Genomics Reporting Implementation Guide
3.0.0 - release International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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

Resource Profile: Molecular Biomarker

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker Version: 3.0.0
Active as of 2024-11-19 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.

Contents:

Scope and Usage

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).

Biomarker Ontology

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.

Molecular Biomarker Ontology with examples

Biomarker Categories

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

Other Guidance

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.

Usage:

Formal Views of Profile Content

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

This structure is derived from Observation

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation Observation
... 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 | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
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
.... 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)

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Observation.codeexampleMolecularBiomarkerCodeVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-code-vs
from this IG
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:biomarker-category.value[x]exampleMolecularBiomarkerCategoryVS (a valid code from Molecular Biomarker Ontology Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs
from this IG
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* Observation Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... 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.

.... 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:mbCategory 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://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
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 Code for the biomarker
Binding: Molecular Biomarker Codes (example)
... 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 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 Σ 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 Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... 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:biomarker-category Σ 0..* BackboneElement Biomarker Category
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://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] Σ 1..1 CodeableConcept cell receptor | antigen | protein | immune stain
Binding: Molecular Biomarker Categories (example)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:mbCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexampleMolecularBiomarkerCodeVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-code-vs
from this IG
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.codeexamplePattern: LOINC Code 48018-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:biomarker-category.codeexamplePattern: biomarker-category
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:biomarker-category.value[x]exampleMolecularBiomarkerCategoryVS (a valid code from Molecular Biomarker Ontology Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs
from this IG

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* Observation Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
... contained 0..* Resource Contained, inline Resources
... extension 0..* Extension Additional content defined by implementations
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business Identifier for observation
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) Part of referenced event
... status ?!Σ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... 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:mbCategory 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://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 Σ 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 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 Code for the biomarker
Binding: Molecular Biomarker Codes (example)
... 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 0..1 Actual result
.... valueQuantity Quantity
.... valueCodeableConcept CodeableConcept
.... valueString string
.... valueBoolean boolean
.... valueInteger integer
.... valueRange Range
.... valueRatio Ratio
.... valueSampledData SampledData
.... valueTime time
.... valueDateTime dateTime
.... valuePeriod Period
... dataAbsentReason C 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note 0..* Annotation Comments about the observation
... bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method 0..1 CodeableConcept How it was done
Binding: ObservationMethods (example): Methods for simple observations.

... specimen 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
obs-3: Must have at least a low or a high or text
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... low C 0..1 SimpleQuantity Low Range, if relevant
.... high C 0..1 SimpleQuantity High Range, if relevant
.... type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1 Range Applicable age range, if relevant
.... text 0..1 string Text based reference range in an observation
... hasMember Σ 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group
... Slices 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 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 Σ 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 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:gene-studied Σ 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 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:biomarker-category Σ 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 Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-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] Σ 1..1 CodeableConcept cell receptor | antigen | protein | immune stain
Binding: Molecular Biomarker Categories (example)
..... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:mbCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexampleMolecularBiomarkerCodeVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-code-vs
from this IG
Observation.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
from the FHIR Standard
Observation.methodexampleObservationMethods
http://hl7.org/fhir/ValueSet/observation-methods
from the FHIR Standard
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
http://hl7.org/fhir/ValueSet/referencerange-meaning
from the FHIR Standard
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
http://hl7.org/fhir/ValueSet/referencerange-appliesto
from the FHIR Standard
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:gene-studied.codeexamplePattern: LOINC Code 48018-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:gene-studied.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:gene-studied.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:biomarker-category.codeexamplePattern: biomarker-category
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:biomarker-category.value[x]exampleMolecularBiomarkerCategoryVS (a valid code from Molecular Biomarker Ontology Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs
from this IG
Observation.component:biomarker-category.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:biomarker-category.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-3errorObservation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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 Observation

Summary

Mandatory: 4 elements(3 nested mandatory elements)

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of Observation.category
  • The element 1 is sliced based on the value of Observation.derivedFrom
  • The element 1 is sliced based on the value of Observation.component

Differential View

This structure is derived from Observation

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation Observation
... 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 | Media | QuestionnaireResponse | Observation | MolecularSequence) Related measurements the observation is made from
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
.... 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)

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Observation.codeexampleMolecularBiomarkerCodeVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-code-vs
from this IG
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:biomarker-category.value[x]exampleMolecularBiomarkerCategoryVS (a valid code from Molecular Biomarker Ontology Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs
from this IG

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* Observation Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... 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.

.... 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:mbCategory 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://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
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 Code for the biomarker
Binding: Molecular Biomarker Codes (example)
... 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 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 Σ 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 Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... 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:biomarker-category Σ 0..* BackboneElement Biomarker Category
..... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
..... code Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://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] Σ 1..1 CodeableConcept cell receptor | antigen | protein | immune stain
Binding: Molecular Biomarker Categories (example)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:mbCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexampleMolecularBiomarkerCodeVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-code-vs
from this IG
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.codeexamplePattern: LOINC Code 48018-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:biomarker-category.codeexamplePattern: biomarker-category
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:biomarker-category.value[x]exampleMolecularBiomarkerCategoryVS (a valid code from Molecular Biomarker Ontology Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs
from this IG

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C 0..* Observation Measurements and simple assertions
obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present
obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... language 0..1 code Language of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguages Max Binding
... text 0..1 Narrative Text summary of the resource, for human interpretation
... contained 0..* Resource Contained, inline Resources
... extension 0..* Extension Additional content defined by implementations
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Business Identifier for observation
... basedOn Σ 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest) Fulfills plan, proposal or order
... partOf Σ 0..* Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy) Part of referenced event
... status ?!Σ 1..1 code registered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... 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:mbCategory 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://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 Σ 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 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 Code for the biomarker
Binding: Molecular Biomarker Codes (example)
... 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 0..1 Actual result
.... valueQuantity Quantity
.... valueCodeableConcept CodeableConcept
.... valueString string
.... valueBoolean boolean
.... valueInteger integer
.... valueRange Range
.... valueRatio Ratio
.... valueSampledData SampledData
.... valueTime time
.... valueDateTime dateTime
.... valuePeriod Period
... dataAbsentReason C 0..1 CodeableConcept Why the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation 0..* CodeableConcept High, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note 0..* Annotation Comments about the observation
... bodySite 0..1 CodeableConcept Observed body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method 0..1 CodeableConcept How it was done
Binding: ObservationMethods (example): Methods for simple observations.

... specimen 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
obs-3: Must have at least a low or a high or text
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... low C 0..1 SimpleQuantity Low Range, if relevant
.... high C 0..1 SimpleQuantity High Range, if relevant
.... type 0..1 CodeableConcept Reference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..* CodeableConcept Reference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1 Range Applicable age range, if relevant
.... text 0..1 string Text based reference range in an observation
... hasMember Σ 0..* Reference(Observation | QuestionnaireResponse | MolecularSequence) Related resource that belongs to the Observation group
... Slices 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 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 Σ 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 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:gene-studied Σ 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 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:biomarker-category Σ 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 Σ 1..1 CodeableConcept Type of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
....... id 0..1 string Unique id for inter-element referencing
....... extension 0..* Extension Additional content defined by implementations
....... system 1..1 uri Identity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-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] Σ 1..1 CodeableConcept cell receptor | antigen | protein | immune stain
Binding: Molecular Biomarker Categories (example)
..... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Observation.statusrequiredObservationStatus
http://hl7.org/fhir/ValueSet/observation-status|4.0.1
from the FHIR Standard
Observation.categorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:labCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:mbCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.category:geCategorypreferredObservationCategoryCodes
http://hl7.org/fhir/ValueSet/observation-category
from the FHIR Standard
Observation.codeexampleMolecularBiomarkerCodeVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-code-vs
from this IG
Observation.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
from the FHIR Standard
Observation.methodexampleObservationMethods
http://hl7.org/fhir/ValueSet/observation-methods
from the FHIR Standard
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
http://hl7.org/fhir/ValueSet/referencerange-meaning
from the FHIR Standard
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
http://hl7.org/fhir/ValueSet/referencerange-appliesto
from the FHIR Standard
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:gene-studied.codeexamplePattern: LOINC Code 48018-6
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:gene-studied.value[x]extensibleHGNCVS
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/hgnc-vs
from this IG
Observation.component:gene-studied.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:gene-studied.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard
Observation.component:biomarker-category.codeexamplePattern: biomarker-category
http://hl7.org/fhir/ValueSet/observation-codes
from the FHIR Standard
Observation.component:biomarker-category.value[x]exampleMolecularBiomarkerCategoryVS (a valid code from Molecular Biomarker Ontology Codes)
http://hl7.org/fhir/uv/genomics-reporting/ValueSet/molecular-biomarker-category-vs
from this IG
Observation.component:biomarker-category.dataAbsentReasonextensibleDataAbsentReason
http://hl7.org/fhir/ValueSet/data-absent-reason
from the FHIR Standard
Observation.component:biomarker-category.interpretationextensibleObservationInterpretationCodes
http://hl7.org/fhir/ValueSet/observation-interpretation
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorObservationIf 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-4errorObservationIf 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-5errorObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceObservationA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
obs-3errorObservation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
obs-6errorObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
obs-7errorObservationIf 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 Observation

Summary

Mandatory: 4 elements(3 nested mandatory elements)

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of Observation.category
  • The element 1 is sliced based on the value of Observation.derivedFrom
  • The element 1 is sliced based on the value of Observation.component

 

Other representations of profile: CSV, Excel, Schematron