name	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	0..*	GenomicImplication	Genomic Annotation
Observation.code	1..1	CodeableConcept	genomic-annotation Required Pattern: `{ "coding" : [ { "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code" : "genomic-annotation" } ] }`
Observation.component	0..*	BackboneElement	Component results
Observation.component.Slices for extension			Content/Rules for all slices
Observation.component.Slices for extension.extension:knowledgebase-ancestry-group	0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component			Content/Rules for all slices
Observation.Slices for component.component:population-allele-frequency	0..*	BackboneElement	Population Allele Frequency
Observation.Slices for component.component:population-allele-frequency.Slices for extension			Content/Rules for all slices
Observation.Slices for component.component:population-allele-frequency.Slices for extension.extension:knowledgebase-ancestry-group	0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component.component:population-allele-frequency.code	1..1	CodeableConcept	population-allele-frequency Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "92821-8" } ] }`
Observation.Slices for component.component:population-allele-frequency.value[x]	1..1	Quantity	Actual component result
Observation.Slices for component.component:conservation-score	0..*	BackboneElement	conservation score
Observation.Slices for component.component:conservation-score.Slices for extension			Content/Rules for all slices
Observation.Slices for component.component:conservation-score.Slices for extension.extension:knowledgebase-ancestry-group	0..1	CodeableConcept	Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Observation.Slices for component.component:conservation-score.code	1..1	CodeableConcept	conservation-score Required Pattern: `{ "coding" : [ { "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs", "code" : "conservation-score" } ] }`
Observation.Slices for component.component:conservation-score.value[x]	1..1	Quantity	Actual component result
Documentation for this format

Snapshot View