Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/sequence-phase-relationship | Version: 3.0.0-ballot | |||
| Active as of 2023-12-18 | Computable Name: SequencePhaseRelationship | |||
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Indicates whether two entities are in Cis (same strand) or Trans (opposite strand) relationship to each other.
A sequence phase relationship asserts a specific type of relationship between two variants or haplotypes.
Humans inherit a copy of each autosome from mother and father - each cell contains, for instance, a maternally-derived and a paternally-derived chromosome 7. We refer to the two chromosomes as 'homologous', and we can refer to each of the chromosomes as 'homologs'.
Where a person has two variants (or haplotypes) on chromosome 7, those variants can both be on the same homolog (i.e. both variants are on the maternally-derived chromosome), or those variants can be on different homologs (i.e. one variant is on the maternally-derived chromosome and one variant is on the paternally-derived chromosome).
Where the two variants are on the same homolog, the variants are said to be in a 'Cis' relationship. Where the two variants are on different homologs, the variants are said to be in a 'Trans' relationship.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from GenomicFinding
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Observation | GenomicFinding | |||
  code | 1..1 | CodeableConcept | 82120-7 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: 82120-7 | |
 value[x] | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required) | |
| method | 0..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) | |
 derivedFrom:variant | 0..* | Reference(Variant) | Variant in the relationship | |
| derivedFrom:haplotype | 0..* | Reference(Haplotype) | Haplotype in the relationship | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet |
| Observation.value[x] | required | SequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes) |
| Observation.method | extensible | LOINC LL4050-2 |
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | GenomicFinding | Measurements and simple assertions |
 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: ObservationCategoryCodes (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 | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
 Slices for category | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
 category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
  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 | |
 category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| 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/v2-0074 | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| code | Σ | 1..1 | CodeableConcept | 82120-7 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: 82120-7 | |
| value[x] | ΣC | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required) |
| method | 0..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) | |
| Slices for derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() |
 derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant in the relationship |
 derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype in the relationship |
| Slices for component | Σ | 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 | Σ | 0..* | BackboneElement | Gene Studied |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
 code | Σ | 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] | Σ | 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:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |
| value[x] | Σ | 1..1 | CodeableConcept | Example: 1q21.1 |
| component:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 62374-4 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: 62374-4 | |
| value[x] | Σ | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible) |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code |
| Observation.status | required | ObservationStatus |
| Observation.category | preferred | ObservationCategoryCodes |
| Observation.category:labCategory | preferred | ObservationCategoryCodes |
| Observation.category:geCategory | preferred | ObservationCategoryCodes |
| Observation.code | example | Pattern: LOINC code 82120-7 |
| Observation.value[x] | required | SequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes) |
| Observation.method | extensible | LOINC LL4050-2 |
| 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:cytogenetic-location.code | example | Pattern: LOINC code 48001-2 |
| Observation.component:reference-sequence-assembly.code | example | Pattern: LOINC code 62374-4 |
| Observation.component:reference-sequence-assembly.value[x] | extensible | LOINC LL1040-6 |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty() | |
| dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
| dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Observation | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
| obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | GenomicFinding | Measurements and simple assertions | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by pattern:url | |||||
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (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 | Genomic Study) | Part of referenced event | ||||
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| Slices for category | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
 extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | Σ | 0..1 | string | Plain text representation of the concept | ||||
| category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | Σ | 0..1 | string | Plain text representation of the concept | ||||
| code | Σ | 1..1 | CodeableConcept | 82120-7 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: 82120-7 | |||||
| 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 | |||||
| subject | Σ | 0..1 | Reference(Patient | Group | Device | Location) | Who and/or what the observation is about | ||||
| focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
 effective[x] | Σ | 0..1 | Clinically relevant time/time-period for observation | |||||
| effectiveDateTime | dateTime | |||||||
| effectivePeriod | Period | |||||||
| effectiveTiming | Timing | |||||||
| effectiveInstant | instant | |||||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation | ||||
| value[x] | ΣC | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note | 0..* | 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 | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) | |||||
| 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 | ||||
| Slices for derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() | ||||
| derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant in the relationship | ||||
| derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype in the relationship | ||||
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
| component:All Slices | Content/Rules for all slices | |||||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] | Σ | 0..1 | Actual component result | |||||
| valueQuantity | Quantity | |||||||
| valueCodeableConcept | CodeableConcept | |||||||
| valueString | string | |||||||
| valueBoolean | boolean | |||||||
| valueInteger | integer | |||||||
| valueRange | Range | |||||||
| valueRatio | Ratio | |||||||
| valueSampledData | SampledData | |||||||
| valueTime | time | |||||||
| valueDateTime | dateTime | |||||||
| valuePeriod | Period | |||||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-studied | Σ | 0..* | BackboneElement | Gene Studied | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 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] | Σ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Example: 1q21.1 | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | ||||
| Observation.language | preferred | CommonLanguages
| ||||
| Observation.status | required | ObservationStatus | ||||
| Observation.category | preferred | ObservationCategoryCodes | ||||
| Observation.category:labCategory | preferred | ObservationCategoryCodes | ||||
| Observation.category:geCategory | preferred | ObservationCategoryCodes | ||||
| Observation.code | example | Pattern: LOINC code 82120-7 | ||||
| Observation.value[x] | required | SequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes) | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructures | ||||
| Observation.method | extensible | LOINC LL4050-2 | ||||
| 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:cytogenetic-location.code | example | Pattern: LOINC code 48001-2 | ||||
| Observation.component:cytogenetic-location.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:cytogenetic-location.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:reference-sequence-assembly.code | example | Pattern: LOINC code 62374-4 | ||||
| Observation.component:reference-sequence-assembly.value[x] | extensible | LOINC LL1040-6 | ||||
| Observation.component:reference-sequence-assembly.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:reference-sequence-assembly.interpretation | extensible | ObservationInterpretationCodes |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty() | |
| dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
| dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Observation | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text : low.exists() or high.exists() or text.exists() | |
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
| obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
This structure is derived from GenomicFinding
Differential View
This structure is derived from GenomicFinding
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | GenomicFinding | |||
| code | 1..1 | CodeableConcept | 82120-7 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: 82120-7 | |
| value[x] | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required) | |
| method | 0..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) | |
| derivedFrom:variant | 0..* | Reference(Variant) | Variant in the relationship | |
| derivedFrom:haplotype | 0..* | Reference(Haplotype) | Haplotype in the relationship | |
| Documentation for this format | ||||
| Path | Conformance | ValueSet |
| Observation.value[x] | required | SequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes) |
| Observation.method | extensible | LOINC LL4050-2 |
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Observation | C | 0..* | GenomicFinding | Measurements and simple assertions |
| 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: ObservationCategoryCodes (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 | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. |
| Slices for category | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| 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 | |
| category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| 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/v2-0074 | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| code | Σ | 1..1 | CodeableConcept | 82120-7 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: 82120-7 | |
| value[x] | ΣC | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required) |
| method | 0..1 | CodeableConcept | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) | |
| Slices for derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() |
| derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant in the relationship |
| derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype in the relationship |
| Slices for component | Σ | 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 | Σ | 0..* | BackboneElement | Gene Studied |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 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] | Σ | 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:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |
| value[x] | Σ | 1..1 | CodeableConcept | Example: 1q21.1 |
| component:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code | Σ | 1..1 | CodeableConcept | 62374-4 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: 62374-4 | |
| value[x] | Σ | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible) |
| Documentation for this format | ||||
| Path | Conformance | ValueSet / Code |
| Observation.status | required | ObservationStatus |
| Observation.category | preferred | ObservationCategoryCodes |
| Observation.category:labCategory | preferred | ObservationCategoryCodes |
| Observation.category:geCategory | preferred | ObservationCategoryCodes |
| Observation.code | example | Pattern: LOINC code 82120-7 |
| Observation.value[x] | required | SequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes) |
| Observation.method | extensible | LOINC LL4050-2 |
| 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:cytogenetic-location.code | example | Pattern: LOINC code 48001-2 |
| Observation.component:reference-sequence-assembly.code | example | Pattern: LOINC code 62374-4 |
| Observation.component:reference-sequence-assembly.value[x] | extensible | LOINC LL1040-6 |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty() | |
| dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
| dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Observation | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
| obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| Observation | C | 0..* | GenomicFinding | Measurements and simple assertions | ||||
| id | Σ | 0..1 | id | Logical id of this artifact | ||||
| meta | Σ | 0..1 | Meta | Metadata about the resource | ||||
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created | ||||
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained | 0..* | Resource | Contained, inline Resources | |||||
| Slices for extension | 0..* | Extension | Extension Slice: Unordered, Open by pattern:url | |||||
| secondary-finding | 0..1 | CodeableConcept | Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement.
For more detail, please see:
https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: ObservationCategoryCodes (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 | Genomic Study) | Part of referenced event | ||||
| status | ?!Σ | 1..1 | code | registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. | ||||
| Slices for category | 2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| category:labCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | Σ | 0..1 | string | Plain text representation of the concept | ||||
| category:geCategory | 1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding | Σ | 1..1 | Coding | Code defined by a terminology system Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | Σ | 0..1 | string | Plain text representation of the concept | ||||
| code | Σ | 1..1 | CodeableConcept | 82120-7 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: 82120-7 | |||||
| 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 | |||||
| subject | Σ | 0..1 | Reference(Patient | Group | Device | Location) | Who and/or what the observation is about | ||||
| focus | Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record | ||||
| encounter | Σ | 0..1 | Reference(Encounter) | Healthcare event during which this observation is made | ||||
| effective[x] | Σ | 0..1 | Clinically relevant time/time-period for observation | |||||
| effectiveDateTime | dateTime | |||||||
| effectivePeriod | Period | |||||||
| effectiveTiming | Timing | |||||||
| effectiveInstant | instant | |||||||
| issued | Σ | 0..1 | instant | Date/Time this version was made available | ||||
| performer | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson) | Who is responsible for the observation | ||||
| value[x] | ΣC | 1..1 | CodeableConcept | Cis | Trans | Indeterminate | Unknown Binding: Sequence Phase Relationships (required) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note | 0..* | 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 | Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible) | |||||
| 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 | ||||
| Slices for derivedFrom | Σ | 0..* | Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence) | Related measurements the observation is made from Slice: Unordered, Open by profile:resolve() | ||||
| derivedFrom:variant | Σ | 0..* | Reference(Variant) | Variant in the relationship | ||||
| derivedFrom:haplotype | Σ | 0..* | Reference(Haplotype) | Haplotype in the relationship | ||||
| Slices for component | Σ | 0..* | BackboneElement | Component results Slice: Unordered, Open by pattern:code | ||||
| component:All Slices | Content/Rules for all slices | |||||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] | Σ | 0..1 | Actual component result | |||||
| valueQuantity | Quantity | |||||||
| valueCodeableConcept | CodeableConcept | |||||||
| valueString | string | |||||||
| valueBoolean | boolean | |||||||
| valueInteger | integer | |||||||
| valueRange | Range | |||||||
| valueRatio | Ratio | |||||||
| valueSampledData | SampledData | |||||||
| valueTime | time | |||||||
| valueDateTime | dateTime | |||||||
| valuePeriod | Period | |||||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:conclusion-string | Σ | 0..1 | BackboneElement | Clinical Conclusion | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: conclusion-string | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 0..1 | string | Summary conclusion (interpretation/impression) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:gene-studied | Σ | 0..* | BackboneElement | Gene Studied | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 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] | Σ | 1..1 | CodeableConcept | The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:cytogenetic-location | Σ | 0..* | BackboneElement | Cytogenetic (Chromosome) Location | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 48001-2 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | Example: 1q21.1 | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| component:reference-sequence-assembly | Σ | 0..* | BackboneElement | Human Reference Sequence Assembly | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Extension | |||||
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| code | Σ | 1..1 | CodeableConcept | 62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| coding | 1..* | Coding | Code defined by a terminology system Fixed Value: (complex) | |||||
| id | 0..1 | string | Unique id for inter-element referencing | |||||
| extension | 0..* | Extension | Additional content defined by implementations | |||||
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |||||
| version | 0..1 | string | Version of the system - if relevant | |||||
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: 62374-4 | |||||
| display | 0..1 | string | Representation defined by the system | |||||
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |||||
| text | 0..1 | string | Plain text representation of the concept | |||||
| value[x] | Σ | 1..1 | CodeableConcept | GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible) | ||||
| dataAbsentReason | C | 0..1 | CodeableConcept | Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation | 0..* | CodeableConcept | High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| referenceRange | 0..* | See referenceRange (Observation) | Provides guide for interpretation of component result | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | ||||
| Observation.language | preferred | CommonLanguages
| ||||
| Observation.status | required | ObservationStatus | ||||
| Observation.category | preferred | ObservationCategoryCodes | ||||
| Observation.category:labCategory | preferred | ObservationCategoryCodes | ||||
| Observation.category:geCategory | preferred | ObservationCategoryCodes | ||||
| Observation.code | example | Pattern: LOINC code 82120-7 | ||||
| Observation.value[x] | required | SequencePhaseRelationshipVS (a valid code from Sequence Phase Relationship Codes) | ||||
| Observation.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.bodySite | example | SNOMEDCTBodyStructures | ||||
| Observation.method | extensible | LOINC LL4050-2 | ||||
| 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:cytogenetic-location.code | example | Pattern: LOINC code 48001-2 | ||||
| Observation.component:cytogenetic-location.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:cytogenetic-location.interpretation | extensible | ObservationInterpretationCodes | ||||
| Observation.component:reference-sequence-assembly.code | example | Pattern: LOINC code 62374-4 | ||||
| Observation.component:reference-sequence-assembly.value[x] | extensible | LOINC LL1040-6 | ||||
| Observation.component:reference-sequence-assembly.dataAbsentReason | extensible | DataAbsentReason | ||||
| Observation.component:reference-sequence-assembly.interpretation | extensible | ObservationInterpretationCodes |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Observation | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Observation | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty() | |
| dom-4 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
| dom-5 | error | Observation | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Observation | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| obs-3 | error | Observation.referenceRange | Must have at least a low or a high or text : low.exists() or high.exists() or text.exists() | |
| obs-6 | error | Observation | dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty() | |
| obs-7 | error | Observation | If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty() |
This structure is derived from GenomicFinding
Other representations of profile: CSV, Excel, Schematron
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
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