minimal Common Oncology Data Elements (mCODE) Implementation Guide
3.0.0 - STU3 Release
minimal Common Oncology Data Elements (mCODE) Implementation Guide
3.0.0 - STU3 Release
This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v3.0.0: STU 3) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions
| Official URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-region-studied | Version: 3.0.0 | |||
| Draft as of 2023-10-25 | Maturity Level: 1 | Computable Name: GenomicRegionStudied | ||
A subset of genes or genomic regions of interest in a targeted resequencing study.
This profile identifies a specific region analyzed for gene mutations or variants in a given genomic test. For example, exome sequencing tests could analyze multiple non-contiguous regions. Each region is designated by a range of start and end location and referencing a coordinate system which is 0-based or 1-based.
RegionStudied is noted at the GenomicsReport level and not directly tied to a given GenomicVariant.
Observation resources associated with an in-scope patient with DiagnosticReport.code LOINC 53041-0 SHALL conform to this profile. Beyond this requirement, a producer of resources SHOULD ensure that any resource instance associated with an in-scope patient that would reasonably be expected to conform to this profile SHOULD be published in this form.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from RegionStudied
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Observation | 0..* | RegionStudied | Region Studied | |
  status | S | 1..1 | code | registered | preliminary | final | amended + |
| category | S | 1..* | CodeableConcept | Classification of type of observation |
  category:labCategory | 1..1 | CodeableConcept | Classification of type of observation 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 | |
 coding | 1..1 | Coding | Code defined by a terminology system | |
| code | S | 1..1 | CodeableConcept | 53041-0 |
 subject | S | 1..1 | Reference(Cancer Patient Profile) | Who and/or what the observation is about |
 Slices for effective[x] | S | 0..1 | dateTime, Period, Timing, instant | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this |
 effective[x]:effectiveDateTime | S | 0..1 | dateTime | Clinically relevant time/time-period for observation |
| value[x] | 0..0 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | ||
| dataAbsentReason | S | 0..1 | CodeableConcept | Why the result is missing |
| component | S | 0..* | BackboneElement | Component results |
| component:gene-studied | S | 0..1 | BackboneElement | Gene Studied |
 code | S | 1..1 | CodeableConcept | 48018-6 |
| value[x] | S | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. |
| component:gene-mutations | S | 0..1 | BackboneElement | Gene Mutations ID |
| code | S | 1..1 | CodeableConcept | 36908-2 |
| value[x] | S | 1..1 | CodeableConcept | Actual component result |
| component:region-description | S | 0..1 | BackboneElement | Region Description |
| code | S | 1..1 | CodeableConcept | 81293-3 |
| value[x] | S | 0..1 | string | Actual component result |
| component:ranges-examined | S | 0..* | BackboneElement | Range(s) of DNA sequence examined |
| code | S | 1..1 | CodeableConcept | 51959-5 |
| value[x] | S | 0..1 | Range | Actual component result |
| component:coordinate-system | S | 0..1 | BackboneElement | Coordinate System |
| code | S | 1..1 | CodeableConcept | 92822-6 |
| value[x] | S | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting |
 component:genomic-ref-seq | S | 0..1 | BackboneElement | Genomic Reference Sequence |
 code | S | 1..1 | CodeableConcept | 48013-7 |
| value[x] | S | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier. |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | RegionStudied | Region Studied |
 implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |
| body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
 modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
| Slices for category | S | 1..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. |
 category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following | |
| 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 | |
  coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| code | SΣ | 1..1 | CodeableConcept | 53041-0 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: 53041-0 | |
| subject | SΣ | 1..1 | Reference(Cancer Patient Profile) | Who and/or what the observation is about |
| Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this | |
 effectiveDateTime | dateTime | |||
| effectivePeriod | Period | |||
| effectiveTiming | Timing | |||
| effectiveInstant | instant | |||
| effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation |
| dataAbsentReason | SC | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| Slices for component | SΣ | 0..* | 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. |
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
| component:gene-studied | SΣ | 0..1 | BackboneElement | Gene Studied |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |
| value[x] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) |
| component:gene-mutations | SΣ | 0..1 | BackboneElement | Gene Mutations ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 36908-2 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: 36908-2 | |
| value[x] | SΣ | 1..1 | CodeableConcept | Actual component result Binding: Human Genome Variation Society (HGVS) Nomenclature (required) |
| component:region-description | SΣ | 0..1 | BackboneElement | Region Description |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 81293-3 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: 81293-3 | |
| value[x] | SΣ | 0..1 | string | Actual component result |
| component:region-coverage | Σ | 0..1 | BackboneElement | Region Coverage |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | region-coverage 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: region-coverage | |
| component:ranges-examined | SΣ | 0..* | BackboneElement | Range(s) of DNA sequence examined |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 51959-5 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: 51959-5 | |
| value[x] | SΣ | 0..1 | Range | Actual component result |
| component:coordinate-system | SΣ | 0..1 | BackboneElement | Coordinate System |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 92822-6 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: 92822-6 | |
| value[x] | SΣ | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) |
| component:genomic-ref-seq | SΣ | 0..1 | BackboneElement | Genomic Reference Sequence |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 48013-7 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: 48013-7 | |
| value[x] | SΣ | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier. Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG) |
| component:uncallable-regions | Σ | 0..* | BackboneElement | Uncallable Sub-regions |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | uncallable-regions 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: uncallable-regions | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code |
| Observation.status | required | ObservationStatus |
| Observation.category | preferred | ObservationCategoryCodes |
| Observation.category:labCategory | preferred | Pattern: laboratory |
| Observation.code | example | Pattern: LOINC code 53041-0 |
| Observation.dataAbsentReason | extensible | DataAbsentReason |
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) |
| Observation.component:conclusion-string.code | example | Pattern: conclusion-string |
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6 |
| Observation.component:gene-studied.value[x] | extensible | HGNCVS |
| Observation.component:gene-mutations.code | example | Pattern: LOINC code 36908-2 |
| Observation.component:gene-mutations.value[x] | required | HGVSVS |
| Observation.component:region-description.code | example | Pattern: LOINC code 81293-3 |
| Observation.component:region-coverage.code | example | Pattern: region-coverage |
| Observation.component:ranges-examined.code | example | Pattern: LOINC code 51959-5 |
| Observation.component:coordinate-system.code | example | Pattern: LOINC code 92822-6 |
| Observation.component:coordinate-system.value[x] | extensible | LOINC LL5323-2 |
| Observation.component:genomic-ref-seq.code | example | Pattern: LOINC code 48013-7 |
| Observation.component:genomic-ref-seq.value[x] | example | |
| Observation.component:uncallable-regions.code | example | Pattern: uncallable-regions |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | RegionStudied | Region Studied | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
 Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |||||
| body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
| basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event | ||||
| status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| Slices for category | S | 1..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | ||||
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | Σ | 0..1 | string | Plain text representation of the concept | ||||
| code | SΣ | 1..1 | CodeableConcept | 53041-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53041-0 | |||||
| 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 | |||||
| subject | SΣ | 1..1 | Reference(Cancer Patient Profile) | Who and/or what the observation is about | ||||
| focus | ΣTU | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
| Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this | |||||
| effectiveDateTime | dateTime | |||||||
| effectivePeriod | Period | |||||||
| effectiveTiming | Timing | |||||||
| effectiveInstant | instant | |||||||
| effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation | ||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation | ||||
| dataAbsentReason | SC | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note | 0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |||||
| bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |||||
| method | 0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen | 0..1 | Reference(Specimen) | Specimen used for this observation | |||||
| device | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
| referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| low | C | 0..1 | SimpleQuantity | Low Range, if relevant | ||||
| high | C | 0..1 | SimpleQuantity | High Range, if relevant | ||||
| type | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
| appliesTo | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
| age | 0..1 | Range | Applicable age range, if relevant | |||||
| text | 0..1 | string | Text based reference range in an observation | |||||
| hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from | ||||
| Slices for component | SΣ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
| component:All Slices | Content/Rules for all slices | |||||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-studied | SΣ | 0..1 | BackboneElement | Gene Studied | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | SΣ | 1..1 | CodeableConcept | 48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-mutations | SΣ | 0..1 | BackboneElement | Gene Mutations 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 | SΣ | 1..1 | CodeableConcept | 36908-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 36908-2 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 1..1 | CodeableConcept | Actual component result Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:region-description | SΣ | 0..1 | BackboneElement | Region Description | ||||
| 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 | SΣ | 1..1 | CodeableConcept | 81293-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81293-3 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 0..1 | string | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:region-coverage | Σ | 0..1 | BackboneElement | Region Coverage | ||||
| 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 | region-coverage Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: region-coverage | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | Quantity | 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:ranges-examined | SΣ | 0..* | BackboneElement | Range(s) of DNA sequence examined | ||||
| 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 | SΣ | 1..1 | CodeableConcept | 51959-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51959-5 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 0..1 | Range | 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:coordinate-system | SΣ | 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 | SΣ | 1..1 | CodeableConcept | 92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:genomic-ref-seq | SΣ | 0..1 | BackboneElement | Genomic Reference Sequence | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | SΣ | 1..1 | CodeableConcept | 48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier. Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:uncallable-regions | Σ | 0..* | BackboneElement | Uncallable Sub-regions | ||||
| 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 | uncallable-regions Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: uncallable-regions | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | Range | Must be inside the range given by 'ranges examined' in the given reference sequence and coordinate system. | ||||
| 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 | ||||
| Observation.language | preferred | CommonLanguages
| ||||
| Observation.status | required | ObservationStatus | ||||
| Observation.category | preferred | ObservationCategoryCodes | ||||
| Observation.category:labCategory | preferred | Pattern: laboratory | ||||
| Observation.code | example | Pattern: LOINC code 53041-0 | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructures | ||||
| Observation.method | example | ObservationMethods | ||||
| Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodes | ||||
| Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodes | ||||
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) | ||||
| Observation.component.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:conclusion-string.code | example | Pattern: conclusion-string | ||||
| Observation.component:conclusion-string.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:conclusion-string.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6 | ||||
| Observation.component:gene-studied.value[x] | extensible | HGNCVS | ||||
| Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:gene-studied.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:gene-mutations.code | example | Pattern: LOINC code 36908-2 | ||||
| Observation.component:gene-mutations.value[x] | required | HGVSVS | ||||
| Observation.component:gene-mutations.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:gene-mutations.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:region-description.code | example | Pattern: LOINC code 81293-3 | ||||
| Observation.component:region-description.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:region-description.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:region-coverage.code | example | Pattern: region-coverage | ||||
| Observation.component:region-coverage.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:region-coverage.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:ranges-examined.code | example | Pattern: LOINC code 51959-5 | ||||
| Observation.component:ranges-examined.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:ranges-examined.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:coordinate-system.code | example | Pattern: LOINC code 92822-6 | ||||
| Observation.component:coordinate-system.value[x] | extensible | LOINC LL5323-2 | ||||
| Observation.component:coordinate-system.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:coordinate-system.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:genomic-ref-seq.code | example | Pattern: LOINC code 48013-7 | ||||
| Observation.component:genomic-ref-seq.value[x] | example | |||||
| Observation.component:genomic-ref-seq.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:genomic-ref-seq.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:uncallable-regions.code | example | Pattern: uncallable-regions | ||||
| Observation.component:uncallable-regions.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:uncallable-regions.interpretation | extensible | ObservationInterpretationCodes |
This structure is derived from RegionStudied
Differential View
This structure is derived from RegionStudied
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | 0..* | RegionStudied | Region Studied | |
| status | S | 1..1 | code | registered | preliminary | final | amended + |
| category | S | 1..* | CodeableConcept | Classification of type of observation |
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation 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 | |
| coding | 1..1 | Coding | Code defined by a terminology system | |
| code | S | 1..1 | CodeableConcept | 53041-0 |
| subject | S | 1..1 | Reference(Cancer Patient Profile) | Who and/or what the observation is about |
| Slices for effective[x] | S | 0..1 | dateTime, Period, Timing, instant | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this |
| effective[x]:effectiveDateTime | S | 0..1 | dateTime | Clinically relevant time/time-period for observation |
| value[x] | 0..0 | Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, Period | ||
| dataAbsentReason | S | 0..1 | CodeableConcept | Why the result is missing |
| component | S | 0..* | BackboneElement | Component results |
| component:gene-studied | S | 0..1 | BackboneElement | Gene Studied |
| code | S | 1..1 | CodeableConcept | 48018-6 |
| value[x] | S | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. |
| component:gene-mutations | S | 0..1 | BackboneElement | Gene Mutations ID |
| code | S | 1..1 | CodeableConcept | 36908-2 |
| value[x] | S | 1..1 | CodeableConcept | Actual component result |
| component:region-description | S | 0..1 | BackboneElement | Region Description |
| code | S | 1..1 | CodeableConcept | 81293-3 |
| value[x] | S | 0..1 | string | Actual component result |
| component:ranges-examined | S | 0..* | BackboneElement | Range(s) of DNA sequence examined |
| code | S | 1..1 | CodeableConcept | 51959-5 |
| value[x] | S | 0..1 | Range | Actual component result |
| component:coordinate-system | S | 0..1 | BackboneElement | Coordinate System |
| code | S | 1..1 | CodeableConcept | 92822-6 |
| value[x] | S | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting |
| component:genomic-ref-seq | S | 0..1 | BackboneElement | Genomic Reference Sequence |
| code | S | 1..1 | CodeableConcept | 48013-7 |
| value[x] | S | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier. |
| Documentation for this format | ||||
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | RegionStudied | Region Studied |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |
| body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
| Slices for category | S | 1..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. |
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following | |
| 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 | |
| coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |
| code | SΣ | 1..1 | CodeableConcept | 53041-0 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: 53041-0 | |
| subject | SΣ | 1..1 | Reference(Cancer Patient Profile) | Who and/or what the observation is about |
| Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this | |
| effectiveDateTime | dateTime | |||
| effectivePeriod | Period | |||
| effectiveTiming | Timing | |||
| effectiveInstant | instant | |||
| effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation |
| dataAbsentReason | SC | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| Slices for component | SΣ | 0..* | 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. |
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |
| component:gene-studied | SΣ | 0..1 | BackboneElement | Gene Studied |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |
| value[x] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) |
| component:gene-mutations | SΣ | 0..1 | BackboneElement | Gene Mutations ID |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 36908-2 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: 36908-2 | |
| value[x] | SΣ | 1..1 | CodeableConcept | Actual component result Binding: Human Genome Variation Society (HGVS) Nomenclature (required) |
| component:region-description | SΣ | 0..1 | BackboneElement | Region Description |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 81293-3 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: 81293-3 | |
| value[x] | SΣ | 0..1 | string | Actual component result |
| component:region-coverage | Σ | 0..1 | BackboneElement | Region Coverage |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | region-coverage 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: region-coverage | |
| component:ranges-examined | SΣ | 0..* | BackboneElement | Range(s) of DNA sequence examined |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 51959-5 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: 51959-5 | |
| value[x] | SΣ | 0..1 | Range | Actual component result |
| component:coordinate-system | SΣ | 0..1 | BackboneElement | Coordinate System |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 92822-6 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: 92822-6 | |
| value[x] | SΣ | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) |
| component:genomic-ref-seq | SΣ | 0..1 | BackboneElement | Genomic Reference Sequence |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | SΣ | 1..1 | CodeableConcept | 48013-7 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: 48013-7 | |
| value[x] | SΣ | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier. Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG) |
| component:uncallable-regions | Σ | 0..* | BackboneElement | Uncallable Sub-regions |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | uncallable-regions 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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: uncallable-regions | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code |
| Observation.status | required | ObservationStatus |
| Observation.category | preferred | ObservationCategoryCodes |
| Observation.category:labCategory | preferred | Pattern: laboratory |
| Observation.code | example | Pattern: LOINC code 53041-0 |
| Observation.dataAbsentReason | extensible | DataAbsentReason |
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) |
| Observation.component:conclusion-string.code | example | Pattern: conclusion-string |
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6 |
| Observation.component:gene-studied.value[x] | extensible | HGNCVS |
| Observation.component:gene-mutations.code | example | Pattern: LOINC code 36908-2 |
| Observation.component:gene-mutations.value[x] | required | HGVSVS |
| Observation.component:region-description.code | example | Pattern: LOINC code 81293-3 |
| Observation.component:region-coverage.code | example | Pattern: region-coverage |
| Observation.component:ranges-examined.code | example | Pattern: LOINC code 51959-5 |
| Observation.component:coordinate-system.code | example | Pattern: LOINC code 92822-6 |
| Observation.component:coordinate-system.value[x] | extensible | LOINC LL5323-2 |
| Observation.component:genomic-ref-seq.code | example | Pattern: LOINC code 48013-7 |
| Observation.component:genomic-ref-seq.value[x] | example | |
| Observation.component:uncallable-regions.code | example | Pattern: uncallable-regions |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | RegionStudied | Region Studied | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding. | |||||
| body-structure | 0..1 | Reference(BodyStructure) | Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite | |||||
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier | Σ | 0..* | Identifier | Business Identifier for observation | ||||
| basedOn | Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| partOf | Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) | Part of referenced event | ||||
| status | ?!SΣ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| Slices for category | S | 1..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | ||||
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | Σ | 0..1 | string | Plain text representation of the concept | ||||
| code | SΣ | 1..1 | CodeableConcept | 53041-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 53041-0 | |||||
| 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 | |||||
| subject | SΣ | 1..1 | Reference(Cancer Patient Profile) | Who and/or what the observation is about | ||||
| focus | ΣTU | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
| Slices for effective[x] | SΣ | 0..1 | Clinically relevant time/time-period for observation Slice: Unordered, Open by type:$this | |||||
| effectiveDateTime | dateTime | |||||||
| effectivePeriod | Period | |||||||
| effectiveTiming | Timing | |||||||
| effectiveInstant | instant | |||||||
| effective[x]:effectiveDateTime | SΣ | 0..1 | dateTime | Clinically relevant time/time-period for observation | ||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation | ||||
| dataAbsentReason | SC | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note | 0..* | CodedAnnotation | Comments about the Observation that also contain a coded type | |||||
| bodySite | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |||||
| method | 0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen | 0..1 | Reference(Specimen) | Specimen used for this observation | |||||
| device | 0..1 | Reference(Device | DeviceMetric) | (Measurement) Device | |||||
| referenceRange | C | 0..* | BackboneElement | Provides guide for interpretation | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| low | C | 0..1 | SimpleQuantity | Low Range, if relevant | ||||
| high | C | 0..1 | SimpleQuantity | High Range, if relevant | ||||
| type | 0..1 | CodeableConcept | Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range. | |||||
| appliesTo | 0..* | CodeableConcept | Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to. | |||||
| age | 0..1 | Range | Applicable age range, if relevant | |||||
| text | 0..1 | string | Text based reference range in an observation | |||||
| hasMember | Σ | 0..* | Reference(Observation | QuestionnaireResponse | MolecularSequence) | Related resource that belongs to the Observation group | ||||
| derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from | ||||
| Slices for component | SΣ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
| component:All Slices | Content/Rules for all slices | |||||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | 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. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-studied | SΣ | 0..1 | BackboneElement | Gene Studied | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | SΣ | 1..1 | CodeableConcept | 48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-mutations | SΣ | 0..1 | BackboneElement | Gene Mutations 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 | SΣ | 1..1 | CodeableConcept | 36908-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 36908-2 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 1..1 | CodeableConcept | Actual component result Binding: Human Genome Variation Society (HGVS) Nomenclature (required) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:region-description | SΣ | 0..1 | BackboneElement | Region Description | ||||
| 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 | SΣ | 1..1 | CodeableConcept | 81293-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 81293-3 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 0..1 | string | Actual component result | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:region-coverage | Σ | 0..1 | BackboneElement | Region Coverage | ||||
| 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 | region-coverage Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: region-coverage | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | Quantity | 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:ranges-examined | SΣ | 0..* | BackboneElement | Range(s) of DNA sequence examined | ||||
| 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 | SΣ | 1..1 | CodeableConcept | 51959-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 51959-5 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 0..1 | Range | 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:coordinate-system | SΣ | 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 | SΣ | 1..1 | CodeableConcept | 92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 92822-6 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 1..1 | CodeableConcept | 0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:genomic-ref-seq | SΣ | 0..1 | BackboneElement | Genomic Reference Sequence | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | SΣ | 1..1 | CodeableConcept | 48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48013-7 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | SΣ | 1..1 | CodeableConcept | Versioned genomic reference sequence identifier. Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:uncallable-regions | Σ | 0..* | BackboneElement | Uncallable Sub-regions | ||||
| 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 | uncallable-regions Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: uncallable-regions | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | Range | Must be inside the range given by 'ranges examined' in the given reference sequence and coordinate system. | ||||
| 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 | ||||
| Observation.language | preferred | CommonLanguages
| ||||
| Observation.status | required | ObservationStatus | ||||
| Observation.category | preferred | ObservationCategoryCodes | ||||
| Observation.category:labCategory | preferred | Pattern: laboratory | ||||
| Observation.code | example | Pattern: LOINC code 53041-0 | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructures | ||||
| Observation.method | example | ObservationMethods | ||||
| Observation.referenceRange.type | preferred | ObservationReferenceRangeMeaningCodes | ||||
| Observation.referenceRange.appliesTo | example | ObservationReferenceRangeAppliesToCodes | ||||
| Observation.component.code | example | LOINCCodes (a valid code from LOINC) | ||||
| Observation.component.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:conclusion-string.code | example | Pattern: conclusion-string | ||||
| Observation.component:conclusion-string.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:conclusion-string.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:gene-studied.code | example | Pattern: LOINC code 48018-6 | ||||
| Observation.component:gene-studied.value[x] | extensible | HGNCVS | ||||
| Observation.component:gene-studied.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:gene-studied.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:gene-mutations.code | example | Pattern: LOINC code 36908-2 | ||||
| Observation.component:gene-mutations.value[x] | required | HGVSVS | ||||
| Observation.component:gene-mutations.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:gene-mutations.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:region-description.code | example | Pattern: LOINC code 81293-3 | ||||
| Observation.component:region-description.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:region-description.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:region-coverage.code | example | Pattern: region-coverage | ||||
| Observation.component:region-coverage.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:region-coverage.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:ranges-examined.code | example | Pattern: LOINC code 51959-5 | ||||
| Observation.component:ranges-examined.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:ranges-examined.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:coordinate-system.code | example | Pattern: LOINC code 92822-6 | ||||
| Observation.component:coordinate-system.value[x] | extensible | LOINC LL5323-2 | ||||
| Observation.component:coordinate-system.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:coordinate-system.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:genomic-ref-seq.code | example | Pattern: LOINC code 48013-7 | ||||
| Observation.component:genomic-ref-seq.value[x] | example | |||||
| Observation.component:genomic-ref-seq.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:genomic-ref-seq.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:uncallable-regions.code | example | Pattern: uncallable-regions | ||||
| Observation.component:uncallable-regions.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:uncallable-regions.interpretation | extensible | ObservationInterpretationCodes |
This structure is derived from RegionStudied
Other representations of profile: CSV, Excel, Schematron
IG © 2019+ HL7 International / Clinical Interoperability Council. Package hl7.fhir.us.mcode#3.0.0 based on FHIR 4.0.1. Generated 2023-10-25
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