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 Implication ( Abstract )

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

Properties common to genomic implications expressed as computable discrete elements.

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

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

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

- `derivedFrom` is a required field that provides an explicit reference from an implication to the variant(s) / haplotype(s) / genotype(s) / molecular biomarker(s) from which the implication is derived.
- `workflow-relatedArtifact (base extension) (component)` supports conveying references to citations, supporting documentation and other information relevant to the asserted implication, such as documentation which applies to the full implication Observation or to the component level information specific to the component's code and value (such as documentation supporting a specific clinical significance or evidence level value).
- `evidence-level (component)` indicates the strength of the evidence behind the asserted implication.
- `clinical-significance (component)` indicates the clinical impact of an implication.
- `knowledge-base (component)` indicates the database from which the annotation is derived. Annotations are obtained from different knowledge bases (e.g. Clinvar, gnomAD, 1000 Genomes). Knowledge bases continue to evolve, with new ones being developed, and existing ones being updated/revised.
- `annotation-pipeline (component)` indicates the name of the data pipeline that processed the genomic data file.

#### evidence-level versus clinical-significance

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

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

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

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

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

#### Differentiating AND vs OR

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

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

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

Implication fields affected by this guidance include:

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

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

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

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

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

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

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

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

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

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

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

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

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

Usages:

- Derived from this Profile: Diagnostic Implication, Genomic Annotation, Molecular Consequence and Therapeutic Implication

You can also check for usages in the FHIR IG Statistics

### Formal Views of Profile Content

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

- Key Elements Table
- Differential Table
- Snapshot Table
- Statistics/References
- All

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

#### Terminology Bindings

Path | Status | Usage | ValueSet | Version | Source
Observation.status | Base | required | ObservationStatus | 📍4.0.1 | FHIR Std.
Observation.category | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:conclusion-string.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​value[x] | Base | example | Evidence Level Examples | 📦4.0.0-cibuild | This IG
Observation.component:clinical-significance.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:clinical-significance.​value[x] | Base | example | LOINC Answer Codes for LL4034-6 | ∅ | unknown?
Observation.component:knowledge-base.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:knowledge-base.​value[x] | Base | example | Knowledge Base Version Codes | 📦4.0.0-cibuild | This IG
Observation.component:annotation-pipeline.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.

#### Constraints

Id | Grade | Path(s) | Description | Expression
dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources | `contained.contained.empty()`
dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource | `contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()`
dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated | `contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()`
dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label | `contained.meta.security.empty()`
dom-6 | best practice | Observation | A resource should have narrative for robust management | `text.`div`.exists()`
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children | `hasValue() or (children().count() > id.count())`
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both | `extension.exists() != value.exists()`
obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present | `dataAbsentReason.empty() or value.empty()`
obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present | `value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()`

This structure is derived from GenomicBase

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation |  | 0..* | GenomicBase | This is an abstract profile. Child profiles: DiagnosticImplication, GenomicAnnotation, MolecularConsequence, TherapeuticImplication Measurements and simple assertions
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
value[x] |  | 0..0 |  | Actual result
derivedFrom |  | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from
Slices for derivedFrom |  |  |  | Content/Rules for all slices
derivedFrom:variant |  | 0..* | Reference(Variant) | Variant the implication is derived from
derivedFrom:genotype |  | 0..* | Reference(Genotype) | Genotype the implication is derived from
derivedFrom:haplotype |  | 0..* | Reference(Haplotype) | Haplotype the implication is derived from
derivedFrom:biomarker |  | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from
component |  | 0..* | BackboneElement | Component results
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
Slices for component |  |  |  | Content/Rules for all slices
component:evidence-level |  | 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
code |  | 1..1 | CodeableConcept | 93044-6 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: 93044-6
value[x] |  | 1..1 | CodeableConcept | 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar
component:clinical-significance |  | 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
code |  | 1..1 | CodeableConcept | 53037-8 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: 53037-8
value[x] |  | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (example)
component:knowledge-base |  | 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
code |  | 1..1 | CodeableConcept | knowledge-base 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: knowledge-base
value[x] |  | 1..1 | CodeableConcept | Actual component result Binding: Knowledge Base Version Codes (example)
component:annotation-pipeline |  | 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
code |  | 1..1 | CodeableConcept | annotation-pipeline 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: annotation-pipeline
value[x] |  | 1..1 | CodeableConcept | Actual component result
Documentation for this format

#### Terminology Bindings (Differential)

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

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

#### Terminology Bindings

Path | Status | Usage | ValueSet | Version | Source
Observation.language | Base | preferred | Common Languages | 📍4.0.1 | FHIR Std.
Observation.status | Base | required | ObservationStatus | 📍4.0.1 | FHIR Std.
Observation.category | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.bodySite | Base | example | SNOMED CT Body Structures | 📍4.0.1 | FHIR Std.
Observation.method | Base | example | Observation Methods | 📍4.0.1 | FHIR Std.
Observation.referenceRange.​type | Base | preferred | Observation Reference Range Meaning Codes | 📍4.0.1 | FHIR Std.
Observation.referenceRange.​appliesTo | Base | example | Observation Reference Range Applies To Codes | 📍4.0.1 | FHIR Std.
Observation.component.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:conclusion-string.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:conclusion-string.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​value[x] | Base | example | Evidence Level Examples | 📦4.0.0-cibuild | This IG
Observation.component:evidence-level.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:clinical-significance.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:clinical-significance.​value[x] | Base | example | LOINC Answer Codes for LL4034-6 | ∅ | unknown?
Observation.component:clinical-significance.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:clinical-significance.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:knowledge-base.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:knowledge-base.​value[x] | Base | example | Knowledge Base Version Codes | 📦4.0.0-cibuild | This IG
Observation.component:knowledge-base.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:knowledge-base.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:annotation-pipeline.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:annotation-pipeline.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:annotation-pipeline.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.

#### Constraints

Id | Grade | Path(s) | Description | Expression
dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources | `contained.contained.empty()`
dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource | `contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()`
dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated | `contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()`
dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label | `contained.meta.security.empty()`
dom-6 | best practice | Observation | A resource should have narrative for robust management | `text.`div`.exists()`
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children | `hasValue() or (children().count() > id.count())`
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both | `extension.exists() != value.exists()`
obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text | `low.exists() or high.exists() or text.exists()`
obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present | `dataAbsentReason.empty() or value.empty()`
obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present | `value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()`

This structure is derived from GenomicBase

Summary

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

Structures

This structure refers to these other structures:

- Variant (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant)
- Genotype (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype)
- Haplotype (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype)
- Molecular Biomarker (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker)

Extensions

This structure refers to these extensions:

- http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact|5.2.0

Maturity: 2

Key Elements View

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

#### Terminology Bindings

Path | Status | Usage | ValueSet | Version | Source
Observation.status | Base | required | ObservationStatus | 📍4.0.1 | FHIR Std.
Observation.category | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:conclusion-string.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​value[x] | Base | example | Evidence Level Examples | 📦4.0.0-cibuild | This IG
Observation.component:clinical-significance.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:clinical-significance.​value[x] | Base | example | LOINC Answer Codes for LL4034-6 | ∅ | unknown?
Observation.component:knowledge-base.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:knowledge-base.​value[x] | Base | example | Knowledge Base Version Codes | 📦4.0.0-cibuild | This IG
Observation.component:annotation-pipeline.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.

#### Constraints

Id | Grade | Path(s) | Description | Expression
dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources | `contained.contained.empty()`
dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource | `contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()`
dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated | `contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()`
dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label | `contained.meta.security.empty()`
dom-6 | best practice | Observation | A resource should have narrative for robust management | `text.`div`.exists()`
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children | `hasValue() or (children().count() > id.count())`
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both | `extension.exists() != value.exists()`
obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present | `dataAbsentReason.empty() or value.empty()`
obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present | `value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()`

Differential View

This structure is derived from GenomicBase

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation |  | 0..* | GenomicBase | This is an abstract profile. Child profiles: DiagnosticImplication, GenomicAnnotation, MolecularConsequence, TherapeuticImplication Measurements and simple assertions
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
value[x] |  | 0..0 |  | Actual result
derivedFrom |  | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from
Slices for derivedFrom |  |  |  | Content/Rules for all slices
derivedFrom:variant |  | 0..* | Reference(Variant) | Variant the implication is derived from
derivedFrom:genotype |  | 0..* | Reference(Genotype) | Genotype the implication is derived from
derivedFrom:haplotype |  | 0..* | Reference(Haplotype) | Haplotype the implication is derived from
derivedFrom:biomarker |  | 0..* | Reference(Molecular Biomarker) | MolecularBiomarker the implication is derived from
component |  | 0..* | BackboneElement | Component results
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
Slices for component |  |  |  | Content/Rules for all slices
component:evidence-level |  | 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
code |  | 1..1 | CodeableConcept | 93044-6 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: 93044-6
value[x] |  | 1..1 | CodeableConcept | 1A | 1B | 2A | 2B | 3 | 4 | 4-star | 3-star | 2-star | 1-star | no-star Binding: Evidence Level Examples (example): PharmGKB or ClinVar
component:clinical-significance |  | 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
code |  | 1..1 | CodeableConcept | 53037-8 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: 53037-8
value[x] |  | 1..1 | CodeableConcept | Pathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign Binding: LOINC Answer List LL4034-6 (example)
component:knowledge-base |  | 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
code |  | 1..1 | CodeableConcept | knowledge-base 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: knowledge-base
value[x] |  | 1..1 | CodeableConcept | Actual component result Binding: Knowledge Base Version Codes (example)
component:annotation-pipeline |  | 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
code |  | 1..1 | CodeableConcept | annotation-pipeline 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: annotation-pipeline
value[x] |  | 1..1 | CodeableConcept | Actual component result
Documentation for this format

#### Terminology Bindings (Differential)

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

Snapshot View

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

#### Terminology Bindings

Path | Status | Usage | ValueSet | Version | Source
Observation.language | Base | preferred | Common Languages | 📍4.0.1 | FHIR Std.
Observation.status | Base | required | ObservationStatus | 📍4.0.1 | FHIR Std.
Observation.category | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍4.0.1 | FHIR Std.
Observation.code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.bodySite | Base | example | SNOMED CT Body Structures | 📍4.0.1 | FHIR Std.
Observation.method | Base | example | Observation Methods | 📍4.0.1 | FHIR Std.
Observation.referenceRange.​type | Base | preferred | Observation Reference Range Meaning Codes | 📍4.0.1 | FHIR Std.
Observation.referenceRange.​appliesTo | Base | example | Observation Reference Range Applies To Codes | 📍4.0.1 | FHIR Std.
Observation.component.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:conclusion-string.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:conclusion-string.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​value[x] | Base | example | Evidence Level Examples | 📦4.0.0-cibuild | This IG
Observation.component:evidence-level.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:evidence-level.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:clinical-significance.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:clinical-significance.​value[x] | Base | example | LOINC Answer Codes for LL4034-6 | ∅ | unknown?
Observation.component:clinical-significance.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:clinical-significance.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:knowledge-base.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:knowledge-base.​value[x] | Base | example | Knowledge Base Version Codes | 📦4.0.0-cibuild | This IG
Observation.component:knowledge-base.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:knowledge-base.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:annotation-pipeline.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:annotation-pipeline.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:annotation-pipeline.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.

#### Constraints

Id | Grade | Path(s) | Description | Expression
dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources | `contained.contained.empty()`
dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource | `contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()`
dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated | `contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()`
dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label | `contained.meta.security.empty()`
dom-6 | best practice | Observation | A resource should have narrative for robust management | `text.`div`.exists()`
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children | `hasValue() or (children().count() > id.count())`
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both | `extension.exists() != value.exists()`
obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text | `low.exists() or high.exists() or text.exists()`
obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present | `dataAbsentReason.empty() or value.empty()`
obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present | `value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()`

This structure is derived from GenomicBase

Summary

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

Structures

This structure refers to these other structures:

- Variant (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant)
- Genotype (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype)
- Haplotype (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype)
- Molecular Biomarker (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker)

Extensions

This structure refers to these extensions:

- http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact|5.2.0

Maturity: 2

Other representations of profile: CSV, Excel, Schematron