FHIR Osiris Implementation Guide
2.1.0 - ci-build
FHIR Osiris Implementation Guide
2.1.0 - ci-build
FHIR Osiris Implementation Guide - Local Development build (v2.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions
| Official URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/fusion | Version: 2.1.0 | |||
| Draft as of 2024-03-21 | Computable Name: Fusion | |||
Observation of a Gene Fusion derived from a SequencingAnalysis. The Fusion profile indicates the pathogenicity, the actionability and if the fusion has occured in the reading frame.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Observation
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Observation | Observation | |||
  spanning-pairs | S | 0..1 | integer | Number of reads pairs spanning the fusion URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs |
   value[x] | 0..1 | integer | Value of extension | |
| split-reads | S | 0..1 | integer | Number of reads containing the fusion point URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads |
| value[x] | 0..1 | integer | Value of extension | |
 code | 1..1 | CodeableConcept | Type of the fusion event. eg: translocation, readthrough Binding: Fusion Type Value Set (required) | |
 subject | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about | |
 Slices for derivedFrom | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference | |
 derivedFrom:fusion-molecular-sequences | 0..2 | Reference(5 Prime Molecular Sequence | 3 Prime Molecular Sequence) | Five prime and three prime positions of the fusion | |
 derivedFrom:analysis | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation | |
 Slices for component | 1..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | |
  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:gene-studied | 0..* | BackboneElement | Gene studied [ID] | |
| 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: 48018-6 | |
| value[x] | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible) | |
 component:in-frame | 1..1 | BackboneElement | Specify whether the fusion is in frame | |
| 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: 95123-6 | |
| value[x] | 0..1 | boolean | Actual component result | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet | URI |
| Observation.code | required | FusionTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/FusionTypefrom this IG | |
| Observation.component:pathogenicity.value[x] | required | Pathogenicityhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/Pathogenicityfrom this IG | |
| Observation.component:gene-studied.value[x] | extensible | HGNChttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc |
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | Observation | Measurements and simple assertions 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 obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| spanning-pairs | S | 0..1 | integer | Number of reads pairs spanning the fusion URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs |
  extension | 0..0 | |||
| url | 1..1 | uri | "https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs" | |
| value[x] | 0..1 | integer | Value of extension | |
| split-reads | S | 0..1 | integer | Number of reads containing the fusion point URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads |
| extension | 0..0 | |||
| url | 1..1 | uri | "https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads" | |
| value[x] | 0..1 | integer | Value of extension | |
 modifierExtension | ?!N | 0..* | Extension | Extensions that cannot be ignored Slice: Unordered, Open by value:url |
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
| code | Σ | 1..1 | CodeableConcept | Type of the fusion event. eg: translocation, readthrough Binding: Fusion Type Value Set (required) |
| subject | ΣC | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about ref-1: SHALL have a contained resource if a local reference is provided |
 value[x] | ΣC | 0..1 | Actual 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 result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| Slices for derivedFrom | ΣC | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference ref-1: SHALL have a contained resource if a local reference is provided |
| derivedFrom:fusion-molecular-sequences | ΣC | 0..2 | Reference(5 Prime Molecular Sequence | 3 Prime Molecular Sequence) | Five prime and three prime positions of the fusion ref-1: SHALL have a contained resource if a local reference is provided |
| derivedFrom:analysis | ΣC | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation ref-1: SHALL have a contained resource if a local reference is provided |
| Slices for component | Σ | 1..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code |
| component:All Slices | Content/Rules for all slices | |||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board |
| 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 |
| 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 |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? |
| 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 |
| 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 |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board |
| 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 |
| 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) |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:gene-studied | Σ | 0..* | BackboneElement | Gene studied [ID] |
| 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 |
| 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) |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:in-frame | Σ | 1..1 | BackboneElement | Specify whether the fusion is in frame |
| 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 |
| 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: 95123-6 | |
| 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. |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code | URI |
| Observation.status | required | ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1from the FHIR Standard | |
| Observation.code | required | FusionTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/FusionTypefrom this IG | |
| Observation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component.code | example | LOINCCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:actionability.code | example | Pattern: LOINC code 93348-1http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:actionability.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:proposed-for-orientation.code | example | Pattern: C0449889http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:proposed-for-orientation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:pathogenicity.code | example | Pattern: LOINC code 74019-1http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:pathogenicity.value[x] | required | Pathogenicityhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/Pathogenicityfrom this IG | |
| Observation.component:pathogenicity.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:gene-studied.value[x] | extensible | HGNChttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc | |
| Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:in-frame.code | example | Pattern: LOINC code 95123-6http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:in-frame.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | Observation | Measurements and simple assertions 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 obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
| Slices for extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| spanning-pairs | S | 0..1 | integer | Number of reads pairs spanning the fusion URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..0 | |||||||
| url | 1..1 | uri | "https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs" | |||||
| value[x] | 0..1 | integer | Value of extension | |||||
| split-reads | S | 0..1 | integer | Number of reads containing the fusion point URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..0 | |||||||
| url | 1..1 | uri | "https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads" | |||||
| value[x] | 0..1 | integer | Value of extension | |||||
| modifierExtension | ?!N | 0..* | Extension | Extensions that cannot be ignored Slice: Unordered, Open by value:url | ||||
| identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
| basedOn | ΣC | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order ref-1: SHALL have a contained resource if a local reference is provided | ||||
| partOf | ΣC | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event ref-1: SHALL have a contained resource if a local reference is provided | ||||
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| category | 0..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| code | Σ | 1..1 | CodeableConcept | Type of the fusion event. eg: translocation, readthrough Binding: Fusion Type Value Set (required) | ||||
| subject | ΣC | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about ref-1: SHALL have a contained resource if a local reference is provided | ||||
| focus | ΣC | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record ref-1: SHALL have a contained resource if a local reference is provided | ||||
| encounter | ΣC | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made ref-1: SHALL have a contained resource if a local reference is provided | ||||
| effective[x] | Σ | 0..1 | Clinically relevant time/time-period for observation | |||||
| effectiveDateTime | dateTime | |||||||
| effectivePeriod | Period | |||||||
| effectiveTiming | Timing | |||||||
| effectiveInstant | instant | |||||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | ΣC | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation ref-1: SHALL have a contained resource if a local reference is provided | ||||
| value[x] | ΣC | 0..1 | Actual 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 result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note | 0..* | 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 | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen | C | 0..1 | Reference(Specimen) | Specimen used for this observation ref-1: SHALL have a contained resource if a local reference is provided | ||||
| device | C | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device ref-1: SHALL have a contained resource if a local reference is provided | ||||
| 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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| low | C | 0..1 | SimpleQuantity | Low Range, if relevant 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 | ||||
| high | C | 0..1 | SimpleQuantity | High Range, if relevant 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 | ||||
| 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 | C | 0..1 | Range | Applicable age range, if relevant rng-2: If present, low SHALL have a lower value than high | ||||
| text | 0..1 | string | Text based reference range in an observation | |||||
| hasMember | ΣC | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group ref-1: SHALL have a contained resource if a local reference is provided | ||||
| Slices for derivedFrom | ΣC | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference ref-1: SHALL have a contained resource if a local reference is provided | ||||
| derivedFrom:fusion-molecular-sequences | ΣC | 0..2 | Reference(5 Prime Molecular Sequence | 3 Prime Molecular Sequence) | Five prime and three prime positions of the fusion ref-1: SHALL have a contained resource if a local reference is provided | ||||
| derivedFrom:analysis | ΣC | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation ref-1: SHALL have a contained resource if a local reference is provided | ||||
| Slices for component | Σ | 1..* | 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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] | Σ | 0..1 | Actual component result | |||||
| valueQuantity | Quantity | |||||||
| valueCodeableConcept | CodeableConcept | |||||||
| valueString | string | |||||||
| valueBoolean | boolean | |||||||
| valueInteger | integer | |||||||
| valueRange | Range | |||||||
| valueRatio | Ratio | |||||||
| valueSampledData | SampledData | |||||||
| valueTime | time | |||||||
| valueDateTime | dateTime | |||||||
| valuePeriod | Period | |||||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component: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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component: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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component: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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-studied | Σ | 0..* | BackboneElement | Gene studied [ID] | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:in-frame | Σ | 1..1 | BackboneElement | Specify whether the fusion is in frame | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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: 95123-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | URI | |||
| Observation.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| Observation.status | required | ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1from the FHIR Standard | ||||
| Observation.category | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-categoryfrom the FHIR Standard | ||||
| Observation.code | required | FusionTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/FusionTypefrom this IG | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-sitefrom the FHIR Standard | ||||
| Observation.method | example | ObservationMethodshttp://hl7.org/fhir/ValueSet/observation-methodsfrom the FHIR Standard | ||||
| Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodeshttp://hl7.org/fhir/ValueSet/referencerange-meaningfrom the FHIR Standard | ||||
| Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodeshttp://hl7.org/fhir/ValueSet/referencerange-appliestofrom the FHIR Standard | ||||
| Observation.component.code | example | LOINCCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:actionability.code | example | Pattern: LOINC code 93348-1http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:actionability.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:actionability.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:proposed-for-orientation.code | example | Pattern: C0449889http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:proposed-for-orientation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:proposed-for-orientation.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:pathogenicity.code | example | Pattern: LOINC code 74019-1http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:pathogenicity.value[x] | required | Pathogenicityhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/Pathogenicityfrom this IG | ||||
| Observation.component:pathogenicity.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:pathogenicity.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:gene-studied.value[x] | extensible | HGNChttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc | ||||
| Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:gene-studied.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:in-frame.code | example | Pattern: LOINC code 95123-6http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:in-frame.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:in-frame.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard |
This structure is derived from Observation
Summary
Mandatory: 4 elements (1 nested mandatory element)
Must-Support: 2 elements
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Slices
This structure defines the following Slices:
Differential View
This structure is derived from Observation
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | Observation | |||
| spanning-pairs | S | 0..1 | integer | Number of reads pairs spanning the fusion URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs |
| value[x] | 0..1 | integer | Value of extension | |
| split-reads | S | 0..1 | integer | Number of reads containing the fusion point URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads |
| value[x] | 0..1 | integer | Value of extension | |
| code | 1..1 | CodeableConcept | Type of the fusion event. eg: translocation, readthrough Binding: Fusion Type Value Set (required) | |
| subject | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about | |
| Slices for derivedFrom | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference | |
| derivedFrom:fusion-molecular-sequences | 0..2 | Reference(5 Prime Molecular Sequence | 3 Prime Molecular Sequence) | Five prime and three prime positions of the fusion | |
| derivedFrom:analysis | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation | |
| Slices for component | 1..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | |
| 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:gene-studied | 0..* | BackboneElement | Gene studied [ID] | |
| 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: 48018-6 | |
| value[x] | 1..1 | CodeableConcept | If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HGNC (extensible) | |
| component:in-frame | 1..1 | BackboneElement | Specify whether the fusion is in frame | |
| 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: 95123-6 | |
| value[x] | 0..1 | boolean | Actual component result | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet | URI |
| Observation.code | required | FusionTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/FusionTypefrom this IG | |
| Observation.component:pathogenicity.value[x] | required | Pathogenicityhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/Pathogenicityfrom this IG | |
| Observation.component:gene-studied.value[x] | extensible | HGNChttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc |
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | Observation | Measurements and simple assertions 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 obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| spanning-pairs | S | 0..1 | integer | Number of reads pairs spanning the fusion URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs |
| extension | 0..0 | |||
| url | 1..1 | uri | "https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs" | |
| value[x] | 0..1 | integer | Value of extension | |
| split-reads | S | 0..1 | integer | Number of reads containing the fusion point URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads |
| extension | 0..0 | |||
| url | 1..1 | uri | "https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads" | |
| value[x] | 0..1 | integer | Value of extension | |
| modifierExtension | ?!N | 0..* | Extension | Extensions that cannot be ignored Slice: Unordered, Open by value:url |
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
| code | Σ | 1..1 | CodeableConcept | Type of the fusion event. eg: translocation, readthrough Binding: Fusion Type Value Set (required) |
| subject | ΣC | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about ref-1: SHALL have a contained resource if a local reference is provided |
| value[x] | ΣC | 0..1 | Actual 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 result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| Slices for derivedFrom | ΣC | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference ref-1: SHALL have a contained resource if a local reference is provided |
| derivedFrom:fusion-molecular-sequences | ΣC | 0..2 | Reference(5 Prime Molecular Sequence | 3 Prime Molecular Sequence) | Five prime and three prime positions of the fusion ref-1: SHALL have a contained resource if a local reference is provided |
| derivedFrom:analysis | ΣC | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation ref-1: SHALL have a contained resource if a local reference is provided |
| Slices for component | Σ | 1..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code |
| component:All Slices | Content/Rules for all slices | |||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:actionability | Σ | 0..1 | BackboneElement | Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board |
| 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 |
| 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 |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:proposed-for-orientation | Σ | 0..1 | BackboneElement | Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? |
| 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 |
| 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 |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:pathogenicity | Σ | 0..1 | BackboneElement | Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board |
| 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 |
| 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) |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:gene-studied | Σ | 0..* | BackboneElement | Gene studied [ID] |
| 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 |
| 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) |
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| component:in-frame | Σ | 1..1 | BackboneElement | Specify whether the fusion is in frame |
| 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 |
| 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: 95123-6 | |
| 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. |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code | URI |
| Observation.status | required | ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1from the FHIR Standard | |
| Observation.code | required | FusionTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/FusionTypefrom this IG | |
| Observation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component.code | example | LOINCCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:actionability.code | example | Pattern: LOINC code 93348-1http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:actionability.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:proposed-for-orientation.code | example | Pattern: C0449889http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:proposed-for-orientation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:pathogenicity.code | example | Pattern: LOINC code 74019-1http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:pathogenicity.value[x] | required | Pathogenicityhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/Pathogenicityfrom this IG | |
| Observation.component:pathogenicity.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:gene-studied.value[x] | extensible | HGNChttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc | |
| Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | |
| Observation.component:in-frame.code | example | Pattern: LOINC code 95123-6http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | |
| Observation.component:in-frame.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | Observation | Measurements and simple assertions 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 obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
| Slices for extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| spanning-pairs | S | 0..1 | integer | Number of reads pairs spanning the fusion URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..0 | |||||||
| url | 1..1 | uri | "https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/spanning-pairs" | |||||
| value[x] | 0..1 | integer | Value of extension | |||||
| split-reads | S | 0..1 | integer | Number of reads containing the fusion point URL: https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..0 | |||||||
| url | 1..1 | uri | "https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/split-reads" | |||||
| value[x] | 0..1 | integer | Value of extension | |||||
| modifierExtension | ?!N | 0..* | Extension | Extensions that cannot be ignored Slice: Unordered, Open by value:url | ||||
| identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
| basedOn | ΣC | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order ref-1: SHALL have a contained resource if a local reference is provided | ||||
| partOf | ΣC | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event ref-1: SHALL have a contained resource if a local reference is provided | ||||
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| category | 0..* | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| code | Σ | 1..1 | CodeableConcept | Type of the fusion event. eg: translocation, readthrough Binding: Fusion Type Value Set (required) | ||||
| subject | ΣC | 0..1 | Reference(Oncology Patient) | Who and/or what the observation is about ref-1: SHALL have a contained resource if a local reference is provided | ||||
| focus | ΣC | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record ref-1: SHALL have a contained resource if a local reference is provided | ||||
| encounter | ΣC | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made ref-1: SHALL have a contained resource if a local reference is provided | ||||
| effective[x] | Σ | 0..1 | Clinically relevant time/time-period for observation | |||||
| effectiveDateTime | dateTime | |||||||
| effectivePeriod | Period | |||||||
| effectiveTiming | Timing | |||||||
| effectiveInstant | instant | |||||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | ΣC | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation ref-1: SHALL have a contained resource if a local reference is provided | ||||
| value[x] | ΣC | 0..1 | Actual 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 result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note | 0..* | 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 | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen | C | 0..1 | Reference(Specimen) | Specimen used for this observation ref-1: SHALL have a contained resource if a local reference is provided | ||||
| device | C | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device ref-1: SHALL have a contained resource if a local reference is provided | ||||
| 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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| low | C | 0..1 | SimpleQuantity | Low Range, if relevant 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 | ||||
| high | C | 0..1 | SimpleQuantity | High Range, if relevant 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 | ||||
| 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 | C | 0..1 | Range | Applicable age range, if relevant rng-2: If present, low SHALL have a lower value than high | ||||
| text | 0..1 | string | Text based reference range in an observation | |||||
| hasMember | ΣC | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group ref-1: SHALL have a contained resource if a local reference is provided | ||||
| Slices for derivedFrom | ΣC | 1..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by pattern:reference ref-1: SHALL have a contained resource if a local reference is provided | ||||
| derivedFrom:fusion-molecular-sequences | ΣC | 0..2 | Reference(5 Prime Molecular Sequence | 3 Prime Molecular Sequence) | Five prime and three prime positions of the fusion ref-1: SHALL have a contained resource if a local reference is provided | ||||
| derivedFrom:analysis | ΣC | 1..1 | Reference(Sequencing Analysis) | Analysis from which come this observation ref-1: SHALL have a contained resource if a local reference is provided | ||||
| Slices for component | Σ | 1..* | 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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] | Σ | 0..1 | Actual component result | |||||
| valueQuantity | Quantity | |||||||
| valueCodeableConcept | CodeableConcept | |||||||
| valueString | string | |||||||
| valueBoolean | boolean | |||||||
| valueInteger | integer | |||||||
| valueRange | Range | |||||||
| valueRatio | Ratio | |||||||
| valueSampledData | SampledData | |||||||
| valueTime | time | |||||||
| valueDateTime | dateTime | |||||||
| valuePeriod | Period | |||||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component: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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component: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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component: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 | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-studied | Σ | 0..* | BackboneElement | Gene studied [ID] | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:in-frame | Σ | 1..1 | BackboneElement | Specify whether the fusion is in frame | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | N | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | ||||
| 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: 95123-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | URI | |||
| Observation.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| Observation.status | required | ObservationStatushttp://hl7.org/fhir/ValueSet/observation-status|4.0.1from the FHIR Standard | ||||
| Observation.category | preferred | ObservationCategoryCodeshttp://hl7.org/fhir/ValueSet/observation-categoryfrom the FHIR Standard | ||||
| Observation.code | required | FusionTypehttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/FusionTypefrom this IG | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-sitefrom the FHIR Standard | ||||
| Observation.method | example | ObservationMethodshttp://hl7.org/fhir/ValueSet/observation-methodsfrom the FHIR Standard | ||||
| Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodeshttp://hl7.org/fhir/ValueSet/referencerange-meaningfrom the FHIR Standard | ||||
| Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodeshttp://hl7.org/fhir/ValueSet/referencerange-appliestofrom the FHIR Standard | ||||
| Observation.component.code | example | LOINCCodes (a valid code from LOINC)http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:actionability.code | example | Pattern: LOINC code 93348-1http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:actionability.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:actionability.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:proposed-for-orientation.code | example | Pattern: C0449889http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:proposed-for-orientation.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:proposed-for-orientation.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:pathogenicity.code | example | Pattern: LOINC code 74019-1http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:pathogenicity.value[x] | required | Pathogenicityhttps://build.fhir.org/ig/arkhn/arkhn-ig-osiris/ValueSet/Pathogenicityfrom this IG | ||||
| Observation.component:pathogenicity.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:pathogenicity.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:gene-studied.value[x] | extensible | HGNChttp://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc | ||||
| Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:gene-studied.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard | ||||
| Observation.component:in-frame.code | example | Pattern: LOINC code 95123-6http://hl7.org/fhir/ValueSet/observation-codesfrom the FHIR Standard | ||||
| Observation.component:in-frame.dataAbsentReason | extensible | DataAbsentReasonhttp://hl7.org/fhir/ValueSet/data-absent-reasonfrom the FHIR Standard | ||||
| Observation.component:in-frame.interpretation | extensible | ObservationInterpretationCodeshttp://hl7.org/fhir/ValueSet/observation-interpretationfrom the FHIR Standard |
This structure is derived from Observation
Summary
Mandatory: 4 elements (1 nested mandatory element)
Must-Support: 2 elements
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Slices
This structure defines the following Slices:
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IG © 2020+ Arkhn. Package arkhn.fhir.uv.osiris#2.1.0 based on FHIR 4.0.1. Generated 2024-03-21
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