Genomic Implication - 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 Implication ( Abstract )

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

Properties common to genomic implications expressed as computable discrete elements.

The Genomic Implication profile is an abstract profile for therapeutic and diagnostic implications and molecular consequences. Implications are relevant information which are derived from the presence of a haplotype, genotype, variant or molecular biomarker. This portion of the implementation guide relies on the content in the General Genomic Reporting and Variant Reporting portions of this implementation guide.

At the heart of many genomic reports are findings (variants, haplotypes, genotypes, biomarkers) and annotations derived from those findings (diagnostic implications, therapeutic implications, predicted molecular consequences, other genomic annotations), as shown in the following figure:

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

derivedFrom is a required field that provides an explicit reference from an implication to the variant(s) / haplotype(s) / genotype(s) / molecular biomarker(s) from which the implication is derived.
workflow-relatedArtifact (base extension) (component) supports conveying references to citations, supporting documentation and other information relevant to the asserted implication, such as documentation which applies to the full implication Observation or to the component level information specific to the component's code and value (such as documentation supporting a specific clinical significance or evidence level value).
evidence-level (component) indicates the strength of the evidence behind the asserted implication.
clinical-significance (component) indicates the clinical impact of an implication.
knowledge-base (component) 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.
annotation-pipeline (component) indicates the name of the data pipeline that processed the genomic data file.

evidence-level versus clinical-significance

evidence-level: The amount of observed support for the association between an implication and a variant / haplotype / genotype / biomarker. There are dozens if not hundreds of evidence-level value sets, generally providing an ordinal range of codes from low evidence (e.g. 'predicted', 'case report', '1-star') to high evidence (e.g. 'professional society guideline', 'expert panel consensus', '1A').

clinical-significance: The clinical impact of an implication on a person's health. There are dozens if not hundreds of clinical-significance value sets, generally providing an ordinal range of codes from low significance (e.g. 'benign') to high significance (e.g. 'pathogenic', 'oncogenic','predictive of drug response').

While evidence and significance are orthogonal concepts, some codes conflate the two (e.g. 'expert panel consensus of strong efficacy', 'strong evidence refutes the clinical utility of this drug', 'case report evidence of pathogenicity'). In general, using discrete evidence and significance codes allow for a more precise characterization of an implication. Where an implementation is using a conflated code, we recommend communicating that code in the evidence-level field.

Examples of other code sets for evidence-level and clinical-significance:

ACMG_Level of evidence
Oncokb levels
US FDA levels
AMP/ASCO/CAP levels
Classification on ClinVar submitted records
Bioportal clinical variant interpretation
CIViC Evidence
CIViC Significance

Differentiating AND vs OR

There are several cases where it is necessary to differentiate 'AND' conditions (e.g. both drug X AND drug Y, in combination, are indicated in the presence of a variant) vs. 'OR' conditions (e.g., either drug X OR drug Y are indicated in the presence of a variant).

This situation is not unique to genomic implications, and arises elsewhere within FHIR (e.g. FHIR Search) and outside of FHIR (e.g., ClinVar submission API condition set). To be consistent with other precedents:

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

Implication fields affected by this guidance include:

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

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

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

Genomic annotations: derivedFrom, evidence-level, population-allele-frequency, conservation-score.

Here are examples of these rules with DiagnosticImplication (but the principles would apply to any Implication):

Example 1: Variant X is pathogenic for Disease Y AND Disease Z (in combination)

Implementation: One DiagnosticImplication with two predicted-phenotype instances for Disease Y and Disease Z that is derivedFrom one Variant for VariantX

Example 2: Variant X might be pathogenic for Disease Y alone, or Disease Z alone

Implementation: Two DiagnosticImplications, one with predicted-phenotype for DiseaseY, second with predicted-phenotype for DiseaseZ, and both are derivedFrom the same Variant for VariantX

Example 3: Variant X AND Variant Y (in combination) are pathogenic for Disease Z

Implementation: One DiagnosticImplications with predicted-phenotype for DiseaseZ that is derivedFrom the two Variants (VariantX and VariantY)

Example 4: Variant X OR Variant Y might be pathogenic for Disease Z

Implementation: Two DiagnosticImplications, each with predicted-phenotype for DiseaseZ, one that is derivedFrom a Variant for VariantX, the other that is derivedFrom a Variant for VariantY

Usages:

Derived from this Profile: Diagnostic Implication, Genomic Annotation, Molecular Consequence and Therapeutic 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..*	GenomicBase	This is an abstract profile. Child profiles: DiagnosticImplication, TherapeuticImplication, GenomicAnnotation, MolecularConsequence 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				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	Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
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		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.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
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.

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 GenomicBase

Name	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	0..*	GenomicBase	This is an abstract profile. Child profiles: DiagnosticImplication, TherapeuticImplication, GenomicAnnotation, MolecularConsequence Measurements and simple assertions
Observation.Slices for extension			Content/Rules for all slices
Observation.Slices for extension.extension:workflow-relatedArtifact	0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.value[x]	0..0		Actual result
Observation.derivedFrom	1..*	Reference(DocumentReference \| ImagingStudy \| Media \| QuestionnaireResponse \| Observation \| MolecularSequence)	Related measurements the observation is made from
Observation.Slices for derivedFrom			Content/Rules for all slices
Observation.Slices for derivedFrom.derivedFrom:variant	0..*	Reference(Variant)	Variant the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:genotype	0..*	Reference(Genotype)	Genotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:haplotype	0..*	Reference(Haplotype)	Haplotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:biomarker	0..*	Reference(Molecular Biomarker)	MolecularBiomarker the implication is derived from
Observation.component	0..*	BackboneElement	Component results
Observation.component.Slices for extension	0..*	Extension	Extension Slice: Unordered, Open by value:url
Observation.component.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			Content/Rules for all slices
Observation.Slices for component.component:evidence-level	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.code	1..1	CodeableConcept	93044-6 Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "93044-6" } ] }`
Observation.Slices for component.component:evidence-level.value[x]	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	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.code	1..1	CodeableConcept	53037-8 Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "53037-8" } ] }`
Observation.Slices for component.component:clinical-significance.value[x]	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	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.code	1..1	CodeableConcept	knowledge-base 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]	1..1	CodeableConcept	Actual component result Binding: Knowledge Base Version Codes (example)
Observation.Slices for component.component:annotation-pipeline	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.code	1..1	CodeableConcept	annotation-pipeline 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]	1..1	CodeableConcept	Actual component result
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
Observation.component:evidence-level.value[x]	Base	example	Evidence Level Examples	📦4.0.0-cibuild	This IG
Observation.component:clinical-significance.value[x]	Base	example	LOINC Answer Codes for LL4034-6	∅	unknown?
Observation.component:knowledge-base.value[x]	Base	example	Knowledge Base Version Codes	📦4.0.0-cibuild	This IG

Description & Constraints Filter:

Observation C 0..* GenomicBase This is an abstract profile. Child profiles: DiagnosticImplication, TherapeuticImplication, GenomicAnnotation, MolecularConsequence
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.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

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.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.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

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.

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 GenomicBase

Summary

Mandatory: 1 element(4 nested mandatory elements)
Prohibited: 1 element

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact|5.4.0

Maturity: 2

Key Elements View

Name	Flags	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicBase	This is an abstract profile. Child profiles: DiagnosticImplication, TherapeuticImplication, GenomicAnnotation, MolecularConsequence 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				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	Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
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		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.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
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.

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 GenomicBase

Name	Card.	Type	Description & Constraints Filter: Bindings Constraints Obligations
Observation	0..*	GenomicBase	This is an abstract profile. Child profiles: DiagnosticImplication, TherapeuticImplication, GenomicAnnotation, MolecularConsequence Measurements and simple assertions
Observation.Slices for extension			Content/Rules for all slices
Observation.Slices for extension.extension:workflow-relatedArtifact	0..*	RelatedArtifact	Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
Observation.value[x]	0..0		Actual result
Observation.derivedFrom	1..*	Reference(DocumentReference \| ImagingStudy \| Media \| QuestionnaireResponse \| Observation \| MolecularSequence)	Related measurements the observation is made from
Observation.Slices for derivedFrom			Content/Rules for all slices
Observation.Slices for derivedFrom.derivedFrom:variant	0..*	Reference(Variant)	Variant the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:genotype	0..*	Reference(Genotype)	Genotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:haplotype	0..*	Reference(Haplotype)	Haplotype the implication is derived from
Observation.Slices for derivedFrom.derivedFrom:biomarker	0..*	Reference(Molecular Biomarker)	MolecularBiomarker the implication is derived from
Observation.component	0..*	BackboneElement	Component results
Observation.component.Slices for extension	0..*	Extension	Extension Slice: Unordered, Open by value:url
Observation.component.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			Content/Rules for all slices
Observation.Slices for component.component:evidence-level	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.code	1..1	CodeableConcept	93044-6 Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "93044-6" } ] }`
Observation.Slices for component.component:evidence-level.value[x]	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	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.code	1..1	CodeableConcept	53037-8 Required Pattern: `{ "coding" : [ { "system" : "http://loinc.org", "code" : "53037-8" } ] }`
Observation.Slices for component.component:clinical-significance.value[x]	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	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.code	1..1	CodeableConcept	knowledge-base 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]	1..1	CodeableConcept	Actual component result Binding: Knowledge Base Version Codes (example)
Observation.Slices for component.component:annotation-pipeline	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.code	1..1	CodeableConcept	annotation-pipeline 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]	1..1	CodeableConcept	Actual component result
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
Observation.component:evidence-level.value[x]	Base	example	Evidence Level Examples	📦4.0.0-cibuild	This IG
Observation.component:clinical-significance.value[x]	Base	example	LOINC Answer Codes for LL4034-6	∅	unknown?
Observation.component:knowledge-base.value[x]	Base	example	Knowledge Base Version Codes	📦4.0.0-cibuild	This IG

Snapshot View