Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot
Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker | Version: 4.0.0-ballot | |||
| Standards status: Trial-use | Maturity Level: 2 | Computable Name: MolecularBiomarker | ||
This profile is used to represent laboratory measurements of human inherent substances such as gene products, antigens and antibodies, and complex chemicals that result from post-translational processing of multi-gene products.
The term 'biomarker' is broad, encompassing observable characteristics that indicate normal or abnormal biological processes and that are often used to assess prognosis or guide therapy. In the broad sense, many clinical and laboratory observations might be considered a 'biomarker'. 'Molecular biomarker' is likewise broad, primarily encompassing laboratory measurements of human inherent substances such as gene products, antigens and antibodies, complex chemicals that result from post-translational processing of multi-gene products, etc. Molecular biomarkers include many different types of measurements, such as presence or absence of a chemical, or the level of a chemical. Here, we are primarily interested in those molecular biomarkers that have associated therapeutic implications, particularly in precision cancer care, including but not limited to: cell receptor levels (e.g. ER, PR, HER2); molecular sequence adjacent observations (e.g. microsatellite instability, tumor mutation burden, gene promoter methylation); cell receptor ligands (e.g. PD-L1); proteins, antigens, and antibodies (e.g. HLA type).
The code is bound to the Molecular Biomarker Codes ValueSet. It is not a comprehensive list of biomarkers and only provides representative examples drawn from LOINC and NCI Thesaurus.
Where the biomarker is a proxy or higher level abstraction for one or more underlying genetic observations, the derivedFrom attribute can be used to reference the source variant(s), haplotype(s) and/or genotype(s).
Component 'gene-studied' is an optional and repeating field for representing the gene or genes from which the observed substance is derived.
Component 'biomarker-category' is a repeating field that provides for a categorization of a given biomarker observation.
In the absence of a well defined and comprehensive value set for molecular biomarkers, we provide general guidance for the construction of a biomarker instance for an arbitrary biomarker. A typical use of this profile includes (1) identify the appropriate observation.code (e.g. drawing from LOINC, NCIt, etc); (2) add an observation.category of 'biomarker-category'; (3) populate component:gene-studied if applicable; (4) optionally populate component:biomarker-category; (5) populate other applicable observation fields similar to how you would populate them for regular lab observations (e.g. include observation.value, observation.effectiveDateTime, etc).
The Molecular Biomarker Ontology code system provides a categorization of biomarkers along several axes. A given lab test can be associated with more than one category within more than one axis. For example, LOINC code 85337-4 represents Estrogen receptor antigen in tissue by immune stain. It can be categorized by physiologic role of cell receptor and antigen; by molecule type of protein; and by method of immune stain.
Biomarker categories can be associated with LOINC value sets to facilitate retrieval, as shown in this non-normative example table.
| Biomarker Category | Example LOINC codes |
|---|---|
| cell receptor | ER, HER2 by IA, HLA class I, PR |
| protein | ER, HER2 by IA, Hgb A2, HLA class I, Neutrophil Ab, PR, PSA, Insulin, Lactoferrin Ab by immunoassay |
| immune stain | ER, Insulin, MSI by immune stain, PD-L1, PR |
If implementers have additional annotations for biomarkers, the Molecular Biomarker profile is defined to allow flexibility. See the section on flexibility for additional guidance, especially the guidance for the Open Slicing allowed on Observation.component.
Usages:
You can also check for usages in the FHIR IG Statistics
Description of Profiles, Differentials, Snapshots and how the different presentations work.
| Name | Flags | Card. | Type | Description & Constraints Filter:   |
|---|---|---|---|---|
  Observation |
C | 0..* | Observation | Measurements and simple assertions Constraints: obs-6, obs-7, obs-8, obs-10, obs-11 |
  implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created |
| contained |
0..* | Resource | Contained, inline Resources | |
 modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| status |
?!Σ | 1..1 | code | registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained 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 |
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 | |
| category:mbCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding |
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://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: biomarker-category | |
| display |
0..1 | string | Representation defined by the system | |
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |
 category:geCategory |
0..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding |
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 | |
| code |
ΣC | 1..1 | CodeableConcept | Code for the biomarker Binding: Molecular Biomarker Codes (example) |
 focus |
?!Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record |
 value[x] |
ΣC | 0..1 | Actual result | |
| valueQuantity |
Quantity | |||
| valueCodeableConcept |
CodeableConcept | |||
| valueString |
string | |||
| valueBoolean |
boolean | |||
| valueInteger |
integer | |||
| valueRange |
Range | |||
| valueRatio |
Ratio | |||
| valueSampledData |
SampledData | |||
| valueTime |
time | |||
| valueDateTime |
dateTime | |||
| valuePeriod |
Period | |||
| valueAttachment |
Attachment | |||
| valueReference |
Reference(MolecularSequence) | |||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| Slices for derivedFrom |
Σ | 0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() |
 derivedFrom:variant |
Σ | 0..* | Reference(Variant) | Variant the biomarker is derived from |
| derivedFrom:genotype |
Σ | 0..* | Reference(Genotype) | Genotype the biomarker is derived from |
 derivedFrom:haplotype |
Σ | 0..* | Reference(Haplotype) | Haplotype the biomarker is derived from |
 Slices for component |
ΣC | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code |
 component:All Slices |
Content/Rules for all slices | |||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| component:gene-studied |
ΣC | 0..* | BackboneElement | Gene Studied |
 modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
 code |
ΣC | 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] |
ΣC | 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:biomarker-category |
ΣC | 0..* | BackboneElement | Biomarker Category |
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| version |
0..1 | string | Version of the system - if relevant | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: biomarker-category | |
| 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] |
ΣC | 1..1 | CodeableConcept | cell receptor | antigen | protein | immune stain Binding: Molecular Biomarker Categories (example) |
| Documentation for this format | ||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.status | Base | required | Observation Status | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:mbCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.code | Base | example | Molecular Biomarker Codes | 📦4.0.0-ballot | This IG |
| Observation.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-ballot | This IG |
| Observation.component:biomarker-category.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:biomarker-category.value[x] | Base | example | Molecular Biomarker Categories | 📦4.0.0-ballot | This IG |
| Id | Grade | Path(s) | Description | Expression |
| 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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())
|
| obs-6 | error | Observation | Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). |
value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
|
| obs-8 | error | Observation | bodyStructure SHALL only be present if Observation.bodySite is not present |
bodySite.exists() implies bodyStructure.empty()
|
| obs-10 | error | Observation | Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present |
component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
|
| obs-11 | error | Observation | if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present |
(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())
|
This structure is derived from Observation
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| Observation |
0..* | Observation | Measurements and simple assertions | |
| Slices for category |
2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding | |
| category:labCategory |
1..1 | CodeableConcept | Classification of type of observation | |
| coding |
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:mbCategory |
1..1 | CodeableConcept | Classification of type of observation | |
| coding |
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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: biomarker-category | |
| category:geCategory |
0..1 | CodeableConcept | Classification of type of observation | |
| coding |
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 |
1..1 | CodeableConcept | Code for the biomarker Binding: Molecular Biomarker Codes (example) | |
| Slices for derivedFrom |
0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() | |
| derivedFrom:variant |
0..* | Reference(Variant) | Variant the biomarker is derived from | |
| derivedFrom:genotype |
0..* | Reference(Genotype) | Genotype the biomarker is derived from | |
| derivedFrom:haplotype |
0..* | Reference(Haplotype) | Haplotype the biomarker is derived from | |
| Slices for component |
0..* | BackboneElement | Component results Slice: Unordered, Open by value:code | |
| component:gene-studied |
0..* | BackboneElement | Gene Studied | |
| code |
1..1 | CodeableConcept | 48018-6 Required Pattern: At least the following | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |
| value[x] |
1..1 | CodeableConcept | 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:biomarker-category |
0..* | BackboneElement | Biomarker Category | |
| code |
1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: biomarker-category | |
| value[x] |
1..1 | CodeableConcept | cell receptor | antigen | protein | immune stain Binding: Molecular Biomarker Categories (example) | |
| Documentation for this format | ||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.code | Base | example | Molecular Biomarker Codes | 📦4.0.0-ballot | This IG |
| Observation.component:gene-studied.value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-ballot | This IG |
| Observation.component:biomarker-category.value[x] | Base | example | Molecular Biomarker Categories | 📦4.0.0-ballot | This IG |
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| Observation |
C | 0..* | Observation | Measurements and simple assertions Constraints: obs-6, obs-7, obs-8, obs-10, obs-11 | ||||
| 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: AllLanguages (required): IETF language tag for a human language
| |||||
| text |
0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
 extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
Σ | 0..* | Identifier | Business Identifier for observation | ||||
| instantiates[x] |
Σ | 0..1 | canonical(ObservationDefinition), Reference(ObservationDefinition) | Instantiates FHIR ObservationDefinition | ||||
| basedOn |
Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| triggeredBy |
0..* | BackboneElement | Triggering observation(s) | |||||
| 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 | ||||
| observation |
Σ | 1..1 | Reference(Observation) | Triggering observation | ||||
| type |
Σ | 1..1 | code | reflex | repeat | re-run Binding: TriggeredBytype (required): The type of TriggeredBy Observation. | ||||
| reason |
0..1 | string | Reason that the observation was triggered | |||||
| partOf |
Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | GenomicStudy) | Part of referenced event | ||||
| status |
?!Σ | 1..1 | code | registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained 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 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
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 |
0..1 | string | Plain text representation of the concept | |||||
| category:mbCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id |
0..1 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
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://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: biomarker-category | |||||
| 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 | |||||
| category:geCategory |
0..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id |
0..1 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
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 |
0..1 | string | Plain text representation of the concept | |||||
| code |
ΣC | 1..1 | CodeableConcept | Code for the biomarker Binding: Molecular Biomarker Codes (example) | ||||
| subject |
Σ | 0..1 | Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct) | 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 | ||||
| organizer |
ΣC | 0..1 | boolean | This observation organizes/groups a set of sub-observations | ||||
| 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 | HealthcareService) | Who is responsible for the observation | ||||
| value[x] |
ΣC | 0..1 | Actual result | |||||
| valueQuantity |
Quantity | |||||||
| valueCodeableConcept |
CodeableConcept | |||||||
| valueString |
string | |||||||
| valueBoolean |
boolean | |||||||
| valueInteger |
integer | |||||||
| valueRange |
Range | |||||||
| valueRatio |
Ratio | |||||||
| valueSampledData |
SampledData | |||||||
| valueTime |
time | |||||||
| valueDateTime |
dateTime | |||||||
| valuePeriod |
Period | |||||||
| valueAttachment |
Attachment | |||||||
| valueReference |
Reference(MolecularSequence) | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note |
0..* | Annotation | Comments about the observation | |||||
| bodySite |
C | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts | ||||
| bodyStructure |
C | 0..1 | Reference(BodyStructure) | Observed body structure | ||||
| method |
0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen |
C | 0..1 | Reference(Specimen | Group) | Specimen used for this observation Constraints: obs-9 | ||||
| device |
0..1 | Reference(Device | DeviceMetric) | A reference to the device that generates the measurements or the device settings for the device | |||||
| referenceRange |
C | 0..* | BackboneElement | Provides guide for interpretation Constraints: obs-3 | ||||
| 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(6.0.0-ballot3) | Low Range, if relevant | ||||
| high |
C | 0..1 | SimpleQuantity(6.0.0-ballot3) | High Range, if relevant | ||||
| normalValue |
0..1 | CodeableConcept | Normal value, if relevant Binding: ObservationReferenceRangeNormalValueCodes (extensible): Codes identifying the normal value of the observation. | |||||
| 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 |
C | 0..1 | markdown | 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 | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() | ||||
| derivedFrom:variant |
Σ | 0..* | Reference(Variant) | Variant the biomarker is derived from | ||||
| derivedFrom:genotype |
Σ | 0..* | Reference(Genotype) | Genotype the biomarker is derived from | ||||
| derivedFrom:haplotype |
Σ | 0..* | Reference(Haplotype) | Haplotype the biomarker is derived from | ||||
| Slices for component |
ΣC | 0..* | BackboneElement | Component results Slice: Unordered, Open by value: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 |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] |
ΣC | 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 | |||||||
| valueAttachment |
Attachment | |||||||
| valueReference |
Reference(MolecularSequence) | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result value 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 value | |||||
| component:gene-studied |
ΣC | 0..* | 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 |
ΣC | 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] |
ΣC | 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 value 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 value | |||||
| component:biomarker-category |
ΣC | 0..* | BackboneElement | Biomarker Category | ||||
| 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 |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: biomarker-category | |||||
| 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] |
ΣC | 1..1 | CodeableConcept | cell receptor | antigen | protein | immune stain Binding: Molecular Biomarker Categories (example) | ||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result value 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 value | |||||
| Documentation for this format | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.language | Base | required | All Languages | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.triggeredBy.type | Base | required | triggered Bytype | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.status | Base | required | Observation Status | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:mbCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.code | Base | example | Molecular Biomarker Codes | 📦4.0.0-ballot | This IG |
| Observation.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.bodySite | Base | example | SNOMED CT Body Structures | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.method | Base | example | Observation Methods | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.normalValue | Base | extensible | Observation Reference Range Normal Value Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.type | Base | preferred | Observation Reference Range Meaning Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.appliesTo | Base | example | Observation Reference Range Applies To Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-ballot | This IG |
| Observation.component:gene-studied.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:biomarker-category.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:biomarker-category.value[x] | Base | example | Molecular Biomarker Categories | 📦4.0.0-ballot | This IG |
| Observation.component:biomarker-category.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:biomarker-category.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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())
|
| 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 | Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). |
value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
|
| obs-8 | error | Observation | bodyStructure SHALL only be present if Observation.bodySite is not present |
bodySite.exists() implies bodyStructure.empty()
|
| obs-9 | error | Observation.specimen | If Observation.specimen is a reference to Group, the group can only have specimens |
(reference.resolve().exists() and reference.resolve() is Group) implies reference.resolve().member.entity.resolve().all($this is Specimen)
|
| obs-10 | error | Observation | Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present |
component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
|
| obs-11 | error | Observation | if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present |
(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())
|
This structure is derived from Observation
Summary
Mandatory: 4 elements(3 nested mandatory elements)
Structures
This structure refers to these other structures:
Slices
This structure defines the following Slices:
Maturity: 2
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| Observation |
C | 0..* | Observation | Measurements and simple assertions Constraints: obs-6, obs-7, obs-8, obs-10, obs-11 |
| implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created |
| contained |
0..* | Resource | Contained, inline Resources | |
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored |
| status |
?!Σ | 1..1 | code | registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained 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 |
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 | |
| category:mbCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding |
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://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: biomarker-category | |
| display |
0..1 | string | Representation defined by the system | |
| userSelected |
0..1 | boolean | If this coding was chosen directly by the user | |
| category:geCategory |
0..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |
| coding |
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 | |
| code |
ΣC | 1..1 | CodeableConcept | Code for the biomarker Binding: Molecular Biomarker Codes (example) |
| focus |
?!Σ | 0..* | Reference(Resource) | What the observation is about, when it is not about the subject of record |
| value[x] |
ΣC | 0..1 | Actual result | |
| valueQuantity |
Quantity | |||
| valueCodeableConcept |
CodeableConcept | |||
| valueString |
string | |||
| valueBoolean |
boolean | |||
| valueInteger |
integer | |||
| valueRange |
Range | |||
| valueRatio |
Ratio | |||
| valueSampledData |
SampledData | |||
| valueTime |
time | |||
| valueDateTime |
dateTime | |||
| valuePeriod |
Period | |||
| valueAttachment |
Attachment | |||
| valueReference |
Reference(MolecularSequence) | |||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. |
| Slices for derivedFrom |
Σ | 0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() |
| derivedFrom:variant |
Σ | 0..* | Reference(Variant) | Variant the biomarker is derived from |
| derivedFrom:genotype |
Σ | 0..* | Reference(Genotype) | Genotype the biomarker is derived from |
| derivedFrom:haplotype |
Σ | 0..* | Reference(Haplotype) | Haplotype the biomarker is derived from |
| Slices for component |
ΣC | 0..* | BackboneElement | Component results Slice: Unordered, Open by value:code |
| component:All Slices |
Content/Rules for all slices | |||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. |
| component:gene-studied |
ΣC | 0..* | BackboneElement | Gene Studied |
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code |
ΣC | 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] |
ΣC | 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:biomarker-category |
ΣC | 0..* | BackboneElement | Biomarker Category |
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| code |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| id |
0..1 | string | Unique id for inter-element referencing | |
| extension |
0..* | Extension | Additional content defined by implementations | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| version |
0..1 | string | Version of the system - if relevant | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: biomarker-category | |
| 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] |
ΣC | 1..1 | CodeableConcept | cell receptor | antigen | protein | immune stain Binding: Molecular Biomarker Categories (example) |
| Documentation for this format | ||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.status | Base | required | Observation Status | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:mbCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.code | Base | example | Molecular Biomarker Codes | 📦4.0.0-ballot | This IG |
| Observation.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-ballot | This IG |
| Observation.component:biomarker-category.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:biomarker-category.value[x] | Base | example | Molecular Biomarker Categories | 📦4.0.0-ballot | This IG |
| Id | Grade | Path(s) | Description | Expression |
| 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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())
|
| obs-6 | error | Observation | Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). |
value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
|
| obs-8 | error | Observation | bodyStructure SHALL only be present if Observation.bodySite is not present |
bodySite.exists() implies bodyStructure.empty()
|
| obs-10 | error | Observation | Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present |
component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
|
| obs-11 | error | Observation | if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present |
(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())
|
Differential View
This structure is derived from Observation
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| Observation |
0..* | Observation | Measurements and simple assertions | |
| Slices for category |
2..* | CodeableConcept | Classification of type of observation Slice: Unordered, Open by value:coding | |
| category:labCategory |
1..1 | CodeableConcept | Classification of type of observation | |
| coding |
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:mbCategory |
1..1 | CodeableConcept | Classification of type of observation | |
| coding |
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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: biomarker-category | |
| category:geCategory |
0..1 | CodeableConcept | Classification of type of observation | |
| coding |
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 |
1..1 | CodeableConcept | Code for the biomarker Binding: Molecular Biomarker Codes (example) | |
| Slices for derivedFrom |
0..* | Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() | |
| derivedFrom:variant |
0..* | Reference(Variant) | Variant the biomarker is derived from | |
| derivedFrom:genotype |
0..* | Reference(Genotype) | Genotype the biomarker is derived from | |
| derivedFrom:haplotype |
0..* | Reference(Haplotype) | Haplotype the biomarker is derived from | |
| Slices for component |
0..* | BackboneElement | Component results Slice: Unordered, Open by value:code | |
| component:gene-studied |
0..* | BackboneElement | Gene Studied | |
| code |
1..1 | CodeableConcept | 48018-6 Required Pattern: At least the following | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://loinc.org | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: 48018-6 | |
| value[x] |
1..1 | CodeableConcept | 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:biomarker-category |
0..* | BackboneElement | Biomarker Category | |
| code |
1..1 | CodeableConcept | Type of component observation (code / type) Required Pattern: At least the following | |
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: biomarker-category | |
| value[x] |
1..1 | CodeableConcept | cell receptor | antigen | protein | immune stain Binding: Molecular Biomarker Categories (example) | |
| Documentation for this format | ||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.code | Base | example | Molecular Biomarker Codes | 📦4.0.0-ballot | This IG |
| Observation.component:gene-studied.value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-ballot | This IG |
| Observation.component:biomarker-category.value[x] | Base | example | Molecular Biomarker Categories | 📦4.0.0-ballot | This IG |
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| Observation |
C | 0..* | Observation | Measurements and simple assertions Constraints: obs-6, obs-7, obs-8, obs-10, obs-11 | ||||
| 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: AllLanguages (required): IETF language tag for a human language
| |||||
| text |
0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
Σ | 0..* | Identifier | Business Identifier for observation | ||||
| instantiates[x] |
Σ | 0..1 | canonical(ObservationDefinition), Reference(ObservationDefinition) | Instantiates FHIR ObservationDefinition | ||||
| basedOn |
Σ | 0..* | Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) | Fulfills plan, proposal or order | ||||
| triggeredBy |
0..* | BackboneElement | Triggering observation(s) | |||||
| 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 | ||||
| observation |
Σ | 1..1 | Reference(Observation) | Triggering observation | ||||
| type |
Σ | 1..1 | code | reflex | repeat | re-run Binding: TriggeredBytype (required): The type of TriggeredBy Observation. | ||||
| reason |
0..1 | string | Reason that the observation was triggered | |||||
| partOf |
Σ | 0..* | Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | GenomicStudy) | Part of referenced event | ||||
| status |
?!Σ | 1..1 | code | registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained 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 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
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 |
0..1 | string | Plain text representation of the concept | |||||
| category:mbCategory |
1..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id |
0..1 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
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://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: biomarker-category | |||||
| 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 | |||||
| category:geCategory |
0..1 | CodeableConcept | Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. | |||||
| id |
0..1 | id | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
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 |
0..1 | string | Plain text representation of the concept | |||||
| code |
ΣC | 1..1 | CodeableConcept | Code for the biomarker Binding: Molecular Biomarker Codes (example) | ||||
| subject |
Σ | 0..1 | Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct) | 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 | ||||
| organizer |
ΣC | 0..1 | boolean | This observation organizes/groups a set of sub-observations | ||||
| 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 | HealthcareService) | Who is responsible for the observation | ||||
| value[x] |
ΣC | 0..1 | Actual result | |||||
| valueQuantity |
Quantity | |||||||
| valueCodeableConcept |
CodeableConcept | |||||||
| valueString |
string | |||||||
| valueBoolean |
boolean | |||||||
| valueInteger |
integer | |||||||
| valueRange |
Range | |||||||
| valueRatio |
Ratio | |||||||
| valueSampledData |
SampledData | |||||||
| valueTime |
time | |||||||
| valueDateTime |
dateTime | |||||||
| valuePeriod |
Period | |||||||
| valueAttachment |
Attachment | |||||||
| valueReference |
Reference(MolecularSequence) | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing. | ||||
| interpretation |
0..* | CodeableConcept | High, low, normal, etc Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations. | |||||
| note |
0..* | Annotation | Comments about the observation | |||||
| bodySite |
C | 0..1 | CodeableConcept | Observed body part Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts | ||||
| bodyStructure |
C | 0..1 | Reference(BodyStructure) | Observed body structure | ||||
| method |
0..1 | CodeableConcept | How it was done Binding: ObservationMethods (example): Methods for simple observations. | |||||
| specimen |
C | 0..1 | Reference(Specimen | Group) | Specimen used for this observation Constraints: obs-9 | ||||
| device |
0..1 | Reference(Device | DeviceMetric) | A reference to the device that generates the measurements or the device settings for the device | |||||
| referenceRange |
C | 0..* | BackboneElement | Provides guide for interpretation Constraints: obs-3 | ||||
| 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(6.0.0-ballot3) | Low Range, if relevant | ||||
| high |
C | 0..1 | SimpleQuantity(6.0.0-ballot3) | High Range, if relevant | ||||
| normalValue |
0..1 | CodeableConcept | Normal value, if relevant Binding: ObservationReferenceRangeNormalValueCodes (extensible): Codes identifying the normal value of the observation. | |||||
| 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 |
C | 0..1 | markdown | 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 | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy) | Related resource from which the observation is made Slice: Unordered, Open by profile:resolve() | ||||
| derivedFrom:variant |
Σ | 0..* | Reference(Variant) | Variant the biomarker is derived from | ||||
| derivedFrom:genotype |
Σ | 0..* | Reference(Genotype) | Genotype the biomarker is derived from | ||||
| derivedFrom:haplotype |
Σ | 0..* | Reference(Haplotype) | Haplotype the biomarker is derived from | ||||
| Slices for component |
ΣC | 0..* | BackboneElement | Component results Slice: Unordered, Open by value: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 |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. | ||||
| value[x] |
ΣC | 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 | |||||||
| valueAttachment |
Attachment | |||||||
| valueReference |
Reference(MolecularSequence) | |||||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result value 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 value | |||||
| component:gene-studied |
ΣC | 0..* | 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 |
ΣC | 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] |
ΣC | 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 value 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 value | |||||
| component:biomarker-category |
ΣC | 0..* | BackboneElement | Biomarker Category | ||||
| 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 |
ΣC | 1..1 | CodeableConcept | Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| coding |
1..* | Coding | Code defined by a terminology system Fixed Value: (Complex) | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| system |
1..1 | uri | Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: biomarker-category | |||||
| 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] |
ΣC | 1..1 | CodeableConcept | cell receptor | antigen | protein | immune stain Binding: Molecular Biomarker Categories (example) | ||||
| dataAbsentReason |
C | 0..1 | CodeableConcept | Why the component result value 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 value | |||||
| Documentation for this format | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| Observation.language | Base | required | All Languages | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.triggeredBy.type | Base | required | triggered Bytype | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.status | Base | required | Observation Status | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:labCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:mbCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.category:geCategory | Base | preferred | Observation Category Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.code | Base | example | Molecular Biomarker Codes | 📦4.0.0-ballot | This IG |
| Observation.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.bodySite | Base | example | SNOMED CT Body Structures | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.method | Base | example | Observation Methods | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.normalValue | Base | extensible | Observation Reference Range Normal Value Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.type | Base | preferred | Observation Reference Range Meaning Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.referenceRange.appliesTo | Base | example | Observation Reference Range Applies To Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.value[x] | Base | extensible | HUGO Gene Nomenclature Committee Gene Names (HGNC) | 📦4.0.0-ballot | This IG |
| Observation.component:gene-studied.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:gene-studied.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:biomarker-category.code | Base | example | LOINC Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:biomarker-category.value[x] | Base | example | Molecular Biomarker Categories | 📦4.0.0-ballot | This IG |
| Observation.component:biomarker-category.dataAbsentReason | Base | extensible | Data Absent Reason | 📍6.0.0-ballot3 | FHIR Std. |
| Observation.component:biomarker-category.interpretation | Base | extensible | Observation Interpretation Codes | 📍6.0.0-ballot3 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| 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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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())
|
| 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 | Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present |
dataAbsentReason.empty() or value.empty()
|
| obs-7 | error | Observation | If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value). |
value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
|
| obs-8 | error | Observation | bodyStructure SHALL only be present if Observation.bodySite is not present |
bodySite.exists() implies bodyStructure.empty()
|
| obs-9 | error | Observation.specimen | If Observation.specimen is a reference to Group, the group can only have specimens |
(reference.resolve().exists() and reference.resolve() is Group) implies reference.resolve().member.entity.resolve().all($this is Specimen)
|
| obs-10 | error | Observation | Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present |
component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
|
| obs-11 | error | Observation | if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present |
(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())
|
This structure is derived from Observation
Summary
Mandatory: 4 elements(3 nested mandatory elements)
Structures
This structure refers to these other structures:
Slices
This structure defines the following Slices:
Maturity: 2
Other representations of profile: CSV, Excel, Schematron
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-ballot based on FHIR 6.0.0-ballot3. Generated 2025-10-16
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