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Merge pull request #3 from aphp/ngr/fullExample
Ngr/full example
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‎input/fml/usages/core/StructureMap-CoreBusiness2Physical.fml

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map "https://aphp.fr/ig/fhir/dm/StructureMap/CoreBusiness2Physical" = "CoreBusiness2Physical"
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/// name = 'CoreBusiness2Physical'
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/// title = 'Alignement de l\'expression de besoin vers le modèle physique du DPI dans le cadre de l\'usage Core'
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// Alignement entre le modèle métier et le ùodèle physique du DPI
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uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QR as source
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uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/CoreDataSet" alias DataSet as target
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uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/CorePatient" alias PatientTable as target
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uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/CoreSejour" alias SejourTable as target
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uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/CoreBiology" alias BiologyTable as target
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uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/CoreClinical" alias ClinicalTable as target
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uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/CoreMedicationAdm" alias MedicationAdmTable as target
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uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/CoreMedicationPre" alias MedicationPreTable as target
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group init(source srcQR : QR, target tgtDS : DataSet) <<types>> {
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srcQR -> tgtDS.logicalid = uuid() "setId";
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srcQR -> tgtDS.patient as tgtPatient,
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tgtDS.sejour as tgtSejour,
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tgtDS.biology as tgtBiol,
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tgtDS.clinical as tgtClin,
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tgtDS.medicationPre as tgtMedPre,
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tgtDS.medicationAdm as tgtMedAdm then {
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srcQR.item as srcSocioDemoDataItem where linkId = '4647259356106' then {
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srcSocioDemoDataItem.item as srcPatientIdItem where linkId = '2958000860428' then {
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srcPatientIdItem.item as srcNomItem where linkId = '8605698058770' then {
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srcNomItem.answer as srcNomAnswer then {
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srcNomAnswer.value : string as srcNomValue -> tgtPatient.name = srcNomValue "SetNomValue";
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} "setNomAnswer" ;
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} "setNom" ;
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srcPatientIdItem.item as srcPrenomItem where linkId = '6214879623503' then {
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srcPrenomItem.answer as srcPrenomAnswer then {
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srcPrenomAnswer.value : string as srcPrenomValue -> tgtPatient.firstName = srcPrenomValue "SetPrenomValue";
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} "setPrenomAnswer" ;
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} "setPrenom" ;
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srcPatientIdItem.item as srcNIRItem where linkId = '5711960356160' then {
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srcNIRItem.answer as srcNIRAnswer then {
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srcNIRAnswer.value : string as srcNIRValue -> tgtPatient.nir = srcNIRValue "SetNIRValue";
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} "setNIRAnswer" ;
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} "setNIR" ;
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srcPatientIdItem.item as srcDDNItem where linkId = '5036133558154' then {
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srcDDNItem.answer as srcDDNAnswer then {
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srcDDNAnswer.value : date as srcDDNValue -> tgtPatient.birthDate = srcDDNValue "SetDDNValue";
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} "setDDNAnswer" ;
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} "setDDN" ;
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srcPatientIdItem.item as srcDDDItem where linkId = '5036133558154' then {
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srcDDDItem.answer as srcDDDAnswer then {
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srcDDDAnswer.value : date as srcDDDValue "SetDDDValue";
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} "setDDDAnswer" ;
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srcDDDItem.item as srcDDDSourceItem where linkId = '9098810065693' then {
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srcDDDSourceItem.answer as srcDDDSourceAnswer then {
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srcDDDSourceAnswer.value : Coding as srcDDDSourceValue "SetDDDSourceValue";
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} "setDDDSourceAnswer" ;
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} "setDDDSource" ;
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} "setDDD" ;
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srcPatientIdItem.item as srcGemRankItem where linkId = '6931296968515' then {
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srcGemRankItem.answer as srcGemRankAnswer then {
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srcGemRankAnswer.value : integer as srcGemRankValue "SetGemRankValue";
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} "setDDNAnswer" ;
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} "setDDN" ;
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} "navigationToPatientId" ;
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srcSocioDemoDataItem.item as srcEnvItem where linkId = '5491974639955' then {
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srcEnvItem.item as srcGeocodItem where linkId = '3816475533472' then {
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srcGeocodItem.item as srcLatItem where linkId = '3709843054556' then {
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srcLatItem.answer as srcLatAnswer then {
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srcLatAnswer.value : decimal as srcLatValue "SetLatValue";
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} "setLatAnswer" ;
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} "setLat" ;
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srcGeocodItem.item as srcLongItem where linkId = '7651448032665' then {
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srcLongItem.answer as srcLongAnswer then {
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srcLongAnswer.value : decimal as srcLongValue "SetLongValue";
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} "setLongAnswer" ;
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} "setLong" ;
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srcGeocodItem.item as srcGeocodDateItem where linkId = '1185653257776' then {
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srcGeocodDateItem.answer as srcGeocodDateAnswer then {
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srcGeocodDateAnswer.value : date as srcGeocodDateValue "SetGeocodDateValue";
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} "setGeocodDateAnswer" ;
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} "setGeocodDate" ;
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} "navigationToGeocod" ;
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srcEnvItem.item as srcIrisItem where linkId = '7621032273792' then {
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srcIrisItem.answer as srcIrisAnswer then {
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srcIrisAnswer.value : Coding as srcIrisValue "SetIrisValue";
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} "setIrisAnswer" ;
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srcIrisItem.item as srcIrisDateItem where linkId = '4999580038872' then {
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srcIrisDateItem.answer as srcIrisDateAnswer then {
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srcIrisDateAnswer.value : date as srcIrisDateValue "SetIrisDateValue";
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} "setIrisDateAnswer" ;
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} "setIrisDate" ;
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} "setIris" ;
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} "navigationToEnv" ;
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} "navigationToSocioDemoData" ;
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srcQR.item as srcPMSIDataItem where linkId = '2825244231605' then {
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srcPMSIDataItem.item as srcPMSISexeItem where linkId = '3894630481120' then {
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srcPMSISexeItem.answer as srcPMSISexeAnswer then {
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srcPMSISexeAnswer.value : Coding as srcPMSISexeValueCoding -> tgtPatient.gender = (%srcPMSISexeValueCoding.code) "SetPMSISexeValue" ;
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} "SetPMSISexeAnswer" ;
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} "setPMSISexe" ;
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} "navigationToPMSIData" ;
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} "setTgtVar" ;
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}

‎input/fml/usages/core/StructureMap-CorePhysical2FHIR.fml

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@@ -40,6 +40,7 @@ group patient(source srcPatient : PatientTable, target tgtPatient : FHIRPatient)
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srcPatient -> tgtPatient.id = uuid() "setId";
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srcPatient.patientNi as srcNi -> tgtPatient.meta as tgtMeta then setPatientMeta(srcNi, tgtMeta) "setMeta"; // copie la valeur du champ patientNi de la table Patient dans l'élément id de la ressource FHIR Patient
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srcPatient -> tgtPatient.name as tgtPatientName then setHumainName(srcPatient, tgtPatientName) "setHumainName";
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srcPatient -> tgtPatient.identifier as tgtPatientIdentifier then setHumainNir(srcPatient, tgtPatientIdentifier) "setHumainNir" ;
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srcPatient.gender as srcPatientGender -> tgtPatient.gender = translate(srcPatientGender, 'https://aphp.fr/ig/fhir/dm/ConceptMap/DpiGender2Hl7Gender', 'code') "setGender"; // traduit la valeur du champ gender de la table Patient dans l'élément gender de la ressource FHIR Patient
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srcPatient.birthDate as srcPatientBirthDate -> tgtPatient.birthDate = srcPatientBirthDate "setBirthDate"; // copie la valeur du champ birthDate de la table Patient dans l'élément birthDate de la ressource FHIR Patient
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}
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tgtPatientName.text = (%srcPatientFirstName + ' ' + %srcPatientName) "setFirstNameAndText";
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} "setName";}
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group setHumainNir(source srcPatient : PatientTable, target tgtPatientIdentifier) {
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srcPatient.nir as srcPatientNir -> tgtPatientIdentifier.use = 'official',
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tgtPatientIdentifier.type = cc('https://hl7.fr/ig/fhir/core/CodeSystem/fr-core-cs-v2-0203', 'INS-NIR'),
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tgtPatientIdentifier.system = 'urn:oid:1.2.250.1.213.1.4.8',
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tgtPatientIdentifier.value = srcPatientNir "setNir" ;
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}
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group encounter(source srcSejour : SejourTable, source srcPatient : FHIRPatient, target tgtEncounter : FHIREncounter) {
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srcSejour -> tgtEncounter.id = uuid() "setId";
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srcSejour.sejourNi as srcNi -> tgtEncounter.meta as tgtMeta then setEncounterMeta(srcNi, tgtMeta) "setMeta"; // copie la valeur du champ patientNi de la table Patient dans l'élément id de la ressource FHIR Patient

‎input/fsh/applications/dpi/codesystems/CodeSystem-DpiEncounterType.fsh

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CodeSystem: DpiEncounterType
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Title: "Dpi Encounter type"
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Description: "TODO"
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Title: "DPI Type de séjour"
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Description: "Type de séjour"
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* ^status = #active
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* ^content = #complete

‎input/fsh/applications/dpi/logicals/StructureDefinition-CorePatient.fsh

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* firstName 0..1 string "FIRST_NAME"
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* gender 0..1 string "GENDER"
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* birthDate 0..1 date "BIRTH_DATE"
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* nir 0..1 string "NIR"

‎input/fsh/semantic-layer/codesystems/CodeSystem-SemanticLayerEncounterType.fsh

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CodeSystem: SemanticLayerEncounterType
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Title: "Semantic layer encounter type"
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Description: "TODO"
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Description: "Semantic layer encounter type"
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* ^status = #active
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* ^content = #complete

‎input/fsh/semantic-layer/profiles/StructureDefinition-DMObservationLaboratoryTCA.fsh

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Profil des résultats de TCA - socle commun des EDS
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"""
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* code = $loinc#50197-3 "aPTT panel - Platelet poor plasma" (exactly)
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* code = $loinc#50197-3 "Temps de céphaline activée panel [-] Plasma pauvre en plaquettes ; Numérique" (exactly)
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* component ^slicing.discriminator[0].type = #value
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* component ^slicing.discriminator[=].path = "code"

‎input/fsh/semantic-layer/profiles/StructureDefinition-DMObservationLaboratoryUremie.fsh

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Profil des résultats d'urémie du socle commun des EDS
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"""
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* code = $loinc#22664-7 "Urea [Moles/volume] in Serum or Plasma" (exactly)
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* code = $loinc#22664-7 "Urée [Moles/Volume] Sérum/Plasma ; Numérique" (exactly)
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* value[x] only Quantity
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* valueQuantity.value ^short = "Valeur mesurée"

‎input/fsh/usages/core/conceptmaps/ConceptMap-hl7Gender2OhdsiGender.fsh

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Instance: hl7Gender2OhdsiGender
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InstanceOf: ConceptMap
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Usage: #definition
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* title = "HL7 Gender to OHDSI Gender"
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* name = "Hl7Gender2OhdsiGender"
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* description = "L'objectif de cet alignement est rendre possible la conversion d'un code 'gender' d'HL7 vers son équivalent dans OHDSI"
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* experimental = false
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* status = #active
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* group[0]
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* source = "https://hl7.fr/ig/fhir/core/ValueSet/fr-core-vs-patient-gender-INS"
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* target = "https://fhir-terminology.ohdsi.org"
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* element[0]
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* code = #male
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* display = "Male"
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* target[0]
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* code = #8507
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* display = "MALE"
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* equivalence = #equivalent
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* element[+]
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* code = #female
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* display = "Female"
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* target[0]
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* code = #8532
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* display = "FEMALE"
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* equivalence = #equivalent

‎input/images-source/core-mpd.plantuml

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* {field} FIRST_NAME VARCHAR2 (50) NULL
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* {field} GENDER CHAR (1) NULL
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* {field} BIRTH_DATE DATE NULL
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* {field} NIR VARCHAR2 (13) NULL
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}
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entity CORE.SEJOUR {

‎input/pagecontent/StructureDefinition-DMObservationBodyHeight-intro.md

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<table style="width: 100%">
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<tr><th>Nom</th><th>Description</th></tr>
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<tr><td><a href="dm-core.html#variables-socles">Socles pour les EDSH</a></td><td>Les variables socles pour les EDSH.</td></tr>
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<tr><td><a href="dm-core.html">Socles pour les EDSH</a></td><td>Les variables socles pour les EDSH.</td></tr>
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</table>
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### Exemples

‎input/pagecontent/StructureDefinition-DMObservationBodyWeight-intro.md

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<table style="width: 100%">
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<tr><th>Nom</th><th>Description</th></tr>
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<tr><td><a href="dm-core.html#variables-socles">Socles pour les EDSH</a></td><td>Les variables socles pour les EDSH.</td></tr>
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<tr><td><a href="dm-core.html">Socles pour les EDSH</a></td><td>Les variables socles pour les EDSH.</td></tr>
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</table>
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### Exemples

‎input/pagecontent/use-core-conception-fhir.md

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* Taille : [DMObservationBodyHeight]
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* Poids : [DMObservationBodyWeight]
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##### L'alignement
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Une fois les éléments pertinents de la source identifiés (périmètre final) et les profils FHIR élaborés, il est possible de formaliser les règles d'alignement des premiers vers les seconds via la rédaction d'une structureMap.
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Vous pouvez trouver l'alignement formel entre le modèle physique et les profils FHIR [ici](StructureMap-CorePhysical2FHIR.html)
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{% include markdown-link-references.md %}

‎input/pagecontent/use-core-exemple-bout-en-bout.md

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<ol>
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<li><a href="Questionnaire-UsageCore.html">Questionnaire des exigences</a></li>
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<li><a href="QuestionnaireResponse-qr-test-usage-core.html">QuestionnaireResponse des exigences</a></li>
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<li><a href="StructureMap-CoreBusiness2Physical.html">StructureMap de génération du dataset depuis la QuestionnaireResponse</a></li>
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<li>DataSet Patient généré par l'éxecution de la StructureMap sur le QuestionnaireResponse :
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<pre>{
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"patient" : {
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"name" : "doe",
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"firstName" : "john",
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"gender" : "h",
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"birthDate" : "1948-07-16",
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"nir" : "1234567890123"
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}
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}</pre></li>
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<li><a href="StructureMap-CorePhysical2FHIR.html">StructureMap de génération de la ressource Patient depuis le datasetPatient</a></li>
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<li><a href="Patient-8f005d60-b59b-47f7-b04a-f877378f8d68.html">Patient généré par l'éxecution de la StructureMap sur le dataset patient</a></li>
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<li><a href="StructureMap-CoreFHIRPatient2OMOP.html">StructureMap de génération de l'entrée OMOP depuis la ressource Patient</a></li>
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<li>Entrée de la table OMOP générée par l'éxecution de la StructureMap sur la ressource Patient : <pre>{
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"person" : {
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"gender_concept_id" : {
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"reference" : "Concept/8507"
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},
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"year_of_birth" : 1948,
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"month_of_birth" : 7,
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"day_of_birth" : 16,
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"birth_datetime" : "1948-07-16",
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"person_source_value" : "8f005d60-b59b-47f7-b04a-f877378f8d68",
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"gender_source_value" : "male"
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}
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}</pre></li>
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</ol>
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‎input/pagecontent/use-core-instruction.md

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##### Périmètre final
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L'alignement entre le modèle "physique" (modèle de l'application DPI) et le modèle métier issu des exigences en donnée de l'usage permet d'identifier les tables et les champs d'intérêt.
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L'alignement du modèle métier, issu des exigences en donnée de l'usage, vers le modèle "physique" (modèle de l'application DPI) permet d'identifier les tables et les champs d'intérêt.
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<!-- If the image below is not wrapped in a div tag, the publisher tries to wrap text around the image, which is not desired. -->
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<div style="text-align: center;">{%include core-map.svg%}</div>
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Vous pouvez trouver l'alignement formel entre le modèle physique et les profils FHIR : [Modèle physique vers FHIR](StructureMap-CorePhysical2FHIR.html)
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Vous pouvez trouver l'alignement formel entre le modèle métier et le modèle physique : [Modèle métier vers modèle physique](StructureMap-CoreBusiness2Physical.html)
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#### Profilage des données
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‎input/pagecontent/use-core.md

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#### Conception de la livraison des données (OMOP)
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{% include use-core-conception-omop.md %}
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{% include use-core-conception-omop.md %}
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#### Exemple de synthèse
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{% include use-core-exemple-bout-en-bout.md %}

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