Onconova Implementation Guide
0.2.0 - ci-build

Onconova Implementation Guide - Local Development build (v0.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Resource Profile: Genomic Variant Profile

Official URL: http://onconova.github.io/fhir/StructureDefinition/onconova-genomic-variant Version: 0.2.0
Active as of 2025-10-17 Computable Name: OnconovaGenomicVariant

A profile representing a genomic variant identified for a cancer patient.

This profile extends the base mCODE GenomicVariant profile (which in turn profiles the Genomics Reporting Variant profile) to include specific constraints and extensions relevant to Onconova.

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..* GenomicVariant(4.0.0) Variant
Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
Constraints: ext-1
.... 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.
Constraints: ext-1
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Constraints: ext-1
.... extension:genePanel 0..1 string Gene Panel
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-gene-panel
Constraints: ext-1
.... extension:hgvsVersion 1..1 string HGVS Version
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-hgvs-version
Constraints: ext-1
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
Constraints: ext-1
... Slices for category S 1..* 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.

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id 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
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
... code SΣ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject SΣ 0..1 Reference(Cancer Patient Profile(0.2.0)) Who and/or what the observation is about
... Slices for effective[x] SΣ 0..1 dateTime Clinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime SΣ 0..1 dateTime Clinically relevant time/time-period for observation
... Slices for value[x] SΣC 0..1 CodeableConcept Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... method S 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 0..1 Reference(Human Specimen Profile(4.0.0)) Specimen used for this observation
... Slices for component SΣ 2..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
.... component:conclusion-string Σ 0..1 BackboneElement Clinical Conclusion
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:gene-studied SΣ 0..* BackboneElement Gene Studied
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48018-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNCVS (2.0.0) (extensible)
.... component:cytogenetic-location SΣ 0..* BackboneElement Cytogenetic (Chromosome) Location
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Example: 1q21.1
.... component:reference-sequence-assembly Σ 0..* BackboneElement Human Reference Sequence Assembly
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 62374-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:coding-hgvs Σ 0..1 BackboneElement Coding (cDNA) Change - cHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'c.' string, e.g. NM_005228.5:c.2369C>T
Binding: HGVSVS (2.0.0) (required)
.... component:genomic-hgvs SΣ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: HGVSVS (2.0.0) (required)
.... component:cytogenomic-nomenclature SΣ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq Σ 0..1 BackboneElement Genomic Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end Σ 0..1 BackboneElement Exact Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:inner-start-end Σ 0..1 BackboneElement Inner Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:outer-start-end Σ 0..1 BackboneElement Outer Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:coordinate-system Σ 0..1 BackboneElement Coordinate System
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
.... component:ref-allele Σ 0..1 BackboneElement Genomic Ref Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:alt-allele Σ 0..1 BackboneElement Genomic Alt Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:coding-change-type SΣ 0..1 BackboneElement Coding DNA Change Type
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNAChangeTypeVS (2.0.0) (extensible): Concepts in sequence ontology under SO:0002072
.... component:genomic-source-class SΣ 0..1 BackboneElement Genomic Source Class
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 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 SΣ 0..1 BackboneElement Sample Allelic Frequency
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 0..1 Quantity Relative frequency in the sample
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth Σ 0..1 BackboneElement Allelic Read Depth
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:allelic-state SΣ 0..1 BackboneElement Allelic State
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance Σ 0..1 BackboneElement Variant Inheritance
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept variant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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-inheritance
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: VariantInheritanceVS (2.0.0) (extensible)
.... component:variation-code SΣ 0..* BackboneElement Variation Code
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... component:chromosome-identifier Σ 0..* BackboneElement Chromosome Identifier
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48000-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:protein-hgvs SΣ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: HGVSVS (2.0.0) (required)
.... component:amino-acid-change-type SΣ 0..1 BackboneElement Amino Acid Change Type
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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: 48006-1
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: LOINC Answer List LL380-7 (extensible)
.... component:molecular-consequence SΣ 0..1 BackboneElement Molecular Consequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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: molecular-consequence
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: MolecularConsequenceVS (2.0.0) (extensible): Concepts in sequence ontology under SO:0001537.
.... component:copy-number SΣ 0..1 BackboneElement Genomic Structural Variant Copy Number
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣC 0..1 Quantity Actual component result
Constraints: cnt-3
.... component:variant-confidence-status Σ 0..1 BackboneElement Variant Confidence Status
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept High | Intermediate | Low
Binding: VariantConfidenceStatusVS (2.0.0) (required)
.... component:nucleotidesCount SΣ 1..1 BackboneElement Length of of the variant in nNucleotides
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 integer Actual component result
.... component:geneRegion SΣ 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible ​ LOINC Answer Codes for LL1040-6 (missing link) 📦 unknown?
Observation.component:coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible Variant Inheritances 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variation-code.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required ​ LOINC Answer Codes for LL2938-0 (missing link) 📦 unknown?
Observation.component:protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:amino-acid-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​value[x] Base extensible ​ LOINC Answer Codes for LL380-7 (missing link) 📦 unknown?
Observation.component:molecular-consequence.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:molecular-consequence.​value[x] Base extensible Molecular Consequence 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:copy-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:nucleotidesCount.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:geneRegion.​code Base example LOINC Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
cnt-3 error Observation.component:copy-number.value[x] There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error Observation.implicitRules, Observation.extension, Observation.extension:secondary-finding, Observation.extension:body-structure, Observation.extension:genePanel, Observation.extension:hgvsVersion, Observation.modifierExtension, Observation.status, Observation.category, Observation.category:labCategory, Observation.category:labCategory.coding, Observation.code, Observation.subject, Observation.effective[x], Observation.effective[x]:effectiveDateTime, Observation.value[x], Observation.value[x]:valueCodeableConcept, Observation.dataAbsentReason, Observation.method, Observation.specimen, Observation.component, Observation.component.modifierExtension, Observation.component.code, Observation.component:conclusion-string, Observation.component:conclusion-string.modifierExtension, Observation.component:conclusion-string.code, Observation.component:gene-studied, Observation.component:gene-studied.modifierExtension, Observation.component:gene-studied.code, Observation.component:gene-studied.value[x], Observation.component:cytogenetic-location, Observation.component:cytogenetic-location.modifierExtension, Observation.component:cytogenetic-location.code, Observation.component:cytogenetic-location.value[x], Observation.component:reference-sequence-assembly, Observation.component:reference-sequence-assembly.modifierExtension, Observation.component:reference-sequence-assembly.code, Observation.component:reference-sequence-assembly.value[x], Observation.component:coding-hgvs, Observation.component:coding-hgvs.modifierExtension, Observation.component:coding-hgvs.code, Observation.component:coding-hgvs.value[x], Observation.component:genomic-hgvs, Observation.component:genomic-hgvs.modifierExtension, Observation.component:genomic-hgvs.code, Observation.component:genomic-hgvs.value[x], Observation.component:cytogenomic-nomenclature, Observation.component:cytogenomic-nomenclature.modifierExtension, Observation.component:cytogenomic-nomenclature.code, Observation.component:cytogenomic-nomenclature.value[x], Observation.component:genomic-ref-seq, Observation.component:genomic-ref-seq.modifierExtension, Observation.component:genomic-ref-seq.code, Observation.component:genomic-ref-seq.value[x], Observation.component:transcript-ref-seq, Observation.component:transcript-ref-seq.modifierExtension, Observation.component:transcript-ref-seq.code, Observation.component:transcript-ref-seq.value[x], Observation.component:exact-start-end, Observation.component:exact-start-end.modifierExtension, Observation.component:exact-start-end.code, Observation.component:inner-start-end, Observation.component:inner-start-end.modifierExtension, Observation.component:inner-start-end.code, Observation.component:outer-start-end, Observation.component:outer-start-end.modifierExtension, Observation.component:outer-start-end.code, Observation.component:coordinate-system, Observation.component:coordinate-system.modifierExtension, Observation.component:coordinate-system.code, Observation.component:coordinate-system.value[x], Observation.component:ref-allele, Observation.component:ref-allele.modifierExtension, Observation.component:ref-allele.code, Observation.component:alt-allele, Observation.component:alt-allele.modifierExtension, Observation.component:alt-allele.code, Observation.component:coding-change-type, Observation.component:coding-change-type.modifierExtension, Observation.component:coding-change-type.code, Observation.component:coding-change-type.value[x], Observation.component:genomic-source-class, Observation.component:genomic-source-class.modifierExtension, Observation.component:genomic-source-class.code, Observation.component:genomic-source-class.value[x], Observation.component:sample-allelic-frequency, Observation.component:sample-allelic-frequency.modifierExtension, Observation.component:sample-allelic-frequency.code, Observation.component:sample-allelic-frequency.value[x], Observation.component:sample-allelic-frequency.value[x].comparator, Observation.component:sample-allelic-frequency.value[x].system, Observation.component:allelic-read-depth, Observation.component:allelic-read-depth.modifierExtension, Observation.component:allelic-read-depth.code, Observation.component:allelic-state, Observation.component:allelic-state.modifierExtension, Observation.component:allelic-state.code, Observation.component:allelic-state.value[x], Observation.component:variant-inheritance, Observation.component:variant-inheritance.modifierExtension, Observation.component:variant-inheritance.code, Observation.component:variant-inheritance.value[x], Observation.component:variation-code, Observation.component:variation-code.modifierExtension, Observation.component:variation-code.code, Observation.component:variation-code.value[x], Observation.component:chromosome-identifier, Observation.component:chromosome-identifier.modifierExtension, Observation.component:chromosome-identifier.code, Observation.component:chromosome-identifier.value[x], Observation.component:protein-hgvs, Observation.component:protein-hgvs.modifierExtension, Observation.component:protein-hgvs.code, Observation.component:protein-hgvs.value[x], Observation.component:amino-acid-change-type, Observation.component:amino-acid-change-type.modifierExtension, Observation.component:amino-acid-change-type.code, Observation.component:amino-acid-change-type.value[x], Observation.component:molecular-consequence, Observation.component:molecular-consequence.modifierExtension, Observation.component:molecular-consequence.code, Observation.component:molecular-consequence.value[x], Observation.component:copy-number, Observation.component:copy-number.modifierExtension, Observation.component:copy-number.code, Observation.component:copy-number.value[x], Observation.component:variant-confidence-status, Observation.component:variant-confidence-status.modifierExtension, Observation.component:variant-confidence-status.code, Observation.component:variant-confidence-status.value[x], Observation.component:nucleotidesCount, Observation.component:nucleotidesCount.modifierExtension, Observation.component:nucleotidesCount.code, Observation.component:nucleotidesCount.value[x], Observation.component:geneRegion, Observation.component:geneRegion.modifierExtension, Observation.component:geneRegion.code, Observation.component:geneRegion.value[x] All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error Observation.extension, Observation.extension:secondary-finding, Observation.extension:body-structure, Observation.extension:genePanel, Observation.extension:hgvsVersion, Observation.modifierExtension, Observation.component.modifierExtension, Observation.component:conclusion-string.modifierExtension, Observation.component:gene-studied.modifierExtension, Observation.component:cytogenetic-location.modifierExtension, Observation.component:reference-sequence-assembly.modifierExtension, Observation.component:coding-hgvs.modifierExtension, Observation.component:genomic-hgvs.modifierExtension, Observation.component:cytogenomic-nomenclature.modifierExtension, Observation.component:genomic-ref-seq.modifierExtension, Observation.component:transcript-ref-seq.modifierExtension, Observation.component:exact-start-end.modifierExtension, Observation.component:inner-start-end.modifierExtension, Observation.component:outer-start-end.modifierExtension, Observation.component:coordinate-system.modifierExtension, Observation.component:ref-allele.modifierExtension, Observation.component:alt-allele.modifierExtension, Observation.component:coding-change-type.modifierExtension, Observation.component:genomic-source-class.modifierExtension, Observation.component:sample-allelic-frequency.modifierExtension, Observation.component:allelic-read-depth.modifierExtension, Observation.component:allelic-state.modifierExtension, Observation.component:variant-inheritance.modifierExtension, Observation.component:variation-code.modifierExtension, Observation.component:chromosome-identifier.modifierExtension, Observation.component:protein-hgvs.modifierExtension, Observation.component:amino-acid-change-type.modifierExtension, Observation.component:molecular-consequence.modifierExtension, Observation.component:copy-number.modifierExtension, Observation.component:variant-confidence-status.modifierExtension, Observation.component:nucleotidesCount.modifierExtension, Observation.component:geneRegion.modifierExtension Must have either extensions or value[x], not both extension.exists() != value.exists()
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicVariant

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant(4.0.0) Variant
... extension 1..* Extension Extension
... Slices for extension Content/Rules for all slices
.... extension:genePanel 0..1 string Gene Panel
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-gene-panel
.... extension:hgvsVersion 1..1 string HGVS Version
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-hgvs-version
... status 1..1 code registered | preliminary | final | amended +
Required Pattern: final
... effective[x] 0..1 dateTime Clinically relevant time/time-period for observation
... component 2..* BackboneElement Component results
... Slices for component Content/Rules for all slices
.... component:coding-hgvs 0..1 BackboneElement Coding (cDNA) Change - cHGVS
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'c.' string, e.g. NM_005228.5:c.2369C>T
.... component:genomic-hgvs 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
.... component:protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
.... component:nucleotidesCount S 1..1 BackboneElement Length of of the variant in nNucleotides
..... code S 1..1 CodeableConcept Type of component observation (code / type)
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://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
..... value[x] S 0..1 integer Actual component result
.... component:geneRegion S 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
..... code S 1..1 CodeableConcept Type of component observation (code / type)
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://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
..... value[x] S 0..1 string Actual component result

doco Documentation for this format

Constraints

Id Grade Path(s) Description Expression
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant(4.0.0) Variant
Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
Constraints: ext-1
.... 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.
Constraints: ext-1
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Constraints: ext-1
.... extension:genePanel 0..1 string Gene Panel
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-gene-panel
Constraints: ext-1
.... extension:hgvsVersion 1..1 string HGVS Version
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-hgvs-version
Constraints: ext-1
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
Constraints: ext-1
... identifier Σ 0..* Identifier Business Identifier for observation
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) Part of referenced event
... status ?!SΣ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Required Pattern: final
... Slices for category S 1..* 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.

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id 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
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Constraints: ext-1
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text Σ 0..1 string Plain text representation of the concept
... code SΣ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject SΣ 0..1 Reference(Cancer Patient Profile(0.2.0)) Who and/or what the observation is about
... focus Σ 0..* Reference(Resource) What the observation is about, when it is not about the subject of record
... encounter Σ 0..1 Reference(Encounter) Healthcare event during which this observation is made
... Slices for effective[x] SΣ 0..1 dateTime Clinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime SΣ 0..1 dateTime Clinically relevant time/time-period for observation
... issued Σ 0..1 instant Date/Time this version was made available
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation
... Slices for value[x] SΣC 0..1 CodeableConcept Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
... note 0..* CodedAnnotation(2.0.0) Comments about the Observation that also contain a coded type
... bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
... method S 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 0..1 Reference(Human Specimen Profile(4.0.0)) Specimen used for this observation
... device 0..1 Reference(Device | DeviceMetric) (Measurement) Device
... referenceRange C 0..* BackboneElement Not used in this profile
Constraints: obs-3
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
.... low C 0..1 SimpleQuantity(4.0.1) Low Range, if relevant
.... high C 0..1 SimpleQuantity(4.0.1) High Range, if relevant
.... type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
.... appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
.... age 0..1 Range Applicable age range, if relevant
.... text 0..1 string Text based reference range in an observation
... hasMember Σ 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Not used in this profile
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
... Slices for component SΣ 2..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
..... value[x] Σ 0..1 Actual component result
...... valueQuantity Quantity
...... valueCodeableConcept CodeableConcept
...... valueString string
...... valueBoolean boolean
...... valueInteger integer
...... valueRange Range
...... valueRatio Ratio
...... valueSampledData SampledData
...... valueTime time
...... valueDateTime dateTime
...... valuePeriod Period
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:conclusion-string Σ 0..1 BackboneElement Clinical Conclusion
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Summary conclusion (interpretation/impression)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:gene-studied SΣ 0..* BackboneElement Gene Studied
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48018-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNCVS (2.0.0) (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:cytogenetic-location SΣ 0..* BackboneElement Cytogenetic (Chromosome) Location
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Example: 1q21.1
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:reference-sequence-assembly Σ 0..* BackboneElement Human Reference Sequence Assembly
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 62374-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coding-hgvs Σ 0..1 BackboneElement Coding (cDNA) Change - cHGVS
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'c.' string, e.g. NM_005228.5:c.2369C>T
Binding: HGVSVS (2.0.0) (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-hgvs SΣ 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
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: HGVSVS (2.0.0) (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:cytogenomic-nomenclature SΣ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-ref-seq Σ 0..1 BackboneElement Genomic Reference Sequence
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:exact-start-end Σ 0..1 BackboneElement Exact Start-End
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:inner-start-end Σ 0..1 BackboneElement Inner Start-End
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Imprecise variant inner-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:outer-start-end Σ 0..1 BackboneElement Outer Start-End
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Imprecise variant outer-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coordinate-system Σ 0..1 BackboneElement Coordinate System
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:ref-allele Σ 0..1 BackboneElement Genomic Ref Allele
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:alt-allele Σ 0..1 BackboneElement Genomic Alt Allele
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coding-change-type SΣ 0..1 BackboneElement Coding DNA Change Type
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNAChangeTypeVS (2.0.0) (extensible): Concepts in sequence ontology under SO:0002072
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-source-class SΣ 0..1 BackboneElement Genomic Source Class
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:sample-allelic-frequency SΣ 0..1 BackboneElement Sample Allelic Frequency
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 0..1 Quantity Relative frequency in the sample
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Constraints: ext-1
...... value Σ 0..1 decimal Numerical value (with implicit precision)
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... unit Σ 0..1 string Unit representation
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code Σ 0..1 code Coded form of the unit
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:allelic-read-depth Σ 0..1 BackboneElement Allelic Read Depth
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Quantity Unfiltered count of supporting reads
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:allelic-state SΣ 0..1 BackboneElement Allelic State
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variant-inheritance Σ 0..1 BackboneElement Variant Inheritance
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept variant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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-inheritance
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: VariantInheritanceVS (2.0.0) (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variation-code SΣ 0..* BackboneElement Variation Code
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:chromosome-identifier Σ 0..* BackboneElement Chromosome Identifier
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48000-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:protein-hgvs SΣ 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
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: HGVSVS (2.0.0) (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:amino-acid-change-type SΣ 0..1 BackboneElement Amino Acid Change Type
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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: 48006-1
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: LOINC Answer List LL380-7 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:molecular-consequence SΣ 0..1 BackboneElement Molecular Consequence
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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: molecular-consequence
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: MolecularConsequenceVS (2.0.0) (extensible): Concepts in sequence ontology under SO:0001537.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:copy-number SΣ 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
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣC 0..1 Quantity Actual component result
Constraints: cnt-3
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variant-confidence-status Σ 0..1 BackboneElement Variant Confidence Status
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept High | Intermediate | Low
Binding: VariantConfidenceStatusVS (2.0.0) (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:nucleotidesCount SΣ 1..1 BackboneElement Length of of the variant in nNucleotides
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 integer Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:geneRegion SΣ 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base preferred Common Languages 📍4.0.1 FHIR Std.
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📍4.0.1 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📍4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:gene-studied.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible ​ LOINC Answer Codes for LL1040-6 (missing link) 📦 unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:coding-change-type.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible Variant Inheritances 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variant-inheritance.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variation-code.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required ​ LOINC Answer Codes for LL2938-0 (missing link) 📦 unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​value[x] Base extensible ​ LOINC Answer Codes for LL380-7 (missing link) 📦 unknown?
Observation.component:amino-acid-change-type.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:molecular-consequence.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:molecular-consequence.​value[x] Base extensible Molecular Consequence 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:molecular-consequence.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:molecular-consequence.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:nucleotidesCount.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:nucleotidesCount.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:nucleotidesCount.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:geneRegion.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:geneRegion.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:geneRegion.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
cnt-3 error Observation.component:copy-number.value[x] There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error Observation.meta, Observation.implicitRules, Observation.language, Observation.text, Observation.extension, Observation.extension:secondary-finding, Observation.extension:body-structure, Observation.extension:genePanel, Observation.extension:hgvsVersion, Observation.modifierExtension, Observation.identifier, Observation.basedOn, Observation.partOf, Observation.status, Observation.category, Observation.category:labCategory, Observation.category:labCategory.extension, Observation.category:labCategory.coding, Observation.category:labCategory.text, Observation.code, Observation.subject, Observation.focus, Observation.encounter, Observation.effective[x], Observation.effective[x]:effectiveDateTime, Observation.issued, Observation.performer, Observation.value[x], Observation.value[x]:valueCodeableConcept, Observation.dataAbsentReason, Observation.interpretation, Observation.note, Observation.bodySite, Observation.method, Observation.specimen, Observation.device, Observation.referenceRange, Observation.referenceRange.extension, Observation.referenceRange.modifierExtension, Observation.referenceRange.low, Observation.referenceRange.high, Observation.referenceRange.type, Observation.referenceRange.appliesTo, Observation.referenceRange.age, Observation.referenceRange.text, Observation.hasMember, Observation.derivedFrom, Observation.component, Observation.component.extension, Observation.component.modifierExtension, Observation.component.code, Observation.component.value[x], Observation.component.dataAbsentReason, Observation.component.interpretation, Observation.component.referenceRange, Observation.component:conclusion-string, Observation.component:conclusion-string.extension, Observation.component:conclusion-string.modifierExtension, Observation.component:conclusion-string.code, Observation.component:conclusion-string.value[x], Observation.component:conclusion-string.dataAbsentReason, Observation.component:conclusion-string.interpretation, Observation.component:conclusion-string.referenceRange, Observation.component:gene-studied, Observation.component:gene-studied.extension, Observation.component:gene-studied.modifierExtension, Observation.component:gene-studied.code, Observation.component:gene-studied.value[x], Observation.component:gene-studied.dataAbsentReason, Observation.component:gene-studied.interpretation, Observation.component:gene-studied.referenceRange, Observation.component:cytogenetic-location, Observation.component:cytogenetic-location.extension, Observation.component:cytogenetic-location.modifierExtension, Observation.component:cytogenetic-location.code, Observation.component:cytogenetic-location.value[x], Observation.component:cytogenetic-location.dataAbsentReason, Observation.component:cytogenetic-location.interpretation, Observation.component:cytogenetic-location.referenceRange, Observation.component:reference-sequence-assembly, Observation.component:reference-sequence-assembly.extension, Observation.component:reference-sequence-assembly.modifierExtension, Observation.component:reference-sequence-assembly.code, Observation.component:reference-sequence-assembly.value[x], Observation.component:reference-sequence-assembly.dataAbsentReason, Observation.component:reference-sequence-assembly.interpretation, Observation.component:reference-sequence-assembly.referenceRange, Observation.component:coding-hgvs, Observation.component:coding-hgvs.extension, Observation.component:coding-hgvs.modifierExtension, Observation.component:coding-hgvs.code, Observation.component:coding-hgvs.value[x], Observation.component:coding-hgvs.dataAbsentReason, Observation.component:coding-hgvs.interpretation, Observation.component:coding-hgvs.referenceRange, Observation.component:genomic-hgvs, Observation.component:genomic-hgvs.extension, Observation.component:genomic-hgvs.modifierExtension, Observation.component:genomic-hgvs.code, Observation.component:genomic-hgvs.value[x], Observation.component:genomic-hgvs.dataAbsentReason, Observation.component:genomic-hgvs.interpretation, Observation.component:genomic-hgvs.referenceRange, Observation.component:cytogenomic-nomenclature, Observation.component:cytogenomic-nomenclature.extension, Observation.component:cytogenomic-nomenclature.modifierExtension, Observation.component:cytogenomic-nomenclature.code, Observation.component:cytogenomic-nomenclature.value[x], Observation.component:cytogenomic-nomenclature.dataAbsentReason, Observation.component:cytogenomic-nomenclature.interpretation, Observation.component:cytogenomic-nomenclature.referenceRange, Observation.component:genomic-ref-seq, Observation.component:genomic-ref-seq.extension, Observation.component:genomic-ref-seq.modifierExtension, Observation.component:genomic-ref-seq.code, Observation.component:genomic-ref-seq.value[x], Observation.component:genomic-ref-seq.dataAbsentReason, Observation.component:genomic-ref-seq.interpretation, Observation.component:genomic-ref-seq.referenceRange, Observation.component:transcript-ref-seq, Observation.component:transcript-ref-seq.extension, Observation.component:transcript-ref-seq.modifierExtension, Observation.component:transcript-ref-seq.code, Observation.component:transcript-ref-seq.value[x], Observation.component:transcript-ref-seq.dataAbsentReason, Observation.component:transcript-ref-seq.interpretation, Observation.component:transcript-ref-seq.referenceRange, Observation.component:exact-start-end, Observation.component:exact-start-end.extension, Observation.component:exact-start-end.modifierExtension, Observation.component:exact-start-end.code, Observation.component:exact-start-end.value[x], Observation.component:exact-start-end.dataAbsentReason, Observation.component:exact-start-end.interpretation, Observation.component:exact-start-end.referenceRange, Observation.component:inner-start-end, Observation.component:inner-start-end.extension, Observation.component:inner-start-end.modifierExtension, Observation.component:inner-start-end.code, Observation.component:inner-start-end.value[x], Observation.component:inner-start-end.dataAbsentReason, Observation.component:inner-start-end.interpretation, Observation.component:inner-start-end.referenceRange, Observation.component:outer-start-end, Observation.component:outer-start-end.extension, Observation.component:outer-start-end.modifierExtension, Observation.component:outer-start-end.code, Observation.component:outer-start-end.value[x], Observation.component:outer-start-end.dataAbsentReason, Observation.component:outer-start-end.interpretation, Observation.component:outer-start-end.referenceRange, Observation.component:coordinate-system, Observation.component:coordinate-system.extension, Observation.component:coordinate-system.modifierExtension, Observation.component:coordinate-system.code, Observation.component:coordinate-system.value[x], Observation.component:coordinate-system.dataAbsentReason, Observation.component:coordinate-system.interpretation, Observation.component:coordinate-system.referenceRange, Observation.component:ref-allele, Observation.component:ref-allele.extension, Observation.component:ref-allele.modifierExtension, Observation.component:ref-allele.code, Observation.component:ref-allele.value[x], Observation.component:ref-allele.dataAbsentReason, Observation.component:ref-allele.interpretation, Observation.component:ref-allele.referenceRange, Observation.component:alt-allele, Observation.component:alt-allele.extension, Observation.component:alt-allele.modifierExtension, Observation.component:alt-allele.code, Observation.component:alt-allele.value[x], Observation.component:alt-allele.dataAbsentReason, Observation.component:alt-allele.interpretation, Observation.component:alt-allele.referenceRange, Observation.component:coding-change-type, Observation.component:coding-change-type.extension, Observation.component:coding-change-type.modifierExtension, Observation.component:coding-change-type.code, Observation.component:coding-change-type.value[x], Observation.component:coding-change-type.dataAbsentReason, Observation.component:coding-change-type.interpretation, Observation.component:coding-change-type.referenceRange, Observation.component:genomic-source-class, Observation.component:genomic-source-class.extension, Observation.component:genomic-source-class.modifierExtension, Observation.component:genomic-source-class.code, Observation.component:genomic-source-class.value[x], Observation.component:genomic-source-class.dataAbsentReason, Observation.component:genomic-source-class.interpretation, Observation.component:genomic-source-class.referenceRange, Observation.component:sample-allelic-frequency, Observation.component:sample-allelic-frequency.extension, Observation.component:sample-allelic-frequency.modifierExtension, Observation.component:sample-allelic-frequency.code, Observation.component:sample-allelic-frequency.value[x], Observation.component:sample-allelic-frequency.value[x].extension, Observation.component:sample-allelic-frequency.value[x].value, Observation.component:sample-allelic-frequency.value[x].comparator, Observation.component:sample-allelic-frequency.value[x].unit, Observation.component:sample-allelic-frequency.value[x].system, Observation.component:sample-allelic-frequency.value[x].code, Observation.component:sample-allelic-frequency.dataAbsentReason, Observation.component:sample-allelic-frequency.interpretation, Observation.component:sample-allelic-frequency.referenceRange, Observation.component:allelic-read-depth, Observation.component:allelic-read-depth.extension, Observation.component:allelic-read-depth.modifierExtension, Observation.component:allelic-read-depth.code, Observation.component:allelic-read-depth.value[x], Observation.component:allelic-read-depth.dataAbsentReason, Observation.component:allelic-read-depth.interpretation, Observation.component:allelic-read-depth.referenceRange, Observation.component:allelic-state, Observation.component:allelic-state.extension, Observation.component:allelic-state.modifierExtension, Observation.component:allelic-state.code, Observation.component:allelic-state.value[x], Observation.component:allelic-state.dataAbsentReason, Observation.component:allelic-state.interpretation, Observation.component:allelic-state.referenceRange, Observation.component:variant-inheritance, Observation.component:variant-inheritance.extension, Observation.component:variant-inheritance.modifierExtension, Observation.component:variant-inheritance.code, Observation.component:variant-inheritance.value[x], Observation.component:variant-inheritance.dataAbsentReason, Observation.component:variant-inheritance.interpretation, Observation.component:variant-inheritance.referenceRange, Observation.component:variation-code, Observation.component:variation-code.extension, Observation.component:variation-code.modifierExtension, Observation.component:variation-code.code, Observation.component:variation-code.value[x], Observation.component:variation-code.dataAbsentReason, Observation.component:variation-code.interpretation, Observation.component:variation-code.referenceRange, Observation.component:chromosome-identifier, Observation.component:chromosome-identifier.extension, Observation.component:chromosome-identifier.modifierExtension, Observation.component:chromosome-identifier.code, Observation.component:chromosome-identifier.value[x], Observation.component:chromosome-identifier.dataAbsentReason, Observation.component:chromosome-identifier.interpretation, Observation.component:chromosome-identifier.referenceRange, Observation.component:protein-hgvs, Observation.component:protein-hgvs.extension, Observation.component:protein-hgvs.modifierExtension, Observation.component:protein-hgvs.code, Observation.component:protein-hgvs.value[x], Observation.component:protein-hgvs.dataAbsentReason, Observation.component:protein-hgvs.interpretation, Observation.component:protein-hgvs.referenceRange, Observation.component:amino-acid-change-type, Observation.component:amino-acid-change-type.extension, Observation.component:amino-acid-change-type.modifierExtension, Observation.component:amino-acid-change-type.code, Observation.component:amino-acid-change-type.value[x], Observation.component:amino-acid-change-type.dataAbsentReason, Observation.component:amino-acid-change-type.interpretation, Observation.component:amino-acid-change-type.referenceRange, Observation.component:molecular-consequence, Observation.component:molecular-consequence.extension, Observation.component:molecular-consequence.modifierExtension, Observation.component:molecular-consequence.code, Observation.component:molecular-consequence.value[x], Observation.component:molecular-consequence.dataAbsentReason, Observation.component:molecular-consequence.interpretation, Observation.component:molecular-consequence.referenceRange, Observation.component:copy-number, Observation.component:copy-number.extension, Observation.component:copy-number.modifierExtension, Observation.component:copy-number.code, Observation.component:copy-number.value[x], Observation.component:copy-number.dataAbsentReason, Observation.component:copy-number.interpretation, Observation.component:copy-number.referenceRange, Observation.component:variant-confidence-status, Observation.component:variant-confidence-status.extension, Observation.component:variant-confidence-status.modifierExtension, Observation.component:variant-confidence-status.code, Observation.component:variant-confidence-status.value[x], Observation.component:variant-confidence-status.dataAbsentReason, Observation.component:variant-confidence-status.interpretation, Observation.component:variant-confidence-status.referenceRange, Observation.component:nucleotidesCount, Observation.component:nucleotidesCount.extension, Observation.component:nucleotidesCount.modifierExtension, Observation.component:nucleotidesCount.code, Observation.component:nucleotidesCount.value[x], Observation.component:nucleotidesCount.dataAbsentReason, Observation.component:nucleotidesCount.interpretation, Observation.component:nucleotidesCount.referenceRange, Observation.component:geneRegion, Observation.component:geneRegion.extension, Observation.component:geneRegion.modifierExtension, Observation.component:geneRegion.code, Observation.component:geneRegion.value[x], Observation.component:geneRegion.dataAbsentReason, Observation.component:geneRegion.interpretation, Observation.component:geneRegion.referenceRange All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error Observation.extension, Observation.extension:secondary-finding, Observation.extension:body-structure, Observation.extension:genePanel, Observation.extension:hgvsVersion, Observation.modifierExtension, Observation.category:labCategory.extension, Observation.referenceRange.extension, Observation.referenceRange.modifierExtension, Observation.component.extension, Observation.component.modifierExtension, Observation.component:conclusion-string.extension, Observation.component:conclusion-string.modifierExtension, Observation.component:gene-studied.extension, Observation.component:gene-studied.modifierExtension, Observation.component:cytogenetic-location.extension, Observation.component:cytogenetic-location.modifierExtension, Observation.component:reference-sequence-assembly.extension, Observation.component:reference-sequence-assembly.modifierExtension, Observation.component:coding-hgvs.extension, Observation.component:coding-hgvs.modifierExtension, Observation.component:genomic-hgvs.extension, Observation.component:genomic-hgvs.modifierExtension, Observation.component:cytogenomic-nomenclature.extension, Observation.component:cytogenomic-nomenclature.modifierExtension, Observation.component:genomic-ref-seq.extension, Observation.component:genomic-ref-seq.modifierExtension, Observation.component:transcript-ref-seq.extension, Observation.component:transcript-ref-seq.modifierExtension, Observation.component:exact-start-end.extension, Observation.component:exact-start-end.modifierExtension, Observation.component:inner-start-end.extension, Observation.component:inner-start-end.modifierExtension, Observation.component:outer-start-end.extension, Observation.component:outer-start-end.modifierExtension, Observation.component:coordinate-system.extension, Observation.component:coordinate-system.modifierExtension, Observation.component:ref-allele.extension, Observation.component:ref-allele.modifierExtension, Observation.component:alt-allele.extension, Observation.component:alt-allele.modifierExtension, Observation.component:coding-change-type.extension, Observation.component:coding-change-type.modifierExtension, Observation.component:genomic-source-class.extension, Observation.component:genomic-source-class.modifierExtension, Observation.component:sample-allelic-frequency.extension, Observation.component:sample-allelic-frequency.modifierExtension, Observation.component:sample-allelic-frequency.value[x].extension, Observation.component:allelic-read-depth.extension, Observation.component:allelic-read-depth.modifierExtension, Observation.component:allelic-state.extension, Observation.component:allelic-state.modifierExtension, Observation.component:variant-inheritance.extension, Observation.component:variant-inheritance.modifierExtension, Observation.component:variation-code.extension, Observation.component:variation-code.modifierExtension, Observation.component:chromosome-identifier.extension, Observation.component:chromosome-identifier.modifierExtension, Observation.component:protein-hgvs.extension, Observation.component:protein-hgvs.modifierExtension, Observation.component:amino-acid-change-type.extension, Observation.component:amino-acid-change-type.modifierExtension, Observation.component:molecular-consequence.extension, Observation.component:molecular-consequence.modifierExtension, Observation.component:copy-number.extension, Observation.component:copy-number.modifierExtension, Observation.component:variant-confidence-status.extension, Observation.component:variant-confidence-status.modifierExtension, Observation.component:nucleotidesCount.extension, Observation.component:nucleotidesCount.modifierExtension, Observation.component:geneRegion.extension, Observation.component:geneRegion.modifierExtension Must have either extensions or value[x], not both extension.exists() != value.exists()
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-3 error Observation.referenceRange Must have at least a low or a high or text low.exists() or high.exists() or text.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicVariant

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant(4.0.0) Variant
Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
Constraints: ext-1
.... 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.
Constraints: ext-1
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Constraints: ext-1
.... extension:genePanel 0..1 string Gene Panel
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-gene-panel
Constraints: ext-1
.... extension:hgvsVersion 1..1 string HGVS Version
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-hgvs-version
Constraints: ext-1
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
Constraints: ext-1
... Slices for category S 1..* 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.

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id 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
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
... code SΣ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject SΣ 0..1 Reference(Cancer Patient Profile(0.2.0)) Who and/or what the observation is about
... Slices for effective[x] SΣ 0..1 dateTime Clinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime SΣ 0..1 dateTime Clinically relevant time/time-period for observation
... Slices for value[x] SΣC 0..1 CodeableConcept Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... method S 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 0..1 Reference(Human Specimen Profile(4.0.0)) Specimen used for this observation
... Slices for component SΣ 2..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
.... component:conclusion-string Σ 0..1 BackboneElement Clinical Conclusion
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:gene-studied SΣ 0..* BackboneElement Gene Studied
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48018-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNCVS (2.0.0) (extensible)
.... component:cytogenetic-location SΣ 0..* BackboneElement Cytogenetic (Chromosome) Location
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Example: 1q21.1
.... component:reference-sequence-assembly Σ 0..* BackboneElement Human Reference Sequence Assembly
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 62374-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:coding-hgvs Σ 0..1 BackboneElement Coding (cDNA) Change - cHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'c.' string, e.g. NM_005228.5:c.2369C>T
Binding: HGVSVS (2.0.0) (required)
.... component:genomic-hgvs SΣ 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: HGVSVS (2.0.0) (required)
.... component:cytogenomic-nomenclature SΣ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
.... component:genomic-ref-seq Σ 0..1 BackboneElement Genomic Reference Sequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
.... component:exact-start-end Σ 0..1 BackboneElement Exact Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:inner-start-end Σ 0..1 BackboneElement Inner Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:outer-start-end Σ 0..1 BackboneElement Outer Start-End
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:coordinate-system Σ 0..1 BackboneElement Coordinate System
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
.... component:ref-allele Σ 0..1 BackboneElement Genomic Ref Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:alt-allele Σ 0..1 BackboneElement Genomic Alt Allele
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:coding-change-type SΣ 0..1 BackboneElement Coding DNA Change Type
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNAChangeTypeVS (2.0.0) (extensible): Concepts in sequence ontology under SO:0002072
.... component:genomic-source-class SΣ 0..1 BackboneElement Genomic Source Class
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 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 SΣ 0..1 BackboneElement Sample Allelic Frequency
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 0..1 Quantity Relative frequency in the sample
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
.... component:allelic-read-depth Σ 0..1 BackboneElement Allelic Read Depth
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
.... component:allelic-state SΣ 0..1 BackboneElement Allelic State
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance Σ 0..1 BackboneElement Variant Inheritance
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept variant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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-inheritance
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: VariantInheritanceVS (2.0.0) (extensible)
.... component:variation-code SΣ 0..* BackboneElement Variation Code
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
.... component:chromosome-identifier Σ 0..* BackboneElement Chromosome Identifier
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48000-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:protein-hgvs SΣ 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: HGVSVS (2.0.0) (required)
.... component:amino-acid-change-type SΣ 0..1 BackboneElement Amino Acid Change Type
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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: 48006-1
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: LOINC Answer List LL380-7 (extensible)
.... component:molecular-consequence SΣ 0..1 BackboneElement Molecular Consequence
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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: molecular-consequence
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: MolecularConsequenceVS (2.0.0) (extensible): Concepts in sequence ontology under SO:0001537.
.... component:copy-number SΣ 0..1 BackboneElement Genomic Structural Variant Copy Number
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣC 0..1 Quantity Actual component result
Constraints: cnt-3
.... component:variant-confidence-status Σ 0..1 BackboneElement Variant Confidence Status
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept High | Intermediate | Low
Binding: VariantConfidenceStatusVS (2.0.0) (required)
.... component:nucleotidesCount SΣ 1..1 BackboneElement Length of of the variant in nNucleotides
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 integer Actual component result
.... component:geneRegion SΣ 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible ​ LOINC Answer Codes for LL1040-6 (missing link) 📦 unknown?
Observation.component:coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:exact-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:ref-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible Variant Inheritances 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variation-code.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required ​ LOINC Answer Codes for LL2938-0 (missing link) 📦 unknown?
Observation.component:protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:amino-acid-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​value[x] Base extensible ​ LOINC Answer Codes for LL380-7 (missing link) 📦 unknown?
Observation.component:molecular-consequence.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:molecular-consequence.​value[x] Base extensible Molecular Consequence 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:copy-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:nucleotidesCount.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:geneRegion.​code Base example LOINC Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
cnt-3 error Observation.component:copy-number.value[x] There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error Observation.implicitRules, Observation.extension, Observation.extension:secondary-finding, Observation.extension:body-structure, Observation.extension:genePanel, Observation.extension:hgvsVersion, Observation.modifierExtension, Observation.status, Observation.category, Observation.category:labCategory, Observation.category:labCategory.coding, Observation.code, Observation.subject, Observation.effective[x], Observation.effective[x]:effectiveDateTime, Observation.value[x], Observation.value[x]:valueCodeableConcept, Observation.dataAbsentReason, Observation.method, Observation.specimen, Observation.component, Observation.component.modifierExtension, Observation.component.code, Observation.component:conclusion-string, Observation.component:conclusion-string.modifierExtension, Observation.component:conclusion-string.code, Observation.component:gene-studied, Observation.component:gene-studied.modifierExtension, Observation.component:gene-studied.code, Observation.component:gene-studied.value[x], Observation.component:cytogenetic-location, Observation.component:cytogenetic-location.modifierExtension, Observation.component:cytogenetic-location.code, Observation.component:cytogenetic-location.value[x], Observation.component:reference-sequence-assembly, Observation.component:reference-sequence-assembly.modifierExtension, Observation.component:reference-sequence-assembly.code, Observation.component:reference-sequence-assembly.value[x], Observation.component:coding-hgvs, Observation.component:coding-hgvs.modifierExtension, Observation.component:coding-hgvs.code, Observation.component:coding-hgvs.value[x], Observation.component:genomic-hgvs, Observation.component:genomic-hgvs.modifierExtension, Observation.component:genomic-hgvs.code, Observation.component:genomic-hgvs.value[x], Observation.component:cytogenomic-nomenclature, Observation.component:cytogenomic-nomenclature.modifierExtension, Observation.component:cytogenomic-nomenclature.code, Observation.component:cytogenomic-nomenclature.value[x], Observation.component:genomic-ref-seq, Observation.component:genomic-ref-seq.modifierExtension, Observation.component:genomic-ref-seq.code, Observation.component:genomic-ref-seq.value[x], Observation.component:transcript-ref-seq, Observation.component:transcript-ref-seq.modifierExtension, Observation.component:transcript-ref-seq.code, Observation.component:transcript-ref-seq.value[x], Observation.component:exact-start-end, Observation.component:exact-start-end.modifierExtension, Observation.component:exact-start-end.code, Observation.component:inner-start-end, Observation.component:inner-start-end.modifierExtension, Observation.component:inner-start-end.code, Observation.component:outer-start-end, Observation.component:outer-start-end.modifierExtension, Observation.component:outer-start-end.code, Observation.component:coordinate-system, Observation.component:coordinate-system.modifierExtension, Observation.component:coordinate-system.code, Observation.component:coordinate-system.value[x], Observation.component:ref-allele, Observation.component:ref-allele.modifierExtension, Observation.component:ref-allele.code, Observation.component:alt-allele, Observation.component:alt-allele.modifierExtension, Observation.component:alt-allele.code, Observation.component:coding-change-type, Observation.component:coding-change-type.modifierExtension, Observation.component:coding-change-type.code, Observation.component:coding-change-type.value[x], Observation.component:genomic-source-class, Observation.component:genomic-source-class.modifierExtension, Observation.component:genomic-source-class.code, Observation.component:genomic-source-class.value[x], Observation.component:sample-allelic-frequency, Observation.component:sample-allelic-frequency.modifierExtension, Observation.component:sample-allelic-frequency.code, Observation.component:sample-allelic-frequency.value[x], Observation.component:sample-allelic-frequency.value[x].comparator, Observation.component:sample-allelic-frequency.value[x].system, Observation.component:allelic-read-depth, Observation.component:allelic-read-depth.modifierExtension, Observation.component:allelic-read-depth.code, Observation.component:allelic-state, Observation.component:allelic-state.modifierExtension, Observation.component:allelic-state.code, Observation.component:allelic-state.value[x], Observation.component:variant-inheritance, Observation.component:variant-inheritance.modifierExtension, Observation.component:variant-inheritance.code, Observation.component:variant-inheritance.value[x], Observation.component:variation-code, Observation.component:variation-code.modifierExtension, Observation.component:variation-code.code, Observation.component:variation-code.value[x], Observation.component:chromosome-identifier, Observation.component:chromosome-identifier.modifierExtension, Observation.component:chromosome-identifier.code, Observation.component:chromosome-identifier.value[x], Observation.component:protein-hgvs, Observation.component:protein-hgvs.modifierExtension, Observation.component:protein-hgvs.code, Observation.component:protein-hgvs.value[x], Observation.component:amino-acid-change-type, Observation.component:amino-acid-change-type.modifierExtension, Observation.component:amino-acid-change-type.code, Observation.component:amino-acid-change-type.value[x], Observation.component:molecular-consequence, Observation.component:molecular-consequence.modifierExtension, Observation.component:molecular-consequence.code, Observation.component:molecular-consequence.value[x], Observation.component:copy-number, Observation.component:copy-number.modifierExtension, Observation.component:copy-number.code, Observation.component:copy-number.value[x], Observation.component:variant-confidence-status, Observation.component:variant-confidence-status.modifierExtension, Observation.component:variant-confidence-status.code, Observation.component:variant-confidence-status.value[x], Observation.component:nucleotidesCount, Observation.component:nucleotidesCount.modifierExtension, Observation.component:nucleotidesCount.code, Observation.component:nucleotidesCount.value[x], Observation.component:geneRegion, Observation.component:geneRegion.modifierExtension, Observation.component:geneRegion.code, Observation.component:geneRegion.value[x] All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error Observation.extension, Observation.extension:secondary-finding, Observation.extension:body-structure, Observation.extension:genePanel, Observation.extension:hgvsVersion, Observation.modifierExtension, Observation.component.modifierExtension, Observation.component:conclusion-string.modifierExtension, Observation.component:gene-studied.modifierExtension, Observation.component:cytogenetic-location.modifierExtension, Observation.component:reference-sequence-assembly.modifierExtension, Observation.component:coding-hgvs.modifierExtension, Observation.component:genomic-hgvs.modifierExtension, Observation.component:cytogenomic-nomenclature.modifierExtension, Observation.component:genomic-ref-seq.modifierExtension, Observation.component:transcript-ref-seq.modifierExtension, Observation.component:exact-start-end.modifierExtension, Observation.component:inner-start-end.modifierExtension, Observation.component:outer-start-end.modifierExtension, Observation.component:coordinate-system.modifierExtension, Observation.component:ref-allele.modifierExtension, Observation.component:alt-allele.modifierExtension, Observation.component:coding-change-type.modifierExtension, Observation.component:genomic-source-class.modifierExtension, Observation.component:sample-allelic-frequency.modifierExtension, Observation.component:allelic-read-depth.modifierExtension, Observation.component:allelic-state.modifierExtension, Observation.component:variant-inheritance.modifierExtension, Observation.component:variation-code.modifierExtension, Observation.component:chromosome-identifier.modifierExtension, Observation.component:protein-hgvs.modifierExtension, Observation.component:amino-acid-change-type.modifierExtension, Observation.component:molecular-consequence.modifierExtension, Observation.component:copy-number.modifierExtension, Observation.component:variant-confidence-status.modifierExtension, Observation.component:nucleotidesCount.modifierExtension, Observation.component:geneRegion.modifierExtension Must have either extensions or value[x], not both extension.exists() != value.exists()
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

Differential View

This structure is derived from GenomicVariant

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant(4.0.0) Variant
... extension 1..* Extension Extension
... Slices for extension Content/Rules for all slices
.... extension:genePanel 0..1 string Gene Panel
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-gene-panel
.... extension:hgvsVersion 1..1 string HGVS Version
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-hgvs-version
... status 1..1 code registered | preliminary | final | amended +
Required Pattern: final
... effective[x] 0..1 dateTime Clinically relevant time/time-period for observation
... component 2..* BackboneElement Component results
... Slices for component Content/Rules for all slices
.... component:coding-hgvs 0..1 BackboneElement Coding (cDNA) Change - cHGVS
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'c.' string, e.g. NM_005228.5:c.2369C>T
.... component:genomic-hgvs 0..1 BackboneElement Genomic (gDNA) Change - gHGVS
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
.... component:protein-hgvs 0..1 BackboneElement Protein (Amino Acid) Change - pHGVS
..... value[x] 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
.... component:nucleotidesCount S 1..1 BackboneElement Length of of the variant in nNucleotides
..... code S 1..1 CodeableConcept Type of component observation (code / type)
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://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
..... value[x] S 0..1 integer Actual component result
.... component:geneRegion S 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
..... code S 1..1 CodeableConcept Type of component observation (code / type)
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://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
..... value[x] S 0..1 string Actual component result

doco Documentation for this format

Constraints

Id Grade Path(s) Description Expression
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Observation C 0..* GenomicVariant(4.0.0) Variant
Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.
Additional BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
Constraints: ext-1
.... 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.
Constraints: ext-1
.... extension:body-structure 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
Constraints: ext-1
.... extension:genePanel 0..1 string Gene Panel
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-gene-panel
Constraints: ext-1
.... extension:hgvsVersion 1..1 string HGVS Version
URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-hgvs-version
Constraints: ext-1
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
Constraints: ext-1
... identifier Σ 0..* Identifier Business Identifier for observation
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) Part of referenced event
... status ?!SΣ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.
Required Pattern: final
... Slices for category S 1..* 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.

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id 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
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Constraints: ext-1
..... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text Σ 0..1 string Plain text representation of the concept
... code SΣ 1..1 CodeableConcept 69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
..... version 0..1 string Version of the system - if relevant
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69548-6
..... display 0..1 string Representation defined by the system
..... userSelected 0..1 boolean If this coding was chosen directly by the user
.... text 0..1 string Plain text representation of the concept
... subject SΣ 0..1 Reference(Cancer Patient Profile(0.2.0)) Who and/or what the observation is about
... focus Σ 0..* Reference(Resource) What the observation is about, when it is not about the subject of record
... encounter Σ 0..1 Reference(Encounter) Healthcare event during which this observation is made
... Slices for effective[x] SΣ 0..1 dateTime Clinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime SΣ 0..1 dateTime Clinically relevant time/time-period for observation
... issued Σ 0..1 instant Date/Time this version was made available
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) Who is responsible for the observation
... Slices for value[x] SΣC 0..1 CodeableConcept Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC 0..1 CodeableConcept Indeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
... note 0..* CodedAnnotation(2.0.0) Comments about the Observation that also contain a coded type
... bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
... method S 0..1 CodeableConcept Sequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S 0..1 Reference(Human Specimen Profile(4.0.0)) Specimen used for this observation
... device 0..1 Reference(Device | DeviceMetric) (Measurement) Device
... referenceRange C 0..* BackboneElement Not used in this profile
Constraints: obs-3
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
.... low C 0..1 SimpleQuantity(4.0.1) Low Range, if relevant
.... high C 0..1 SimpleQuantity(4.0.1) High Range, if relevant
.... type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
.... appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
.... age 0..1 Range Applicable age range, if relevant
.... text 0..1 string Text based reference range in an observation
... hasMember Σ 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Not used in this profile
... derivedFrom Σ 0..* Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
... Slices for component SΣ 2..* BackboneElement Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
..... value[x] Σ 0..1 Actual component result
...... valueQuantity Quantity
...... valueCodeableConcept CodeableConcept
...... valueString string
...... valueBoolean boolean
...... valueInteger integer
...... valueRange Range
...... valueRatio Ratio
...... valueSampledData SampledData
...... valueTime time
...... valueDateTime dateTime
...... valuePeriod Period
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:conclusion-string Σ 0..1 BackboneElement Clinical Conclusion
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept conclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: conclusion-string
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Summary conclusion (interpretation/impression)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:gene-studied SΣ 0..* BackboneElement Gene Studied
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48018-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HGNCVS (2.0.0) (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:cytogenetic-location SΣ 0..* BackboneElement Cytogenetic (Chromosome) Location
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Example: 1q21.1
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:reference-sequence-assembly Σ 0..* BackboneElement Human Reference Sequence Assembly
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 62374-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept GRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coding-hgvs Σ 0..1 BackboneElement Coding (cDNA) Change - cHGVS
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48004-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'c.' string, e.g. NM_005228.5:c.2369C>T
Binding: HGVSVS (2.0.0) (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-hgvs SΣ 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
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: HGVSVS (2.0.0) (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:cytogenomic-nomenclature SΣ 0..1 BackboneElement Cytogenomic Nomenclature (ISCN)
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Actual component result
Binding Description: (example): Binding not yet defined
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-ref-seq Σ 0..1 BackboneElement Genomic Reference Sequence
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48013-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned genomic reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:transcript-ref-seq Σ 0..1 BackboneElement Reference Transcript
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 51958-7
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Versioned transcript reference sequence identifier
Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:exact-start-end Σ 0..1 BackboneElement Exact Start-End
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81254-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Range in question. 'High' can be omitted for single nucleotide variants.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:inner-start-end Σ 0..1 BackboneElement Inner Start-End
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81302-2
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Imprecise variant inner-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:outer-start-end Σ 0..1 BackboneElement Outer Start-End
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 81301-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Range Imprecise variant outer-bounding range
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coordinate-system Σ 0..1 BackboneElement Coordinate System
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 92822-6
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept 0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:ref-allele Σ 0..1 BackboneElement Genomic Ref Allele
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69547-8
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:alt-allele Σ 0..1 BackboneElement Genomic Alt Allele
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 69551-0
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 string Normalized string per the VCF format.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:coding-change-type SΣ 0..1 BackboneElement Coding DNA Change Type
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48019-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNAChangeTypeVS (2.0.0) (extensible): Concepts in sequence ontology under SO:0002072
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:genomic-source-class SΣ 0..1 BackboneElement Genomic Source Class
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:sample-allelic-frequency SΣ 0..1 BackboneElement Sample Allelic Frequency
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 0..1 Quantity Relative frequency in the sample
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
Constraints: ext-1
...... value Σ 0..1 decimal Numerical value (with implicit precision)
...... comparator ?!Σ 0..1 code < | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.
...... unit Σ 0..1 string Unit representation
...... system ΣC 0..1 uri System that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code Σ 0..1 code Coded form of the unit
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:allelic-read-depth Σ 0..1 BackboneElement Allelic Read Depth
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 82121-5
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 0..1 Quantity Unfiltered count of supporting reads
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:allelic-state SΣ 0..1 BackboneElement Allelic State
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variant-inheritance Σ 0..1 BackboneElement Variant Inheritance
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept variant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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-inheritance
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Maternal | Paternal | Unknown
Binding: VariantInheritanceVS (2.0.0) (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variation-code SΣ 0..* BackboneElement Variation Code
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept ClinVar ID or similar
Binding Description: (example): Multiple bindings acceptable
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:chromosome-identifier Σ 0..* BackboneElement Chromosome Identifier
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept 48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://loinc.org
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: 48000-4
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:protein-hgvs SΣ 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
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣ 1..1 CodeableConcept A valid HGVS-formatted (version >=21.1) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: HGVSVS (2.0.0) (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:amino-acid-change-type SΣ 0..1 BackboneElement Amino Acid Change Type
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept 48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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: 48006-1
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: LOINC Answer List LL380-7 (extensible)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:molecular-consequence SΣ 0..1 BackboneElement Molecular Consequence
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept molecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id 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: molecular-consequence
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 1..1 CodeableConcept stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: MolecularConsequenceVS (2.0.0) (extensible): Concepts in sequence ontology under SO:0001537.
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:copy-number SΣ 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
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 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] SΣC 0..1 Quantity Actual component result
Constraints: cnt-3
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:variant-confidence-status Σ 0..1 BackboneElement Variant Confidence Status
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code Σ 1..1 CodeableConcept variant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display 0..1 string Representation defined by the system
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] Σ 1..1 CodeableConcept High | Intermediate | Low
Binding: VariantConfidenceStatusVS (2.0.0) (required)
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:nucleotidesCount SΣ 1..1 BackboneElement Length of of the variant in nNucleotides
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C709
....... display 1..1 string Representation defined by the system
Fixed Value: Nucleotides
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 integer Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result
.... component:geneRegion SΣ 1..1 BackboneElement Region (exon, intron, etc.) of the gene affected by the variant
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
Constraints: ext-1
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
Constraints: ext-1
..... code SΣ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.
Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
....... version 0..1 string Version of the system - if relevant
....... code 1..1 code Symbol in syntax defined by the system
Fixed Value: C13445
....... display 1..1 string Representation defined by the system
Fixed Value: Gene Feature
....... userSelected 0..1 boolean If this coding was chosen directly by the user
...... text 0..1 string Plain text representation of the concept
..... value[x] SΣ 0..1 string Actual component result
..... dataAbsentReason C 0..1 CodeableConcept Why the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
..... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
..... referenceRange 0..* See referenceRange (Observation) Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Observation.language Base preferred Common Languages 📍4.0.1 FHIR Std.
Observation.status Base required ObservationStatus 📍4.0.1 FHIR Std.
Observation.category Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.category:labCategory Base preferred Observation Category Codes 📍4.0.1 FHIR Std.
Observation.code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.value[x]:valueCodeableConcept Base required ​ LOINC Answer Codes for LL1971-2 (missing link) 📦 unknown?
Observation.dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Observation.method Base extensible ​ LOINC Answer Codes for LL4048-6 (missing link) 📦 unknown?
Observation.referenceRange.​type Base preferred Observation Reference Range Meaning Codes 📍4.0.1 FHIR Std.
Observation.referenceRange.​appliesTo Base example Observation Reference Range Applies To Codes 📍4.0.1 FHIR Std.
Observation.component.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:conclusion-string.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​value[x] Base extensible HUGO Gene Nomenclature Committee Gene Names (HGNC) 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:gene-studied.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:gene-studied.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenetic-location.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​value[x] Base extensible ​ LOINC Answer Codes for LL1040-6 (missing link) 📦 unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:coding-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coding-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x] Base example Not Stated Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​value[x] Base example Not Stated Unknown
Observation.component:transcript-ref-seq.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:transcript-ref-seq.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:exact-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:inner-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:outer-start-end.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​value[x] Base extensible ​ LOINC Answer Codes for LL5323-2 (missing link) 📦 unknown?
Observation.component:coordinate-system.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coordinate-system.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:ref-allele.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:alt-allele.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​value[x] Base extensible DNA Change Type 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:coding-change-type.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:coding-change-type.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​value[x] Base extensible ​ LOINC Answer Codes for LL378-1 (missing link) 📦 unknown?
Observation.component:genomic-source-class.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:genomic-source-class.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator Base required QuantityComparator 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:allelic-read-depth.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​value[x] Base extensible ​ LOINC Answer Codes for LL381-5 (missing link) 📦 unknown?
Observation.component:allelic-state.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:allelic-state.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​value[x] Base extensible Variant Inheritances 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variant-inheritance.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-inheritance.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variation-code.​value[x] Base example Not Stated Unknown
Observation.component:variation-code.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variation-code.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​value[x] Base required ​ LOINC Answer Codes for LL2938-0 (missing link) 📦 unknown?
Observation.component:chromosome-identifier.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:chromosome-identifier.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​value[x] Base required Human Genome Variation Society (HGVS) Nomenclature 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:protein-hgvs.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:protein-hgvs.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​value[x] Base extensible ​ LOINC Answer Codes for LL380-7 (missing link) 📦 unknown?
Observation.component:amino-acid-change-type.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:amino-acid-change-type.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:molecular-consequence.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:molecular-consequence.​value[x] Base extensible Molecular Consequence 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:molecular-consequence.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:molecular-consequence.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:copy-number.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:copy-number.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:copy-number.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​value[x] Base required Variant Confidence Status 📍2.0.0 Genomics Reporting Implementation Guide v2.0
Observation.component:variant-confidence-status.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:variant-confidence-status.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:nucleotidesCount.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:nucleotidesCount.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:nucleotidesCount.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.
Observation.component:geneRegion.​code Base example LOINC Codes 📍4.0.1 FHIR Std.
Observation.component:geneRegion.​dataAbsentReason Base extensible DataAbsentReason 📍4.0.1 FHIR Std.
Observation.component:geneRegion.​interpretation Base extensible Observation Interpretation Codes 📍4.0.1 FHIR Std.

Constraints

Id Grade Path(s) Description Expression
cnt-3 error Observation.component:copy-number.value[x] There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2 error Observation If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Observation If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Observation If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Observation If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Observation A resource should have narrative for robust management text.`div`.exists()
ele-1 error Observation.meta, Observation.implicitRules, Observation.language, Observation.text, Observation.extension, Observation.extension:secondary-finding, Observation.extension:body-structure, Observation.extension:genePanel, Observation.extension:hgvsVersion, Observation.modifierExtension, Observation.identifier, Observation.basedOn, Observation.partOf, Observation.status, Observation.category, Observation.category:labCategory, Observation.category:labCategory.extension, Observation.category:labCategory.coding, Observation.category:labCategory.text, Observation.code, Observation.subject, Observation.focus, Observation.encounter, Observation.effective[x], Observation.effective[x]:effectiveDateTime, Observation.issued, Observation.performer, Observation.value[x], Observation.value[x]:valueCodeableConcept, Observation.dataAbsentReason, Observation.interpretation, Observation.note, Observation.bodySite, Observation.method, Observation.specimen, Observation.device, Observation.referenceRange, Observation.referenceRange.extension, Observation.referenceRange.modifierExtension, Observation.referenceRange.low, Observation.referenceRange.high, Observation.referenceRange.type, Observation.referenceRange.appliesTo, Observation.referenceRange.age, Observation.referenceRange.text, Observation.hasMember, Observation.derivedFrom, Observation.component, Observation.component.extension, Observation.component.modifierExtension, Observation.component.code, Observation.component.value[x], Observation.component.dataAbsentReason, Observation.component.interpretation, Observation.component.referenceRange, Observation.component:conclusion-string, Observation.component:conclusion-string.extension, Observation.component:conclusion-string.modifierExtension, Observation.component:conclusion-string.code, Observation.component:conclusion-string.value[x], Observation.component:conclusion-string.dataAbsentReason, Observation.component:conclusion-string.interpretation, Observation.component:conclusion-string.referenceRange, Observation.component:gene-studied, Observation.component:gene-studied.extension, Observation.component:gene-studied.modifierExtension, Observation.component:gene-studied.code, Observation.component:gene-studied.value[x], Observation.component:gene-studied.dataAbsentReason, Observation.component:gene-studied.interpretation, Observation.component:gene-studied.referenceRange, Observation.component:cytogenetic-location, Observation.component:cytogenetic-location.extension, Observation.component:cytogenetic-location.modifierExtension, Observation.component:cytogenetic-location.code, Observation.component:cytogenetic-location.value[x], Observation.component:cytogenetic-location.dataAbsentReason, Observation.component:cytogenetic-location.interpretation, Observation.component:cytogenetic-location.referenceRange, Observation.component:reference-sequence-assembly, Observation.component:reference-sequence-assembly.extension, Observation.component:reference-sequence-assembly.modifierExtension, Observation.component:reference-sequence-assembly.code, Observation.component:reference-sequence-assembly.value[x], Observation.component:reference-sequence-assembly.dataAbsentReason, Observation.component:reference-sequence-assembly.interpretation, Observation.component:reference-sequence-assembly.referenceRange, Observation.component:coding-hgvs, Observation.component:coding-hgvs.extension, Observation.component:coding-hgvs.modifierExtension, Observation.component:coding-hgvs.code, Observation.component:coding-hgvs.value[x], Observation.component:coding-hgvs.dataAbsentReason, Observation.component:coding-hgvs.interpretation, Observation.component:coding-hgvs.referenceRange, Observation.component:genomic-hgvs, Observation.component:genomic-hgvs.extension, Observation.component:genomic-hgvs.modifierExtension, Observation.component:genomic-hgvs.code, Observation.component:genomic-hgvs.value[x], Observation.component:genomic-hgvs.dataAbsentReason, Observation.component:genomic-hgvs.interpretation, Observation.component:genomic-hgvs.referenceRange, Observation.component:cytogenomic-nomenclature, Observation.component:cytogenomic-nomenclature.extension, Observation.component:cytogenomic-nomenclature.modifierExtension, Observation.component:cytogenomic-nomenclature.code, Observation.component:cytogenomic-nomenclature.value[x], Observation.component:cytogenomic-nomenclature.dataAbsentReason, Observation.component:cytogenomic-nomenclature.interpretation, Observation.component:cytogenomic-nomenclature.referenceRange, Observation.component:genomic-ref-seq, Observation.component:genomic-ref-seq.extension, Observation.component:genomic-ref-seq.modifierExtension, Observation.component:genomic-ref-seq.code, Observation.component:genomic-ref-seq.value[x], Observation.component:genomic-ref-seq.dataAbsentReason, Observation.component:genomic-ref-seq.interpretation, Observation.component:genomic-ref-seq.referenceRange, Observation.component:transcript-ref-seq, Observation.component:transcript-ref-seq.extension, Observation.component:transcript-ref-seq.modifierExtension, Observation.component:transcript-ref-seq.code, Observation.component:transcript-ref-seq.value[x], Observation.component:transcript-ref-seq.dataAbsentReason, Observation.component:transcript-ref-seq.interpretation, Observation.component:transcript-ref-seq.referenceRange, Observation.component:exact-start-end, Observation.component:exact-start-end.extension, Observation.component:exact-start-end.modifierExtension, Observation.component:exact-start-end.code, Observation.component:exact-start-end.value[x], Observation.component:exact-start-end.dataAbsentReason, Observation.component:exact-start-end.interpretation, Observation.component:exact-start-end.referenceRange, Observation.component:inner-start-end, Observation.component:inner-start-end.extension, Observation.component:inner-start-end.modifierExtension, Observation.component:inner-start-end.code, Observation.component:inner-start-end.value[x], Observation.component:inner-start-end.dataAbsentReason, Observation.component:inner-start-end.interpretation, Observation.component:inner-start-end.referenceRange, Observation.component:outer-start-end, Observation.component:outer-start-end.extension, Observation.component:outer-start-end.modifierExtension, Observation.component:outer-start-end.code, Observation.component:outer-start-end.value[x], Observation.component:outer-start-end.dataAbsentReason, Observation.component:outer-start-end.interpretation, Observation.component:outer-start-end.referenceRange, Observation.component:coordinate-system, Observation.component:coordinate-system.extension, Observation.component:coordinate-system.modifierExtension, Observation.component:coordinate-system.code, Observation.component:coordinate-system.value[x], Observation.component:coordinate-system.dataAbsentReason, Observation.component:coordinate-system.interpretation, Observation.component:coordinate-system.referenceRange, Observation.component:ref-allele, Observation.component:ref-allele.extension, Observation.component:ref-allele.modifierExtension, Observation.component:ref-allele.code, Observation.component:ref-allele.value[x], Observation.component:ref-allele.dataAbsentReason, Observation.component:ref-allele.interpretation, Observation.component:ref-allele.referenceRange, Observation.component:alt-allele, Observation.component:alt-allele.extension, Observation.component:alt-allele.modifierExtension, Observation.component:alt-allele.code, Observation.component:alt-allele.value[x], Observation.component:alt-allele.dataAbsentReason, Observation.component:alt-allele.interpretation, Observation.component:alt-allele.referenceRange, Observation.component:coding-change-type, Observation.component:coding-change-type.extension, Observation.component:coding-change-type.modifierExtension, Observation.component:coding-change-type.code, Observation.component:coding-change-type.value[x], Observation.component:coding-change-type.dataAbsentReason, Observation.component:coding-change-type.interpretation, Observation.component:coding-change-type.referenceRange, Observation.component:genomic-source-class, Observation.component:genomic-source-class.extension, Observation.component:genomic-source-class.modifierExtension, Observation.component:genomic-source-class.code, Observation.component:genomic-source-class.value[x], Observation.component:genomic-source-class.dataAbsentReason, Observation.component:genomic-source-class.interpretation, Observation.component:genomic-source-class.referenceRange, Observation.component:sample-allelic-frequency, Observation.component:sample-allelic-frequency.extension, Observation.component:sample-allelic-frequency.modifierExtension, Observation.component:sample-allelic-frequency.code, Observation.component:sample-allelic-frequency.value[x], Observation.component:sample-allelic-frequency.value[x].extension, Observation.component:sample-allelic-frequency.value[x].value, Observation.component:sample-allelic-frequency.value[x].comparator, Observation.component:sample-allelic-frequency.value[x].unit, Observation.component:sample-allelic-frequency.value[x].system, Observation.component:sample-allelic-frequency.value[x].code, Observation.component:sample-allelic-frequency.dataAbsentReason, Observation.component:sample-allelic-frequency.interpretation, Observation.component:sample-allelic-frequency.referenceRange, Observation.component:allelic-read-depth, Observation.component:allelic-read-depth.extension, Observation.component:allelic-read-depth.modifierExtension, Observation.component:allelic-read-depth.code, Observation.component:allelic-read-depth.value[x], Observation.component:allelic-read-depth.dataAbsentReason, Observation.component:allelic-read-depth.interpretation, Observation.component:allelic-read-depth.referenceRange, Observation.component:allelic-state, Observation.component:allelic-state.extension, Observation.component:allelic-state.modifierExtension, Observation.component:allelic-state.code, Observation.component:allelic-state.value[x], Observation.component:allelic-state.dataAbsentReason, Observation.component:allelic-state.interpretation, Observation.component:allelic-state.referenceRange, Observation.component:variant-inheritance, Observation.component:variant-inheritance.extension, Observation.component:variant-inheritance.modifierExtension, Observation.component:variant-inheritance.code, Observation.component:variant-inheritance.value[x], Observation.component:variant-inheritance.dataAbsentReason, Observation.component:variant-inheritance.interpretation, Observation.component:variant-inheritance.referenceRange, Observation.component:variation-code, Observation.component:variation-code.extension, Observation.component:variation-code.modifierExtension, Observation.component:variation-code.code, Observation.component:variation-code.value[x], Observation.component:variation-code.dataAbsentReason, Observation.component:variation-code.interpretation, Observation.component:variation-code.referenceRange, Observation.component:chromosome-identifier, Observation.component:chromosome-identifier.extension, Observation.component:chromosome-identifier.modifierExtension, Observation.component:chromosome-identifier.code, Observation.component:chromosome-identifier.value[x], Observation.component:chromosome-identifier.dataAbsentReason, Observation.component:chromosome-identifier.interpretation, Observation.component:chromosome-identifier.referenceRange, Observation.component:protein-hgvs, Observation.component:protein-hgvs.extension, Observation.component:protein-hgvs.modifierExtension, Observation.component:protein-hgvs.code, Observation.component:protein-hgvs.value[x], Observation.component:protein-hgvs.dataAbsentReason, Observation.component:protein-hgvs.interpretation, Observation.component:protein-hgvs.referenceRange, Observation.component:amino-acid-change-type, Observation.component:amino-acid-change-type.extension, Observation.component:amino-acid-change-type.modifierExtension, Observation.component:amino-acid-change-type.code, Observation.component:amino-acid-change-type.value[x], Observation.component:amino-acid-change-type.dataAbsentReason, Observation.component:amino-acid-change-type.interpretation, Observation.component:amino-acid-change-type.referenceRange, Observation.component:molecular-consequence, Observation.component:molecular-consequence.extension, Observation.component:molecular-consequence.modifierExtension, Observation.component:molecular-consequence.code, Observation.component:molecular-consequence.value[x], Observation.component:molecular-consequence.dataAbsentReason, Observation.component:molecular-consequence.interpretation, Observation.component:molecular-consequence.referenceRange, Observation.component:copy-number, Observation.component:copy-number.extension, Observation.component:copy-number.modifierExtension, Observation.component:copy-number.code, Observation.component:copy-number.value[x], Observation.component:copy-number.dataAbsentReason, Observation.component:copy-number.interpretation, Observation.component:copy-number.referenceRange, Observation.component:variant-confidence-status, Observation.component:variant-confidence-status.extension, Observation.component:variant-confidence-status.modifierExtension, Observation.component:variant-confidence-status.code, Observation.component:variant-confidence-status.value[x], Observation.component:variant-confidence-status.dataAbsentReason, Observation.component:variant-confidence-status.interpretation, Observation.component:variant-confidence-status.referenceRange, Observation.component:nucleotidesCount, Observation.component:nucleotidesCount.extension, Observation.component:nucleotidesCount.modifierExtension, Observation.component:nucleotidesCount.code, Observation.component:nucleotidesCount.value[x], Observation.component:nucleotidesCount.dataAbsentReason, Observation.component:nucleotidesCount.interpretation, Observation.component:nucleotidesCount.referenceRange, Observation.component:geneRegion, Observation.component:geneRegion.extension, Observation.component:geneRegion.modifierExtension, Observation.component:geneRegion.code, Observation.component:geneRegion.value[x], Observation.component:geneRegion.dataAbsentReason, Observation.component:geneRegion.interpretation, Observation.component:geneRegion.referenceRange All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error Observation.extension, Observation.extension:secondary-finding, Observation.extension:body-structure, Observation.extension:genePanel, Observation.extension:hgvsVersion, Observation.modifierExtension, Observation.category:labCategory.extension, Observation.referenceRange.extension, Observation.referenceRange.modifierExtension, Observation.component.extension, Observation.component.modifierExtension, Observation.component:conclusion-string.extension, Observation.component:conclusion-string.modifierExtension, Observation.component:gene-studied.extension, Observation.component:gene-studied.modifierExtension, Observation.component:cytogenetic-location.extension, Observation.component:cytogenetic-location.modifierExtension, Observation.component:reference-sequence-assembly.extension, Observation.component:reference-sequence-assembly.modifierExtension, Observation.component:coding-hgvs.extension, Observation.component:coding-hgvs.modifierExtension, Observation.component:genomic-hgvs.extension, Observation.component:genomic-hgvs.modifierExtension, Observation.component:cytogenomic-nomenclature.extension, Observation.component:cytogenomic-nomenclature.modifierExtension, Observation.component:genomic-ref-seq.extension, Observation.component:genomic-ref-seq.modifierExtension, Observation.component:transcript-ref-seq.extension, Observation.component:transcript-ref-seq.modifierExtension, Observation.component:exact-start-end.extension, Observation.component:exact-start-end.modifierExtension, Observation.component:inner-start-end.extension, Observation.component:inner-start-end.modifierExtension, Observation.component:outer-start-end.extension, Observation.component:outer-start-end.modifierExtension, Observation.component:coordinate-system.extension, Observation.component:coordinate-system.modifierExtension, Observation.component:ref-allele.extension, Observation.component:ref-allele.modifierExtension, Observation.component:alt-allele.extension, Observation.component:alt-allele.modifierExtension, Observation.component:coding-change-type.extension, Observation.component:coding-change-type.modifierExtension, Observation.component:genomic-source-class.extension, Observation.component:genomic-source-class.modifierExtension, Observation.component:sample-allelic-frequency.extension, Observation.component:sample-allelic-frequency.modifierExtension, Observation.component:sample-allelic-frequency.value[x].extension, Observation.component:allelic-read-depth.extension, Observation.component:allelic-read-depth.modifierExtension, Observation.component:allelic-state.extension, Observation.component:allelic-state.modifierExtension, Observation.component:variant-inheritance.extension, Observation.component:variant-inheritance.modifierExtension, Observation.component:variation-code.extension, Observation.component:variation-code.modifierExtension, Observation.component:chromosome-identifier.extension, Observation.component:chromosome-identifier.modifierExtension, Observation.component:protein-hgvs.extension, Observation.component:protein-hgvs.modifierExtension, Observation.component:amino-acid-change-type.extension, Observation.component:amino-acid-change-type.modifierExtension, Observation.component:molecular-consequence.extension, Observation.component:molecular-consequence.modifierExtension, Observation.component:copy-number.extension, Observation.component:copy-number.modifierExtension, Observation.component:variant-confidence-status.extension, Observation.component:variant-confidence-status.modifierExtension, Observation.component:nucleotidesCount.extension, Observation.component:nucleotidesCount.modifierExtension, Observation.component:geneRegion.extension, Observation.component:geneRegion.modifierExtension Must have either extensions or value[x], not both extension.exists() != value.exists()
o-var-req-1 error Observation The subject element is required and must be provided. subject.exists() and subject.resolve().is(Patient)
o-var-req-2 error Observation The effectiveDateTime element is required and must be provided. effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3 error Observation The genes extension is required and must be provided. component.where(code.coding.code = '48018-6').exists()
o-var-req-4 error Observation At least one HGVS representation (coding, protein, or genomic) must be provided. component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-3 error Observation.referenceRange Must have at least a low or a high or text low.exists() or high.exists() or text.exists()
obs-6 error Observation dataAbsentReason SHALL only be present if Observation.value[x] is not present dataAbsentReason.empty() or value.empty()
obs-7 error Observation If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicVariant

 

Other representations of profile: CSV, Excel, Schematron