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: Sequence Phase Relationship

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship | Version: 4.0.0-cibuild
Standards status: Trial-use | Maturity Level: 2 | Computable Name: SequencePhaseRelationship
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.

Indicates whether two entities are in Cis (same strand) or Trans (opposite strand) relationship to each other.

A sequence phase relationship asserts a specific type of relationship between two variants or haplotypes.

Humans inherit a copy of each autosome from mother and father - each cell contains, for instance, a maternally-derived and a paternally-derived chromosome 7. We refer to the two chromosomes as 'homologous', and we can refer to each of the chromosomes as 'homologs'.

Where a person has two variants (or haplotypes) on chromosome 7, those variants can both be on the same homolog (i.e. both variants are on the maternally-derived chromosome), or those variants can be on different homologs (i.e. one variant is on the maternally-derived chromosome and one variant is on the paternally-derived chromosome).

Where the two variants are on the same homolog, the variants are said to be in a 'Cis' relationship. Where the two variants are on different homologs, the variants are said to be in a 'Trans' relationship.

Usages:

- Refer to this Profile: Genomic Report
- Examples for this Profile: Observation/SequencePhaseRelationExample1

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..* | GenomicFinding | 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
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 | 82120-7 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: 82120-7
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 C | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required)
method |  | 0..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
Slices for derivedFrom | Σ | 0..* | 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 in the relationship
derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype in the relationship
Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code
component:All Slices |  |  |  | Content/Rules for all slices
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:gene-studied | Σ | 0..* | BackboneElement | Gene Studied
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 48018-6 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: 48018-6
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 | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 48001-2 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: 48001-2
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 | Example: 1q21.1
component:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 62374-4 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: 62374-4
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 | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
component:chromosome-identifier | Σ | 0..* | BackboneElement | Chromosome Identifier
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 48000-4 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: 48000-4
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 | Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
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.value[x] | Base | required | Sequence Phase Relationships | 📦4.0.0-cibuild | This IG
Observation.method | Base | extensible | LOINC Answer Codes for LL4050-2 | ∅ | unknown?
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:gene-studied.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:gene-studied.​value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-cibuild | This IG
Observation.component:cytogenetic-location.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] | Base | extensible | LOINC Answer Codes for LL1040-6 | ∅ | unknown?
Observation.component:chromosome-identifier.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:chromosome-identifier.​value[x] | Base | required | LOINC Answer Codes for LL2938-0 | ∅ | unknown?

#### 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 GenomicFinding

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation |  | 0..* | GenomicFinding | Measurements and simple assertions
code |  | 1..1 | CodeableConcept | 82120-7 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: 82120-7
value[x] |  | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required)
method |  | 0..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
Slices for derivedFrom |  |  |  | Content/Rules for all slices
derivedFrom:variant |  | 0..* | Reference(Variant) | Variant in the relationship
derivedFrom:haplotype |  | 0..* | Reference(Haplotype) | Haplotype in the relationship
Documentation for this format

#### Terminology Bindings (Differential)

Path | Status | Usage | ValueSet | Version | Source
Observation.value[x] | Base | required | Sequence Phase Relationships | 📦4.0.0-cibuild | This IG
Observation.method | Base | extensible | LOINC Answer Codes for LL4050-2 | ∅ | unknown?

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation | C | 0..* | GenomicFinding | 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
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 | 82120-7 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: 82120-7
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
subject | Σ | 0..1 | Reference(Patient | Group | Device | Location) | Who and/or what the observation is about
focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record
encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made
effective[x] | Σ | 0..1 |  | Clinically relevant time/time-period for observation
effectiveDateTime |  |  | dateTime |
effectivePeriod |  |  | Period |
effectiveTiming |  |  | Timing |
effectiveInstant |  |  | instant |
issued | Σ | 0..1 | instant | Date/Time this version was made available
performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation
value[x] | Σ C | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required)
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 | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
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 | 0..* | 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 in the relationship
derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype in the relationship
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
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 | 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:gene-studied | Σ | 0..* | BackboneElement | Gene Studied
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 | 48018-6 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: 48018-6
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 | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
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:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location
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 | 48001-2 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: 48001-2
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 | Example: 1q21.1
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:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly
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 | 62374-4 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: 62374-4
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 | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
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:chromosome-identifier | Σ | 0..* | BackboneElement | Chromosome Identifier
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 | 48000-4 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: 48000-4
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 | Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
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.value[x] | Base | required | Sequence Phase Relationships | 📦4.0.0-cibuild | This IG
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 | extensible | LOINC Answer Codes for LL4050-2 | ∅ | unknown?
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:gene-studied.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:gene-studied.​value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-cibuild | This IG
Observation.component:gene-studied.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:gene-studied.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:cytogenetic-location.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:cytogenetic-location.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] | Base | extensible | LOINC Answer Codes for LL1040-6 | ∅ | unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:chromosome-identifier.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:chromosome-identifier.​value[x] | Base | required | LOINC Answer Codes for LL2938-0 | ∅ | unknown?
Observation.component:chromosome-identifier.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:chromosome-identifier.​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 GenomicFinding

Summary

Mandatory: 1 element

Structures

This structure refers to these other structures:

- Variant (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant)
- Haplotype (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype)

Maturity: 2

Key Elements View

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation | C | 0..* | GenomicFinding | 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
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 | 82120-7 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: 82120-7
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 C | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required)
method |  | 0..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
Slices for derivedFrom | Σ | 0..* | 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 in the relationship
derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype in the relationship
Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code
component:All Slices |  |  |  | Content/Rules for all slices
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:gene-studied | Σ | 0..* | BackboneElement | Gene Studied
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 48018-6 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: 48018-6
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 | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 48001-2 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: 48001-2
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 | Example: 1q21.1
component:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 62374-4 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: 62374-4
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 | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
component:chromosome-identifier | Σ | 0..* | BackboneElement | Chromosome Identifier
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | 48000-4 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: 48000-4
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 | Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
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.value[x] | Base | required | Sequence Phase Relationships | 📦4.0.0-cibuild | This IG
Observation.method | Base | extensible | LOINC Answer Codes for LL4050-2 | ∅ | unknown?
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:gene-studied.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:gene-studied.​value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-cibuild | This IG
Observation.component:cytogenetic-location.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] | Base | extensible | LOINC Answer Codes for LL1040-6 | ∅ | unknown?
Observation.component:chromosome-identifier.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:chromosome-identifier.​value[x] | Base | required | LOINC Answer Codes for LL2938-0 | ∅ | unknown?

#### 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 GenomicFinding

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation |  | 0..* | GenomicFinding | Measurements and simple assertions
code |  | 1..1 | CodeableConcept | 82120-7 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: 82120-7
value[x] |  | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required)
method |  | 0..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
Slices for derivedFrom |  |  |  | Content/Rules for all slices
derivedFrom:variant |  | 0..* | Reference(Variant) | Variant in the relationship
derivedFrom:haplotype |  | 0..* | Reference(Haplotype) | Haplotype in the relationship
Documentation for this format

#### Terminology Bindings (Differential)

Path | Status | Usage | ValueSet | Version | Source
Observation.value[x] | Base | required | Sequence Phase Relationships | 📦4.0.0-cibuild | This IG
Observation.method | Base | extensible | LOINC Answer Codes for LL4050-2 | ∅ | unknown?

Snapshot View

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
Observation | C | 0..* | GenomicFinding | 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
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 | 82120-7 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: 82120-7
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
subject | Σ | 0..1 | Reference(Patient | Group | Device | Location) | Who and/or what the observation is about
focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record
encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made
effective[x] | Σ | 0..1 |  | Clinically relevant time/time-period for observation
effectiveDateTime |  |  | dateTime |
effectivePeriod |  |  | Period |
effectiveTiming |  |  | Timing |
effectiveInstant |  |  | instant |
issued | Σ | 0..1 | instant | Date/Time this version was made available
performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation
value[x] | Σ C | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required)
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 | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
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 | 0..* | 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 in the relationship
derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype in the relationship
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
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 | 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:gene-studied | Σ | 0..* | BackboneElement | Gene Studied
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 | 48018-6 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: 48018-6
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 | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
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:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location
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 | 48001-2 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: 48001-2
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 | Example: 1q21.1
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:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly
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 | 62374-4 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: 62374-4
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 | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
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:chromosome-identifier | Σ | 0..* | BackboneElement | Chromosome Identifier
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 | 48000-4 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: 48000-4
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 | Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
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.value[x] | Base | required | Sequence Phase Relationships | 📦4.0.0-cibuild | This IG
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 | extensible | LOINC Answer Codes for LL4050-2 | ∅ | unknown?
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:gene-studied.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:gene-studied.​value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-cibuild | This IG
Observation.component:gene-studied.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:gene-studied.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:cytogenetic-location.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:cytogenetic-location.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] | Base | extensible | LOINC Answer Codes for LL1040-6 | ∅ | unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation | Base | extensible | Observation Interpretation Codes | 📍4.0.1 | FHIR Std.
Observation.component:chromosome-identifier.​code | Base | example | LOINC Codes | 📍4.0.1 | FHIR Std.
Observation.component:chromosome-identifier.​value[x] | Base | required | LOINC Answer Codes for LL2938-0 | ∅ | unknown?
Observation.component:chromosome-identifier.​dataAbsentReason | Base | extensible | DataAbsentReason | 📍4.0.1 | FHIR Std.
Observation.component:chromosome-identifier.​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 GenomicFinding

Summary

Mandatory: 1 element

Structures

This structure refers to these other structures:

- Variant (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant)
- Haplotype (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype)

Maturity: 2

Other representations of profile: CSV, Excel, Schematron