<status value="draft" /> <description value="The core resource of the Genomic study which holds the genomic study and related profiles together. . Its the main procedure resource to represent a Genomic case. The genomic case includes both laboratory process(es) aswell as the data analysis which are both referenced from this profile." /> <purpose value="The purpose of this profile is to be part of the MVP-GDR project with the goal to evaluate FHIR as a standard to meet our needs for genomic data. It should therefore be known that the information model itself has been created for the purpose of making this evaluation. The information model is therefore not ready for implementation in a production environment and ready to be used to store resource data." /> <fhirVersion value="4.0.1" /> <kind value="resource" /> <abstract value="false" /> <type value="Procedure" /> <baseDefinition value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study" /> <derivation value="constraint" /> <differential> <element id="Procedure.extension:genomic-laboratory-process"> <path value="Procedure.extension" /> <sliceName value="genomic-laboratory-process" /> <type> <code value="Extension" /> <profile value="https://karolinskafhirserver.org/fhir/StructureDefinition/KarolinskaGenomicLaboratoryProcessExtension" /> </type> <isModifier value="false" /> </element> <element id="Procedure.identifier"> <path value="Procedure.identifier" /> <slicing> <discriminator> <type value="value" /> <path value="type.coding.code" /> </discriminator> <rules value="open" /> </slicing> <min value="1" /> </element> <element id="Procedure.identifier.value"> <path value="Procedure.identifier.value" /> <requirements value="Used for CaseID" /> </element> <element id="Procedure.identifier:requester-case-identifier"> <path value="Procedure.identifier" /> <sliceName value="requester-case-identifier" /> <definition value="Business identifiers assigned to this procedure by the requester" /> <max value="1" /> </element> <element id="Procedure.identifier:requester-case-identifier.type"> <path value="Procedure.identifier.type" /> <min value="1" /> </element> <element id="Procedure.identifier:requester-case-identifier.type.coding"> <path value="Procedure.identifier.type.coding" /> <min value="1" /> <max value="1" /> </element> <element id="Procedure.identifier:requester-case-identifier.type.coding.system"> <path value="Procedure.identifier.type.coding.system" /> <min value="1" /> <fixedUri value="http://terminology.hl7.org/CodeSystem/v2-0203" /> </element> <element id="Procedure.identifier:requester-case-identifier.type.coding.code"> <path value="Procedure.identifier.type.coding.code" /> <definition value="An identifier for a request where the identifier is issued by the person or service making the request." /> <min value="1" /> <fixedCode value="PLAC" /> </element> <element id="Procedure.identifier:requester-case-identifier.type.coding.display"> <path value="Procedure.identifier.type.coding.display" /> <min value="1" /> <fixedString value="Placer Identifier" /> </element> <element id="Procedure.identifier:requester-case-identifier.system"> <path value="Procedure.identifier.system" /> <min value="1" /> <fixedUri value="http://mdk.regionstockholm.se/starlims/kliniskgenetik/id" /> </element> <element id="Procedure.identifier:requester-case-identifier.value"> <path value="Procedure.identifier.value" /> <min value="1" /> </element> <element id="Procedure.identifier:laboratory-case-identifier"> <path value="Procedure.identifier" /> <sliceName value="laboratory-case-identifier" /> <definition value="Business identifiers assigned to this procedure by the performer/laboratory" /> <min value="1" /> <max value="1" /> </element> <element id="Procedure.identifier:laboratory-case-identifier.type"> <path value="Procedure.identifier.type" /> <min value="1" /> </element> <element id="Procedure.identifier:laboratory-case-identifier.type.coding"> <path value="Procedure.identifier.type.coding" /> <min value="1" /> <max value="1" /> </element> <element id="Procedure.identifier:laboratory-case-identifier.type.coding.system"> <path value="Procedure.identifier.type.coding.system" /> <min value="1" /> <fixedUri value="http://terminology.hl7.org/CodeSystem/v2-0203" /> </element> <element id="Procedure.identifier:laboratory-case-identifier.type.coding.code"> <path value="Procedure.identifier.type.coding.code" /> <definition value="An identifier for a request where the identifier is issued by the person, or service, that produces the observations or fulfills the request." /> <min value="1" /> <fixedCode value="FILL" /> </element> <element id="Procedure.identifier:laboratory-case-identifier.type.coding.display"> <path value="Procedure.identifier.type.coding.display" /> <min value="1" /> <fixedString value="Filler Identifier" /> </element> <element id="Procedure.identifier:laboratory-case-identifier.system"> <path value="Procedure.identifier.system" /> <min value="1" /> <fixedUri value="http://mdk.regionstockholm.se/gmck/clarity-lims/id" /> </element> <element id="Procedure.identifier:laboratory-case-identifier.value"> <path value="Procedure.identifier.value" /> <min value="1" /> </element> <element id="Procedure.instantiatesCanonical"> <path value="Procedure.instantiatesCanonical" /> <requirements value="Removed for this MVP." /> <max value="0" /> </element> <element id="Procedure.instantiatesUri"> <path value="Procedure.instantiatesUri" /> <requirements value="Removed for this MVP" /> <max value="0" /> </element> <element id="Procedure.basedOn"> <path value="Procedure.basedOn" /> <comment value="Placeholder for future use. Can be used to point to a referral (serviceRequest instance), or to hold a logical reference (Referral ID) to link the case to the referral(s) and referral data." /> <requirements value="Not used in MVP but is kept as a placeholder to show the possibility to connect this Genomic Study to a service request." /> </element> <element id="Procedure.status"> <path value="Procedure.status" /> <comment value="The following statuses can be used to represent the status of the procedure: preparation in-progress not-done on-hold stopped completed entered-in-error unknown" /> <requirements value="We only use completed in MVP - The use case of the GDR is to store completed analyses. Not to store analysis thats still in progress etc." /> <fixedCode value="completed" /> </element> <element id="Procedure.category.coding.system"> <path value="Procedure.category.coding.system" /> <min value="1" /> <fixedUri value="http://snomed.info/sct" /> </element> <element id="Procedure.category.coding.code"> <path value="Procedure.category.coding.code" /> <min value="1" /> <fixedCode value="405824009" /> </element> <element id="Procedure.category.coding.display"> <path value="Procedure.category.coding.display" /> <min value="1" /> <fixedString value="Genetic test (procedure)" /> </element> <element id="Procedure.code"> <path value="Procedure.code" /> <definition value="The specific procedure that is performed. Use text if the exact nature of the procedure cannot be coded (e.g. "Panel Sequencing", Whole Genome Sequencing, Whole Exome Sequencing etc.)." /> <comment value="Should be used to represent the type of Genomic study performed. Preferably a code from a defined value set should be used. If not applivable the text element can be used." /> <requirements value="Used to specify the type of analysis. WGS, Exome, Panel etc. Should use snomed CT" /> </element> <element id="Procedure.subject"> <path value="Procedure.subject" /> <comment value="Should be used to point to the Karolinska Patient resource. We do not want to create a seperate patient-resource." /> <type> <code value="Reference" /> <targetProfile value="https://karolinskafhirserver.org/fhir/StructureDefinition/KarolinskaPatientGenomics" /> </type> </element> <element id="Procedure.encounter"> <path value="Procedure.encounter" /> <requirements value="Could be used to connect the analysis to the encounter in which the analysis was ordered. Karolinska PAS-ID and at which unit and at which time the encounter occurred." /> <max value="0" /> </element> <element id="Procedure.performed[x]"> <path value="Procedure.performed[x]" /> <requirements value="dateTime of when the case was started." /> </element> <element id="Procedure.asserter"> <path value="Procedure.asserter" /> <definition value="Individual who is making the procedure statement. https" /> <max value="0" /> </element> <element id="Procedure.performer.actor"> <path value="Procedure.performer.actor" /> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Organization" /> </type> </element> <element id="Procedure.performer.actor.type"> <path value="Procedure.performer.actor.type" /> <fixedUri value="Organization" /> </element> <element id="Procedure.performer.actor.identifier.system"> <path value="Procedure.performer.actor.identifier.system" /> <min value="1" /> <fixedUri value="http://gmck.se/clarity-lims" /> </element> <element id="Procedure.performer.actor.identifier.value"> <path value="Procedure.performer.actor.identifier.value" /> <min value="1" /> </element> <element id="Procedure.performer.actor.display"> <path value="Procedure.performer.actor.display" /> <min value="1" /> </element> <element id="Procedure.performer.onBehalfOf"> <path value="Procedure.performer.onBehalfOf" /> <min value="1" /> </element> <element id="Procedure.performer.onBehalfOf.type"> <path value="Procedure.performer.onBehalfOf.type" /> <fixedUri value="Organization" /> </element> <element id="Procedure.performer.onBehalfOf.identifier.system"> <path value="Procedure.performer.onBehalfOf.identifier.system" /> <min value="1" /> <fixedUri value="http://gmck.se/clarity-lims" /> </element> <element id="Procedure.performer.onBehalfOf.identifier.value"> <path value="Procedure.performer.onBehalfOf.identifier.value" /> <min value="1" /> </element> <element id="Procedure.performer.onBehalfOf.display"> <path value="Procedure.performer.onBehalfOf.display" /> <min value="1" /> </element> <element id="Procedure.reasonCode"> <path value="Procedure.reasonCode" /> <max value="0" /> </element> <element id="Procedure.reasonReference"> <path value="Procedure.reasonReference" /> <requirements value="Not used in MVP - But in future can be used to categorize the ptotential diagnosis as the reason to perform the service." /> <max value="0" /> </element> </differential> </StructureDefinition>