GenomeX Data Exchange FHIR IG
0.2.0 - draft

GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions

Resource Profile: GDX Variant

Official URL: http://mitre.org/gdx/StructureDefinition/GdxVariant Version: 0.2.0
Draft as of 2025-12-17 Computable Name: GdxVariant

GenomeX subset of variant profile.

For additional details on how to use this profile, please review the Variant Reporting page in the Genomics Reporting Implemention Guide.

Usages:

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.

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* Variant Variant
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 ?!SΣ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category S 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 SΣ 1..1 CodeableConcept 69548-6
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: 69548-6
..... 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
... subject SΣ 1..1 Reference(GDX Patient) Who and/or what the observation is about
... Slices for effective[x] SΣ 0..1 Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
.... effective[x]:effectiveDateTime SΣ 0..1 dateTime Clinically relevant time/time-period for observation
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization) Who is responsible for the observation
... Slices for value[x] SΣC 0..1 Actual result
Slice: Unordered, Closed by type:$this
.... valueQuantity Quantity
.... valueCodeableConcept CodeableConcept
.... valueString string
.... valueBoolean boolean
.... valueInteger integer
.... valueRange Range
.... valueRatio Ratio
.... valueSampledData SampledData
.... valueTime time
.... valueDateTime dateTime
.... valuePeriod Period
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... specimen S 0..1 Reference(Specimen) Specimen used for this observation
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
... Slices for component SΣ 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
...... 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 SΣ 0..* BackboneElement Gene Studied
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 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] SΣ 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 SΣ 0..* BackboneElement Human Reference Sequence Assembly
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 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] SΣ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:representative-coding-hgvs Σ 0..1 BackboneElement DNA change (c.HGVS)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48004-6
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: 48004-6
....... 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 A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:genomic-hgvs Σ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81290-9
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: 81290-9
....... 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 A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:cytogenomic-nomenclature Σ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81291-7
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: 81291-7
....... 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 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq Σ 0..1 BackboneElement Genomic Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48013-7
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: 48013-7
....... 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 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-protein-ref-seq Σ 0..1 BackboneElement Protein Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept protein-ref-seq
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: protein-ref-seq
....... 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 Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 51958-7
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: 51958-7
....... 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 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end Σ 0..1 BackboneElement Exact Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81254-5
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: 81254-5
....... 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:inner-start-end Σ 0..1 BackboneElement Inner Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81302-2
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: 81302-2
....... 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
.... component:outer-start-end Σ 0..1 BackboneElement Outer Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81301-4
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: 81301-4
....... 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
.... component:coordinate-system Σ 0..1 BackboneElement Coordinate System
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 92822-6
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: 92822-6
....... 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 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
.... component:ref-allele Σ 0..1 BackboneElement Genomic Ref Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:alt-allele Σ 0..1 BackboneElement Genomic Alt Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69551-0
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: 69551-0
....... 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:coding-change-type SΣ 0..1 BackboneElement Coding DNA Change Type
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48019-4
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: 48019-4
....... 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] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
.... component:genomic-source-class Σ 0..1 BackboneElement Genomic Source Class
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48002-0
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: 48002-0
....... 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 Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
.... component:sample-allelic-frequency Σ 0..1 BackboneElement Sample Allelic Frequency
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81258-6
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: 81258-6
....... 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
.... component:allelic-read-depth Σ 0..1 BackboneElement Allelic Read Depth
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82121-5
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: 82121-5
....... 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:allelic-state Σ 0..1 BackboneElement Allelic State
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 53034-5
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: 53034-5
....... 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 Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance Σ 0..1 BackboneElement Origin of germline genetic variant
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 94186-4
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: 94186-4
....... 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 Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
.... component:variant-inheritance-basis Σ 0..1 BackboneElement Evidential basis for variant inheritance
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Basis for allelic phase
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: 82309-6
....... 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 Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
.... component:variation-code Σ 0..* BackboneElement Variation Code
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81252-9
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: 81252-9
....... 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 ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... 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)
.... component:representative-protein-hgvs Σ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48005-3
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: 48005-3
....... 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 A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:copy-number Σ 0..1 BackboneElement Genomic Structural Variant Copy Number
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82155-3
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: 82155-3
....... 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:variant-confidence-status Σ 0..1 BackboneElement Variant Confidence Status
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-confidence-status
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: variant-confidence-status
....... 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 High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:repeat-motif Σ 0..* BackboneElement Repeat Motif
..... Slices for extension Content/Rules for all slices
...... extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-motif
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: repeat-motif
....... 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 string CAG
.... component:repeat-number Σ 0..* BackboneElement Repeat Number
..... Slices for extension Content/Rules for all slices
...... extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-number
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: repeat-number
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 Quantity 40

doco 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]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component: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) 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
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:representative-coding-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:genomic-source-class.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variation-code.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State 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?
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:copy-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:repeat-motif.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.

Constraints

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

This structure is derived from Variant

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation 0..* Variant Variant
... basedOn 0..* Reference(Genomic Service Request) Fulfills plan, proposal or order
... status S 1..1 code registered | preliminary | final | amended +
... category S 2..* CodeableConcept Classification of type of observation
... subject S 1..1 Reference(GDX Patient) Who and/or what the observation is about
... Slices for effective[x] S 0..1 dateTime, Period, Timing, instant Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effective[x]:effectiveDateTime S 0..1 dateTime Clinically relevant time/time-period for observation
... performer 0..* Reference(Practitioner | PractitionerRole | Organization) Who is responsible for the observation
... value[x] S 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual result
... dataAbsentReason S 0..1 CodeableConcept Why the result is missing
... specimen S 0..1 Reference(Specimen) Specimen used for this observation
... component S 0..* BackboneElement Component results
... Slices for component Content/Rules for all slices
.... component:gene-studied S 0..* BackboneElement Gene Studied
..... code S 1..1 CodeableConcept 48018-6
..... value[x] S 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.
.... component:reference-sequence-assembly S 0..* BackboneElement Human Reference Sequence Assembly
..... code S 1..1 CodeableConcept 62374-4
..... value[x] S 1..1 CodeableConcept GRCh37 | GRCh38 | ...
.... component:coding-change-type S 0..1 BackboneElement Coding DNA Change Type
..... code S 1..1 CodeableConcept 48019-4
..... value[x] S 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* Variant Variant
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 BindingsPurpose
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 pattern: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(Genomic Service Request) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) Part of referenced event
... status ?!SΣ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category S 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 SΣ 1..1 CodeableConcept 69548-6
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: 69548-6
..... 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
... subject SΣ 1..1 Reference(GDX Patient) 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
... Slices for effective[x] SΣ 0..1 Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
.... effective[x]:effectiveDateTime SΣ 0..1 dateTime Clinically relevant time/time-period for observation
... issued Σ 0..1 instant Date/Time this version was made available
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization) Who is responsible for the observation
... Slices for value[x] SΣC 0..1 Actual result
Slice: Unordered, Closed by type:$this
.... valueQuantity Quantity
.... valueCodeableConcept CodeableConcept
.... valueString string
.... valueBoolean boolean
.... valueInteger integer
.... valueRange Range
.... valueRatio Ratio
.... valueSampledData SampledData
.... valueTime time
.... valueDateTime dateTime
.... valuePeriod Period
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 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 Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 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 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
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
... Slices for component SΣ 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 SΣ 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 SΣ 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] SΣ 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 SΣ 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 SΣ 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] SΣ 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:representative-coding-hgvs Σ 0..1 BackboneElement DNA change (c.HGVS)
..... 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 48004-6
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: 48004-6
....... 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 A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (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
.... component:genomic-hgvs Σ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... 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 81290-9
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: 81290-9
....... 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 A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (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
.... component:cytogenomic-nomenclature Σ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... 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 81291-7
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: 81291-7
....... 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 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
..... 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:genomic-ref-seq Σ 0..1 BackboneElement Genomic Reference Sequence
..... 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 48013-7
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: 48013-7
....... 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 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... 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:representative-protein-ref-seq Σ 0..1 BackboneElement Protein Reference Sequence
..... 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 protein-ref-seq
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: protein-ref-seq
....... 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 Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... 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:representative-transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... 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 51958-7
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: 51958-7
....... 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 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... 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:exact-start-end Σ 0..1 BackboneElement Exact Start-End
..... 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 81254-5
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: 81254-5
....... 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 Range Range in question. 'High' can be omitted for single nucleotide variants.
..... 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:inner-start-end Σ 0..1 BackboneElement Inner Start-End
..... 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 81302-2
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: 81302-2
....... 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 0..1 Range Imprecise variant inner-bounding range
..... 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:outer-start-end Σ 0..1 BackboneElement Outer Start-End
..... 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 81301-4
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: 81301-4
....... 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 0..1 Range Imprecise variant outer-bounding range
..... 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:coordinate-system Σ 0..1 BackboneElement Coordinate System
..... 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 92822-6
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: 92822-6
....... 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 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (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:ref-allele Σ 0..1 BackboneElement Genomic Ref Allele
..... 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 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... 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:alt-allele Σ 0..1 BackboneElement Genomic Alt Allele
..... 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 69551-0
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: 69551-0
....... 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 Normalized string per the VCF format.
..... 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:coding-change-type SΣ 0..1 BackboneElement Coding DNA Change Type
..... 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 SΣ 1..1 CodeableConcept 48019-4
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: 48019-4
....... 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] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
..... 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:genomic-source-class Σ 0..1 BackboneElement Genomic Source Class
..... 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 48002-0
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: 48002-0
....... 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 Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (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:sample-allelic-frequency Σ 0..1 BackboneElement Sample Allelic Frequency
..... 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 81258-6
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: 81258-6
....... 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 0..1 Quantity Relative frequency in the sample
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
...... value Σ 0..1 decimal Numerical value (with implicit precision)
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... unit Σ 0..1 string Unit representation
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code Σ 0..1 code Coded form of the unit
..... 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:allelic-read-depth Σ 0..1 BackboneElement Allelic Read Depth
..... 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 82121-5
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: 82121-5
....... 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 Quantity Unfiltered count of supporting reads
..... 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:allelic-state Σ 0..1 BackboneElement Allelic State
..... 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 53034-5
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: 53034-5
....... 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 Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (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:variant-inheritance Σ 0..1 BackboneElement Origin of germline genetic variant
..... 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 94186-4
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: 94186-4
....... 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 Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (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:variant-inheritance-basis Σ 0..1 BackboneElement Evidential basis for variant inheritance
..... 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 Basis for allelic phase
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: 82309-6
....... 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 Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (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:variation-code Σ 0..* BackboneElement Variation Code
..... 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 81252-9
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: 81252-9
....... 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 ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
..... 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 Extension
..... 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
.... component:representative-protein-hgvs Σ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... 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 48005-3
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: 48005-3
....... 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 A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (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
.... component:copy-number Σ 0..1 BackboneElement Genomic Structural Variant Copy Number
..... 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 82155-3
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: 82155-3
....... 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 Actual component result
...... valueQuantity Quantity
...... valueRange Range
..... 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:variant-confidence-status Σ 0..1 BackboneElement Variant Confidence Status
..... 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 variant-confidence-status
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: variant-confidence-status
....... 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 High | Intermediate | Low
Binding: Variant Confidence Status (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
.... component:repeat-motif Σ 0..* BackboneElement Repeat Motif
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-motif
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: repeat-motif
....... 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 string CAG
..... 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:repeat-number Σ 0..* BackboneElement Repeat Number
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-number
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: repeat-number
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 Quantity 40
..... 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

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]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
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 LL4048-6 ∅ 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) 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
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:representative-coding-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:representative-coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:coding-change-type.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variant-inheritance-basis.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variation-code.​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.
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:representative-protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-motif.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-motif.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:repeat-motif.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-number.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:repeat-number.​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 Variant

Summary

Mandatory: 1 element
Must-Support: 19 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of Observation.effective[x]

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* Variant Variant
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 ?!SΣ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category S 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 SΣ 1..1 CodeableConcept 69548-6
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: 69548-6
..... 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
... subject SΣ 1..1 Reference(GDX Patient) Who and/or what the observation is about
... Slices for effective[x] SΣ 0..1 Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
.... effective[x]:effectiveDateTime SΣ 0..1 dateTime Clinically relevant time/time-period for observation
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization) Who is responsible for the observation
... Slices for value[x] SΣC 0..1 Actual result
Slice: Unordered, Closed by type:$this
.... valueQuantity Quantity
.... valueCodeableConcept CodeableConcept
.... valueString string
.... valueBoolean boolean
.... valueInteger integer
.... valueRange Range
.... valueRatio Ratio
.... valueSampledData SampledData
.... valueTime time
.... valueDateTime dateTime
.... valuePeriod Period
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... specimen S 0..1 Reference(Specimen) Specimen used for this observation
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
... Slices for component SΣ 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
...... 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 SΣ 0..* BackboneElement Gene Studied
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 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] SΣ 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 SΣ 0..* BackboneElement Human Reference Sequence Assembly
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 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] SΣ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:representative-coding-hgvs Σ 0..1 BackboneElement DNA change (c.HGVS)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48004-6
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: 48004-6
....... 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 A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:genomic-hgvs Σ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81290-9
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: 81290-9
....... 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 A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:cytogenomic-nomenclature Σ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81291-7
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: 81291-7
....... 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 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq Σ 0..1 BackboneElement Genomic Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48013-7
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: 48013-7
....... 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 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-protein-ref-seq Σ 0..1 BackboneElement Protein Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept protein-ref-seq
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: protein-ref-seq
....... 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 Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 51958-7
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: 51958-7
....... 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 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end Σ 0..1 BackboneElement Exact Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81254-5
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: 81254-5
....... 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:inner-start-end Σ 0..1 BackboneElement Inner Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81302-2
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: 81302-2
....... 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
.... component:outer-start-end Σ 0..1 BackboneElement Outer Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81301-4
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: 81301-4
....... 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
.... component:coordinate-system Σ 0..1 BackboneElement Coordinate System
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 92822-6
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: 92822-6
....... 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 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
.... component:ref-allele Σ 0..1 BackboneElement Genomic Ref Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:alt-allele Σ 0..1 BackboneElement Genomic Alt Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 69551-0
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: 69551-0
....... 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:coding-change-type SΣ 0..1 BackboneElement Coding DNA Change Type
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code SΣ 1..1 CodeableConcept 48019-4
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: 48019-4
....... 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] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
.... component:genomic-source-class Σ 0..1 BackboneElement Genomic Source Class
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48002-0
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: 48002-0
....... 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 Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
.... component:sample-allelic-frequency Σ 0..1 BackboneElement Sample Allelic Frequency
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81258-6
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: 81258-6
....... 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
.... component:allelic-read-depth Σ 0..1 BackboneElement Allelic Read Depth
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82121-5
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: 82121-5
....... 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:allelic-state Σ 0..1 BackboneElement Allelic State
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 53034-5
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: 53034-5
....... 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 Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance Σ 0..1 BackboneElement Origin of germline genetic variant
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 94186-4
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: 94186-4
....... 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 Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
.... component:variant-inheritance-basis Σ 0..1 BackboneElement Evidential basis for variant inheritance
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Basis for allelic phase
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: 82309-6
....... 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 Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
.... component:variation-code Σ 0..* BackboneElement Variation Code
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 81252-9
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: 81252-9
....... 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 ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... 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)
.... component:representative-protein-hgvs Σ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 48005-3
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: 48005-3
....... 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 A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:copy-number Σ 0..1 BackboneElement Genomic Structural Variant Copy Number
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept 82155-3
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: 82155-3
....... 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:variant-confidence-status Σ 0..1 BackboneElement Variant Confidence Status
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept variant-confidence-status
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: variant-confidence-status
....... 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 High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:repeat-motif Σ 0..* BackboneElement Repeat Motif
..... Slices for extension Content/Rules for all slices
...... extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-motif
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: repeat-motif
....... 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 string CAG
.... component:repeat-number Σ 0..* BackboneElement Repeat Number
..... Slices for extension Content/Rules for all slices
...... extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-number
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: repeat-number
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 Quantity 40

doco 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]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component: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) 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
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:representative-coding-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:genomic-source-class.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variation-code.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State 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?
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:copy-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:repeat-motif.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.

Constraints

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

Differential View

This structure is derived from Variant

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation 0..* Variant Variant
... basedOn 0..* Reference(Genomic Service Request) Fulfills plan, proposal or order
... status S 1..1 code registered | preliminary | final | amended +
... category S 2..* CodeableConcept Classification of type of observation
... subject S 1..1 Reference(GDX Patient) Who and/or what the observation is about
... Slices for effective[x] S 0..1 dateTime, Period, Timing, instant Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effective[x]:effectiveDateTime S 0..1 dateTime Clinically relevant time/time-period for observation
... performer 0..* Reference(Practitioner | PractitionerRole | Organization) Who is responsible for the observation
... value[x] S 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period Actual result
... dataAbsentReason S 0..1 CodeableConcept Why the result is missing
... specimen S 0..1 Reference(Specimen) Specimen used for this observation
... component S 0..* BackboneElement Component results
... Slices for component Content/Rules for all slices
.... component:gene-studied S 0..* BackboneElement Gene Studied
..... code S 1..1 CodeableConcept 48018-6
..... value[x] S 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.
.... component:reference-sequence-assembly S 0..* BackboneElement Human Reference Sequence Assembly
..... code S 1..1 CodeableConcept 62374-4
..... value[x] S 1..1 CodeableConcept GRCh37 | GRCh38 | ...
.... component:coding-change-type S 0..1 BackboneElement Coding DNA Change Type
..... code S 1..1 CodeableConcept 48019-4
..... value[x] S 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* Variant Variant
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 BindingsPurpose
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 pattern: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(Genomic Service Request) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) Part of referenced event
... status ?!SΣ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category S 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 SΣ 1..1 CodeableConcept 69548-6
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: 69548-6
..... 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
... subject SΣ 1..1 Reference(GDX Patient) 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
... Slices for effective[x] SΣ 0..1 Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
.... effective[x]:effectiveDateTime SΣ 0..1 dateTime Clinically relevant time/time-period for observation
... issued Σ 0..1 instant Date/Time this version was made available
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization) Who is responsible for the observation
... Slices for value[x] SΣC 0..1 Actual result
Slice: Unordered, Closed by type:$this
.... valueQuantity Quantity
.... valueCodeableConcept CodeableConcept
.... valueString string
.... valueBoolean boolean
.... valueInteger integer
.... valueRange Range
.... valueRatio Ratio
.... valueSampledData SampledData
.... valueTime time
.... valueDateTime dateTime
.... valuePeriod Period
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 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 Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 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 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
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
Slice: Unordered, Open by profile:resolve()
... Slices for component SΣ 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 SΣ 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 SΣ 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] SΣ 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 SΣ 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 SΣ 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] SΣ 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:representative-coding-hgvs Σ 0..1 BackboneElement DNA change (c.HGVS)
..... 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 48004-6
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: 48004-6
....... 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 A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (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
.... component:genomic-hgvs Σ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... 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 81290-9
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: 81290-9
....... 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 A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (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
.... component:cytogenomic-nomenclature Σ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... 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 81291-7
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: 81291-7
....... 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 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
..... 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:genomic-ref-seq Σ 0..1 BackboneElement Genomic Reference Sequence
..... 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 48013-7
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: 48013-7
....... 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 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... 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:representative-protein-ref-seq Σ 0..1 BackboneElement Protein Reference Sequence
..... 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 protein-ref-seq
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: protein-ref-seq
....... 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 Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... 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:representative-transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... 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 51958-7
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: 51958-7
....... 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 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... 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:exact-start-end Σ 0..1 BackboneElement Exact Start-End
..... 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 81254-5
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: 81254-5
....... 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 Range Range in question. 'High' can be omitted for single nucleotide variants.
..... 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:inner-start-end Σ 0..1 BackboneElement Inner Start-End
..... 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 81302-2
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: 81302-2
....... 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 0..1 Range Imprecise variant inner-bounding range
..... 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:outer-start-end Σ 0..1 BackboneElement Outer Start-End
..... 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 81301-4
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: 81301-4
....... 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 0..1 Range Imprecise variant outer-bounding range
..... 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:coordinate-system Σ 0..1 BackboneElement Coordinate System
..... 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 92822-6
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: 92822-6
....... 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 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (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:ref-allele Σ 0..1 BackboneElement Genomic Ref Allele
..... 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 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... 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:alt-allele Σ 0..1 BackboneElement Genomic Alt Allele
..... 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 69551-0
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: 69551-0
....... 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 Normalized string per the VCF format.
..... 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:coding-change-type SΣ 0..1 BackboneElement Coding DNA Change Type
..... 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 SΣ 1..1 CodeableConcept 48019-4
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: 48019-4
....... 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] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072
..... 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:genomic-source-class Σ 0..1 BackboneElement Genomic Source Class
..... 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 48002-0
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: 48002-0
....... 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 Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (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:sample-allelic-frequency Σ 0..1 BackboneElement Sample Allelic Frequency
..... 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 81258-6
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: 81258-6
....... 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 0..1 Quantity Relative frequency in the sample
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
...... value Σ 0..1 decimal Numerical value (with implicit precision)
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... unit Σ 0..1 string Unit representation
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code Σ 0..1 code Coded form of the unit
..... 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:allelic-read-depth Σ 0..1 BackboneElement Allelic Read Depth
..... 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 82121-5
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: 82121-5
....... 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 Quantity Unfiltered count of supporting reads
..... 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:allelic-state Σ 0..1 BackboneElement Allelic State
..... 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 53034-5
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: 53034-5
....... 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 Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (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:variant-inheritance Σ 0..1 BackboneElement Origin of germline genetic variant
..... 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 94186-4
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: 94186-4
....... 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 Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (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:variant-inheritance-basis Σ 0..1 BackboneElement Evidential basis for variant inheritance
..... 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 Basis for allelic phase
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: 82309-6
....... 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 Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (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:variation-code Σ 0..* BackboneElement Variation Code
..... 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 81252-9
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: 81252-9
....... 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 ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
..... 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 Extension
..... 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
.... component:representative-protein-hgvs Σ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... 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 48005-3
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: 48005-3
....... 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 A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (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
.... component:copy-number Σ 0..1 BackboneElement Genomic Structural Variant Copy Number
..... 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 82155-3
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: 82155-3
....... 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 Actual component result
...... valueQuantity Quantity
...... valueRange Range
..... 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:variant-confidence-status Σ 0..1 BackboneElement Variant Confidence Status
..... 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 variant-confidence-status
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: variant-confidence-status
....... 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 High | Intermediate | Low
Binding: Variant Confidence Status (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
.... component:repeat-motif Σ 0..* BackboneElement Repeat Motif
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-motif
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: repeat-motif
....... 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 string CAG
..... 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:repeat-number Σ 0..* BackboneElement Repeat Number
..... id 0..1 string Unique id for inter-element referencing
..... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
...... extension:repeat-motif-order 0..1 positiveInt Repeat Motif Order
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept repeat-number
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: repeat-number
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 Quantity 40
..... 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

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]:valueCodeableConcept Base required LOINC Answer Codes for LL1971-2 ∅ unknown?
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 LL4048-6 ∅ 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) 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
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:representative-coding-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:representative-coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:representative-coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not State Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not State Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-protein-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:representative-protein-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not State Unknown
Observation.component:representative-transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:representative-transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible LOINC Answer Codes for LL5323-2 ∅ unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:coding-change-type.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible LOINC Answer Codes for LL378-1 ∅ unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible LOINC Answer Codes for LL381-5 ∅ unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible LOINC Answer Codes for LL5489-1 ∅ unknown?
Observation.component:variant-inheritance.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible LOINC Answer Codes for LL4050-2 ∅ unknown?
Observation.component:variant-inheritance-basis.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-inheritance-basis.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not State Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variation-code.​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.
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:representative-protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:representative-protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦3.0.0-ballot Genomics Reporting Implementation Guide v3.0
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-motif.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-motif.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:repeat-motif.​interpretation Base extensible Observation Interpretation Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📦4.0.1 FHIR Std.
Observation.component:repeat-number.​dataAbsentReason Base extensible DataAbsentReason 📦4.0.1 FHIR Std.
Observation.component:repeat-number.​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 Variant

Summary

Mandatory: 1 element
Must-Support: 19 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of Observation.effective[x]

 

Other representations of profile: CSV, Excel, Schematron