Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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: 3.0.1-SNAPSHOT
Active as of 2024-07-15 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.

Usage:

Formal Views of Profile Content

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

This structure is derived from GenomicFinding

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation GenomicFinding
... 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)
.... derivedFrom:variant 0..* Reference(Variant) Variant in the relationship
.... derivedFrom:haplotype 0..* Reference(Haplotype) Haplotype in the relationship

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Observation.value[x]requiredSequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/sequence-phase-relationship-vs
from this IG
Observation.methodextensibleLOINC LL4050-2
http://loinc.org/vs/LL4050-2
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* GenomicFinding Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension Content/Rules for all slices
.... 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.


.... 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
... 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
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
.... 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
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
... code Σ 1..1 CodeableConcept 82120-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] ΣC 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 pattern: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
...... 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: conclusion-string
.... 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
...... 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: 48018-6
..... 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
...... 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: 48001-2
..... 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
...... 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: 62374-4
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexamplePattern: LOINC Code 82120-7
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.value[x]requiredSequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/sequence-phase-relationship-vs
from this IG
Observation.methodextensibleLOINC LL4050-2
http://loinc.org/vs/LL4050-2
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.codeexamplePattern: LOINC Code 48018-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:cytogenetic-location.codeexamplePattern: LOINC Code 48001-2
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:reference-sequence-assembly.codeexamplePattern: LOINC Code 62374-4
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:reference-sequence-assembly.value[x]extensibleLOINC LL1040-6
http://loinc.org/vs/LL1040-6

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* GenomicFinding Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... 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 BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by pattern:url
.... 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.


.... 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] ΣC 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
obs-3: Must have at least a low or a high or text
.... 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 Low Range, if relevant
.... high C 0..1 SimpleQuantity 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 pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Extension
..... 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 Extension
..... 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 Extension
..... 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 Extension
..... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexamplePattern: LOINC Code 82120-7
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.value[x]requiredSequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/sequence-phase-relationship-vs
from this IG
Observation.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
from the FHIR Standard
Observation.methodextensibleLOINC LL4050-2
http://loinc.org/vs/LL4050-2
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
http://hl7.org/fhir/ValueSet/referencerange-meaning
from the FHIR Standard
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
http://hl7.org/fhir/ValueSet/referencerange-appliesto
from the FHIR Standard
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:conclusion-string.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:gene-studied.codeexamplePattern: LOINC Code 48018-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:gene-studied.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:gene-studied.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:cytogenetic-location.codeexamplePattern: LOINC Code 48001-2
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:cytogenetic-location.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:cytogenetic-location.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:reference-sequence-assembly.codeexamplePattern: LOINC Code 62374-4
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:reference-sequence-assembly.value[x]extensibleLOINC LL1040-6
http://loinc.org/vs/LL1040-6
Observation.component:reference-sequence-assembly.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:reference-sequence-assembly.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-3errorObservation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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

Differential View

This structure is derived from GenomicFinding

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation GenomicFinding
... 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)
.... derivedFrom:variant 0..* Reference(Variant) Variant in the relationship
.... derivedFrom:haplotype 0..* Reference(Haplotype) Haplotype in the relationship

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Observation.value[x]requiredSequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/sequence-phase-relationship-vs
from this IG
Observation.methodextensibleLOINC LL4050-2
http://loinc.org/vs/LL4050-2

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* GenomicFinding Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension Content/Rules for all slices
.... 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.


.... 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
... 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
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
.... 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
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: GE
... code Σ 1..1 CodeableConcept 82120-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


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] ΣC 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 pattern: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
...... 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: conclusion-string
.... 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
...... 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: 48018-6
..... 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
...... 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: 48001-2
..... 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
...... 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: 62374-4
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexamplePattern: LOINC Code 82120-7
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.value[x]requiredSequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/sequence-phase-relationship-vs
from this IG
Observation.methodextensibleLOINC LL4050-2
http://loinc.org/vs/LL4050-2
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.codeexamplePattern: LOINC Code 48018-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:cytogenetic-location.codeexamplePattern: LOINC Code 48001-2
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:reference-sequence-assembly.codeexamplePattern: LOINC Code 62374-4
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:reference-sequence-assembly.value[x]extensibleLOINC LL1040-6
http://loinc.org/vs/LL1040-6

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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()

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* GenomicFinding Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... 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 BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by pattern:url
.... 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.


.... 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] ΣC 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
obs-3: Must have at least a low or a high or text
.... 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 Low Range, if relevant
.... high C 0..1 SimpleQuantity 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 pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Extension
..... 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
.