Name Flags Card. Type Description & Constraints doco
. . Observation 0 .. * Genomics Base Observation
. . . bodySite 0..1 Reference(BodyStructure) Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
. . . observation-secondaryFinding 0..1 CodeableConcept Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible)
. . . basedOn 0..* Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)
. . . status 1 .. 1 code
. . . category 1..* CodeableConcept Required Pattern: At least the following
. . . . coding 1..* Coding Code defined by a terminology system
Fixed Value: (complex)
. . . . . system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
. . . . . code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
. . . code 1..1 CodeableConcept
. . . subject 0..1 Reference(Patient | Group | Location)
. . . effectiveDateTime 0 .. 1 dateTime Clinically relevant time/time-period for observation
. . . issued 0 .. 1 instant Date/Time this version was made available
. . . performer 0..1 Reference(Practitioner | Organization | Patient | RelatedPerson) Who is responsible for the observation
. . . interpretation 0 .. 0
. . . component 0..* BackboneElement
. . . . interpretation 0 .. 0

doco Documentation for this format
<status value="draft" /> <experimental value="false" /> <date value="2017-05-20T00:00:00-04:00" /> <publisher value="HL7 Clinical Genomics WG" /> <description value="Observation-related profiles" /> <fhirVersion value="4.0.1" /> <mapping> <identity value="workflow" /> <uri value="http://hl7.org/fhir/workflow" /> <name value="Workflow Pattern" /> </mapping> <mapping> <identity value="sct-concept" /> <uri value="http://snomed.info/conceptdomain" /> <name value="SNOMED CT Concept Domain Binding" /> </mapping> <mapping> <identity value="v2" /> <uri value="http://hl7.org/v2" /> <name value="HL7 v2 Mapping" /> </mapping> <mapping> <identity value="rim" /> <uri value="http://hl7.org/v3" /> <name value="RIM Mapping" /> </mapping> <mapping> <identity value="w5" /> <uri value="http://hl7.org/fhir/fivews" /> <name value="FiveWs Pattern Mapping" /> </mapping> <mapping> <identity value="sct-attr" /> <uri value="http://snomed.org/attributebinding" /> <name value="SNOMED CT Attribute Binding" /> </mapping> <kind value="resource" /> <abstract value="false" /> <type value="Observation" /> <baseDefinition value="http://hl7.org/fhir/StructureDefinition/Observation" /> <derivation value="constraint" /> <differential> <element id="Observation"> <path value="Observation" /> <short value="Genomics Base Observation" /> <definition value="Base profile that defines characteristics shared by all genetic observations." /> <mustSupport value="false" /> </element> <element id="Observation.meta"> <path value="Observation.meta" /> </element> <element id="Observation.meta.profile"> <path value="Observation.meta.profile" /> <type> <code value="canonical" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/StructureDefinition" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Variant" /> </type> </element> <element id="Observation.extension"> <path value="Observation.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <rules value="open" /> </slicing> </element> <element id="Observation.extension:BodyStructure"> <path value="Observation.extension" /> <sliceName value="BodyStructure" /> <definition value="Allows associating observations to a particular portion of the patient - a fetus, a tumor, a lesion, etc." /> <type> <code value="Extension" /> <profile value="http://hl7.org/fhir/StructureDefinition/bodySite" /> </type> <mustSupport value="false" /> </element> <element id="Observation.extension:SecondaryFinding"> <path value="Observation.extension" /> <sliceName value="SecondaryFinding" /> <definition value="Allows flagging observations that should be considered secondary findings." /> <type> <code value="Extension" /> <profile value="http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding" /> </type> <mustSupport value="false" /> </element> <element id="Observation.basedOn"> <path value="Observation.basedOn" /> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/CarePlan" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/DeviceRequest" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/ImmunizationRecommendation" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/MedicationRequest" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/NutritionOrder" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/ServiceRequest" /> </type> <mustSupport value="false" /> </element> <element id="Observation.status"> <path value="Observation.status" /> <comment value="… This should generally be 'completed' or 'revised'." /> <mustSupport value="false" /> </element> <element id="Observation.category"> <path value="Observation.category" /> <comment value="… This should be populated with 'lab'." /> <min value="1" /> <patternCodeableConcept> <coding> <system value="http://terminology.hl7.org/CodeSystem/observation-category" /> <code value="laboratory" /> <display value="Laboratory" /> </coding> </patternCodeableConcept> <mustSupport value="false" /> </element> <element id="Observation.code"> <path value="Observation.code" /> <mustSupport value="false" /> </element> <element id="Observation.code.coding"> <path value="Observation.code.coding" /> <fixedCoding> <system value="http://loinc.org" /> <code value="69548-6" /> <display value="Genetic variant assessment" /> </fixedCoding> </element> <element id="Observation.code.coding.system"> <path value="Observation.code.coding.system" /> <code> <system value="http://loinc.org" /> <code value="69548-6" /> <display value="Genetic variant assessment" /> </code> </element> <element id="Observation.subject"> <path value="Observation.subject" /> <comment value="… This must be the same patient as on the DiagnosticReport unless combining data from multiple fetuses or family members in a single report." /> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Patient" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Group" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Location" /> </type> <mustSupport value="false" /> </element> <element id="Observation.effective[x]"> <path value="Observation.effective[x]" /> <slicing> <discriminator> <type value="type" /> <path value="$this" /> </discriminator> </slicing> </element> <element id="Observation.effective[x]:effectiveDateTime"> <path value="Observation.effective[x]" /> <sliceName value="effectiveDateTime" /> <type> <code value="dateTime" /> </type> <mustSupport value="false" /> </element> <element id="Observation.issued"> <path value="Observation.issued" /> <mustSupport value="false" /> </element> <element id="Observation.performer"> <path value="Observation.performer" /> <max value="1" /> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Practitioner" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Organization" /> </type> <mustSupport value="false" /> </element> <element id="Observation.interpretation"> <path value="Observation.interpretation" /> <max value="0" /> <mustSupport value="false" /> </element> <element id="Observation.note.author[x]"> <path value="Observation.note.author[x]" /> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Practitioner" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Patient" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/RelatedPerson" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Organization" /> </type> <type> <code value="string" /> </type> </element> <element id="Observation.specimen"> <path value="Observation.specimen" /> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Specimen" /> </type> </element> <element id="Observation.component"> <path value="Observation.component" /> <label value="variants reference assembly if applicable" /> <mustSupport value="false" /> </element> <element id="Observation.component.code.coding"> <path value="Observation.component.code.coding" /> <code> <system value="http://loinc.org" /> <code value="62374-4" /> <display value="Human reference sequence assembly version" /> </code> <code> <system value="http://loinc.org" /> <code value="48000-4" /> <display value="Chromosome [ID]" /> </code> <code> <system value="http://loinc.org" /> <code value="48013-7" /> <display value="Genomic reference sequence [ID]" /> </code> <code> <system value="http://loinc.org" /> <code value="69547-8" /> <display value="Genomic reference allele [ID]" /> </code> <code> <system value="http://loinc.org" /> <code value="69551-0" /> <display value="Genomic alt allele [ID]" /> </code> <code> <system value="http://loinc.org" /> <code value="92882-6" /> <display value="Genomic coordinate system [Type]" /> </code> <code> <system value="http://loinc.org" /> <code value="81254-5" /> <display value="Genomic allele start-end" /> </code> <code> <system value="http://loinc.org" /> <code value="48002-0" /> <display value="Genomic source class [Type]" /> </code> <code> <system value="http://loinc.org" /> <code value="53034-5" /> <display value="Allelic state" /> </code> <code> <system value="http://loinc.org" /> <code value="48018-6" /> <display value="Gene studied [ID]" /> </code> <code> <system value="http://loinc.org" /> <code value="81290-9" /> <display value="Genomic DNA change (gHGVS)" /> </code> <code> <system value="http://loinc.org" /> <code value="51958-7" /> <display value="Transcript reference sequence [ID]" /> </code> <code> <system value="http://loinc.org" /> <code value="48004-6" /> <display value="DNA change (c.DNA)" /> </code> <code> <system value="http://loinc.org" /> <code value="48019-4" /> <display value="DNA change type" /> </code> <code> <system value="http://loinc.org" /> <code value="81255-2" /> <display value="dbSNP [ID]" /> </code> <code> <system value="http://loinc.org" /> <code value="79742-3" /> <display value="Inheritance pattern based on family history" /> </code> <code> <system value="http://loinc.org" /> <code value="48005-3" /> <display value="Amino acid change (pHGVS)" /> </code> <code> <system value="http://loinc.org" /> <code value="48006-1" /> <display value="Amino acid chnage [Type]" /> </code> <min value="1" /> </element> <element id="Observation.component.interpretation"> <path value="Observation.component.interpretation" /> <max value="0" /> <mustSupport value="false" /> </element> </differential> </StructureDefinition>