GenomeX Data Exchange FHIR IG
0.2.0 - draft
GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions
Official URL: http://mitre.org/gdx/StructureDefinition/GdxVariant | Version: 0.2.0 | |||
Draft as of 2024-12-18 | Computable Name: GdxVariant |
GenomeX subset of variant profile.
For additional details on how to use this profile, please review the Variant Reporting page in the Genomics Reporting Implemention Guide.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Variant
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | 0..* | Variant | Variant | |
basedOn | 0..* | Reference(Genomic Service Request) | Fulfills plan, proposal or order | |
status | S | 1..1 | code | registered | preliminary | final | amended + |
category | S | 2..* | CodeableConcept | Classification of type of observation |
code | S | 1..1 | CodeableConcept | 69548-6 |
subject | S | 1..1 | Reference(GDX Patient) | Who and/or what the observation is about |
Slices for effective[x] | S | 0..1 | dateTime, Period, Timing, instant | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this |
effective[x]:effectiveDateTime | S | 0..1 | dateTime | Clinically relevant time/time-period for observation |
performer | 0..* | Reference(Practitioner | PractitionerRole | Organization) | Who is responsible for the observation | |
value[x] | S | 0..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual result |
dataAbsentReason | S | 0..1 | CodeableConcept | Why the result is missing |
specimen | S | 0..1 | Reference(Specimen) | Specimen used for this observation |
component | S | 0..* | BackboneElement | Component results |
Slices for component | Content/Rules for all slices | |||
component:gene-studied | S | 0..* | BackboneElement | Gene Studied |
code | S | 1..1 | CodeableConcept | 48018-6 |
value[x] | S | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. |
component:reference-sequence-assembly | S | 0..* | BackboneElement | Human Reference Sequence Assembly |
code | S | 1..1 | CodeableConcept | 62374-4 |
value[x] | S | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... |
component:coding-change-type | S | 0..1 | BackboneElement | Coding DNA Change Type |
code | S | 1..1 | CodeableConcept | 48019-4 |
value[x] | S | 1..1 | CodeableConcept | deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) |
Documentation for this format |
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | C | 0..* | Variant | Variant dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: 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 dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present |
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children |
Slices for extension | Content/Rules for all slices | |||
secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
basedOn | Σ | 0..* | Reference(Genomic Service Request) | Fulfills plan, proposal or order ele-1: All FHIR elements must have a @value or children |
status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. ele-1: All FHIR elements must have a @value or children |
Slices for category | S | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. ele-1: All FHIR elements must have a @value or children |
category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. ele-1: All FHIR elements must have a @value or children | |
coding | Σ | 1..1 | Coding | Code defined by a terminology system ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. ele-1: All FHIR elements must have a @value or children | |
coding | Σ | 1..1 | Coding | Code defined by a terminology system ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
code | SΣ | 1..1 | CodeableConcept | 69548-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |
subject | SΣ | 1..1 | Reference(GDX Patient) | Who and/or what the observation is about ele-1: All FHIR elements must have a @value or children |
Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this ele-1: All FHIR elements must have a @value or children | |
effectiveDateTime | dateTime | |||
effectivePeriod | Period | |||
effectiveTiming | Timing | |||
effectiveInstant | instant | |||
effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation ele-1: All FHIR elements must have a @value or children |
performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization) | Who is responsible for the observation ele-1: All FHIR elements must have a @value or children |
Slices for value[x] | SΣC | 0..1 | Actual result Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children | |
valueQuantity | Quantity | |||
valueCodeableConcept | CodeableConcept | |||
valueString | string | |||
valueBoolean | boolean | |||
valueInteger | integer | |||
valueRange | Range | |||
valueRatio | Ratio | |||
valueSampledData | SampledData | |||
valueTime | time | |||
valueDateTime | dateTime | |||
valuePeriod | Period | |||
value[x]:valueCodeableConcept | ΣC | 0..1 | CodeableConcept | Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required) ele-1: All FHIR elements must have a @value or children |
dataAbsentReason | SC | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. ele-1: All FHIR elements must have a @value or children |
specimen | S | 0..1 | Reference(Specimen) | Specimen used for this observation ele-1: All FHIR elements must have a @value or children |
derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() ele-1: All FHIR elements must have a @value or children |
Slices for component | SΣ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code ele-1: All FHIR elements must have a @value or children |
component:All Slices | Content/Rules for all slices | |||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children |
component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
component:gene-studied | SΣ | 0..* | BackboneElement | Gene Studied ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | SΣ | 1..1 | CodeableConcept | 48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |
value[x] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) ele-1: All FHIR elements must have a @value or children |
component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |
value[x] | Σ | 1..1 | CodeableConcept | Example: 1q21.1 ele-1: All FHIR elements must have a @value or children |
component:reference-sequence-assembly | SΣ | 0..* | BackboneElement | Human Reference Sequence Assembly ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | SΣ | 1..1 | CodeableConcept | 62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |
value[x] | SΣ | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible) ele-1: All FHIR elements must have a @value or children |
component:representative-coding-hgvs | Σ | 0..1 | BackboneElement | DNA change (c.HGVS) ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48004-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T. Binding: Human Genome Variation Society (HGVS) Nomenclature (required) ele-1: All FHIR elements must have a @value or children |
component:genomic-hgvs | Σ | 0..1 | BackboneElement | Genomic (gDNA) Change - gHGVS ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81290-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required) ele-1: All FHIR elements must have a @value or children |
component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature (ISCN) ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81291-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined ele-1: All FHIR elements must have a @value or children |
component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic Reference Sequence ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |
value[x] | Σ | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) ele-1: All FHIR elements must have a @value or children |
component:representative-protein-ref-seq | Σ | 0..1 | BackboneElement | Protein Reference Sequence ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | protein-ref-seq Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: protein-ref-seq | |
value[x] | Σ | 1..1 | CodeableConcept | Versioned protein reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) ele-1: All FHIR elements must have a @value or children |
component:representative-transcript-ref-seq | Σ | 0..1 | BackboneElement | Reference Transcript ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 51958-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |
value[x] | Σ | 1..1 | CodeableConcept | Versioned transcript reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) ele-1: All FHIR elements must have a @value or children |
component:exact-start-end | Σ | 0..1 | BackboneElement | Exact Start-End ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81254-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81254-5 | |
component:inner-start-end | Σ | 0..1 | BackboneElement | Inner Start-End ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81302-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81302-2 | |
component:outer-start-end | Σ | 0..1 | BackboneElement | Outer Start-End ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81301-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81301-4 | |
component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |
value[x] | Σ | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) ele-1: All FHIR elements must have a @value or children |
component:ref-allele | Σ | 0..1 | BackboneElement | Genomic Ref Allele ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 69547-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |
component:alt-allele | Σ | 0..1 | BackboneElement | Genomic Alt Allele ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 69551-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |
component:coding-change-type | SΣ | 0..1 | BackboneElement | Coding DNA Change Type ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | SΣ | 1..1 | CodeableConcept | 48019-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |
value[x] | SΣ | 1..1 | CodeableConcept | deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072 ele-1: All FHIR elements must have a @value or children |
component:genomic-source-class | Σ | 0..1 | BackboneElement | Genomic Source Class ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48002-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |
value[x] | Σ | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible) ele-1: All FHIR elements must have a @value or children |
component:sample-allelic-frequency | Σ | 0..1 | BackboneElement | Sample Allelic Frequency ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81258-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |
component:allelic-read-depth | Σ | 0..1 | BackboneElement | Allelic Read Depth ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 82121-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5 | |
component:allelic-state | Σ | 0..1 | BackboneElement | Allelic State ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 53034-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53034-5 | |
value[x] | Σ | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible) ele-1: All FHIR elements must have a @value or children |
component:variant-inheritance | Σ | 0..1 | BackboneElement | Origin of germline genetic variant ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 94186-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 94186-4 | |
value[x] | Σ | 1..1 | CodeableConcept | Maternal | Paternal | Unknown Binding: LOINC Answer List LL5489-1 (extensible) ele-1: All FHIR elements must have a @value or children |
component:variant-inheritance-basis | Σ | 0..1 | BackboneElement | Evidential basis for variant inheritance ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | Basis for allelic phase Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82309-6 | |
value[x] | Σ | 1..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) ele-1: All FHIR elements must have a @value or children |
component:variation-code | Σ | 0..* | BackboneElement | Variation Code ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81252-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |
value[x] | Σ | 1..1 | CodeableConcept | ClinVar ID or similar Binding Description (No ValueSet): (example): Multiple bindings acceptable ele-1: All FHIR elements must have a @value or children |
component:chromosome-identifier | Σ | 0..* | BackboneElement | Chromosome Identifier ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48000-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48000-4 | |
value[x] | Σ | 1..1 | CodeableConcept | Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required) ele-1: All FHIR elements must have a @value or children |
component:representative-protein-hgvs | Σ | 0..1 | BackboneElement | Protein (Amino Acid) Change - pHGVS ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48005-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) Binding: Human Genome Variation Society (HGVS) Nomenclature (required) ele-1: All FHIR elements must have a @value or children |
component:copy-number | Σ | 0..1 | BackboneElement | Genomic Structural Variant Copy Number ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 82155-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3 | |
component:variant-confidence-status | Σ | 0..1 | BackboneElement | Variant Confidence Status ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | variant-confidence-status Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-confidence-status | |
value[x] | Σ | 1..1 | CodeableConcept | High | Intermediate | Low Binding: Variant Confidence Status (required) ele-1: All FHIR elements must have a @value or children |
component:repeat-motif | Σ | 0..* | BackboneElement | Repeat Motif ele-1: All FHIR elements must have a @value or children |
Slices for extension | Content/Rules for all slices | |||
repeat-motif-order | 0..1 | positiveInt | Repeat Motif Order URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | repeat-motif Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: repeat-motif | |
value[x] | Σ | 1..1 | string | CAG ele-1: All FHIR elements must have a @value or children |
component:repeat-number | Σ | 0..* | BackboneElement | Repeat Number ele-1: All FHIR elements must have a @value or children |
Slices for extension | Content/Rules for all slices | |||
repeat-motif-order | 0..1 | positiveInt | Repeat Motif Order URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | repeat-number Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: repeat-number | |
value[x] | Σ | 1..1 | Quantity | 40 ele-1: All FHIR elements must have a @value or children |
Documentation for this format |
Path | Conformance | ValueSet / Code | URI |
Observation.status | required | ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1 from the FHIR Standard | |
Observation.category | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | |
Observation.category:labCategory | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | |
Observation.category:geCategory | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | |
Observation.code | example | Pattern: LOINC Code 69548-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.value[x]:valueCodeableConcept | required | LOINC LL1971-2http://loinc.org/vs/LL1971-2 | |
Observation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | |
Observation.component.code | example | LOINCCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:conclusion-string.code | example | Pattern: conclusion-stringhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:gene-studied.code | example | Pattern: LOINC Code 48018-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:gene-studied.value[x] | extensible | HGNCVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs | |
Observation.component:cytogenetic-location.code | example | Pattern: LOINC Code 48001-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:reference-sequence-assembly.code | example | Pattern: LOINC Code 62374-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:reference-sequence-assembly.value[x] | extensible | LOINC LL1040-6http://loinc.org/vs/LL1040-6 | |
Observation.component:representative-coding-hgvs.code | example | Pattern: LOINC Code 48004-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:representative-coding-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | |
Observation.component:genomic-hgvs.code | example | Pattern: LOINC Code 81290-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:genomic-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | |
Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC Code 81291-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:cytogenomic-nomenclature.value[x] | example | ||
Observation.component:genomic-ref-seq.code | example | Pattern: LOINC Code 48013-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:genomic-ref-seq.value[x] | example | ||
Observation.component:representative-protein-ref-seq.code | example | Pattern: protein-ref-seqhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:representative-protein-ref-seq.value[x] | example | ||
Observation.component:representative-transcript-ref-seq.code | example | Pattern: LOINC Code 51958-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:representative-transcript-ref-seq.value[x] | example | ||
Observation.component:exact-start-end.code | example | Pattern: LOINC Code 81254-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:inner-start-end.code | example | Pattern: LOINC Code 81302-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:outer-start-end.code | example | Pattern: LOINC Code 81301-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coordinate-system.code | example | Pattern: LOINC Code 92822-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coordinate-system.value[x] | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | |
Observation.component:ref-allele.code | example | Pattern: LOINC Code 69547-8http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:alt-allele.code | example | Pattern: LOINC Code 69551-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coding-change-type.code | example | Pattern: LOINC Code 48019-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coding-change-type.value[x] | extensible | DNAChangeTypeVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs | |
Observation.component:genomic-source-class.code | example | Pattern: LOINC Code 48002-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1http://loinc.org/vs/LL378-1 | |
Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC Code 81258-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:allelic-read-depth.code | example | Pattern: LOINC Code 82121-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:allelic-state.code | example | Pattern: LOINC Code 53034-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5http://loinc.org/vs/LL381-5 | |
Observation.component:variant-inheritance.code | example | Pattern: LOINC Code 94186-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-inheritance.value[x] | extensible | LOINC LL5489-1http://loinc.org/vs/LL5489-1 | |
Observation.component:variant-inheritance-basis.code | example | Pattern: LOINC Code 82309-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-inheritance-basis.value[x] | extensible | LOINC LL4050-2http://loinc.org/vs/LL4050-2 | |
Observation.component:variation-code.code | example | Pattern: LOINC Code 81252-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variation-code.value[x] | example | ||
Observation.component:chromosome-identifier.code | example | Pattern: LOINC Code 48000-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:chromosome-identifier.value[x] | required | LOINC LL2938-0http://loinc.org/vs/LL2938-0 | |
Observation.component:representative-protein-hgvs.code | example | Pattern: LOINC Code 48005-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:representative-protein-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | |
Observation.component:copy-number.code | example | Pattern: LOINC Code 82155-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-confidence-status.code | example | Pattern: variant-confidence-statushttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-confidence-status.value[x] | required | VariantConfidenceStatusVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs | |
Observation.component:repeat-motif.code | example | Pattern: repeat-motifhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:repeat-number.code | example | Pattern: repeat-numberhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard |
Id | Grade | Path(s) | Details | Requirements |
dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty() | |
dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
dom-6 | best practice | Observation | A resource should have narrative for robust management : text.`div`.exists() | |
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
Name | Flags | Card. | Type | Description & Constraints | ||||
---|---|---|---|---|---|---|---|---|
Observation | C | 0..* | Variant | Variant obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present | ||||
id | Σ | 0..1 | id | Logical id of this artifact | ||||
meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
contained | 0..* | Resource | Contained, inline Resources | |||||
Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by pattern:url | |||||
secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |||||
body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
basedOn | Σ | 0..* | Reference(Genomic Service Request) | Fulfills plan, proposal or order | ||||
partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) | Part of referenced event | ||||
status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
Slices for category | S | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | ||||
category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | Σ | 0..1 | string | Plain text representation of the concept | ||||
category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | Σ | 0..1 | string | Plain text representation of the concept | ||||
code | SΣ | 1..1 | CodeableConcept | 69548-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
subject | SΣ | 1..1 | Reference(GDX Patient) | Who and/or what the observation is about | ||||
focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this | |||||
effectiveDateTime | dateTime | |||||||
effectivePeriod | Period | |||||||
effectiveTiming | Timing | |||||||
effectiveInstant | instant | |||||||
effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation | ||||
issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization) | Who is responsible for the observation | ||||
Slices for value[x] | SΣC | 0..1 | Actual result Slice: Unordered, Closed by type:$this | |||||
valueQuantity | Quantity | |||||||
valueCodeableConcept | CodeableConcept | |||||||
valueString | string | |||||||
valueBoolean | boolean | |||||||
valueInteger | integer | |||||||
valueRange | Range | |||||||
valueRatio | Ratio | |||||||
valueSampledData | SampledData | |||||||
valueTime | time | |||||||
valueDateTime | dateTime | |||||||
valuePeriod | Period | |||||||
value[x]:valueCodeableConcept | ΣC | 0..1 | CodeableConcept | Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required) | ||||
dataAbsentReason | SC | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
note | 0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |||||
bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |||||
method | 0..1 | CodeableConcept | Sequencing | SNP array | PCR | Computational analysis | ... Binding: LOINC Answer List LL4048-6 (extensible) | |||||
specimen | S | 0..1 | Reference(Specimen) | Specimen used for this observation | ||||
device | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation obs-3: Must have at least a low or a high or text | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
low | C | 0..1 | SimpleQuantity | Low Range, if relevant | ||||
high | C | 0..1 | SimpleQuantity | High Range, if relevant | ||||
type | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
appliesTo | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
age | 0..1 | Range | Applicable age range, if relevant | |||||
text | 0..1 | string | Text based reference range in an observation | |||||
hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() | ||||
Slices for component | SΣ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
component:All Slices | Content/Rules for all slices | |||||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
value[x] | Σ | 0..1 | Actual component result | |||||
valueQuantity | Quantity | |||||||
valueCodeableConcept | CodeableConcept | |||||||
valueString | string | |||||||
valueBoolean | boolean | |||||||
valueInteger | integer | |||||||
valueRange | Range | |||||||
valueRatio | Ratio | |||||||
valueSampledData | SampledData | |||||||
valueTime | time | |||||||
valueDateTime | dateTime | |||||||
valuePeriod | Period | |||||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:gene-studied | SΣ | 0..* | BackboneElement | Gene Studied | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | SΣ | 1..1 | CodeableConcept | 48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Example: 1q21.1 | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:reference-sequence-assembly | SΣ | 0..* | BackboneElement | Human Reference Sequence Assembly | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | SΣ | 1..1 | CodeableConcept | 62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | SΣ | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:representative-coding-hgvs | Σ | 0..1 | BackboneElement | DNA change (c.HGVS) | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48004-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T. Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:genomic-hgvs | Σ | 0..1 | BackboneElement | Genomic (gDNA) Change - gHGVS | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81290-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature (ISCN) | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81291-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic Reference Sequence | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:representative-protein-ref-seq | Σ | 0..1 | BackboneElement | Protein Reference Sequence | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | protein-ref-seq Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: protein-ref-seq | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Versioned protein reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:representative-transcript-ref-seq | Σ | 0..1 | BackboneElement | Reference Transcript | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 51958-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Versioned transcript reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:exact-start-end | Σ | 0..1 | BackboneElement | Exact Start-End | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81254-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81254-5 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Range | Range in question. 'High' can be omitted for single nucleotide variants. | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:inner-start-end | Σ | 0..1 | BackboneElement | Inner Start-End | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81302-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81302-2 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Range | Imprecise variant inner-bounding range | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:outer-start-end | Σ | 0..1 | BackboneElement | Outer Start-End | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81301-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81301-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Range | Imprecise variant outer-bounding range | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:ref-allele | Σ | 0..1 | BackboneElement | Genomic Ref Allele | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 69547-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | string | Normalized string per the VCF format. | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:alt-allele | Σ | 0..1 | BackboneElement | Genomic Alt Allele | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 69551-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | string | Normalized string per the VCF format. | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:coding-change-type | SΣ | 0..1 | BackboneElement | Coding DNA Change Type | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | SΣ | 1..1 | CodeableConcept | 48019-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | SΣ | 1..1 | CodeableConcept | deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072 | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:genomic-source-class | Σ | 0..1 | BackboneElement | Genomic Source Class | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48002-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:sample-allelic-frequency | Σ | 0..1 | BackboneElement | Sample Allelic Frequency | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81258-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Quantity | Relative frequency in the sample | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
value | Σ | 0..1 | decimal | Numerical value (with implicit precision) | ||||
comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented. | ||||
unit | Σ | 0..1 | string | Unit representation | ||||
system | ΣC | 0..1 | uri | System that defines coded unit form Required Pattern: http://unitsofmeasure.org | ||||
code | Σ | 0..1 | code | Coded form of the unit | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:allelic-read-depth | Σ | 0..1 | BackboneElement | Allelic Read Depth | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 82121-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Quantity | Unfiltered count of supporting reads | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:allelic-state | Σ | 0..1 | BackboneElement | Allelic State | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 53034-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53034-5 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:variant-inheritance | Σ | 0..1 | BackboneElement | Origin of germline genetic variant | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 94186-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 94186-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Maternal | Paternal | Unknown Binding: LOINC Answer List LL5489-1 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:variant-inheritance-basis | Σ | 0..1 | BackboneElement | Evidential basis for variant inheritance | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | Basis for allelic phase Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82309-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:variation-code | Σ | 0..* | BackboneElement | Variation Code | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81252-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | ClinVar ID or similar Binding Description (No ValueSet): (example): Multiple bindings acceptable | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:chromosome-identifier | Σ | 0..* | BackboneElement | Chromosome Identifier | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48000-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48000-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:representative-protein-hgvs | Σ | 0..1 | BackboneElement | Protein (Amino Acid) Change - pHGVS | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48005-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:copy-number | Σ | 0..1 | BackboneElement | Genomic Structural Variant Copy Number | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 82155-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Actual component result | |||||
valueQuantity | Quantity | |||||||
valueRange | Range | |||||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:variant-confidence-status | Σ | 0..1 | BackboneElement | Variant Confidence Status | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | variant-confidence-status Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-confidence-status | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | High | Intermediate | Low Binding: Variant Confidence Status (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:repeat-motif | Σ | 0..* | BackboneElement | Repeat Motif | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
repeat-motif-order | 0..1 | positiveInt | Repeat Motif Order URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | repeat-motif Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: repeat-motif | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | string | CAG | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:repeat-number | Σ | 0..* | BackboneElement | Repeat Number | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
repeat-motif-order | 0..1 | positiveInt | Repeat Motif Order URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | repeat-number Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: repeat-number | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | Quantity | 40 | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
Documentation for this format |
Path | Conformance | ValueSet / Code | URI | |||
Observation.language | preferred | CommonLanguageshttp://hl7.org/fhir/ValueSet/languages from the FHIR Standard
| ||||
Observation.status | required | ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1 from the FHIR Standard | ||||
Observation.category | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | ||||
Observation.category:labCategory | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | ||||
Observation.category:geCategory | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | ||||
Observation.code | example | Pattern: LOINC Code 69548-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.value[x]:valueCodeableConcept | required | LOINC LL1971-2http://loinc.org/vs/LL1971-2 | ||||
Observation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.bodySite | example | SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-site from the FHIR Standard | ||||
Observation.method | extensible | LOINC LL4048-6http://loinc.org/vs/LL4048-6 | ||||
Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodeshttp://hl7.org/fhir/ValueSet/referencerange-meaning from the FHIR Standard | ||||
Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodeshttp://hl7.org/fhir/ValueSet/referencerange-appliesto from the FHIR Standard | ||||
Observation.component.code | example | LOINCCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:conclusion-string.code | example | Pattern: conclusion-stringhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:conclusion-string.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:conclusion-string.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:gene-studied.code | example | Pattern: LOINC Code 48018-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:gene-studied.value[x] | extensible | HGNCVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs | ||||
Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:gene-studied.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:cytogenetic-location.code | example | Pattern: LOINC Code 48001-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:cytogenetic-location.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:cytogenetic-location.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:reference-sequence-assembly.code | example | Pattern: LOINC Code 62374-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:reference-sequence-assembly.value[x] | extensible | LOINC LL1040-6http://loinc.org/vs/LL1040-6 | ||||
Observation.component:reference-sequence-assembly.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:reference-sequence-assembly.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:representative-coding-hgvs.code | example | Pattern: LOINC Code 48004-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:representative-coding-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | ||||
Observation.component:representative-coding-hgvs.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:representative-coding-hgvs.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:genomic-hgvs.code | example | Pattern: LOINC Code 81290-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:genomic-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | ||||
Observation.component:genomic-hgvs.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:genomic-hgvs.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC Code 81291-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:cytogenomic-nomenclature.value[x] | example | |||||
Observation.component:cytogenomic-nomenclature.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:cytogenomic-nomenclature.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:genomic-ref-seq.code | example | Pattern: LOINC Code 48013-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:genomic-ref-seq.value[x] | example | |||||
Observation.component:genomic-ref-seq.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:genomic-ref-seq.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:representative-protein-ref-seq.code | example | Pattern: protein-ref-seqhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:representative-protein-ref-seq.value[x] | example | |||||
Observation.component:representative-protein-ref-seq.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:representative-protein-ref-seq.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:representative-transcript-ref-seq.code | example | Pattern: LOINC Code 51958-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:representative-transcript-ref-seq.value[x] | example | |||||
Observation.component:representative-transcript-ref-seq.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:representative-transcript-ref-seq.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:exact-start-end.code | example | Pattern: LOINC Code 81254-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:exact-start-end.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:exact-start-end.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:inner-start-end.code | example | Pattern: LOINC Code 81302-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:inner-start-end.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:inner-start-end.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:outer-start-end.code | example | Pattern: LOINC Code 81301-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:outer-start-end.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:outer-start-end.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:coordinate-system.code | example | Pattern: LOINC Code 92822-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:coordinate-system.value[x] | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | ||||
Observation.component:coordinate-system.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:coordinate-system.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:ref-allele.code | example | Pattern: LOINC Code 69547-8http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:ref-allele.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:ref-allele.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:alt-allele.code | example | Pattern: LOINC Code 69551-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:alt-allele.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:alt-allele.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:coding-change-type.code | example | Pattern: LOINC Code 48019-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:coding-change-type.value[x] | extensible | DNAChangeTypeVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs | ||||
Observation.component:coding-change-type.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:coding-change-type.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:genomic-source-class.code | example | Pattern: LOINC Code 48002-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1http://loinc.org/vs/LL378-1 | ||||
Observation.component:genomic-source-class.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:genomic-source-class.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC Code 81258-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparatorhttp://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1 from the FHIR Standard | ||||
Observation.component:sample-allelic-frequency.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:sample-allelic-frequency.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:allelic-read-depth.code | example | Pattern: LOINC Code 82121-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:allelic-read-depth.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:allelic-read-depth.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:allelic-state.code | example | Pattern: LOINC Code 53034-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5http://loinc.org/vs/LL381-5 | ||||
Observation.component:allelic-state.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:allelic-state.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:variant-inheritance.code | example | Pattern: LOINC Code 94186-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:variant-inheritance.value[x] | extensible | LOINC LL5489-1http://loinc.org/vs/LL5489-1 | ||||
Observation.component:variant-inheritance.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:variant-inheritance.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:variant-inheritance-basis.code | example | Pattern: LOINC Code 82309-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:variant-inheritance-basis.value[x] | extensible | LOINC LL4050-2http://loinc.org/vs/LL4050-2 | ||||
Observation.component:variant-inheritance-basis.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:variant-inheritance-basis.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:variation-code.code | example | Pattern: LOINC Code 81252-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:variation-code.value[x] | example | |||||
Observation.component:variation-code.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:variation-code.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:chromosome-identifier.code | example | Pattern: LOINC Code 48000-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:chromosome-identifier.value[x] | required | LOINC LL2938-0http://loinc.org/vs/LL2938-0 | ||||
Observation.component:chromosome-identifier.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:chromosome-identifier.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:representative-protein-hgvs.code | example | Pattern: LOINC Code 48005-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:representative-protein-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | ||||
Observation.component:representative-protein-hgvs.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:representative-protein-hgvs.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:copy-number.code | example | Pattern: LOINC Code 82155-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:copy-number.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:copy-number.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:variant-confidence-status.code | example | Pattern: variant-confidence-statushttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:variant-confidence-status.value[x] | required | VariantConfidenceStatusVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs | ||||
Observation.component:variant-confidence-status.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:variant-confidence-status.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:repeat-motif.code | example | Pattern: repeat-motifhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:repeat-motif.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:repeat-motif.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:repeat-number.code | example | Pattern: repeat-numberhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:repeat-number.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:repeat-number.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard |
Id | Grade | Path(s) | Details | Requirements |
dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty() | |
dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
dom-6 | best practice | Observation | A resource should have narrative for robust management : text.`div`.exists() | |
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text : low.exists() or high.exists() or text.exists() | |
obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
This structure is derived from Variant
Summary
Mandatory: 1 element
Must-Support: 19 elements
Structures
This structure refers to these other structures:
Slices
This structure defines the following Slices:
Differential View
This structure is derived from Variant
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | 0..* | Variant | Variant | |
basedOn | 0..* | Reference(Genomic Service Request) | Fulfills plan, proposal or order | |
status | S | 1..1 | code | registered | preliminary | final | amended + |
category | S | 2..* | CodeableConcept | Classification of type of observation |
code | S | 1..1 | CodeableConcept | 69548-6 |
subject | S | 1..1 | Reference(GDX Patient) | Who and/or what the observation is about |
Slices for effective[x] | S | 0..1 | dateTime, Period, Timing, instant | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this |
effective[x]:effectiveDateTime | S | 0..1 | dateTime | Clinically relevant time/time-period for observation |
performer | 0..* | Reference(Practitioner | PractitionerRole | Organization) | Who is responsible for the observation | |
value[x] | S | 0..1 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | Actual result |
dataAbsentReason | S | 0..1 | CodeableConcept | Why the result is missing |
specimen | S | 0..1 | Reference(Specimen) | Specimen used for this observation |
component | S | 0..* | BackboneElement | Component results |
Slices for component | Content/Rules for all slices | |||
component:gene-studied | S | 0..* | BackboneElement | Gene Studied |
code | S | 1..1 | CodeableConcept | 48018-6 |
value[x] | S | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. |
component:reference-sequence-assembly | S | 0..* | BackboneElement | Human Reference Sequence Assembly |
code | S | 1..1 | CodeableConcept | 62374-4 |
value[x] | S | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... |
component:coding-change-type | S | 0..1 | BackboneElement | Coding DNA Change Type |
code | S | 1..1 | CodeableConcept | 48019-4 |
value[x] | S | 1..1 | CodeableConcept | deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) |
Documentation for this format |
Key Elements View
Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
Observation | C | 0..* | Variant | Variant dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: 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 dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present |
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children |
Slices for extension | Content/Rules for all slices | |||
secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
basedOn | Σ | 0..* | Reference(Genomic Service Request) | Fulfills plan, proposal or order ele-1: All FHIR elements must have a @value or children |
status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. ele-1: All FHIR elements must have a @value or children |
Slices for category | S | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. ele-1: All FHIR elements must have a @value or children |
category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. ele-1: All FHIR elements must have a @value or children | |
coding | Σ | 1..1 | Coding | Code defined by a terminology system ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. ele-1: All FHIR elements must have a @value or children | |
coding | Σ | 1..1 | Coding | Code defined by a terminology system ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
code | SΣ | 1..1 | CodeableConcept | 69548-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |
subject | SΣ | 1..1 | Reference(GDX Patient) | Who and/or what the observation is about ele-1: All FHIR elements must have a @value or children |
Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this ele-1: All FHIR elements must have a @value or children | |
effectiveDateTime | dateTime | |||
effectivePeriod | Period | |||
effectiveTiming | Timing | |||
effectiveInstant | instant | |||
effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation ele-1: All FHIR elements must have a @value or children |
performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization) | Who is responsible for the observation ele-1: All FHIR elements must have a @value or children |
Slices for value[x] | SΣC | 0..1 | Actual result Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children | |
valueQuantity | Quantity | |||
valueCodeableConcept | CodeableConcept | |||
valueString | string | |||
valueBoolean | boolean | |||
valueInteger | integer | |||
valueRange | Range | |||
valueRatio | Ratio | |||
valueSampledData | SampledData | |||
valueTime | time | |||
valueDateTime | dateTime | |||
valuePeriod | Period | |||
value[x]:valueCodeableConcept | ΣC | 0..1 | CodeableConcept | Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required) ele-1: All FHIR elements must have a @value or children |
dataAbsentReason | SC | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. ele-1: All FHIR elements must have a @value or children |
specimen | S | 0..1 | Reference(Specimen) | Specimen used for this observation ele-1: All FHIR elements must have a @value or children |
derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() ele-1: All FHIR elements must have a @value or children |
Slices for component | SΣ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code ele-1: All FHIR elements must have a @value or children |
component:All Slices | Content/Rules for all slices | |||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children |
component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
component:gene-studied | SΣ | 0..* | BackboneElement | Gene Studied ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | SΣ | 1..1 | CodeableConcept | 48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |
value[x] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) ele-1: All FHIR elements must have a @value or children |
component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |
value[x] | Σ | 1..1 | CodeableConcept | Example: 1q21.1 ele-1: All FHIR elements must have a @value or children |
component:reference-sequence-assembly | SΣ | 0..* | BackboneElement | Human Reference Sequence Assembly ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | SΣ | 1..1 | CodeableConcept | 62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |
value[x] | SΣ | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible) ele-1: All FHIR elements must have a @value or children |
component:representative-coding-hgvs | Σ | 0..1 | BackboneElement | DNA change (c.HGVS) ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48004-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T. Binding: Human Genome Variation Society (HGVS) Nomenclature (required) ele-1: All FHIR elements must have a @value or children |
component:genomic-hgvs | Σ | 0..1 | BackboneElement | Genomic (gDNA) Change - gHGVS ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81290-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required) ele-1: All FHIR elements must have a @value or children |
component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature (ISCN) ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81291-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined ele-1: All FHIR elements must have a @value or children |
component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic Reference Sequence ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |
value[x] | Σ | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) ele-1: All FHIR elements must have a @value or children |
component:representative-protein-ref-seq | Σ | 0..1 | BackboneElement | Protein Reference Sequence ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | protein-ref-seq Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: protein-ref-seq | |
value[x] | Σ | 1..1 | CodeableConcept | Versioned protein reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) ele-1: All FHIR elements must have a @value or children |
component:representative-transcript-ref-seq | Σ | 0..1 | BackboneElement | Reference Transcript ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 51958-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |
value[x] | Σ | 1..1 | CodeableConcept | Versioned transcript reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) ele-1: All FHIR elements must have a @value or children |
component:exact-start-end | Σ | 0..1 | BackboneElement | Exact Start-End ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81254-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81254-5 | |
component:inner-start-end | Σ | 0..1 | BackboneElement | Inner Start-End ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81302-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81302-2 | |
component:outer-start-end | Σ | 0..1 | BackboneElement | Outer Start-End ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81301-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81301-4 | |
component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |
value[x] | Σ | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) ele-1: All FHIR elements must have a @value or children |
component:ref-allele | Σ | 0..1 | BackboneElement | Genomic Ref Allele ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 69547-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |
component:alt-allele | Σ | 0..1 | BackboneElement | Genomic Alt Allele ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 69551-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |
component:coding-change-type | SΣ | 0..1 | BackboneElement | Coding DNA Change Type ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | SΣ | 1..1 | CodeableConcept | 48019-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |
value[x] | SΣ | 1..1 | CodeableConcept | deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072 ele-1: All FHIR elements must have a @value or children |
component:genomic-source-class | Σ | 0..1 | BackboneElement | Genomic Source Class ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48002-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |
value[x] | Σ | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible) ele-1: All FHIR elements must have a @value or children |
component:sample-allelic-frequency | Σ | 0..1 | BackboneElement | Sample Allelic Frequency ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81258-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |
component:allelic-read-depth | Σ | 0..1 | BackboneElement | Allelic Read Depth ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 82121-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5 | |
component:allelic-state | Σ | 0..1 | BackboneElement | Allelic State ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 53034-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53034-5 | |
value[x] | Σ | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible) ele-1: All FHIR elements must have a @value or children |
component:variant-inheritance | Σ | 0..1 | BackboneElement | Origin of germline genetic variant ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 94186-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 94186-4 | |
value[x] | Σ | 1..1 | CodeableConcept | Maternal | Paternal | Unknown Binding: LOINC Answer List LL5489-1 (extensible) ele-1: All FHIR elements must have a @value or children |
component:variant-inheritance-basis | Σ | 0..1 | BackboneElement | Evidential basis for variant inheritance ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | Basis for allelic phase Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82309-6 | |
value[x] | Σ | 1..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) ele-1: All FHIR elements must have a @value or children |
component:variation-code | Σ | 0..* | BackboneElement | Variation Code ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 81252-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |
value[x] | Σ | 1..1 | CodeableConcept | ClinVar ID or similar Binding Description (No ValueSet): (example): Multiple bindings acceptable ele-1: All FHIR elements must have a @value or children |
component:chromosome-identifier | Σ | 0..* | BackboneElement | Chromosome Identifier ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48000-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48000-4 | |
value[x] | Σ | 1..1 | CodeableConcept | Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required) ele-1: All FHIR elements must have a @value or children |
component:representative-protein-hgvs | Σ | 0..1 | BackboneElement | Protein (Amino Acid) Change - pHGVS ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 48005-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) Binding: Human Genome Variation Society (HGVS) Nomenclature (required) ele-1: All FHIR elements must have a @value or children |
component:copy-number | Σ | 0..1 | BackboneElement | Genomic Structural Variant Copy Number ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | 82155-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3 | |
component:variant-confidence-status | Σ | 0..1 | BackboneElement | Variant Confidence Status ele-1: All FHIR elements must have a @value or children |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | variant-confidence-status Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-confidence-status | |
value[x] | Σ | 1..1 | CodeableConcept | High | Intermediate | Low Binding: Variant Confidence Status (required) ele-1: All FHIR elements must have a @value or children |
component:repeat-motif | Σ | 0..* | BackboneElement | Repeat Motif ele-1: All FHIR elements must have a @value or children |
Slices for extension | Content/Rules for all slices | |||
repeat-motif-order | 0..1 | positiveInt | Repeat Motif Order URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | repeat-motif Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: repeat-motif | |
value[x] | Σ | 1..1 | string | CAG ele-1: All FHIR elements must have a @value or children |
component:repeat-number | Σ | 0..* | BackboneElement | Repeat Number ele-1: All FHIR elements must have a @value or children |
Slices for extension | Content/Rules for all slices | |||
repeat-motif-order | 0..1 | positiveInt | Repeat Motif Order URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
code | Σ | 1..1 | CodeableConcept | repeat-number Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children Required Pattern: At least the following |
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: repeat-number | |
value[x] | Σ | 1..1 | Quantity | 40 ele-1: All FHIR elements must have a @value or children |
Documentation for this format |
Path | Conformance | ValueSet / Code | URI |
Observation.status | required | ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1 from the FHIR Standard | |
Observation.category | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | |
Observation.category:labCategory | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | |
Observation.category:geCategory | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | |
Observation.code | example | Pattern: LOINC Code 69548-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.value[x]:valueCodeableConcept | required | LOINC LL1971-2http://loinc.org/vs/LL1971-2 | |
Observation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | |
Observation.component.code | example | LOINCCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:conclusion-string.code | example | Pattern: conclusion-stringhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:gene-studied.code | example | Pattern: LOINC Code 48018-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:gene-studied.value[x] | extensible | HGNCVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs | |
Observation.component:cytogenetic-location.code | example | Pattern: LOINC Code 48001-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:reference-sequence-assembly.code | example | Pattern: LOINC Code 62374-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:reference-sequence-assembly.value[x] | extensible | LOINC LL1040-6http://loinc.org/vs/LL1040-6 | |
Observation.component:representative-coding-hgvs.code | example | Pattern: LOINC Code 48004-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:representative-coding-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | |
Observation.component:genomic-hgvs.code | example | Pattern: LOINC Code 81290-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:genomic-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | |
Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC Code 81291-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:cytogenomic-nomenclature.value[x] | example | ||
Observation.component:genomic-ref-seq.code | example | Pattern: LOINC Code 48013-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:genomic-ref-seq.value[x] | example | ||
Observation.component:representative-protein-ref-seq.code | example | Pattern: protein-ref-seqhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:representative-protein-ref-seq.value[x] | example | ||
Observation.component:representative-transcript-ref-seq.code | example | Pattern: LOINC Code 51958-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:representative-transcript-ref-seq.value[x] | example | ||
Observation.component:exact-start-end.code | example | Pattern: LOINC Code 81254-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:inner-start-end.code | example | Pattern: LOINC Code 81302-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:outer-start-end.code | example | Pattern: LOINC Code 81301-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coordinate-system.code | example | Pattern: LOINC Code 92822-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coordinate-system.value[x] | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | |
Observation.component:ref-allele.code | example | Pattern: LOINC Code 69547-8http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:alt-allele.code | example | Pattern: LOINC Code 69551-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coding-change-type.code | example | Pattern: LOINC Code 48019-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:coding-change-type.value[x] | extensible | DNAChangeTypeVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs | |
Observation.component:genomic-source-class.code | example | Pattern: LOINC Code 48002-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1http://loinc.org/vs/LL378-1 | |
Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC Code 81258-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:allelic-read-depth.code | example | Pattern: LOINC Code 82121-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:allelic-state.code | example | Pattern: LOINC Code 53034-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5http://loinc.org/vs/LL381-5 | |
Observation.component:variant-inheritance.code | example | Pattern: LOINC Code 94186-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-inheritance.value[x] | extensible | LOINC LL5489-1http://loinc.org/vs/LL5489-1 | |
Observation.component:variant-inheritance-basis.code | example | Pattern: LOINC Code 82309-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-inheritance-basis.value[x] | extensible | LOINC LL4050-2http://loinc.org/vs/LL4050-2 | |
Observation.component:variation-code.code | example | Pattern: LOINC Code 81252-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variation-code.value[x] | example | ||
Observation.component:chromosome-identifier.code | example | Pattern: LOINC Code 48000-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:chromosome-identifier.value[x] | required | LOINC LL2938-0http://loinc.org/vs/LL2938-0 | |
Observation.component:representative-protein-hgvs.code | example | Pattern: LOINC Code 48005-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:representative-protein-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | |
Observation.component:copy-number.code | example | Pattern: LOINC Code 82155-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-confidence-status.code | example | Pattern: variant-confidence-statushttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:variant-confidence-status.value[x] | required | VariantConfidenceStatusVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs | |
Observation.component:repeat-motif.code | example | Pattern: repeat-motifhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | |
Observation.component:repeat-number.code | example | Pattern: repeat-numberhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard |
Id | Grade | Path(s) | Details | Requirements |
dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty() | |
dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
dom-6 | best practice | Observation | A resource should have narrative for robust management : text.`div`.exists() | |
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
Snapshot View
Name | Flags | Card. | Type | Description & Constraints | ||||
---|---|---|---|---|---|---|---|---|
Observation | C | 0..* | Variant | Variant obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present | ||||
id | Σ | 0..1 | id | Logical id of this artifact | ||||
meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
contained | 0..* | Resource | Contained, inline Resources | |||||
Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by pattern:url | |||||
secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |||||
body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
basedOn | Σ | 0..* | Reference(Genomic Service Request) | Fulfills plan, proposal or order | ||||
partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | Genomic Study) | Part of referenced event | ||||
status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
Slices for category | S | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | ||||
category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | Σ | 0..1 | string | Plain text representation of the concept | ||||
category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | Σ | 0..1 | string | Plain text representation of the concept | ||||
code | SΣ | 1..1 | CodeableConcept | 69548-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
subject | SΣ | 1..1 | Reference(GDX Patient) | Who and/or what the observation is about | ||||
focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this | |||||
effectiveDateTime | dateTime | |||||||
effectivePeriod | Period | |||||||
effectiveTiming | Timing | |||||||
effectiveInstant | instant | |||||||
effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation | ||||
issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization) | Who is responsible for the observation | ||||
Slices for value[x] | SΣC | 0..1 | Actual result Slice: Unordered, Closed by type:$this | |||||
valueQuantity | Quantity | |||||||
valueCodeableConcept | CodeableConcept | |||||||
valueString | string | |||||||
valueBoolean | boolean | |||||||
valueInteger | integer | |||||||
valueRange | Range | |||||||
valueRatio | Ratio | |||||||
valueSampledData | SampledData | |||||||
valueTime | time | |||||||
valueDateTime | dateTime | |||||||
valuePeriod | Period | |||||||
value[x]:valueCodeableConcept | ΣC | 0..1 | CodeableConcept | Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required) | ||||
dataAbsentReason | SC | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
note | 0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |||||
bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |||||
method | 0..1 | CodeableConcept | Sequencing | SNP array | PCR | Computational analysis | ... Binding: LOINC Answer List LL4048-6 (extensible) | |||||
specimen | S | 0..1 | Reference(Specimen) | Specimen used for this observation | ||||
device | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation obs-3: Must have at least a low or a high or text | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
low | C | 0..1 | SimpleQuantity | Low Range, if relevant | ||||
high | C | 0..1 | SimpleQuantity | High Range, if relevant | ||||
type | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
appliesTo | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
age | 0..1 | Range | Applicable age range, if relevant | |||||
text | 0..1 | string | Text based reference range in an observation | |||||
hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() | ||||
Slices for component | SΣ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
component:All Slices | Content/Rules for all slices | |||||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
value[x] | Σ | 0..1 | Actual component result | |||||
valueQuantity | Quantity | |||||||
valueCodeableConcept | CodeableConcept | |||||||
valueString | string | |||||||
valueBoolean | boolean | |||||||
valueInteger | integer | |||||||
valueRange | Range | |||||||
valueRatio | Ratio | |||||||
valueSampledData | SampledData | |||||||
valueTime | time | |||||||
valueDateTime | dateTime | |||||||
valuePeriod | Period | |||||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:gene-studied | SΣ | 0..* | BackboneElement | Gene Studied | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | SΣ | 1..1 | CodeableConcept | 48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Example: 1q21.1 | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:reference-sequence-assembly | SΣ | 0..* | BackboneElement | Human Reference Sequence Assembly | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | SΣ | 1..1 | CodeableConcept | 62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | SΣ | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:representative-coding-hgvs | Σ | 0..1 | BackboneElement | DNA change (c.HGVS) | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48004-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48004-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T. Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:genomic-hgvs | Σ | 0..1 | BackboneElement | Genomic (gDNA) Change - gHGVS | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81290-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81290-9 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature (ISCN) | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81291-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81291-7 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic Reference Sequence | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:representative-protein-ref-seq | Σ | 0..1 | BackboneElement | Protein Reference Sequence | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | protein-ref-seq Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: protein-ref-seq | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Versioned protein reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:representative-transcript-ref-seq | Σ | 0..1 | BackboneElement | Reference Transcript | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 51958-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51958-7 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Versioned transcript reference sequence identifier Binding Description (No ValueSet): (example): Multiple bindings acceptable (NCBI or LRG) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:exact-start-end | Σ | 0..1 | BackboneElement | Exact Start-End | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81254-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81254-5 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Range | Range in question. 'High' can be omitted for single nucleotide variants. | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:inner-start-end | Σ | 0..1 | BackboneElement | Inner Start-End | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81302-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81302-2 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Range | Imprecise variant inner-bounding range | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:outer-start-end | Σ | 0..1 | BackboneElement | Outer Start-End | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81301-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81301-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Range | Imprecise variant outer-bounding range | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:ref-allele | Σ | 0..1 | BackboneElement | Genomic Ref Allele | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 69547-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | string | Normalized string per the VCF format. | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:alt-allele | Σ | 0..1 | BackboneElement | Genomic Alt Allele | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 69551-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | string | Normalized string per the VCF format. | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:coding-change-type | SΣ | 0..1 | BackboneElement | Coding DNA Change Type | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | SΣ | 1..1 | CodeableConcept | 48019-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48019-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | SΣ | 1..1 | CodeableConcept | deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072 | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:genomic-source-class | Σ | 0..1 | BackboneElement | Genomic Source Class | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48002-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48002-0 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:sample-allelic-frequency | Σ | 0..1 | BackboneElement | Sample Allelic Frequency | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81258-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81258-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Quantity | Relative frequency in the sample | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
value | Σ | 0..1 | decimal | Numerical value (with implicit precision) | ||||
comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented. | ||||
unit | Σ | 0..1 | string | Unit representation | ||||
system | ΣC | 0..1 | uri | System that defines coded unit form Required Pattern: http://unitsofmeasure.org | ||||
code | Σ | 0..1 | code | Coded form of the unit | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:allelic-read-depth | Σ | 0..1 | BackboneElement | Allelic Read Depth | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 82121-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Quantity | Unfiltered count of supporting reads | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:allelic-state | Σ | 0..1 | BackboneElement | Allelic State | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 53034-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53034-5 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:variant-inheritance | Σ | 0..1 | BackboneElement | Origin of germline genetic variant | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 94186-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 94186-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Maternal | Paternal | Unknown Binding: LOINC Answer List LL5489-1 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:variant-inheritance-basis | Σ | 0..1 | BackboneElement | Evidential basis for variant inheritance | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | Basis for allelic phase Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82309-6 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:variation-code | Σ | 0..* | BackboneElement | Variation Code | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 81252-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81252-9 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | ClinVar ID or similar Binding Description (No ValueSet): (example): Multiple bindings acceptable | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:chromosome-identifier | Σ | 0..* | BackboneElement | Chromosome Identifier | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48000-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48000-4 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:representative-protein-hgvs | Σ | 0..1 | BackboneElement | Protein (Amino Acid) Change - pHGVS | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 48005-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48005-3 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:copy-number | Σ | 0..1 | BackboneElement | Genomic Structural Variant Copy Number | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | 82155-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3 | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 0..1 | Actual component result | |||||
valueQuantity | Quantity | |||||||
valueRange | Range | |||||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:variant-confidence-status | Σ | 0..1 | BackboneElement | Variant Confidence Status | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Extension | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | variant-confidence-status Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-confidence-status | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | CodeableConcept | High | Intermediate | Low Binding: Variant Confidence Status (required) | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:repeat-motif | Σ | 0..* | BackboneElement | Repeat Motif | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
repeat-motif-order | 0..1 | positiveInt | Repeat Motif Order URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | repeat-motif Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: repeat-motif | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | string | CAG | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
component:repeat-number | Σ | 0..* | BackboneElement | Repeat Number | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
repeat-motif-order | 0..1 | positiveInt | Repeat Motif Order URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order | |||||
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
code | Σ | 1..1 | CodeableConcept | repeat-number Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
id | 0..1 | string | Unique id for inter-element referencing | |||||
extension | 0..* | Extension | Additional content defined by implementations | |||||
system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
version | 0..1 | string | Version of the system - if relevant | |||||
code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: repeat-number | |||||
display | 0..1 | string | Representation defined by the system | |||||
userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
text | 0..1 | string | Plain text representation of the concept | |||||
value[x] | Σ | 1..1 | Quantity | 40 | ||||
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
Documentation for this format |
Path | Conformance | ValueSet / Code | URI | |||
Observation.language | preferred | CommonLanguageshttp://hl7.org/fhir/ValueSet/languages from the FHIR Standard
| ||||
Observation.status | required | ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1 from the FHIR Standard | ||||
Observation.category | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | ||||
Observation.category:labCategory | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | ||||
Observation.category:geCategory | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard | ||||
Observation.code | example | Pattern: LOINC Code 69548-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.value[x]:valueCodeableConcept | required | LOINC LL1971-2http://loinc.org/vs/LL1971-2 | ||||
Observation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.bodySite | example | SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-site from the FHIR Standard | ||||
Observation.method | extensible | LOINC LL4048-6http://loinc.org/vs/LL4048-6 | ||||
Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodeshttp://hl7.org/fhir/ValueSet/referencerange-meaning from the FHIR Standard | ||||
Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodeshttp://hl7.org/fhir/ValueSet/referencerange-appliesto from the FHIR Standard | ||||
Observation.component.code | example | LOINCCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:conclusion-string.code | example | Pattern: conclusion-stringhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:conclusion-string.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:conclusion-string.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:gene-studied.code | example | Pattern: LOINC Code 48018-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:gene-studied.value[x] | extensible | HGNCVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs | ||||
Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:gene-studied.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:cytogenetic-location.code | example | Pattern: LOINC Code 48001-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:cytogenetic-location.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:cytogenetic-location.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:reference-sequence-assembly.code | example | Pattern: LOINC Code 62374-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:reference-sequence-assembly.value[x] | extensible | LOINC LL1040-6http://loinc.org/vs/LL1040-6 | ||||
Observation.component:reference-sequence-assembly.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:reference-sequence-assembly.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:representative-coding-hgvs.code | example | Pattern: LOINC Code 48004-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:representative-coding-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | ||||
Observation.component:representative-coding-hgvs.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:representative-coding-hgvs.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:genomic-hgvs.code | example | Pattern: LOINC Code 81290-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:genomic-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | ||||
Observation.component:genomic-hgvs.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:genomic-hgvs.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC Code 81291-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:cytogenomic-nomenclature.value[x] | example | |||||
Observation.component:cytogenomic-nomenclature.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:cytogenomic-nomenclature.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:genomic-ref-seq.code | example | Pattern: LOINC Code 48013-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:genomic-ref-seq.value[x] | example | |||||
Observation.component:genomic-ref-seq.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:genomic-ref-seq.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:representative-protein-ref-seq.code | example | Pattern: protein-ref-seqhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:representative-protein-ref-seq.value[x] | example | |||||
Observation.component:representative-protein-ref-seq.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:representative-protein-ref-seq.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:representative-transcript-ref-seq.code | example | Pattern: LOINC Code 51958-7http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:representative-transcript-ref-seq.value[x] | example | |||||
Observation.component:representative-transcript-ref-seq.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:representative-transcript-ref-seq.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:exact-start-end.code | example | Pattern: LOINC Code 81254-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:exact-start-end.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:exact-start-end.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:inner-start-end.code | example | Pattern: LOINC Code 81302-2http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:inner-start-end.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:inner-start-end.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:outer-start-end.code | example | Pattern: LOINC Code 81301-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:outer-start-end.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:outer-start-end.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:coordinate-system.code | example | Pattern: LOINC Code 92822-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:coordinate-system.value[x] | extensible | LOINC LL5323-2http://loinc.org/vs/LL5323-2 | ||||
Observation.component:coordinate-system.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:coordinate-system.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:ref-allele.code | example | Pattern: LOINC Code 69547-8http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:ref-allele.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:ref-allele.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:alt-allele.code | example | Pattern: LOINC Code 69551-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:alt-allele.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:alt-allele.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:coding-change-type.code | example | Pattern: LOINC Code 48019-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:coding-change-type.value[x] | extensible | DNAChangeTypeVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type-vs | ||||
Observation.component:coding-change-type.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:coding-change-type.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:genomic-source-class.code | example | Pattern: LOINC Code 48002-0http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1http://loinc.org/vs/LL378-1 | ||||
Observation.component:genomic-source-class.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:genomic-source-class.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC Code 81258-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparatorhttp://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1 from the FHIR Standard | ||||
Observation.component:sample-allelic-frequency.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:sample-allelic-frequency.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:allelic-read-depth.code | example | Pattern: LOINC Code 82121-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:allelic-read-depth.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:allelic-read-depth.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:allelic-state.code | example | Pattern: LOINC Code 53034-5http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5http://loinc.org/vs/LL381-5 | ||||
Observation.component:allelic-state.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:allelic-state.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:variant-inheritance.code | example | Pattern: LOINC Code 94186-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:variant-inheritance.value[x] | extensible | LOINC LL5489-1http://loinc.org/vs/LL5489-1 | ||||
Observation.component:variant-inheritance.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:variant-inheritance.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:variant-inheritance-basis.code | example | Pattern: LOINC Code 82309-6http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:variant-inheritance-basis.value[x] | extensible | LOINC LL4050-2http://loinc.org/vs/LL4050-2 | ||||
Observation.component:variant-inheritance-basis.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:variant-inheritance-basis.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:variation-code.code | example | Pattern: LOINC Code 81252-9http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:variation-code.value[x] | example | |||||
Observation.component:variation-code.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:variation-code.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:chromosome-identifier.code | example | Pattern: LOINC Code 48000-4http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:chromosome-identifier.value[x] | required | LOINC LL2938-0http://loinc.org/vs/LL2938-0 | ||||
Observation.component:chromosome-identifier.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:chromosome-identifier.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:representative-protein-hgvs.code | example | Pattern: LOINC Code 48005-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:representative-protein-hgvs.value[x] | required | HGVSVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs-vs | ||||
Observation.component:representative-protein-hgvs.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:representative-protein-hgvs.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:copy-number.code | example | Pattern: LOINC Code 82155-3http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:copy-number.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:copy-number.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:variant-confidence-status.code | example | Pattern: variant-confidence-statushttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:variant-confidence-status.value[x] | required | VariantConfidenceStatusVShttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-confidence-status-vs | ||||
Observation.component:variant-confidence-status.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:variant-confidence-status.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:repeat-motif.code | example | Pattern: repeat-motifhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:repeat-motif.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:repeat-motif.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard | ||||
Observation.component:repeat-number.code | example | Pattern: repeat-numberhttp://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard | ||||
Observation.component:repeat-number.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard | ||||
Observation.component:repeat-number.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard |
Id | Grade | Path(s) | Details | Requirements |
dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty() | |
dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
dom-6 | best practice | Observation | A resource should have narrative for robust management : text.`div`.exists() | |
ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text : low.exists() or high.exists() or text.exists() | |
obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
This structure is derived from Variant
Summary
Mandatory: 1 element
Must-Support: 19 elements
Structures
This structure refers to these other structures:
Slices
This structure defines the following Slices:
Other representations of profile: CSV, Excel, Schematron