Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created
Slices for extension |  |  |  | Content/Rules for all slices
extension:secondary-finding |  | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure |  | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category |  | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory |  | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
category:geCategory |  | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
code | Σ | 1..1 | CodeableConcept | genomic-annotation Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: genomic-annotation
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant the implication is derived from
derivedFrom:genotype | Σ | 0..* | Reference(Genotype) | Genotype the implication is derived from
derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype the implication is derived from
derivedFrom:biomarker | Σ | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from
Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code
component:All Slices |  |  |  | Content/Rules for all slices
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
component:evidence-level | Σ | 0..* | BackboneElement | Level of Evidence
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93044-6
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 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
component:clinical-significance | Σ | 0..1 | BackboneElement | Clinical significance
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (example)
component:knowledge-base | Σ | 0..1 | BackboneElement | Knowledge Base
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | knowledge-base Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: knowledge-base
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Knowledge Base Version Codes (example)
component:annotation-pipeline | Σ | 0..1 | BackboneElement | Annotation Pipeline
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | annotation-pipeline Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: annotation-pipeline
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result
component:population-allele-frequency | Σ | 0..* | BackboneElement | Population Allele Frequency
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | population-allele-frequency Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92821-8
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | Quantity | Actual component result
component:conservation-score | Σ | 0..* | BackboneElement | conservation score
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | conservation-score Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conservation-score
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 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 | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation |  | 0..* | GenomicImplication | Genomic Annotation
code |  | 1..1 | CodeableConcept | genomic-annotation Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: genomic-annotation
component |  | 0..* | BackboneElement | Component results
Slices for extension |  |  |  | Content/Rules for all slices
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Slices for component |  |  |  | Content/Rules for all slices
component:population-allele-frequency |  | 0..* | BackboneElement | Population Allele Frequency
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact(5.2.0) | Documentation relevant to the 'parent' resource
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
code |  | 1..1 | CodeableConcept | population-allele-frequency Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92821-8
value[x] |  | 1..1 | Quantity | Actual component result
component:conservation-score |  | 0..* | BackboneElement | conservation score
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact(5.2.0) | Documentation relevant to the 'parent' resource
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
code |  | 1..1 | CodeableConcept | conservation-score Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conservation-score
value[x] |  | 1..1 | Quantity | Actual component result
Documentation for this format

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation | C | 0..* | GenomicImplication | Genomic Annotation Constraints: obs-6, obs-7
id | Σ | 0..1 | id | Logical id of this artifact
meta | Σ | 0..1 | Meta | Metadata about the resource
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created
language |  | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
Additional Bindings | Purpose
AllLanguages | Max Binding
text |  | 0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained |  | 0..* | Resource | Contained, inline Resources
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:secondary-finding |  | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure |  | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
identifier | Σ | 0..* | Identifier | Business Identifier for observation
basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order
partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) | Part of referenced event
status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category |  | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory |  | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text | Σ | 0..1 | string | Plain text representation of the concept
category:geCategory |  | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text | Σ | 0..1 | string | Plain text representation of the concept
code | Σ | 1..1 | CodeableConcept | genomic-annotation Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: genomic-annotation
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
subject | Σ | 0..1 | Reference(Patient | Group | Device | Location) | Who and/or what the observation is about
focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record
encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made
effective[x] | Σ | 0..1 |  | Clinically relevant time/time-period for observation
effectiveDateTime |  |  | dateTime |
effectivePeriod |  |  | Period |
effectiveTiming |  |  | Timing |
effectiveInstant |  |  | instant |
issued | Σ | 0..1 | instant | Date/Time this version was made available
performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation
dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
note |  | 0..* | CodedAnnotation | Comments about the Observation that also contain a coded type
bodySite |  | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method |  | 0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations.
specimen |  | 0..1 | Reference(Specimen) | Specimen used for this observation
device |  | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device
referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation Constraints: obs-3
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
low | C | 0..1 | SimpleQuantity(4.0.1) | Low Range, if relevant
high | C | 0..1 | SimpleQuantity(4.0.1) | High Range, if relevant
type |  | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
appliesTo |  | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
age |  | 0..1 | Range | Applicable age range, if relevant
text |  | 0..1 | string | Text based reference range in an observation
hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group
Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant the implication is derived from
derivedFrom:genotype | Σ | 0..* | Reference(Genotype) | Genotype the implication is derived from
derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype the implication is derived from
derivedFrom:biomarker | Σ | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from
Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code
component:All Slices |  |  |  | Content/Rules for all slices
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
value[x] | Σ | 0..1 |  | Actual component result
valueQuantity |  |  | Quantity |
valueCodeableConcept |  |  | CodeableConcept |
valueString |  |  | string |
valueBoolean |  |  | boolean |
valueInteger |  |  | integer |
valueRange |  |  | Range |
valueRatio |  |  | Ratio |
valueSampledData |  |  | SampledData |
valueTime |  |  | time |
valueDateTime |  |  | dateTime |
valuePeriod |  |  | Period |
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:evidence-level | Σ | 0..* | BackboneElement | Level of Evidence
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93044-6
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 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
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:clinical-significance | Σ | 0..1 | BackboneElement | Clinical significance
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (example)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:knowledge-base | Σ | 0..1 | BackboneElement | Knowledge Base
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | knowledge-base Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: knowledge-base
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Knowledge Base Version Codes (example)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:annotation-pipeline | Σ | 0..1 | BackboneElement | Annotation Pipeline
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | annotation-pipeline Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: annotation-pipeline
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:population-allele-frequency | Σ | 0..* | BackboneElement | Population Allele Frequency
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | population-allele-frequency Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92821-8
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | Quantity | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:conservation-score | Σ | 0..* | BackboneElement | conservation score
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | conservation-score Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conservation-score
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | Quantity | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
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()`

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
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created
Slices for extension |  |  |  | Content/Rules for all slices
extension:secondary-finding |  | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure |  | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category |  | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory |  | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
category:geCategory |  | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
code | Σ | 1..1 | CodeableConcept | genomic-annotation Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: genomic-annotation
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant the implication is derived from
derivedFrom:genotype | Σ | 0..* | Reference(Genotype) | Genotype the implication is derived from
derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype the implication is derived from
derivedFrom:biomarker | Σ | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from
Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code
component:All Slices |  |  |  | Content/Rules for all slices
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
component:evidence-level | Σ | 0..* | BackboneElement | Level of Evidence
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93044-6
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 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
component:clinical-significance | Σ | 0..1 | BackboneElement | Clinical significance
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (example)
component:knowledge-base | Σ | 0..1 | BackboneElement | Knowledge Base
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | knowledge-base Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: knowledge-base
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Knowledge Base Version Codes (example)
component:annotation-pipeline | Σ | 0..1 | BackboneElement | Annotation Pipeline
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | annotation-pipeline Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: annotation-pipeline
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result
component:population-allele-frequency | Σ | 0..* | BackboneElement | Population Allele Frequency
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | population-allele-frequency Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92821-8
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | Quantity | Actual component result
component:conservation-score | Σ | 0..* | BackboneElement | conservation score
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | conservation-score Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conservation-score
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 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 | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation |  | 0..* | GenomicImplication | Genomic Annotation
code |  | 1..1 | CodeableConcept | genomic-annotation Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: genomic-annotation
component |  | 0..* | BackboneElement | Component results
Slices for extension |  |  |  | Content/Rules for all slices
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
Slices for component |  |  |  | Content/Rules for all slices
component:population-allele-frequency |  | 0..* | BackboneElement | Population Allele Frequency
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact(5.2.0) | Documentation relevant to the 'parent' resource
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
code |  | 1..1 | CodeableConcept | population-allele-frequency Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92821-8
value[x] |  | 1..1 | Quantity | Actual component result
component:conservation-score |  | 0..* | BackboneElement | conservation score
Slices for extension |  |  |  | Content/Rules for all slices
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact(5.2.0) | Documentation relevant to the 'parent' resource
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
code |  | 1..1 | CodeableConcept | conservation-score Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conservation-score
value[x] |  | 1..1 | Quantity | Actual component result
Documentation for this format

Snapshot View

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation | C | 0..* | GenomicImplication | Genomic Annotation Constraints: obs-6, obs-7
id | Σ | 0..1 | id | Logical id of this artifact
meta | Σ | 0..1 | Meta | Metadata about the resource
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created
language |  | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
Additional Bindings | Purpose
AllLanguages | Max Binding
text |  | 0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained |  | 0..* | Resource | Contained, inline Resources
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:secondary-finding |  | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure |  | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
identifier | Σ | 0..* | Identifier | Business Identifier for observation
basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order
partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) | Part of referenced event
status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category |  | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory |  | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text | Σ | 0..1 | string | Plain text representation of the concept
category:geCategory |  | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text | Σ | 0..1 | string | Plain text representation of the concept
code | Σ | 1..1 | CodeableConcept | genomic-annotation Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: genomic-annotation
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
subject | Σ | 0..1 | Reference(Patient | Group | Device | Location) | Who and/or what the observation is about
focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record
encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made
effective[x] | Σ | 0..1 |  | Clinically relevant time/time-period for observation
effectiveDateTime |  |  | dateTime |
effectivePeriod |  |  | Period |
effectiveTiming |  |  | Timing |
effectiveInstant |  |  | instant |
issued | Σ | 0..1 | instant | Date/Time this version was made available
performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation
dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
note |  | 0..* | CodedAnnotation | Comments about the Observation that also contain a coded type
bodySite |  | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method |  | 0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations.
specimen |  | 0..1 | Reference(Specimen) | Specimen used for this observation
device |  | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device
referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation Constraints: obs-3
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
low | C | 0..1 | SimpleQuantity(4.0.1) | Low Range, if relevant
high | C | 0..1 | SimpleQuantity(4.0.1) | High Range, if relevant
type |  | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
appliesTo |  | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
age |  | 0..1 | Range | Applicable age range, if relevant
text |  | 0..1 | string | Text based reference range in an observation
hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group
Slices for derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant the implication is derived from
derivedFrom:genotype | Σ | 0..* | Reference(Genotype) | Genotype the implication is derived from
derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype the implication is derived from
derivedFrom:biomarker | Σ | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from
Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code
component:All Slices |  |  |  | Content/Rules for all slices
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
value[x] | Σ | 0..1 |  | Actual component result
valueQuantity |  |  | Quantity |
valueCodeableConcept |  |  | CodeableConcept |
valueString |  |  | string |
valueBoolean |  |  | boolean |
valueInteger |  |  | integer |
valueRange |  |  | Range |
valueRatio |  |  | Ratio |
valueSampledData |  |  | SampledData |
valueTime |  |  | time |
valueDateTime |  |  | dateTime |
valuePeriod |  |  | Period |
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:evidence-level | Σ | 0..* | BackboneElement | Level of Evidence
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 93044-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93044-6
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 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
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:clinical-significance | Σ | 0..1 | BackboneElement | Clinical significance
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 53037-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53037-8
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (example)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:knowledge-base | Σ | 0..1 | BackboneElement | Knowledge Base
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | knowledge-base Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: knowledge-base
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Knowledge Base Version Codes (example)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:annotation-pipeline | Σ | 0..1 | BackboneElement | Annotation Pipeline
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | annotation-pipeline Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: annotation-pipeline
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:population-allele-frequency | Σ | 0..* | BackboneElement | Population Allele Frequency
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | population-allele-frequency Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92821-8
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | Quantity | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:conservation-score | Σ | 0..* | BackboneElement | conservation score
id |  | 0..1 | string | Unique id for inter-element referencing
Slices for extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:workflow-relatedArtifact |  | 0..* | RelatedArtifact | Documentation relevant to the 'parent' resource URL: http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact
extension:knowledgebase-ancestry-group |  | 0..1 | CodeableConcept | Knowledgebase Ancestry Group URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/knowledgebase-ancestry-group
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | conservation-score Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (Complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conservation-score
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | Quantity | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation |  | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
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()`

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

Other representations of profile: CSV, Excel, Schematron