FHIR Osiris Implementation Guide
1.1.0 - trial-implementation

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## Resource Profile: Variant Copy Number

Official URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/copy-number | Version: 1.1.0
Draft as of 2025-04-03 | Computable Name: CopyNumber

Observation of a Copy Number variant derived from a SequencingAnalysis. The CopyNumber profile is used to indicate the pathogenicity, the actionability, the loss of heterozygosity, the cytogenetic location, the start - end positions, the reference sequence assembly, the variation code, the segment intensity, the number of copy found and the Copy Number segment size.

Usage:

- Refer to this Resource Profile: Validation and Variant Annotation

### Formal Views of Profile Content

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

- Key Elements Table
- Differential Table
- Snapshot Table
- Statistics/References
- All

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
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 pour extension |  |  |  | Content/Rules for all slices
extension:BodyStructure |  | 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
extension:SecondaryFinding |  | 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
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
status | ?!Σ | 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
category |  | 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 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://terminology.hl7.org/CodeSystem/observation-category
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory
code | Σ | 1..1 | CodeableConcept | Genetic variant assessment 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 | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about ele-1: All FHIR elements must have a @value or children
Slices pour effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children
effective[x]:effectiveDateTime | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation ele-1: All FHIR elements must have a @value or children
performer | Σ | 0..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Who is responsible for the observation ele-1: All FHIR elements must have a @value or children
value[x] | Σ C | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment ele-1: All FHIR elements must have a @value or children
Slices pour derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference ele-1: All FHIR elements must have a @value or children
derivedFrom:Analysis | Σ | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation ele-1: All FHIR elements must have a @value or children
Slices pour component | Σ | 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:gene-studied | Σ | 0..* | BackboneElement | Gene studied ID 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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6
value[x] | Σ | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee 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 | 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 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 | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined ele-1: All FHIR elements must have a @value or children
component:ref-sequence-assembly | Σ | 0..* | BackboneElement | Human reference sequence assembly version 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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs ele-1: All FHIR elements must have a @value or children
component:dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Transcript (cHGVS) 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 | 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 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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society ele-1: All FHIR elements must have a @value or children
component:dna-chg-type | Σ | 0..1 | BackboneElement | 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 | 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 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] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology) ele-1: All FHIR elements must have a @value or children
component:functional-annotation | Σ | 0..* | BackboneElement | Functional Annotation 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation
value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537) Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology) ele-1: All FHIR elements must have a @value or children
component:variation-code | Σ | 0..1 | 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 | 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 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 | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined ele-1: All FHIR elements must have a @value or children
component:dbSNP-id | Σ | 0..1 | BackboneElement | dbSNP ID 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 | 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 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: 81255-2
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-dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Genomic (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 | 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 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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society 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 | 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 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): Genomic source class values ele-1: All FHIR elements must have a @value or children
component:amino-acid-chg | Σ | 0..1 | BackboneElement | 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 | 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 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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society ele-1: All FHIR elements must have a @value or children
component:amino-acid-chg-type | Σ | 0..1 | BackboneElement | Amino acid 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 | 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 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: 48006-1
value[x] | Σ | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required): Amino acid change type values ele-1: All FHIR elements must have a @value or children
component:transcript-ref-seq | Σ | 0..1 | BackboneElement | Transcript reference sequence ID 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 | 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 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 | 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 ID 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 | 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 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 | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined 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 | Sample Sample VAF 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
value[x] | Σ | 1..1 | Quantity | Actual component result ele-1: All FHIR elements must have a @value or children
value | Σ | 1..1 | decimal | Numerical value (with implicit precision) ele-1: All FHIR elements must have a @value or children
comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented. ele-1: All FHIR elements must have a @value or children
system | Σ C | 1..1 | uri | System that defines coded unit form ele-1: All FHIR elements must have a @value or children Fixed Value: http://unitsofmeasure.org
component:allelic-read-depth | Σ | 0..* | 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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5
value[x] | Σ | 1..1 | Quantity | Actual component result ele-1: All FHIR elements must have a @value or children
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 | 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 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): Allelic state type values 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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3
value[x] | C | 1..1 | Count | A measured or measurable amount cnt-3: There SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. ele-1: All FHIR elements must have a @value or children qty-3: If a code for the unit is present, the system SHALL also be present
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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8
value[x] | Σ | 1..1 | string | Actual component result ele-1: All FHIR elements must have a @value or children
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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0
value[x] | Σ | 1..1 | string | Actual component result ele-1: All FHIR elements must have a @value or children
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 | 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 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 | 0-based character | 1-based character Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: exact-start-end
value[x] | Σ | 1..1 | Range | Actual component result ele-1: All FHIR elements must have a @value or children
low | Σ | 1..1 | SimpleQuantity | Exact Start ele-1: All FHIR elements must have a @value or children
high | Σ | 0..1 | SimpleQuantity | Exact End ele-1: All FHIR elements must have a @value or children
component:variant-length | Σ | 0..1 | BackboneElement | Structural variant length 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 | 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 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: 81300-6
value[x] | C | 1..1 | Count | A measured or measurable amount cnt-3: There SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. ele-1: All FHIR elements must have a @value or children qty-3: If a code for the unit is present, the system SHALL also be present
component:outer-start-end | Σ | 0..1 | BackboneElement | Variant outer start and 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: outer-start-end
value[x] | Σ | 1..1 | Range | Actual component result ele-1: All FHIR elements must have a @value or children
low | Σ | 1..1 | SimpleQuantity | Low limit ele-1: All FHIR elements must have a @value or children
high | Σ | 1..1 | SimpleQuantity | High limit ele-1: All FHIR elements must have a @value or children
component:inner-start-end | Σ | 0..1 | BackboneElement | Variant inner start and 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: inner-start-end
value[x] | Σ | 1..1 | Range | Actual component result ele-1: All FHIR elements must have a @value or children
low | Σ | 1..1 | SimpleQuantity | Low limit ele-1: All FHIR elements must have a @value or children
high | Σ | 1..1 | SimpleQuantity | High limit ele-1: All FHIR elements must have a @value or children
component:chromosome-copy-number-change-type | Σ | 0..1 | BackboneElement | Chromosome copy number 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 | 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 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: 62378-5
value[x] | Σ | 1..1 | CodeableConcept | Copy number gain | Copy number loss Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types ele-1: All FHIR elements must have a @value or children
component:arrCGH-ratio | Σ | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] 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 | 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 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: 81299-0
value[x] | C | 1..1 | SimpleQuantity | A fixed quantity (no comparator) ele-1: All FHIR elements must have a @value or children qty-3: If a code for the unit is present, the system SHALL also be present sqty-1: The comparator is not used on a SimpleQuantity
component:complex-var-type | Σ | 0..1 | BackboneElement | Complex variant 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 | 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 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: 81263-6
value[x] | Σ | 1..1 | CodeableConcept | Compound heterozygous | Double heterozygous | Haplotype | Hemizygous Binding: LOINC Answer List LL3999-1 (required): Complex variant type ele-1: All FHIR elements must have a @value or children
component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature 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 ISCN 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:variant-inheritance | Σ | 0..1 | BackboneElement | 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-inheritance
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology) ele-1: All FHIR elements must have a @value or children
component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board 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 | 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 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: 93348-1
value[x] | Σ | 0..1 | boolean | Actual component result ele-1: All FHIR elements must have a @value or children
component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? 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 | 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 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://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889
value[x] | Σ | 0..1 | boolean | Actual component result ele-1: All FHIR elements must have a @value or children
component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board 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 | 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 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: 74019-1
value[x] | Σ | 0..1 | CodeableConcept | Actual component result Binding: Pathogenicity Value Set (required) ele-1: All FHIR elements must have a @value or children
component:loss-of-heterozygosity | Σ | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information 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 | 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 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://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449
value[x] | Σ | 0..1 | boolean | Actual component result ele-1: All FHIR elements must have a @value or children
component:segment-intensity | Σ | 0..1 | BackboneElement | Intensity of the measured signal 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 | 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 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://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930
value[x] | Σ | 0..1 | integer | Actual component result ele-1: All FHIR elements must have a @value or children
Documentation for this format

#### Terminology Bindings

Path | Conformité | ValueSet / Code | URI
Observation.status | required | ObservationStatus `http://hl7.org/fhir/ValueSet/observation-status|4.0.1` from the FHIR Standard
Observation.category | preferred | Pattern: laboratory `http://hl7.org/fhir/ValueSet/observation-category` from the FHIR Standard
Observation.code | example | Pattern: LOINC Code 69548-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.value[x] | required | LOINC LL1971-2 `http://loinc.org/vs/LL1971-2`
Observation.component.code | example | LOINCCodes (a valid code from LOINC) `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:gene-studied.code | example | Pattern: LOINC Code 48018-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:gene-studied.value[x] | extensible | HGNC `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc`
Observation.component:cytogenetic-location.code | example | Pattern: LOINC Code 48001-2 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:cytogenetic-location.value[x] | example |
Observation.component:ref-sequence-assembly.code | example | Pattern: LOINC Code 62374-4 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:ref-sequence-assembly.value[x] | extensible | LOINC LL1040-6 `http://loinc.org/vs/LL1040-6`
Observation.component:dna-chg.code | example | Pattern: LOINC Code 48004-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dna-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:dna-chg-type.code | example | Pattern: LOINC Code 48019-4 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dna-chg-type.value[x] | extensible | DnaChangeType `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type`
Observation.component:functional-annotation.code | example | Pattern: functional-annotation `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:functional-annotation.value[x] | extensible | FunctionalAnnotation `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-annotation`
Observation.component:variation-code.code | example | Pattern: LOINC Code 81252-9 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variation-code.value[x] | example |
Observation.component:dbSNP-id.code | example | Pattern: LOINC Code 81255-2 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dbSNP-id.value[x] | example |
Observation.component:genomic-dna-chg.code | example | Pattern: LOINC Code 81290-9 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-dna-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:genomic-source-class.code | example | Pattern: LOINC Code 48002-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1 `http://loinc.org/vs/LL378-1`
Observation.component:amino-acid-chg.code | example | Pattern: LOINC Code 48005-3 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:amino-acid-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:amino-acid-chg-type.code | example | Pattern: LOINC Code 48006-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:amino-acid-chg-type.value[x] | required | LOINC LL380-7 `http://loinc.org/vs/LL380-7`
Observation.component:transcript-ref-seq.code | example | Pattern: LOINC Code 51958-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:transcript-ref-seq.value[x] | example |
Observation.component:genomic-ref-seq.code | example | Pattern: LOINC Code 48013-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-ref-seq.value[x] | example |
Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC Code 81258-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparator `http://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1` from the FHIR Standard
Observation.component:allelic-read-depth.code | example | Pattern: LOINC Code 82121-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:allelic-state.code | example | Pattern: LOINC Code 53034-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5 `http://loinc.org/vs/LL381-5`
Observation.component:copy-number.code | example | Pattern: LOINC Code 82155-3 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:ref-allele.code | example | Pattern: LOINC Code 69547-8 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:alt-allele.code | example | Pattern: LOINC Code 69551-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:coordinate-system.code | example | Pattern: LOINC Code 92822-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:coordinate-system.value[x] | preferred | LOINC LL5323-2 `http://loinc.org/vs/LL5323-2`
Observation.component:exact-start-end.code | example | Pattern: exact-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variant-length.code | example | Pattern: LOINC Code 81300-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:outer-start-end.code | example | Pattern: outer-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:inner-start-end.code | example | Pattern: inner-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:chromosome-copy-number-change-type.code | example | Pattern: LOINC Code 62378-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:chromosome-copy-number-change-type.value[x] | required | LOINC LL1041-4 `http://loinc.org/vs/LL1041-4`
Observation.component:arrCGH-ratio.code | example | Pattern: LOINC Code 81299-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:complex-var-type.code | example | Pattern: LOINC Code 81263-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:complex-var-type.value[x] | required | LOINC LL3999-1 `http://loinc.org/vs/LL3999-1`
Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC Code 81291-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:cytogenomic-nomenclature.value[x] | example |
Observation.component:variant-inheritance.code | example | Pattern: variant-inheritance `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variant-inheritance.value[x] | extensible | VariantInheritance `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-inheritance`
Observation.component:actionability.code | example | Pattern: LOINC Code 93348-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:proposed-for-orientation.code | example | Pattern: C0449889 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:pathogenicity.code | example | Pattern: LOINC Code 74019-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:pathogenicity.value[x] | required | Pathogenicity `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Pathogenicity` from this IG
Observation.component:loss-of-heterozygosity.code | example | Pattern: C1881449 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:segment-intensity.code | example | Pattern: C2732930 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard

This structure is derived from Variant

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
Observation |  | 0..* | Variant | Variant
subject |  | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about
Slices pour derivedFrom |  | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference
derivedFrom:Analysis |  | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation
Slices pour component |  |  |  | Content/Rules for all slices
component:cytogenetic-location |  | 0..* | BackboneElement | Cytogenetic (chromosome) location
component:ref-sequence-assembly |  | 0..* | BackboneElement | Human reference sequence assembly version
value[x] |  | 1..1 | CodeableConcept | Actual component result
component:variation-code |  | 0..1 | BackboneElement | Variation Code
value[x] |  | 1..1 | CodeableConcept | Actual component result
component:copy-number |  | 0..1 | BackboneElement | Genomic structural variant copy number
value[x] |  | 1..1 | Count | A measured or measurable amount
component:exact-start-end |  | 0..1 | BackboneElement | Exact start-end
value[x] |  |  |  |
low |  | 1..1 | SimpleQuantity | Exact Start
high |  | 0..1 | SimpleQuantity | Exact End
component:variant-length |  | 0..1 | BackboneElement | Structural variant length
component:actionability |  | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1
value[x] |  | 0..1 | boolean | Actual component result
component:proposed-for-orientation |  | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ?
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889
value[x] |  | 0..1 | boolean | Actual component result
component:pathogenicity |  | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1
value[x] |  | 0..1 | CodeableConcept | Actual component result Binding: Pathogenicity Value Set (required)
component:loss-of-heterozygosity |  | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449
value[x] |  | 0..1 | boolean | Actual component result
component:segment-intensity |  | 0..1 | BackboneElement | Intensity of the measured signal
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930
value[x] |  | 0..1 | integer | Actual component result
Documentation for this format

#### Terminology Bindings (Differential)

Path | Conformité | ValueSet | URI
Observation.component:pathogenicity.value[x] | required | Pathogenicity `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Pathogenicity` from this IG

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
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.
Bindings Additionnels | But
AllLanguages | Binding Max
text |  | 0..1 | Narrative | Text summary of the resource, for human interpretation
contained |  | 0..* | Resource | Contained, inline Resources
Slices pour extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:BodyStructure |  | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:SecondaryFinding |  | 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.
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
identifier | Σ | 0..* | Identifier | Business Identifier for observation
basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order
partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event
status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
category |  | 1..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
code | Σ | 1..1 | CodeableConcept | Genetic variant assessment Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
subject | Σ | 0..1 | Reference(Oncology 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 pour effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime | Σ | 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..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Who is responsible for the observation
value[x] | Σ C | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment
dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
note |  | 0..* | Annotation | Comments about the observation
bodySite |  | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method |  | 0..1 | CodeableConcept | Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+ Binding: LOINC Answer List LL4048-6 (extensible): Variant analysis method type
specimen |  | 0..1 | Reference(Specimen) | Specimen examined
device |  | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device
referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation obs-3: Must have at least a low or a high or text
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
low | C | 0..1 | SimpleQuantity | Low Range, if relevant
high | C | 0..1 | SimpleQuantity | High Range, if relevant
type |  | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
appliesTo |  | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
age |  | 0..1 | Range | Applicable age range, if relevant
text |  | 0..1 | string | Text based reference range in an observation
hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group
Slices pour derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference
derivedFrom:Analysis | Σ | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation
Slices pour component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code
component:All Slices |  |  |  | Content/Rules for all slices
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:gene-studied | Σ | 0..* | BackboneElement | Gene studied ID
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
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 | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:ref-sequence-assembly | Σ | 0..* | BackboneElement | Human reference sequence assembly version
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Transcript (cHGVS)
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:dna-chg-type | Σ | 0..1 | BackboneElement | DNA change type
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:functional-annotation | Σ | 0..* | BackboneElement | Functional Annotation
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537) Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:variation-code | Σ | 0..1 | BackboneElement | Variation Code
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:dbSNP-id | Σ | 0..1 | BackboneElement | dbSNP ID
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81255-2
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 | 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:genomic-dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Genomic (gHGVS)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
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 | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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): Genomic source class values
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:amino-acid-chg | Σ | 0..1 | BackboneElement | Amino acid change (pHGVS)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:amino-acid-chg-type | Σ | 0..1 | BackboneElement | Amino acid change type
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48006-1
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required): Amino acid change type values
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:transcript-ref-seq | Σ | 0..1 | BackboneElement | Transcript reference sequence ID
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic reference sequence ID
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 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.
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 | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Sample Sample VAF Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 1..1 | Quantity | Actual component result
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 | 1..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 | Σ C | 1..1 | uri | System that defines coded unit form Fixed Value: 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:allelic-read-depth | Σ | 0..* | BackboneElement | Allelic read depth
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 1..1 | Quantity | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
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 | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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): Allelic state type values
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
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 | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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] | C | 1..1 | Count | A measured or measurable amount cnt-3: There SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. qty-3: If a code for the unit is present, the system SHALL also be present
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:ref-allele | Σ | 0..1 | BackboneElement | Genomic ref allele
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 1..1 | string | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:alt-allele | Σ | 0..1 | BackboneElement | Genomic alt allele
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 1..1 | string | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 0-based character | 1-based character Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:exact-start-end | Σ | 0..1 | BackboneElement | Exact start-end
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id 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
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: exact-start-end
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | Range | Actual component result
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
low | Σ | 1..1 | SimpleQuantity | Exact Start
high | Σ | 0..1 | SimpleQuantity | Exact End
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:variant-length | Σ | 0..1 | BackboneElement | Structural variant length
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81300-6
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] | C | 1..1 | Count | A measured or measurable amount cnt-3: There SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. qty-3: If a code for the unit is present, the system SHALL also be present
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:outer-start-end | Σ | 0..1 | BackboneElement | Variant outer start and end
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: outer-start-end
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | Range | Actual component result
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
low | Σ | 1..1 | SimpleQuantity | Low limit
high | Σ | 1..1 | SimpleQuantity | High limit
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:inner-start-end | Σ | 0..1 | BackboneElement | Variant inner start and end
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: inner-start-end
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | Range | Actual component result
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
low | Σ | 1..1 | SimpleQuantity | Low limit
high | Σ | 1..1 | SimpleQuantity | High limit
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:chromosome-copy-number-change-type | Σ | 0..1 | BackboneElement | Chromosome copy number change type
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62378-5
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 | Copy number gain | Copy number loss Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:arrCGH-ratio | Σ | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio]
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81299-0
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] | C | 1..1 | SimpleQuantity | A fixed quantity (no comparator) qty-3: If a code for the unit is present, the system SHALL also be present sqty-1: The comparator is not used on a SimpleQuantity
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:complex-var-type | Σ | 0..1 | BackboneElement | Complex variant type
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81263-6
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 | Compound heterozygous | Double heterozygous | Haplotype | Hemizygous Binding: LOINC Answer List LL3999-1 (required): Complex variant type
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature
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 | Variant ISCN Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:variant-inheritance | Σ | 0..1 | BackboneElement | Variant Inheritance
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id 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
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-inheritance
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 0..1 | boolean | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ?
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | boolean | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 0..1 | CodeableConcept | Actual component result Binding: Pathogenicity Value Set (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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:loss-of-heterozygosity | Σ | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | boolean | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:segment-intensity | Σ | 0..1 | BackboneElement | Intensity of the measured signal
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | integer | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
Documentation for this format

#### Terminology Bindings

Path | Conformité | ValueSet / Code | URI
Observation.language | preferred | CommonLanguages `http://hl7.org/fhir/ValueSet/languages` from the FHIR Standard
Bindings Additionnels | But
AllLanguages | Binding Max
Observation.status | required | ObservationStatus `http://hl7.org/fhir/ValueSet/observation-status|4.0.1` from the FHIR Standard
Observation.category | preferred | Pattern: laboratory `http://hl7.org/fhir/ValueSet/observation-category` from the FHIR Standard
Observation.code | example | Pattern: LOINC Code 69548-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.value[x] | required | LOINC LL1971-2 `http://loinc.org/vs/LL1971-2`
Observation.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.bodySite | example | SNOMEDCTBodyStructures `http://hl7.org/fhir/ValueSet/body-site` from the FHIR Standard
Observation.method | extensible | LOINC LL4048-6 `http://loinc.org/vs/LL4048-6`
Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodes `http://hl7.org/fhir/ValueSet/referencerange-meaning` from the FHIR Standard
Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodes `http://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 | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:gene-studied.code | example | Pattern: LOINC Code 48018-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:gene-studied.value[x] | extensible | HGNC `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc`
Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:cytogenetic-location.code | example | Pattern: LOINC Code 48001-2 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:cytogenetic-location.value[x] | example |
Observation.component:cytogenetic-location.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:ref-sequence-assembly.code | example | Pattern: LOINC Code 62374-4 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:ref-sequence-assembly.value[x] | extensible | LOINC LL1040-6 `http://loinc.org/vs/LL1040-6`
Observation.component:ref-sequence-assembly.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:dna-chg.code | example | Pattern: LOINC Code 48004-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dna-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:dna-chg.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:dna-chg-type.code | example | Pattern: LOINC Code 48019-4 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dna-chg-type.value[x] | extensible | DnaChangeType `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type`
Observation.component:dna-chg-type.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:functional-annotation.code | example | Pattern: functional-annotation `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:functional-annotation.value[x] | extensible | FunctionalAnnotation `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-annotation`
Observation.component:functional-annotation.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:variation-code.code | example | Pattern: LOINC Code 81252-9 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variation-code.value[x] | example |
Observation.component:variation-code.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:dbSNP-id.code | example | Pattern: LOINC Code 81255-2 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dbSNP-id.value[x] | example |
Observation.component:dbSNP-id.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:genomic-dna-chg.code | example | Pattern: LOINC Code 81290-9 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-dna-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:genomic-dna-chg.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:genomic-source-class.code | example | Pattern: LOINC Code 48002-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1 `http://loinc.org/vs/LL378-1`
Observation.component:genomic-source-class.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:amino-acid-chg.code | example | Pattern: LOINC Code 48005-3 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:amino-acid-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:amino-acid-chg.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:amino-acid-chg-type.code | example | Pattern: LOINC Code 48006-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:amino-acid-chg-type.value[x] | required | LOINC LL380-7 `http://loinc.org/vs/LL380-7`
Observation.component:amino-acid-chg-type.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:transcript-ref-seq.code | example | Pattern: LOINC Code 51958-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:transcript-ref-seq.value[x] | example |
Observation.component:transcript-ref-seq.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:genomic-ref-seq.code | example | Pattern: LOINC Code 48013-7 `http://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 | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC Code 81258-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparator `http://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1` from the FHIR Standard
Observation.component:sample-allelic-frequency.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:allelic-read-depth.code | example | Pattern: LOINC Code 82121-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:allelic-read-depth.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:allelic-state.code | example | Pattern: LOINC Code 53034-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5 `http://loinc.org/vs/LL381-5`
Observation.component:allelic-state.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:copy-number.code | example | Pattern: LOINC Code 82155-3 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:copy-number.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:ref-allele.code | example | Pattern: LOINC Code 69547-8 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:ref-allele.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:alt-allele.code | example | Pattern: LOINC Code 69551-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:alt-allele.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:coordinate-system.code | example | Pattern: LOINC Code 92822-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:coordinate-system.value[x] | preferred | LOINC LL5323-2 `http://loinc.org/vs/LL5323-2`
Observation.component:coordinate-system.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:exact-start-end.code | example | Pattern: exact-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:exact-start-end.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:variant-length.code | example | Pattern: LOINC Code 81300-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variant-length.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:outer-start-end.code | example | Pattern: outer-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:outer-start-end.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:inner-start-end.code | example | Pattern: inner-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:inner-start-end.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:chromosome-copy-number-change-type.code | example | Pattern: LOINC Code 62378-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:chromosome-copy-number-change-type.value[x] | required | LOINC LL1041-4 `http://loinc.org/vs/LL1041-4`
Observation.component:chromosome-copy-number-change-type.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:arrCGH-ratio.code | example | Pattern: LOINC Code 81299-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:arrCGH-ratio.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:complex-var-type.code | example | Pattern: LOINC Code 81263-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:complex-var-type.value[x] | required | LOINC LL3999-1 `http://loinc.org/vs/LL3999-1`
Observation.component:complex-var-type.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC Code 81291-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:cytogenomic-nomenclature.value[x] | example |
Observation.component:cytogenomic-nomenclature.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:variant-inheritance.code | example | Pattern: variant-inheritance `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variant-inheritance.value[x] | extensible | VariantInheritance `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-inheritance`
Observation.component:variant-inheritance.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:actionability.code | example | Pattern: LOINC Code 93348-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:actionability.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:proposed-for-orientation.code | example | Pattern: C0449889 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:proposed-for-orientation.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:pathogenicity.code | example | Pattern: LOINC Code 74019-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:pathogenicity.value[x] | required | Pathogenicity `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Pathogenicity` from this IG
Observation.component:pathogenicity.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:loss-of-heterozygosity.code | example | Pattern: C1881449 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:loss-of-heterozygosity.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:segment-intensity.code | example | Pattern: C2732930 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:segment-intensity.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard

This structure is derived from Variant

Résumé

Mandatory: 2 elements

Structures

This structure refers to these other structures:

- Oncology Patient (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient)
- Sequencing Analysis (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/sequencing-analysis)

Slices

This structure defines the following Slices:

- The element 1 is sliced based on the value of Observation.derivedFrom

Key Elements View

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
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 pour extension |  |  |  | Content/Rules for all slices
extension:BodyStructure |  | 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
extension:SecondaryFinding |  | 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
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
status | ?!Σ | 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
category |  | 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 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://terminology.hl7.org/CodeSystem/observation-category
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory
code | Σ | 1..1 | CodeableConcept | Genetic variant assessment 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 | Σ | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about ele-1: All FHIR elements must have a @value or children
Slices pour effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children
effective[x]:effectiveDateTime | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation ele-1: All FHIR elements must have a @value or children
performer | Σ | 0..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Who is responsible for the observation ele-1: All FHIR elements must have a @value or children
value[x] | Σ C | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment ele-1: All FHIR elements must have a @value or children
Slices pour derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference ele-1: All FHIR elements must have a @value or children
derivedFrom:Analysis | Σ | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation ele-1: All FHIR elements must have a @value or children
Slices pour component | Σ | 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:gene-studied | Σ | 0..* | BackboneElement | Gene studied ID 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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6
value[x] | Σ | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee 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 | 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 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 | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined ele-1: All FHIR elements must have a @value or children
component:ref-sequence-assembly | Σ | 0..* | BackboneElement | Human reference sequence assembly version 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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs ele-1: All FHIR elements must have a @value or children
component:dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Transcript (cHGVS) 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 | 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 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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society ele-1: All FHIR elements must have a @value or children
component:dna-chg-type | Σ | 0..1 | BackboneElement | 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 | 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 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] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology) ele-1: All FHIR elements must have a @value or children
component:functional-annotation | Σ | 0..* | BackboneElement | Functional Annotation 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation
value[x] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537) Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology) ele-1: All FHIR elements must have a @value or children
component:variation-code | Σ | 0..1 | 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 | 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 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 | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined ele-1: All FHIR elements must have a @value or children
component:dbSNP-id | Σ | 0..1 | BackboneElement | dbSNP ID 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 | 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 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: 81255-2
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-dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Genomic (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 | 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 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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society 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 | 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 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): Genomic source class values ele-1: All FHIR elements must have a @value or children
component:amino-acid-chg | Σ | 0..1 | BackboneElement | 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 | 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 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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society ele-1: All FHIR elements must have a @value or children
component:amino-acid-chg-type | Σ | 0..1 | BackboneElement | Amino acid 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 | 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 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: 48006-1
value[x] | Σ | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required): Amino acid change type values ele-1: All FHIR elements must have a @value or children
component:transcript-ref-seq | Σ | 0..1 | BackboneElement | Transcript reference sequence ID 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 | 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 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 | 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 ID 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 | 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 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 | Actual component result Binding Description (No ValueSet): (example): Binding not yet defined 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 | Sample Sample VAF 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
value[x] | Σ | 1..1 | Quantity | Actual component result ele-1: All FHIR elements must have a @value or children
value | Σ | 1..1 | decimal | Numerical value (with implicit precision) ele-1: All FHIR elements must have a @value or children
comparator | ?!Σ | 0..1 | code | < | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented. ele-1: All FHIR elements must have a @value or children
system | Σ C | 1..1 | uri | System that defines coded unit form ele-1: All FHIR elements must have a @value or children Fixed Value: http://unitsofmeasure.org
component:allelic-read-depth | Σ | 0..* | 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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82121-5
value[x] | Σ | 1..1 | Quantity | Actual component result ele-1: All FHIR elements must have a @value or children
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 | 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 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): Allelic state type values 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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 82155-3
value[x] | C | 1..1 | Count | A measured or measurable amount cnt-3: There SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. ele-1: All FHIR elements must have a @value or children qty-3: If a code for the unit is present, the system SHALL also be present
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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69547-8
value[x] | Σ | 1..1 | string | Actual component result ele-1: All FHIR elements must have a @value or children
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 | 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 Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69551-0
value[x] | Σ | 1..1 | string | Actual component result ele-1: All FHIR elements must have a @value or children
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 | 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 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 | 0-based character | 1-based character Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for variants 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: exact-start-end
value[x] | Σ | 1..1 | Range | Actual component result ele-1: All FHIR elements must have a @value or children
low | Σ | 1..1 | SimpleQuantity | Exact Start ele-1: All FHIR elements must have a @value or children
high | Σ | 0..1 | SimpleQuantity | Exact End ele-1: All FHIR elements must have a @value or children
component:variant-length | Σ | 0..1 | BackboneElement | Structural variant length 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 | 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 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: 81300-6
value[x] | C | 1..1 | Count | A measured or measurable amount cnt-3: There SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. ele-1: All FHIR elements must have a @value or children qty-3: If a code for the unit is present, the system SHALL also be present
component:outer-start-end | Σ | 0..1 | BackboneElement | Variant outer start and 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: outer-start-end
value[x] | Σ | 1..1 | Range | Actual component result ele-1: All FHIR elements must have a @value or children
low | Σ | 1..1 | SimpleQuantity | Low limit ele-1: All FHIR elements must have a @value or children
high | Σ | 1..1 | SimpleQuantity | High limit ele-1: All FHIR elements must have a @value or children
component:inner-start-end | Σ | 0..1 | BackboneElement | Variant inner start and 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: inner-start-end
value[x] | Σ | 1..1 | Range | Actual component result ele-1: All FHIR elements must have a @value or children
low | Σ | 1..1 | SimpleQuantity | Low limit ele-1: All FHIR elements must have a @value or children
high | Σ | 1..1 | SimpleQuantity | High limit ele-1: All FHIR elements must have a @value or children
component:chromosome-copy-number-change-type | Σ | 0..1 | BackboneElement | Chromosome copy number 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 | 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 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: 62378-5
value[x] | Σ | 1..1 | CodeableConcept | Copy number gain | Copy number loss Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types ele-1: All FHIR elements must have a @value or children
component:arrCGH-ratio | Σ | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio] 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 | 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 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: 81299-0
value[x] | C | 1..1 | SimpleQuantity | A fixed quantity (no comparator) ele-1: All FHIR elements must have a @value or children qty-3: If a code for the unit is present, the system SHALL also be present sqty-1: The comparator is not used on a SimpleQuantity
component:complex-var-type | Σ | 0..1 | BackboneElement | Complex variant 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 | 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 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: 81263-6
value[x] | Σ | 1..1 | CodeableConcept | Compound heterozygous | Double heterozygous | Haplotype | Hemizygous Binding: LOINC Answer List LL3999-1 (required): Complex variant type ele-1: All FHIR elements must have a @value or children
component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature 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 ISCN 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:variant-inheritance | Σ | 0..1 | BackboneElement | 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 | 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 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
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-inheritance
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology) ele-1: All FHIR elements must have a @value or children
component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board 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 | 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 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: 93348-1
value[x] | Σ | 0..1 | boolean | Actual component result ele-1: All FHIR elements must have a @value or children
component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? 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 | 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 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://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889
value[x] | Σ | 0..1 | boolean | Actual component result ele-1: All FHIR elements must have a @value or children
component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board 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 | 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 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: 74019-1
value[x] | Σ | 0..1 | CodeableConcept | Actual component result Binding: Pathogenicity Value Set (required) ele-1: All FHIR elements must have a @value or children
component:loss-of-heterozygosity | Σ | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information 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 | 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 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://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449
value[x] | Σ | 0..1 | boolean | Actual component result ele-1: All FHIR elements must have a @value or children
component:segment-intensity | Σ | 0..1 | BackboneElement | Intensity of the measured signal 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 | 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 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://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930
value[x] | Σ | 0..1 | integer | Actual component result ele-1: All FHIR elements must have a @value or children
Documentation for this format

#### Terminology Bindings

Path | Conformité | ValueSet / Code | URI
Observation.status | required | ObservationStatus `http://hl7.org/fhir/ValueSet/observation-status|4.0.1` from the FHIR Standard
Observation.category | preferred | Pattern: laboratory `http://hl7.org/fhir/ValueSet/observation-category` from the FHIR Standard
Observation.code | example | Pattern: LOINC Code 69548-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.value[x] | required | LOINC LL1971-2 `http://loinc.org/vs/LL1971-2`
Observation.component.code | example | LOINCCodes (a valid code from LOINC) `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:gene-studied.code | example | Pattern: LOINC Code 48018-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:gene-studied.value[x] | extensible | HGNC `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc`
Observation.component:cytogenetic-location.code | example | Pattern: LOINC Code 48001-2 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:cytogenetic-location.value[x] | example |
Observation.component:ref-sequence-assembly.code | example | Pattern: LOINC Code 62374-4 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:ref-sequence-assembly.value[x] | extensible | LOINC LL1040-6 `http://loinc.org/vs/LL1040-6`
Observation.component:dna-chg.code | example | Pattern: LOINC Code 48004-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dna-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:dna-chg-type.code | example | Pattern: LOINC Code 48019-4 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dna-chg-type.value[x] | extensible | DnaChangeType `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type`
Observation.component:functional-annotation.code | example | Pattern: functional-annotation `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:functional-annotation.value[x] | extensible | FunctionalAnnotation `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-annotation`
Observation.component:variation-code.code | example | Pattern: LOINC Code 81252-9 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variation-code.value[x] | example |
Observation.component:dbSNP-id.code | example | Pattern: LOINC Code 81255-2 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dbSNP-id.value[x] | example |
Observation.component:genomic-dna-chg.code | example | Pattern: LOINC Code 81290-9 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-dna-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:genomic-source-class.code | example | Pattern: LOINC Code 48002-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1 `http://loinc.org/vs/LL378-1`
Observation.component:amino-acid-chg.code | example | Pattern: LOINC Code 48005-3 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:amino-acid-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:amino-acid-chg-type.code | example | Pattern: LOINC Code 48006-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:amino-acid-chg-type.value[x] | required | LOINC LL380-7 `http://loinc.org/vs/LL380-7`
Observation.component:transcript-ref-seq.code | example | Pattern: LOINC Code 51958-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:transcript-ref-seq.value[x] | example |
Observation.component:genomic-ref-seq.code | example | Pattern: LOINC Code 48013-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-ref-seq.value[x] | example |
Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC Code 81258-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparator `http://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1` from the FHIR Standard
Observation.component:allelic-read-depth.code | example | Pattern: LOINC Code 82121-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:allelic-state.code | example | Pattern: LOINC Code 53034-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5 `http://loinc.org/vs/LL381-5`
Observation.component:copy-number.code | example | Pattern: LOINC Code 82155-3 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:ref-allele.code | example | Pattern: LOINC Code 69547-8 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:alt-allele.code | example | Pattern: LOINC Code 69551-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:coordinate-system.code | example | Pattern: LOINC Code 92822-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:coordinate-system.value[x] | preferred | LOINC LL5323-2 `http://loinc.org/vs/LL5323-2`
Observation.component:exact-start-end.code | example | Pattern: exact-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variant-length.code | example | Pattern: LOINC Code 81300-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:outer-start-end.code | example | Pattern: outer-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:inner-start-end.code | example | Pattern: inner-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:chromosome-copy-number-change-type.code | example | Pattern: LOINC Code 62378-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:chromosome-copy-number-change-type.value[x] | required | LOINC LL1041-4 `http://loinc.org/vs/LL1041-4`
Observation.component:arrCGH-ratio.code | example | Pattern: LOINC Code 81299-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:complex-var-type.code | example | Pattern: LOINC Code 81263-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:complex-var-type.value[x] | required | LOINC LL3999-1 `http://loinc.org/vs/LL3999-1`
Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC Code 81291-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:cytogenomic-nomenclature.value[x] | example |
Observation.component:variant-inheritance.code | example | Pattern: variant-inheritance `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variant-inheritance.value[x] | extensible | VariantInheritance `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-inheritance`
Observation.component:actionability.code | example | Pattern: LOINC Code 93348-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:proposed-for-orientation.code | example | Pattern: C0449889 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:pathogenicity.code | example | Pattern: LOINC Code 74019-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:pathogenicity.value[x] | required | Pathogenicity `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Pathogenicity` from this IG
Observation.component:loss-of-heterozygosity.code | example | Pattern: C1881449 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:segment-intensity.code | example | Pattern: C2732930 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard

Differential View

This structure is derived from Variant

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
Observation |  | 0..* | Variant | Variant
subject |  | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about
Slices pour derivedFrom |  | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference
derivedFrom:Analysis |  | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation
Slices pour component |  |  |  | Content/Rules for all slices
component:cytogenetic-location |  | 0..* | BackboneElement | Cytogenetic (chromosome) location
component:ref-sequence-assembly |  | 0..* | BackboneElement | Human reference sequence assembly version
value[x] |  | 1..1 | CodeableConcept | Actual component result
component:variation-code |  | 0..1 | BackboneElement | Variation Code
value[x] |  | 1..1 | CodeableConcept | Actual component result
component:copy-number |  | 0..1 | BackboneElement | Genomic structural variant copy number
value[x] |  | 1..1 | Count | A measured or measurable amount
component:exact-start-end |  | 0..1 | BackboneElement | Exact start-end
value[x] |  |  |  |
low |  | 1..1 | SimpleQuantity | Exact Start
high |  | 0..1 | SimpleQuantity | Exact End
component:variant-length |  | 0..1 | BackboneElement | Structural variant length
component:actionability |  | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1
value[x] |  | 0..1 | boolean | Actual component result
component:proposed-for-orientation |  | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ?
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889
value[x] |  | 0..1 | boolean | Actual component result
component:pathogenicity |  | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1
value[x] |  | 0..1 | CodeableConcept | Actual component result Binding: Pathogenicity Value Set (required)
component:loss-of-heterozygosity |  | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449
value[x] |  | 0..1 | boolean | Actual component result
component:segment-intensity |  | 0..1 | BackboneElement | Intensity of the measured signal
code |  | 1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930
value[x] |  | 0..1 | integer | Actual component result
Documentation for this format

#### Terminology Bindings (Differential)

Path | Conformité | ValueSet | URI
Observation.component:pathogenicity.value[x] | required | Pathogenicity `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Pathogenicity` from this IG

Snapshot View

Nom | Drapeaux | Card. | Type | Description et contraintes
--- | --- | --- | --- | ---
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.
Bindings Additionnels | But
AllLanguages | Binding Max
text |  | 0..1 | Narrative | Text summary of the resource, for human interpretation
contained |  | 0..* | Resource | Contained, inline Resources
Slices pour extension |  | 0..* | Extension | Extension Slice: Unordered, Open by value:url
extension:BodyStructure |  | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:SecondaryFinding |  | 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.
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
identifier | Σ | 0..* | Identifier | Business Identifier for observation
basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order
partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event
status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
category |  | 1..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
code | Σ | 1..1 | CodeableConcept | Genetic variant assessment Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 69548-6
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
subject | Σ | 0..1 | Reference(Oncology 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 pour effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime | Σ | 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..1 | Reference(Practitioner | Organization | Patient | RelatedPerson) | Who is responsible for the observation
value[x] | Σ C | 1..1 | CodeableConcept | Present|Absent|No call|Indeterminate Binding: LOINC Answer List LL1971-2 (required): Genetic Variant Assessment
dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
note |  | 0..* | Annotation | Comments about the observation
bodySite |  | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method |  | 0..1 | CodeableConcept | Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+ Binding: LOINC Answer List LL4048-6 (extensible): Variant analysis method type
specimen |  | 0..1 | Reference(Specimen) | Specimen examined
device |  | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device
referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation obs-3: Must have at least a low or a high or text
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
low | C | 0..1 | SimpleQuantity | Low Range, if relevant
high | C | 0..1 | SimpleQuantity | High Range, if relevant
type |  | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
appliesTo |  | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
age |  | 0..1 | Range | Applicable age range, if relevant
text |  | 0..1 | string | Text based reference range in an observation
hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group
Slices pour derivedFrom | Σ | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference
derivedFrom:Analysis | Σ | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation
Slices pour component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code
component:All Slices |  |  |  | Content/Rules for all slices
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:gene-studied | Σ | 0..* | BackboneElement | Gene studied ID
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible): HGNC: Human Gene Nomenclature Committee
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
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 | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:ref-sequence-assembly | Σ | 0..* | BackboneElement | Human reference sequence assembly version
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: LOINC Answer List LL1040-6 (extensible): Human reference sequence NCBI build IDs
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Transcript (cHGVS)
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:dna-chg-type | Σ | 0..1 | BackboneElement | DNA change type
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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] | Σ | 1..1 | CodeableConcept | Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072) Binding: DNA Change Type (extensible): DNA Change type values (Sequence Ontology)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:functional-annotation | Σ | 0..* | BackboneElement | Functional Annotation
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: functional-annotation
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537) Binding: Functional Annotation (extensible): Functional Annotation (Sequence Ontology)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:variation-code | Σ | 0..1 | BackboneElement | Variation Code
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:dbSNP-id | Σ | 0..1 | BackboneElement | dbSNP ID
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81255-2
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 | 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:genomic-dna-chg | Σ | 0..1 | BackboneElement | DNA Change - Genomic (gHGVS)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
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 | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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): Genomic source class values
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:amino-acid-chg | Σ | 0..1 | BackboneElement | Amino acid change (pHGVS)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | Actual component result Binding: HGVS (required): HGVS: Sequence Variant Nomenclature from the Human Genome Variation Society
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:amino-acid-chg-type | Σ | 0..1 | BackboneElement | Amino acid change type
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48006-1
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation Binding: LOINC Answer List LL380-7 (required): Amino acid change type values
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:transcript-ref-seq | Σ | 0..1 | BackboneElement | Transcript reference sequence ID
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:genomic-ref-seq | Σ | 0..1 | BackboneElement | Genomic reference sequence ID
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 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.
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 | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Sample Sample VAF Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 1..1 | Quantity | Actual component result
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 | 1..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 | Σ C | 1..1 | uri | System that defines coded unit form Fixed Value: 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:allelic-read-depth | Σ | 0..* | BackboneElement | Allelic read depth
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 1..1 | Quantity | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
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 | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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): Allelic state type values
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
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 | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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] | C | 1..1 | Count | A measured or measurable amount cnt-3: There SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. qty-3: If a code for the unit is present, the system SHALL also be present
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:ref-allele | Σ | 0..1 | BackboneElement | Genomic ref allele
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 1..1 | string | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:alt-allele | Σ | 0..1 | BackboneElement | Genomic alt allele
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 1..1 | string | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:coordinate-system | Σ | 0..1 | BackboneElement | Coordinate System
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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 | 0-based character | 1-based character Binding: LOINC Answer List LL5323-2 (preferred): Base coordinate systems start and end measurements for 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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:exact-start-end | Σ | 0..1 | BackboneElement | Exact start-end
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id 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
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: exact-start-end
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | Range | Actual component result
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
low | Σ | 1..1 | SimpleQuantity | Exact Start
high | Σ | 0..1 | SimpleQuantity | Exact End
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:variant-length | Σ | 0..1 | BackboneElement | Structural variant length
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81300-6
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] | C | 1..1 | Count | A measured or measurable amount cnt-3: There SHALL be a code with a value of "1" if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number. qty-3: If a code for the unit is present, the system SHALL also be present
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:outer-start-end | Σ | 0..1 | BackboneElement | Variant outer start and end
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: outer-start-end
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | Range | Actual component result
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
low | Σ | 1..1 | SimpleQuantity | Low limit
high | Σ | 1..1 | SimpleQuantity | High limit
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:inner-start-end | Σ | 0..1 | BackboneElement | Variant inner start and end
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: inner-start-end
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | Range | Actual component result
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url
low | Σ | 1..1 | SimpleQuantity | Low limit
high | Σ | 1..1 | SimpleQuantity | High limit
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:chromosome-copy-number-change-type | Σ | 0..1 | BackboneElement | Chromosome copy number change type
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62378-5
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 | Copy number gain | Copy number loss Binding: LOINC Answer List LL1041-4 (required): Copy Number Change Types
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:arrCGH-ratio | Σ | 0..1 | BackboneElement | Structural variant reported arrCGH [Ratio]
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81299-0
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] | C | 1..1 | SimpleQuantity | A fixed quantity (no comparator) qty-3: If a code for the unit is present, the system SHALL also be present sqty-1: The comparator is not used on a SimpleQuantity
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:complex-var-type | Σ | 0..1 | BackboneElement | Complex variant type
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81263-6
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 | Compound heterozygous | Double heterozygous | Haplotype | Hemizygous Binding: LOINC Answer List LL3999-1 (required): Complex variant type
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:cytogenomic-nomenclature | Σ | 0..1 | BackboneElement | Cytogenomic Nomenclature
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 | Variant ISCN Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:variant-inheritance | Σ | 0..1 | BackboneElement | Variant Inheritance
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
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. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id 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
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: variant-inheritance
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 1..1 | CodeableConcept | Actual component result Binding: Variant Inheritance (extensible): Variant Inheritance (Sequence Ontology)
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 93348-1
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 0..1 | boolean | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ?
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C0449889
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | boolean | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 74019-1
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 0..1 | boolean | If this coding was chosen directly by the user
text |  | 0..1 | string | Plain text representation of the concept
value[x] | Σ | 0..1 | CodeableConcept | Actual component result Binding: Pathogenicity Value Set (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.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:loss-of-heterozygosity | Σ | 0..1 | BackboneElement | Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C1881449
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | boolean | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
component:segment-intensity | Σ | 0..1 | BackboneElement | Intensity of the measured signal
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 | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
coding |  | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex)
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
system |  | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/umls
version |  | 0..1 | string | Version of the system - if relevant
code |  | 1..1 | code | Symbol in syntax defined by the system Fixed Value: C2732930
display |  | 0..1 | string | Representation defined by the system
userSelected |  | 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 | integer | Actual component result
dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
referenceRange |  | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result
Documentation for this format

#### Terminology Bindings

Path | Conformité | ValueSet / Code | URI
Observation.language | preferred | CommonLanguages `http://hl7.org/fhir/ValueSet/languages` from the FHIR Standard
Bindings Additionnels | But
AllLanguages | Binding Max
Observation.status | required | ObservationStatus `http://hl7.org/fhir/ValueSet/observation-status|4.0.1` from the FHIR Standard
Observation.category | preferred | Pattern: laboratory `http://hl7.org/fhir/ValueSet/observation-category` from the FHIR Standard
Observation.code | example | Pattern: LOINC Code 69548-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.value[x] | required | LOINC LL1971-2 `http://loinc.org/vs/LL1971-2`
Observation.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.bodySite | example | SNOMEDCTBodyStructures `http://hl7.org/fhir/ValueSet/body-site` from the FHIR Standard
Observation.method | extensible | LOINC LL4048-6 `http://loinc.org/vs/LL4048-6`
Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodes `http://hl7.org/fhir/ValueSet/referencerange-meaning` from the FHIR Standard
Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodes `http://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 | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:gene-studied.code | example | Pattern: LOINC Code 48018-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:gene-studied.value[x] | extensible | HGNC `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc`
Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:cytogenetic-location.code | example | Pattern: LOINC Code 48001-2 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:cytogenetic-location.value[x] | example |
Observation.component:cytogenetic-location.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:ref-sequence-assembly.code | example | Pattern: LOINC Code 62374-4 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:ref-sequence-assembly.value[x] | extensible | LOINC LL1040-6 `http://loinc.org/vs/LL1040-6`
Observation.component:ref-sequence-assembly.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:dna-chg.code | example | Pattern: LOINC Code 48004-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dna-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:dna-chg.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:dna-chg-type.code | example | Pattern: LOINC Code 48019-4 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dna-chg-type.value[x] | extensible | DnaChangeType `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/dna-change-type`
Observation.component:dna-chg-type.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:functional-annotation.code | example | Pattern: functional-annotation `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:functional-annotation.value[x] | extensible | FunctionalAnnotation `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/functional-annotation`
Observation.component:functional-annotation.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:variation-code.code | example | Pattern: LOINC Code 81252-9 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variation-code.value[x] | example |
Observation.component:variation-code.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:dbSNP-id.code | example | Pattern: LOINC Code 81255-2 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:dbSNP-id.value[x] | example |
Observation.component:dbSNP-id.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:genomic-dna-chg.code | example | Pattern: LOINC Code 81290-9 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-dna-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:genomic-dna-chg.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:genomic-source-class.code | example | Pattern: LOINC Code 48002-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:genomic-source-class.value[x] | extensible | LOINC LL378-1 `http://loinc.org/vs/LL378-1`
Observation.component:genomic-source-class.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:amino-acid-chg.code | example | Pattern: LOINC Code 48005-3 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:amino-acid-chg.value[x] | required | HGVS `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgvs`
Observation.component:amino-acid-chg.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:amino-acid-chg-type.code | example | Pattern: LOINC Code 48006-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:amino-acid-chg-type.value[x] | required | LOINC LL380-7 `http://loinc.org/vs/LL380-7`
Observation.component:amino-acid-chg-type.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:transcript-ref-seq.code | example | Pattern: LOINC Code 51958-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:transcript-ref-seq.value[x] | example |
Observation.component:transcript-ref-seq.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:genomic-ref-seq.code | example | Pattern: LOINC Code 48013-7 `http://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 | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:sample-allelic-frequency.code | example | Pattern: LOINC Code 81258-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:sample-allelic-frequency.value[x].comparator | required | QuantityComparator `http://hl7.org/fhir/ValueSet/quantity-comparator|4.0.1` from the FHIR Standard
Observation.component:sample-allelic-frequency.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:allelic-read-depth.code | example | Pattern: LOINC Code 82121-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:allelic-read-depth.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:allelic-state.code | example | Pattern: LOINC Code 53034-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:allelic-state.value[x] | extensible | LOINC LL381-5 `http://loinc.org/vs/LL381-5`
Observation.component:allelic-state.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:copy-number.code | example | Pattern: LOINC Code 82155-3 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:copy-number.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:ref-allele.code | example | Pattern: LOINC Code 69547-8 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:ref-allele.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:alt-allele.code | example | Pattern: LOINC Code 69551-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:alt-allele.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:coordinate-system.code | example | Pattern: LOINC Code 92822-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:coordinate-system.value[x] | preferred | LOINC LL5323-2 `http://loinc.org/vs/LL5323-2`
Observation.component:coordinate-system.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:exact-start-end.code | example | Pattern: exact-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:exact-start-end.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:variant-length.code | example | Pattern: LOINC Code 81300-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variant-length.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:outer-start-end.code | example | Pattern: outer-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:outer-start-end.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:inner-start-end.code | example | Pattern: inner-start-end `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:inner-start-end.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:chromosome-copy-number-change-type.code | example | Pattern: LOINC Code 62378-5 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:chromosome-copy-number-change-type.value[x] | required | LOINC LL1041-4 `http://loinc.org/vs/LL1041-4`
Observation.component:chromosome-copy-number-change-type.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:arrCGH-ratio.code | example | Pattern: LOINC Code 81299-0 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:arrCGH-ratio.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:complex-var-type.code | example | Pattern: LOINC Code 81263-6 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:complex-var-type.value[x] | required | LOINC LL3999-1 `http://loinc.org/vs/LL3999-1`
Observation.component:complex-var-type.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:cytogenomic-nomenclature.code | example | Pattern: LOINC Code 81291-7 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:cytogenomic-nomenclature.value[x] | example |
Observation.component:cytogenomic-nomenclature.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:variant-inheritance.code | example | Pattern: variant-inheritance `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:variant-inheritance.value[x] | extensible | VariantInheritance `http://hl7.org/fhir/uv/genomics-reporting/ValueSet/variant-inheritance`
Observation.component:variant-inheritance.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:actionability.code | example | Pattern: LOINC Code 93348-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:actionability.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:proposed-for-orientation.code | example | Pattern: C0449889 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:proposed-for-orientation.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:pathogenicity.code | example | Pattern: LOINC Code 74019-1 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:pathogenicity.value[x] | required | Pathogenicity `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Pathogenicity` from this IG
Observation.component:pathogenicity.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:loss-of-heterozygosity.code | example | Pattern: C1881449 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:loss-of-heterozygosity.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard
Observation.component:segment-intensity.code | example | Pattern: C2732930 `http://hl7.org/fhir/ValueSet/observation-codes` from the FHIR Standard
Observation.component:segment-intensity.dataAbsentReason | extensible | DataAbsentReason `http://hl7.org/fhir/ValueSet/data-absent-reason` from the FHIR Standard

This structure is derived from Variant

Résumé

Mandatory: 2 elements

Structures

This structure refers to these other structures:

- Oncology Patient (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient)
- Sequencing Analysis (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/sequencing-analysis)

Slices

This structure defines the following Slices:

- The element 1 is sliced based on the value of Observation.derivedFrom

Other representations of profile: CSV, Excel, Schematron