StructureDefinition UKCore-Observation

Used to represent the bulk of clinical information to be sent alongside a Genomic Test Order, as well as clinical results included within structured Diagnostic Reports.

Observations within Genomics are used to represent a point-in-time observation made about a patient or specimen. This means Observations SHOULD NOT be updated post-submission unless the original Observation has been entered in error or incorrectly coded (in this case, the appropriate status SHALL be used, e.g. entered-in-error or corrected).

For new observations which invalidate previous observations made about a patient, a new Observation resource SHOULD be created, the new observation MAY reference the invalidated observation via the observation-replaces extension.

Profile url FHIR Module Normative Status
https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation UKCore trial-use

idΣ0..1string
metaΣ0..1Meta
implicitRulesΣ ?!0..1uri
language0..1codeBinding
text0..1Narrative
contained0..*Resource
extensionC0..*Extension
modifierExtension?! C0..*Extension
identifierΣ0..*Identifier
basedOnΣ C0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)
partOfΣ C0..*Reference(ImagingStudy | Immunization | MedicationAdministration | MedicationDispense | MedicationStatement | Procedure)
statusS Σ ?!1..1codeBinding
categoryS0..*CodeableConceptBinding
codeS Σ1..1CodeableConceptBinding
subjectS Σ C0..1Reference(Device | Group | Location | Patient)
focusΣ C0..*Reference(Resource)
encounterΣ C0..1Reference(Encounter)
effectiveDateTimedateTime
effectiveInstantinstant
effectivePeriodPeriod
effectiveTimingTiming
issuedΣ0..1instant
performerS Σ C0..*Reference(CareTeam | Organization | Patient | Practitioner | PractitionerRole | RelatedPerson)
valueBooleanboolean
valueCodeableConceptCodeableConcept
valueDateTimedateTime
valueIntegerinteger
valuePeriodPeriod
valueQuantityQuantity
valueRangeRange
valueRatioRatio
valueSampledDataSampledData
valueStringstring
valueTimetime
dataAbsentReasonC0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
note0..*Annotation
bodySite0..1CodeableConceptBinding
method0..1CodeableConceptBinding
specimenC0..1Reference(Specimen)
deviceC0..1Reference(Device | DeviceMetric)
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
lowC0..1SimpleQuantity
highC0..1SimpleQuantity
type0..1CodeableConceptBinding
appliesTo0..*CodeableConcept
ageC0..1Range
text0..1string
hasMemberΣ C0..*Reference(MolecularSequence | Observation | QuestionnaireResponse)
derivedFromΣ C0..*Reference(DocumentReference | ImagingStudy | Media | MolecularSequence | Observation | QuestionnaireResponse)
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
codeΣ1..1CodeableConceptBinding
valueBooleanboolean
valueCodeableConceptCodeableConcept
valueDateTimedateTime
valueIntegerinteger
valuePeriodPeriod
valueQuantityQuantity
valueRangeRange
valueRatioRatio
valueSampledDataSampledData
valueStringstring
valueTimetime
dataAbsentReasonC0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
referenceRange0..*see (referenceRange)


Observation-AutisticBehaviour-Example
Observation-BlastPercentage-Example
Observation-Bruising-Example
Observation-Cellularity-Example
Observation-CellularityKayBurbridge-Example
Observation-DelayedSpeechLanguageDevt-Example
Observation-DiseasePenetrance-Example
Observation-DiseasePenetrancePheobeSmitham-Example
Observation-DutchLipidScore-Example
Observation-EnlargedKidney-Example
Observation-Haemoglobin-Example
Observation-HepaticCysts-Example
Observation-Immunodefficiency-Example
Observation-IntellectualDisabilityMild-Example
Observation-IntellectualDisabilityProfound-Example
Observation-NatureAndAgeOfHearingLoss-Example
Observation-Necrosis-Example
Observation-NecrosisKayBurbridge-Example
Observation-NeoplasticCell-Example
Observation-NeoplasticCellKayBurbridge-Example
Observation-Neutrophils-Example
Observation-GenomicEthnicity-Example
Observation-MultipleRenalCysts-Example
Observation-Nephronophthisis-Example
Observation-NoBoneMarrowTransplantProbandFather-Example
Observation-NoBoneMarrowTransplantProbandMother-Example
Observation-NoFirstTrimesterFetalAnomalies-Example
Observation-NoPregnancy-Example
Observation-NoSecondTrimesterFetalAnomalies-Example
Observation-NoTransfusion-Example
Observation-NoTransfusionProbandFather-Example
Observation-NoTransfusionProbandMother-Example
Observation-NoTransplant-Example
Observation-NonConsanguinousUnion-Example
Observation-NonConsanguinousUnionProband-Example
Observation-NonConsanguinousUnionProbandFather-Example
Observation-NonConsanguinousUnionProbandMother-Example
Observation-NucleatedCellCount-Example
Observation-Platelets-Example
Observation-PregnancyConfirmation-Example
Observation-QueryXanthoma-Example
Observation-RenalInsufficiency-Example
Observation-SimonBroomeCriteria-Example
Observation-TumourType-Example
Observation-TumourTypeKayBurbridge-Example
Observation-UnknownConsanguinousUnionStatus-Example
Observation-WhiteBloodCell-Example
Observation-SampleCellContent-Example
Observation-HistoryOfFetalLoss-Example
Observation-GenomicsVariantSLC52A2-Example

FHIRMDSHL7v2
ObservationRaw specimen/biopsy - Additional specimen/biopsy information, Extracted specimen - Additional specimen information, Further clinical informationOBX segments (may be attached to SPM)
Observation.codePatient - Sexual orientation, Patient - Karyotypic sex, Patient - Pregnancy status, Patient - Fetal karyotypic sex, Patient - Is from consanguinous union, Fetus - Karyotypic sex, Fetus - Is testing for fetal loss from 24 weeks of gestation, PLCM activity - DNA concentration, PLCM activity - DNA quantification, PLCM activity - Test outcome code (Many), Raw specimen/biopsy - Taken alive/post mortem, Diabetic complications, Has absent reflexesOBX-5 with appropriate SNOMED/READ/LOINC code
Observation.componentPatient - Pregnancy gestation period, Patient - Fetal gestation, Patient - Estimated Delivery Date (EDD), Patient - Pregnancy type, Absent reflexes detailOBX-14 (compared with other ORC segments), OBR segments with appropriate codes
Observation.value\[x\]Patient - Height (m), Raw specimen/biopsy - Skin/Bone affected status, Raw specimen/biopsy - Blasts %, Raw specimen/biopsy - Neoplastic cell content (%), Raw specimen/biopsy - Necrosis, Raw specimen/biopsy - Nucleated cell count, Raw specimen/biopsy - Tumour cellularity, Raw specimen/biopsy - Maternal cell contamination (MCC), Previous non genomic report - Test result value comparator, Previous non genomic report - Test result value unit of measure, Genomic ethnicity, ISTH BAT score, MODY probability calculator score, Patient BMI at time of genomic test request, Patient BMI at time of diagnosis, Maternal BMI at time of request, Paternal BMI at time of request, Birth weightOBX-5/6
Observation.referenceRange.lowPrevious non genomic report - Test result reference range lowOBX-7 (before operator)
Observation.referenceRange.highPrevious non genomic report - Test result reference range highOBX-7 (after operator)
Observation.methodPrevious non genomic report - Test result test methodOBX-17
Observation.referenceRange.textPrevious non genomic report - Test result reference range textOBX-7
Observation.interpretationPrevious non genomic report - Test result clinical summaryOBX-8
Observation.bodySiteSubcutaneous fat loss areas, Increased fat deposition areasOBX-5

Additional Guidance

extension:observation-replaces

A core extension on the base HL7 International Observation resource. Used to link to previous Observation resources which have been invalidated by this Observation instance, e.g. for cases where a previously present HPO term is now no longer applicable. For new observations which invalidate previous observations made about a patient, the new Observation resource SHOULD be created, and MAY reference the invalidated observation via the observation-replaces extension.

{
      "url": "http://hl7.org/fhir/StructureDefinition/observation-replaces",
      "valueReference": {
        "reference": "Observation/Observation-IntellectualDisabilityMild-Example"
      }
    }

partOf

To record the device/software that generated an observation. Our recommendation is that this element SHOULD reference the Genomic Study Procedure profile and its extension:genomic-study-analysis SHOULD reference the Procedure resource for the Genomic Study Analysis

"partOf": [
   {
    "reference": "Procedure/Procedure-GenomicStudy-Example"
   }
  ]
    

status

SHOULD be marked as final for most observations unless corrected after submission. Observations within Genomics are used to represent a point-in-time observation made about a patient or specimen. This means Observations should not be updated post-submission unless the original Observation has been entered in error or incorrectly coded (in this case, the appropriate status SHALL be used, e.g. entered-in-error or corrected, respectively).

"status": "final",

code

SHALL be present. SNOMED CT coding is preferred, though it is expected that alternative codings will be used depending on the appropriateness for a particular observation e.g. HPO or other codings found within the HL7 International Genomic Reporting IG as their use may already be widespread within Genomics. If a SNOMED CT equivalent exists for a code regularly captured within another CodeSystem, additional 'coding' elements within 'code' SHOULD be provided to aid analytics.

For 'PCI-6 - Phenotypic details', HPO terms SHALL be used, using codes from the Human Phenotype Ontology.

When recording HPO codes, the Observation.code.coding.system SHALL be fixed to http://human-phenotype-ontology.org

"code": {
        "coding":  [
            {
                "system": "http://human-phenotype-ontology.org",
                "code": "HP:0000105",
                "display": "Enlarged kidney"
            }
        ]
    },

subject

SHALL be present. Reference to the associated Patient. This MAY be through a resource reference if the ID on the central service is known (or provided within the transaction bundle) or through NHS number where this is known and has been traced through PDS
"subject": {
        "reference": "Patient/Patient-MeirLieberman-Example",
        "identifier": {
            "system": "https://fhir.nhs.uk/Id/nhs-number",
            "value": "9449307873"
        }
    },

focus

For recording the what the observation relates to, e.g. Specimen or Condition, when the observation relevant to the focal resource rather than the patient themselves e.g. Sample nucleated cell count.

Note: Tumour type and cellularity observations relate to the collected sample rather than the primary condition being tested for, which means these observations should reference the Specimen resource instead of a Condition

"focus": {
        "reference": "Specimen/Specimen-BloodEDTA-Example"
    },

effectiveDateTime

It is expected that all Observations SHOULD include the effective time the observation was made, if known, to aid interpretation.
"effectiveDateTime": "2022-07-11T09:00:00Z",

value[x]

The value element SHOULD use the most appropriate data type for the observation in question. Using preferred CodeSystems as specified within HL7 International FHIR R4 or the UK Core. For asserting absence of a particular condition/situation, the finding SHOULD be specified within the 'code' element and 'valueBoolean' set to 'false' or 'valueCodeableConcept' set to an appropriate qualifier value code from SNOMED CT.

HPO terms are recorded as being either Absent or Present, this is represented within FHIR by the HPO term being recorded in Observation.code.coding.code, with the Absent/Present status being recorded as Observation.valueBoolean set as false or true respectively.

For an assertion of a particular situation being present, e.g. a Condition or Procedure having been performed, these SHOULD be collected within the relevant clinical resources, alongside additional information needed to inform interpretation.

"valueQuantity": {
        "value": 6.5,
        "system": "http://unitsofmeasure.org",
        "code": "10*12/L"
    }

component

SHOULD be used to group qualifiers of an observation. In particular, details regarding observations related to a pregnancy SHOULD be added as components on a pregnancy status observation.

Examples of how pregnancy information can be captured within Observations (pregnancy status with EDD, gestation etc. recorded as components) will be added to the Fetus Management Clinical Scenario.

"component": [
		{
			"code": {
				"coding": [
					{
						"system": "http://snomed.info/sct",
						"code": "720451000000102",
						"display": "Assisted conception"
					}
				]
			}
		},
		{
			"code": {
				"coding": [
					{
						"system": "http://snomed.info/sct",
						"code": "226081000000107",
						"display": "Gestational age"
					}
				]
			},
			"valueQuantity": {
				"value": 87,
				"unit": "day",
				"system": "http://unitsofmeasure.org",
				"code": "d"
			}
		},
		{
			"code": {
				"coding": [
					{
						"system": "http://snomed.info/sct",
						"code": "161714006",
						"display": "Estimated date of delivery"
					}
				]
			},
			"valueDateTime": "2024-05-01"
		}
	],