Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

Resource Profile: Variant

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant Version: 4.0.0-ballot
Standards status: Trial-use Maturity Level: 2 Computable Name: Variant

Copyright/Legal: This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.

Details about a set of changes in the tested sample compared to a reference sequence.

Scope and Usage

This profile allows a full description of the variant found using properties from a variety of testing approaches and allowing for a variety of descriptive mechanisms. Labs are encouraged to populate what properties they know. In future versions of this implementation guide, HL7 may provide additional guidance on what properties should be sent in which situations and may subdivide Variant into multiple sub-profiles with more specific purpose.

Other Guidance

See Variant Reporting for details on use.

A variety of annotations (see variant implications) can be applied to identified variants, such as: (1) predicted molecular consequences (e.g. a prediction that a variant leads to loss of gene function); (2) diagnostic implications (e.g. presence of a variant indicates increased risk for breast cancer); (3) therapeutic implications (e.g. presence of a somatic variant is associated with sensitivity to a particular drug or eligibility into a clinical trial).

Most human genes are transcribed into multiple transcripts. The molecular consequences profile can be used to indicate transcript-specific predicted consequences, for one or more transcripts. In the Variant instance itself, one can also indicate a representative transcript-level HGVS and/or protein HGVS.

If implementers have additional variant annotations, the Variant profile is defined to allow flexibility. See the section on flexibility for additional guidancem, especially the guidance for the Open Slicing allowed on Observation.component.

Note on Molecular Consequence in STU2

The STU2 Variant profile contained the component slice molecular-consequence, which is no longer present in this profile. The functionality to communicate predicted molecular consequences has been moved to the Molecular Consequence profile. For those that have already implemented the STU2 solution and are in a transition, open slicing allows components above and beyond those specified in the Implementation Guide and therefore the STU2 method of communicating molecular consequence will not cause conformance errors. This approach should be used carefully and only during a transition period to ensure full compatibility with other systems that implement the full features of this 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..* GenomicFinding Variant
Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... contained 0..* Resource Contained, inline Resources
... 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
... status ?!Σ 1..1 code registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
..... coding 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 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 ΣC 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
... focus ?!Σ 0..* Reference(Resource) What the observation is about, when it is not about the subject of record
... Slices for value[x] ΣC 0..1 Actual result
Slice: Unordered, Open 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
.... valueAttachment Attachment
.... valueReference Reference(MolecularSequence)
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason C 0..1 CodeableConcept Why the result value is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) Related resource from which the observation is made
Slice: Unordered, Open by profile:resolve()
... Slices for component ΣC 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
.... component:conclusion-string ΣC 0..1 BackboneElement Clinical Conclusion
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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 ΣC 0..* BackboneElement Gene Studied
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..* BackboneElement Cytogenetic (Chromosome) Location
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Example: 1q21.1
.... component:reference-sequence-assembly ΣC 0..* BackboneElement Human Reference Sequence Assembly
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:chromosome-identifier ΣC 0..* BackboneElement Chromosome Identifier
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:representative-coding-hgvs ΣC 0..1 BackboneElement DNA change (c.HGVS)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq ΣC 0..1 BackboneElement Genomic Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-protein-ref-seq ΣC 0..1 BackboneElement Protein Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-transcript-ref-seq ΣC 0..1 BackboneElement Reference Transcript
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end ΣC 0..1 BackboneElement Exact Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
.... component:inner-start-end ΣC 0..1 BackboneElement Inner Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Range Imprecise variant inner-bounding range
.... component:outer-start-end ΣC 0..1 BackboneElement Outer Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Range Imprecise variant outer-bounding range
.... component:coordinate-system ΣC 0..1 BackboneElement Coordinate System
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Genomic Ref Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 string Normalized string per the VCF format.
.... component:alt-allele ΣC 0..1 BackboneElement Genomic Alt Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 string Normalized string per the VCF format.
.... component:coding-change-type ΣC 0..1 BackboneElement Coding DNA Change Type
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Genomic Source Class
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Sample Allelic Frequency
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Quantity Relative frequency in the sample
...... comparator ?! 0..1 code < | <= | >= | > | ad - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... system C 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth ΣC 0..1 BackboneElement Allelic Read Depth
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Quantity Unfiltered count of supporting reads
.... component:allelic-state ΣC 0..1 BackboneElement Allelic State
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance ΣC 0..1 BackboneElement Origin of germline genetic variant
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
.... component:variant-inheritance-basis ΣC 0..1 BackboneElement Evidential basis for variant inheritance
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
.... component:variation-code ΣC 0..* BackboneElement Variation Code
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... component:representative-protein-hgvs ΣC 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Genomic Structural Variant Copy Number
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Actual component result
...... valueQuantity Quantity
...... valueRange Range
.... component:variant-confidence-status ΣC 0..1 BackboneElement Variant Confidence Status
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:repeat-motif ΣC 0..* BackboneElement Repeat Motif
..... 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 ΣC 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] ΣC 1..1 string CAG
.... component:repeat-number ΣC 0..* BackboneElement Repeat Number
..... 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 ΣC 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] ΣC 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required Observation Status 📍6.0.0-ballot3 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.component.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-ballot This IG
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible ​ LOINC Answer Codes for LL1040-6 (missing link) 📦 unknown?
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required ​ LOINC Answer Codes for LL2938-0 (missing link) 📦 unknown?
Observation.component:representative-coding-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-ballot This IG
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible ​ LOINC Answer Codes for LL5489-1 (missing link) 📦 unknown?
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible ​ LOINC Answer Codes for LL4050-2 (missing link) 📦 unknown?
Observation.component:variation-code.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:copy-number.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-ballot This IG
Observation.component:repeat-motif.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📍6.0.0-ballot3 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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 Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8 error Observation bodyStructure SHALL only be present if Observation.bodySite is not present bodySite.exists() implies bodyStructure.empty()
obs-10 error Observation Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11 error Observation if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present (organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())

This structure is derived from GenomicFinding

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation 0..* GenomicFinding Variant
... code 1..1 CodeableConcept 69548-6
Required Pattern: At least the following
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
... Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period, Attachment, Reference(MolecularSequence) Actual result
Slice: Unordered, Open by type:$this
.... value[x]:valueCodeableConcept 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
.... component:representative-coding-hgvs 0..1 BackboneElement DNA change (c.HGVS)
..... code 1..1 CodeableConcept 48004-6
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
..... value[x] 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 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... code 1..1 CodeableConcept 81290-9
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81290-9
..... value[x] 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 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... code 1..1 CodeableConcept 81291-7
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81291-7
..... value[x] 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq 0..1 BackboneElement Genomic Reference Sequence
..... code 1..1 CodeableConcept 48013-7
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
..... value[x] 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-protein-ref-seq 0..1 BackboneElement Protein Reference Sequence
..... code 1..1 CodeableConcept protein-ref-seq
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: protein-ref-seq
..... value[x] 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-transcript-ref-seq 0..1 BackboneElement Reference Transcript
..... code 1..1 CodeableConcept 51958-7
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
..... value[x] 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end 0..1 BackboneElement Exact Start-End
..... code 1..1 CodeableConcept 81254-5
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
..... value[x] 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
.... component:inner-start-end 0..1 BackboneElement Inner Start-End
..... code 1..1 CodeableConcept 81302-2
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
..... value[x] 0..1 Range Imprecise variant inner-bounding range
.... component:outer-start-end 0..1 BackboneElement Outer Start-End
..... code 1..1 CodeableConcept 81301-4
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
..... value[x] 0..1 Range Imprecise variant outer-bounding range
.... component:coordinate-system 0..1 BackboneElement Coordinate System
..... code 1..1 CodeableConcept 92822-6
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
..... value[x] 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 0..1 BackboneElement Genomic Ref Allele
..... code 1..1 CodeableConcept 69547-8
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
..... value[x] 0..1 string Normalized string per the VCF format.
.... component:alt-allele 0..1 BackboneElement Genomic Alt Allele
..... code 1..1 CodeableConcept 69551-0
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
..... value[x] 0..1 string Normalized string per the VCF format.
.... component:coding-change-type 0..1 BackboneElement Coding DNA Change Type
..... code 1..1 CodeableConcept 48019-4
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
..... value[x] 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 0..1 BackboneElement Genomic Source Class
..... code 1..1 CodeableConcept 48002-0
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48002-0
..... value[x] 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 0..1 BackboneElement Sample Allelic Frequency
..... code 1..1 CodeableConcept 81258-6
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81258-6
..... value[x] 0..1 Quantity Relative frequency in the sample
...... system 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth 0..1 BackboneElement Allelic Read Depth
..... code 1..1 CodeableConcept 82121-5
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
..... value[x] 0..1 Quantity Unfiltered count of supporting reads
.... component:allelic-state 0..1 BackboneElement Allelic State
..... code 1..1 CodeableConcept 53034-5
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 53034-5
..... value[x] 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance 0..1 BackboneElement Origin of germline genetic variant
..... code 1..1 CodeableConcept 94186-4
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 94186-4
..... value[x] 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
.... component:variant-inheritance-basis 0..1 BackboneElement Evidential basis for variant inheritance
..... code 1..1 CodeableConcept Basis for allelic phase
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82309-6
..... value[x] 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
.... component:variation-code 0..* BackboneElement Variation Code
..... code 1..1 CodeableConcept 81252-9
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81252-9
..... value[x] 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... component:representative-protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... code 1..1 CodeableConcept 48005-3
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48005-3
..... value[x] 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 0..1 BackboneElement Genomic Structural Variant Copy Number
..... code 1..1 CodeableConcept 82155-3
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82155-3
..... value[x] 0..1 Actual component result
...... valueQuantity Quantity
...... valueRange Range
.... component:variant-confidence-status 0..1 BackboneElement Variant Confidence Status
..... code 1..1 CodeableConcept variant-confidence-status
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
..... value[x] 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:repeat-motif 0..* BackboneElement Repeat Motif
..... 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
..... code 1..1 CodeableConcept repeat-motif
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: repeat-motif
..... value[x] 1..1 string CAG
.... component:repeat-number 0..* BackboneElement Repeat Number
..... 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
..... code 1..1 CodeableConcept repeat-number
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: repeat-number
..... value[x] 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-ballot This IG
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:variant-inheritance.​value[x] Base extensible ​ LOINC Answer Codes for LL5489-1 (missing link) 📦 unknown?
Observation.component:variant-inheritance-basis.​value[x] Base extensible ​ LOINC Answer Codes for LL4050-2 (missing link) 📦 unknown?
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-ballot This IG
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicFinding Variant
Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
... 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: AllLanguages (required): IETF language tag for a human language
Additional BindingsPurpose
CommonLanguages Starter
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business Identifier for observation
... instantiates[x] Σ 0..1 canonical(ObservationDefinition), Reference(ObservationDefinition) Instantiates FHIR ObservationDefinition
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... triggeredBy 0..* BackboneElement Triggering observation(s)
.... 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
.... observation Σ 1..1 Reference(Observation) Triggering observation
.... type Σ 1..1 code reflex | repeat | re-run
Binding: TriggeredBytype (required): The type of TriggeredBy Observation.
.... reason 0..1 string Reason that the observation was triggered
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | GenomicStudy) Part of referenced event
... status ?!Σ 1..1 code registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
..... id 0..1 id Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding 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 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 id Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding 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 0..1 string Plain text representation of the concept
... code ΣC 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 Σ 0..1 Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct) 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
... organizer ΣC 0..1 boolean This observation organizes/groups a set of sub-observations
... encounter Σ 0..1 Reference(Encounter) Healthcare event during which this observation is made
... effective[x] Σ 0..1 Clinically relevant time/time-period for observation
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
... issued Σ 0..1 instant Date/Time this version was made available
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson | HealthcareService) Who is responsible for the observation
... Slices for value[x] ΣC 0..1 Actual result
Slice: Unordered, Open 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
.... valueAttachment Attachment
.... valueReference Reference(MolecularSequence)
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason C 0..1 CodeableConcept Why the result value 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 C 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts
... bodyStructure C 0..1 Reference(BodyStructure) Observed body structure
... method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen C 0..1 Reference(Specimen | Group) Specimen used for this observation
Constraints: obs-9
... device 0..1 Reference(Device | DeviceMetric) A reference to the device that generates the measurements or the device settings for the 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(6.0.0-ballot3) Low Range, if relevant
.... high C 0..1 SimpleQuantity(6.0.0-ballot3) High Range, if relevant
.... normalValue 0..1 CodeableConcept Normal value, if relevant
Binding: ObservationReferenceRangeNormalValueCodes (extensible): Codes identifying the normal value of the observation.
.... 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 C 0..1 markdown 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 | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) Related resource from which the observation is made
Slice: Unordered, Open by profile:resolve()
... Slices for component ΣC 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
.... component:All Slices Content/Rules for all slices
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
..... value[x] ΣC 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
...... valueAttachment Attachment
...... valueReference Reference(MolecularSequence)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:conclusion-string ΣC 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 ΣC 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] ΣC 0..1 string Summary conclusion (interpretation/impression)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:gene-studied ΣC 0..* BackboneElement Gene Studied
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 value 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 value
.... component:cytogenetic-location ΣC 0..* BackboneElement Cytogenetic (Chromosome) Location
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Example: 1q21.1
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:reference-sequence-assembly ΣC 0..* BackboneElement Human Reference Sequence Assembly
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:chromosome-identifier ΣC 0..* BackboneElement Chromosome Identifier
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 value 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 value
.... component:representative-coding-hgvs ΣC 0..1 BackboneElement DNA change (c.HGVS)
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:genomic-hgvs ΣC 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:cytogenomic-nomenclature ΣC 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... 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 ΣC 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] ΣC 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:genomic-ref-seq ΣC 0..1 BackboneElement Genomic Reference Sequence
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:representative-protein-ref-seq ΣC 0..1 BackboneElement Protein Reference Sequence
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:representative-transcript-ref-seq ΣC 0..1 BackboneElement Reference Transcript
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:exact-start-end ΣC 0..1 BackboneElement Exact Start-End
..... 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 ΣC 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] ΣC 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:inner-start-end ΣC 0..1 BackboneElement Inner Start-End
..... 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 ΣC 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] ΣC 0..1 Range Imprecise variant inner-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:outer-start-end ΣC 0..1 BackboneElement Outer Start-End
..... 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 ΣC 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] ΣC 0..1 Range Imprecise variant outer-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:coordinate-system ΣC 0..1 BackboneElement Coordinate System
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:ref-allele ΣC 0..1 BackboneElement Genomic Ref Allele
..... 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 ΣC 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] ΣC 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:alt-allele ΣC 0..1 BackboneElement Genomic Alt Allele
..... 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 ΣC 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] ΣC 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:coding-change-type ΣC 0..1 BackboneElement Coding DNA Change Type
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:genomic-source-class ΣC 0..1 BackboneElement Genomic Source Class
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:sample-allelic-frequency ΣC 0..1 BackboneElement Sample Allelic Frequency
..... 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 ΣC 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] ΣC 0..1 Quantity Relative frequency in the sample
...... id 0..1 id Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
...... value 0..1 decimal Numerical value (with implicit precision)
...... comparator ?! 0..1 code < | <= | >= | > | ad - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... unit 0..1 string Unit representation
...... system C 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code C 0..1 code Coded form of the unit
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:allelic-read-depth ΣC 0..1 BackboneElement Allelic Read Depth
..... 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 ΣC 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] ΣC 0..1 Quantity Unfiltered count of supporting reads
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:allelic-state ΣC 0..1 BackboneElement Allelic State
..... 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 ΣC 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] ΣC 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:variant-inheritance ΣC 0..1 BackboneElement Origin of germline genetic variant
..... 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 ΣC 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] ΣC 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:variant-inheritance-basis ΣC 0..1 BackboneElement Evidential basis for variant inheritance
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:variation-code ΣC 0..* BackboneElement Variation Code
..... 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 ΣC 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] ΣC 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:representative-protein-hgvs ΣC 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:copy-number ΣC 0..1 BackboneElement Genomic Structural Variant Copy Number
..... 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 ΣC 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] ΣC 0..1 Actual component result
...... valueQuantity Quantity
...... valueRange Range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:variant-confidence-status ΣC 0..1 BackboneElement Variant Confidence Status
..... 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 ΣC 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] ΣC 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:repeat-motif ΣC 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 ΣC 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] ΣC 1..1 string CAG
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:repeat-number ΣC 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 ΣC 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] ΣC 1..1 Quantity 40
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base required All Languages 📍6.0.0-ballot3 FHIR Std.
Observation.triggeredBy.​type Base required triggered Bytype 📍6.0.0-ballot3 FHIR Std.
Observation.status Base required Observation Status 📍6.0.0-ballot3 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📍6.0.0-ballot3 FHIR Std.
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.referenceRange.​normalValue Base extensible Observation Reference Range Normal Value Codes 📍6.0.0-ballot3 FHIR Std.
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📍6.0.0-ballot3 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-ballot This IG
Observation.component:gene-studied.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible ​ LOINC Answer Codes for LL1040-6 (missing link) 📦 unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required ​ LOINC Answer Codes for LL2938-0 (missing link) 📦 unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-coding-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:representative-coding-hgvs.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-ref-seq.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-transcript-ref-seq.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-ballot This IG
Observation.component:coding-change-type.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible ​ LOINC Answer Codes for LL5489-1 (missing link) 📦 unknown?
Observation.component:variant-inheritance.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible ​ LOINC Answer Codes for LL4050-2 (missing link) 📦 unknown?
Observation.component:variant-inheritance-basis.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance-basis.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:variation-code.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:representative-protein-hgvs.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-ballot This IG
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-motif.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-motif.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-motif.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-number.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-number.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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 Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8 error Observation bodyStructure SHALL only be present if Observation.bodySite is not present bodySite.exists() implies bodyStructure.empty()
obs-9 error Observation.specimen If Observation.specimen is a reference to Group, the group can only have specimens (reference.resolve().exists() and reference.resolve() is Group) implies reference.resolve().member.entity.resolve().all($this is Specimen)
obs-10 error Observation Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11 error Observation if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present (organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())

This structure is derived from GenomicFinding

Summary

Mandatory: 0 element(17 nested mandatory elements)

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

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

Maturity: 2

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicFinding Variant
Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... contained 0..* Resource Contained, inline Resources
... 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
... status ?!Σ 1..1 code registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
..... coding 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 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 ΣC 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
... focus ?!Σ 0..* Reference(Resource) What the observation is about, when it is not about the subject of record
... Slices for value[x] ΣC 0..1 Actual result
Slice: Unordered, Open 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
.... valueAttachment Attachment
.... valueReference Reference(MolecularSequence)
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason C 0..1 CodeableConcept Why the result value is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) Related resource from which the observation is made
Slice: Unordered, Open by profile:resolve()
... Slices for component ΣC 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
.... component:conclusion-string ΣC 0..1 BackboneElement Clinical Conclusion
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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 ΣC 0..* BackboneElement Gene Studied
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..* BackboneElement Cytogenetic (Chromosome) Location
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Example: 1q21.1
.... component:reference-sequence-assembly ΣC 0..* BackboneElement Human Reference Sequence Assembly
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:chromosome-identifier ΣC 0..* BackboneElement Chromosome Identifier
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:representative-coding-hgvs ΣC 0..1 BackboneElement DNA change (c.HGVS)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq ΣC 0..1 BackboneElement Genomic Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-protein-ref-seq ΣC 0..1 BackboneElement Protein Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-transcript-ref-seq ΣC 0..1 BackboneElement Reference Transcript
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end ΣC 0..1 BackboneElement Exact Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
.... component:inner-start-end ΣC 0..1 BackboneElement Inner Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Range Imprecise variant inner-bounding range
.... component:outer-start-end ΣC 0..1 BackboneElement Outer Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Range Imprecise variant outer-bounding range
.... component:coordinate-system ΣC 0..1 BackboneElement Coordinate System
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Genomic Ref Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 string Normalized string per the VCF format.
.... component:alt-allele ΣC 0..1 BackboneElement Genomic Alt Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 string Normalized string per the VCF format.
.... component:coding-change-type ΣC 0..1 BackboneElement Coding DNA Change Type
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Genomic Source Class
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Sample Allelic Frequency
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Quantity Relative frequency in the sample
...... comparator ?! 0..1 code < | <= | >= | > | ad - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... system C 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth ΣC 0..1 BackboneElement Allelic Read Depth
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Quantity Unfiltered count of supporting reads
.... component:allelic-state ΣC 0..1 BackboneElement Allelic State
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance ΣC 0..1 BackboneElement Origin of germline genetic variant
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
.... component:variant-inheritance-basis ΣC 0..1 BackboneElement Evidential basis for variant inheritance
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
.... component:variation-code ΣC 0..* BackboneElement Variation Code
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... component:representative-protein-hgvs ΣC 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 ΣC 0..1 BackboneElement Genomic Structural Variant Copy Number
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 0..1 Actual component result
...... valueQuantity Quantity
...... valueRange Range
.... component:variant-confidence-status ΣC 0..1 BackboneElement Variant Confidence Status
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:repeat-motif ΣC 0..* BackboneElement Repeat Motif
..... 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 ΣC 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] ΣC 1..1 string CAG
.... component:repeat-number ΣC 0..* BackboneElement Repeat Number
..... 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 ΣC 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] ΣC 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required Observation Status 📍6.0.0-ballot3 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.component.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-ballot This IG
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible ​ LOINC Answer Codes for LL1040-6 (missing link) 📦 unknown?
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required ​ LOINC Answer Codes for LL2938-0 (missing link) 📦 unknown?
Observation.component:representative-coding-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-ballot This IG
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible ​ LOINC Answer Codes for LL5489-1 (missing link) 📦 unknown?
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible ​ LOINC Answer Codes for LL4050-2 (missing link) 📦 unknown?
Observation.component:variation-code.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:copy-number.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-ballot This IG
Observation.component:repeat-motif.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📍6.0.0-ballot3 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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 Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8 error Observation bodyStructure SHALL only be present if Observation.bodySite is not present bodySite.exists() implies bodyStructure.empty()
obs-10 error Observation Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11 error Observation if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present (organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())

Differential View

This structure is derived from GenomicFinding

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation 0..* GenomicFinding Variant
... code 1..1 CodeableConcept 69548-6
Required Pattern: At least the following
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
... Slices for value[x] 0..1 Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period, Attachment, Reference(MolecularSequence) Actual result
Slice: Unordered, Open by type:$this
.... value[x]:valueCodeableConcept 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
.... component:representative-coding-hgvs 0..1 BackboneElement DNA change (c.HGVS)
..... code 1..1 CodeableConcept 48004-6
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
..... value[x] 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 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... code 1..1 CodeableConcept 81290-9
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81290-9
..... value[x] 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 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... code 1..1 CodeableConcept 81291-7
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81291-7
..... value[x] 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq 0..1 BackboneElement Genomic Reference Sequence
..... code 1..1 CodeableConcept 48013-7
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
..... value[x] 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-protein-ref-seq 0..1 BackboneElement Protein Reference Sequence
..... code 1..1 CodeableConcept protein-ref-seq
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: protein-ref-seq
..... value[x] 1..1 CodeableConcept Versioned protein reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:representative-transcript-ref-seq 0..1 BackboneElement Reference Transcript
..... code 1..1 CodeableConcept 51958-7
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
..... value[x] 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end 0..1 BackboneElement Exact Start-End
..... code 1..1 CodeableConcept 81254-5
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
..... value[x] 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
.... component:inner-start-end 0..1 BackboneElement Inner Start-End
..... code 1..1 CodeableConcept 81302-2
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
..... value[x] 0..1 Range Imprecise variant inner-bounding range
.... component:outer-start-end 0..1 BackboneElement Outer Start-End
..... code 1..1 CodeableConcept 81301-4
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
..... value[x] 0..1 Range Imprecise variant outer-bounding range
.... component:coordinate-system 0..1 BackboneElement Coordinate System
..... code 1..1 CodeableConcept 92822-6
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
..... value[x] 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 0..1 BackboneElement Genomic Ref Allele
..... code 1..1 CodeableConcept 69547-8
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
..... value[x] 0..1 string Normalized string per the VCF format.
.... component:alt-allele 0..1 BackboneElement Genomic Alt Allele
..... code 1..1 CodeableConcept 69551-0
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
..... value[x] 0..1 string Normalized string per the VCF format.
.... component:coding-change-type 0..1 BackboneElement Coding DNA Change Type
..... code 1..1 CodeableConcept 48019-4
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
..... value[x] 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 0..1 BackboneElement Genomic Source Class
..... code 1..1 CodeableConcept 48002-0
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48002-0
..... value[x] 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 0..1 BackboneElement Sample Allelic Frequency
..... code 1..1 CodeableConcept 81258-6
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81258-6
..... value[x] 0..1 Quantity Relative frequency in the sample
...... system 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth 0..1 BackboneElement Allelic Read Depth
..... code 1..1 CodeableConcept 82121-5
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
..... value[x] 0..1 Quantity Unfiltered count of supporting reads
.... component:allelic-state 0..1 BackboneElement Allelic State
..... code 1..1 CodeableConcept 53034-5
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 53034-5
..... value[x] 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance 0..1 BackboneElement Origin of germline genetic variant
..... code 1..1 CodeableConcept 94186-4
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 94186-4
..... value[x] 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
.... component:variant-inheritance-basis 0..1 BackboneElement Evidential basis for variant inheritance
..... code 1..1 CodeableConcept Basis for allelic phase
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82309-6
..... value[x] 1..1 CodeableConcept Directly measured | Family DNA | Family history | Inferred from population data
Binding: LOINC Answer List LL4050-2 (extensible)
.... component:variation-code 0..* BackboneElement Variation Code
..... code 1..1 CodeableConcept 81252-9
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81252-9
..... value[x] 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... component:representative-protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... code 1..1 CodeableConcept 48005-3
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48005-3
..... value[x] 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 0..1 BackboneElement Genomic Structural Variant Copy Number
..... code 1..1 CodeableConcept 82155-3
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82155-3
..... value[x] 0..1 Actual component result
...... valueQuantity Quantity
...... valueRange Range
.... component:variant-confidence-status 0..1 BackboneElement Variant Confidence Status
..... code 1..1 CodeableConcept variant-confidence-status
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
..... value[x] 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
.... component:repeat-motif 0..* BackboneElement Repeat Motif
..... 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
..... code 1..1 CodeableConcept repeat-motif
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: repeat-motif
..... value[x] 1..1 string CAG
.... component:repeat-number 0..* BackboneElement Repeat Number
..... 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
..... code 1..1 CodeableConcept repeat-number
Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: repeat-number
..... value[x] 1..1 Quantity 40

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-ballot This IG
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:variant-inheritance.​value[x] Base extensible ​ LOINC Answer Codes for LL5489-1 (missing link) 📦 unknown?
Observation.component:variant-inheritance-basis.​value[x] Base extensible ​ LOINC Answer Codes for LL4050-2 (missing link) 📦 unknown?
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-ballot This IG

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicFinding Variant
Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
... 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: AllLanguages (required): IETF language tag for a human language
Additional BindingsPurpose
CommonLanguages Starter
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:secondary-finding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business Identifier for observation
... instantiates[x] Σ 0..1 canonical(ObservationDefinition), Reference(ObservationDefinition) Instantiates FHIR ObservationDefinition
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... triggeredBy 0..* BackboneElement Triggering observation(s)
.... 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
.... observation Σ 1..1 Reference(Observation) Triggering observation
.... type Σ 1..1 code reflex | repeat | re-run
Binding: TriggeredBytype (required): The type of TriggeredBy Observation.
.... reason 0..1 string Reason that the observation was triggered
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | GenomicStudy) Part of referenced event
... status ?!Σ 1..1 code registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained
Binding: ObservationStatus (required): Codes providing the status of an observation.
... Slices for category 2..* CodeableConcept Classification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
.... category:labCategory 1..1 CodeableConcept Classification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
..... id 0..1 id Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding 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 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 id Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
..... coding 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 0..1 string Plain text representation of the concept
... code ΣC 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 Σ 0..1 Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct) 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
... organizer ΣC 0..1 boolean This observation organizes/groups a set of sub-observations
... encounter Σ 0..1 Reference(Encounter) Healthcare event during which this observation is made
... effective[x] Σ 0..1 Clinically relevant time/time-period for observation
.... effectiveDateTime dateTime
.... effectivePeriod Period
.... effectiveTiming Timing
.... effectiveInstant instant
... issued Σ 0..1 instant Date/Time this version was made available
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson | HealthcareService) Who is responsible for the observation
... Slices for value[x] ΣC 0..1 Actual result
Slice: Unordered, Open 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
.... valueAttachment Attachment
.... valueReference Reference(MolecularSequence)
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason C 0..1 CodeableConcept Why the result value 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 C 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts
... bodyStructure C 0..1 Reference(BodyStructure) Observed body structure
... method 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen C 0..1 Reference(Specimen | Group) Specimen used for this observation
Constraints: obs-9
... device 0..1 Reference(Device | DeviceMetric) A reference to the device that generates the measurements or the device settings for the 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(6.0.0-ballot3) Low Range, if relevant
.... high C 0..1 SimpleQuantity(6.0.0-ballot3) High Range, if relevant
.... normalValue 0..1 CodeableConcept Normal value, if relevant
Binding: ObservationReferenceRangeNormalValueCodes (extensible): Codes identifying the normal value of the observation.
.... 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 C 0..1 markdown 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 | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) Related resource from which the observation is made
Slice: Unordered, Open by profile:resolve()
... Slices for component ΣC 0..* BackboneElement Component results
Slice: Unordered, Open by value:code
.... component:All Slices Content/Rules for all slices
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
..... value[x] ΣC 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
...... valueAttachment Attachment
...... valueReference Reference(MolecularSequence)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:conclusion-string ΣC 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 ΣC 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] ΣC 0..1 string Summary conclusion (interpretation/impression)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:gene-studied ΣC 0..* BackboneElement Gene Studied
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 value 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 value
.... component:cytogenetic-location ΣC 0..* BackboneElement Cytogenetic (Chromosome) Location
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept Example: 1q21.1
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:reference-sequence-assembly ΣC 0..* BackboneElement Human Reference Sequence Assembly
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:chromosome-identifier ΣC 0..* BackboneElement Chromosome Identifier
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code ΣC 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] ΣC 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 value 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 value
.... component:representative-coding-hgvs ΣC 0..1 BackboneElement DNA change (c.HGVS)
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:genomic-hgvs ΣC 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:cytogenomic-nomenclature ΣC 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... 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 ΣC 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] ΣC 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:genomic-ref-seq ΣC 0..1 BackboneElement Genomic Reference Sequence
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:representative-protein-ref-seq ΣC 0..1 BackboneElement Protein Reference Sequence
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:representative-transcript-ref-seq ΣC 0..1 BackboneElement Reference Transcript
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:exact-start-end ΣC 0..1 BackboneElement Exact Start-End
..... 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 ΣC 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] ΣC 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:inner-start-end ΣC 0..1 BackboneElement Inner Start-End
..... 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 ΣC 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] ΣC 0..1 Range Imprecise variant inner-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:outer-start-end ΣC 0..1 BackboneElement Outer Start-End
..... 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 ΣC 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] ΣC 0..1 Range Imprecise variant outer-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:coordinate-system ΣC 0..1 BackboneElement Coordinate System
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:ref-allele ΣC 0..1 BackboneElement Genomic Ref Allele
..... 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 ΣC 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] ΣC 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:alt-allele ΣC 0..1 BackboneElement Genomic Alt Allele
..... 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 ΣC 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] ΣC 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:coding-change-type ΣC 0..1 BackboneElement Coding DNA Change Type
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:genomic-source-class ΣC 0..1 BackboneElement Genomic Source Class
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:sample-allelic-frequency ΣC 0..1 BackboneElement Sample Allelic Frequency
..... 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 ΣC 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] ΣC 0..1 Quantity Relative frequency in the sample
...... id 0..1 id Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
...... value 0..1 decimal Numerical value (with implicit precision)
...... comparator ?! 0..1 code < | <= | >= | > | ad - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... unit 0..1 string Unit representation
...... system C 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code C 0..1 code Coded form of the unit
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:allelic-read-depth ΣC 0..1 BackboneElement Allelic Read Depth
..... 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 ΣC 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] ΣC 0..1 Quantity Unfiltered count of supporting reads
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:allelic-state ΣC 0..1 BackboneElement Allelic State
..... 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 ΣC 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] ΣC 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:variant-inheritance ΣC 0..1 BackboneElement Origin of germline genetic variant
..... 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 ΣC 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] ΣC 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: LOINC Answer List LL5489-1 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:variant-inheritance-basis ΣC 0..1 BackboneElement Evidential basis for variant inheritance
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:variation-code ΣC 0..* BackboneElement Variation Code
..... 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 ΣC 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] ΣC 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:representative-protein-hgvs ΣC 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... 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 ΣC 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] ΣC 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 value 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 value
.... component:copy-number ΣC 0..1 BackboneElement Genomic Structural Variant Copy Number
..... 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 ΣC 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] ΣC 0..1 Actual component result
...... valueQuantity Quantity
...... valueRange Range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:variant-confidence-status ΣC 0..1 BackboneElement Variant Confidence Status
..... 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 ΣC 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] ΣC 1..1 CodeableConcept High | Intermediate | Low
Binding: Variant Confidence Status (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:repeat-motif ΣC 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 ΣC 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] ΣC 1..1 string CAG
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value
.... component:repeat-number ΣC 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 ΣC 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] ΣC 1..1 Quantity 40
..... dataAbsentReason C 0..1 CodeableConcept Why the component result value 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 value

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base required All Languages 📍6.0.0-ballot3 FHIR Std.
Observation.triggeredBy.​type Base required triggered Bytype 📍6.0.0-ballot3 FHIR Std.
Observation.status Base required Observation Status 📍6.0.0-ballot3 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.category:geCategory Base preferred Observation Category Codes 📍6.0.0-ballot3 FHIR Std.
Observation.code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📍6.0.0-ballot3 FHIR Std.
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.referenceRange.​normalValue Base extensible Observation Reference Range Normal Value Codes 📍6.0.0-ballot3 FHIR Std.
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📍6.0.0-ballot3 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📦4.0.0-ballot This IG
Observation.component:gene-studied.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible ​ LOINC Answer Codes for LL1040-6 (missing link) 📦 unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required ​ LOINC Answer Codes for LL2938-0 (missing link) 📦 unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-coding-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:representative-coding-hgvs.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-protein-ref-seq.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-transcript-ref-seq.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:representative-transcript-ref-seq.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📦4.0.0-ballot This IG
Observation.component:coding-change-type.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible ​ LOINC Answer Codes for LL5489-1 (missing link) 📦 unknown?
Observation.component:variant-inheritance.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance-basis.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance-basis.​value[x] Base extensible ​ LOINC Answer Codes for LL4050-2 (missing link) 📦 unknown?
Observation.component:variant-inheritance-basis.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-inheritance-basis.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:variation-code.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-hgvs.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📦4.0.0-ballot This IG
Observation.component:representative-protein-hgvs.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:representative-protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📦4.0.0-ballot This IG
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-motif.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-motif.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-motif.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-number.​code Base example LOINC Codes 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-number.​dataAbsentReason Base extensible Data Absent Reason 📍6.0.0-ballot3 FHIR Std.
Observation.component:repeat-number.​interpretation Base extensible Observation Interpretation Codes 📍6.0.0-ballot3 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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 Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8 error Observation bodyStructure SHALL only be present if Observation.bodySite is not present bodySite.exists() implies bodyStructure.empty()
obs-9 error Observation.specimen If Observation.specimen is a reference to Group, the group can only have specimens (reference.resolve().exists() and reference.resolve() is Group) implies reference.resolve().member.entity.resolve().all($this is Specimen)
obs-10 error Observation Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11 error Observation if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present (organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())

This structure is derived from GenomicFinding

Summary

Mandatory: 0 element(17 nested mandatory elements)

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

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

Maturity: 2

 

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