R6 Ballot (3rd Draft) Snapshot 3: Connectathon 32 Base

Publish-box (todo) This is Snapshot #3 for FHIR R5 , released to support Connectathon 32 . For a full list of available versions, see the Directory of published versions .

Example MolecularDefinition/example-allelesliced-cyp2c19-literal-only (JSON) MedicationRequest/medrx0324 (Turtle)

Clinical Genomics Pharmacy Work Group Maturity Level : N/A Standards Status : Informative Compartments : No defined compartments Encounter , Patient , Practitioner

Raw JSON ( canonical form Turtle + (+ also see JSON Turtle/RDF Format Specification )

Example of Allele including slices Request using Medication Code for CYP2C19 As Literal Rectal Suppository - Acetaminophen - completed with reasonCode, dispenseRequest and substitution

{ "resourceType" : "MolecularDefinition", "id" : "example-allelesliced-cyp2c19-literal-only", "moleculeType" : { "coding" : [{ "system" : "http://hl7.org/fhir/sequence-type", "code" : "rna", "display" : "RNA Sequence" }] }, "location" : [{ "sequenceLocation" : { "sequenceContext" : { "reference" : "MolecularDefinition/example-sequence-nm0007694-url", "type" : "MolecularDefinition", "display" : "Starting Sequence Resource: (CYP2C19), mRNA, NM_000769.4" }, "coordinateInterval" : { "coordinateSystem" : { "system" : { "coding" : [{ "system" : "http://loinc.org", "code" : "LA30100-4", "display" : "0-based interval counting" }], "text" : "0-based interval counting" } }, "startQuantity" : { "value" : 1015 }, "endQuantity" : { "value" : 1016 } } } }], "representation" : [{ "focus" : { "coding" : [{ "code" : "allele-state", "display" : "Allele State" }] }, "code" : [{ "coding" : [{ "system" : "https://www.pharmvar.org", "version" : "6.2", "code" : "PV00076", "display" : "CYP2C19*1.002" }] }], "literal" : { "value" : "G" } }] } 
@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sct: <http://snomed.info/id/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

[a fhir:MedicationRequest;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "medrx0324"]; # 
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: MedicationRequest</b><a name=\"medrx0324\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource MedicationRequest &quot;medrx0324&quot; </p></div><p><b>identifier</b>: id: 12345689 (use: OFFICIAL)</p><p><b>status</b>: completed</p><p><b>intent</b>: order</p><h3>Medications</h3><table class=\"grid\"><tr><td>-</td><td><b>Concept</b></td></tr><tr><td>*</td><td>Paracetamol 240mg suppository (product) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#322254008)</span></td></tr></table><p><b>subject</b>: <a href=\"patient-example-a.html\">Patient/pat1: Donald Duck</a> &quot;Donald DUCK&quot;</p><p><b>authoredOn</b>: 2015-01-15</p><p><b>requester</b>: <a href=\"practitioner-example-f007-sh.html\">Practitioner/f007: Patrick Pump</a> &quot;Simone HEPS&quot;</p><h3>Reasons</h3><table class=\"grid\"><tr><td>-</td><td><b>Concept</b></td></tr><tr><td>*</td><td>Scarlet Fever (disorder) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#30242009)</span></td></tr></table><blockquote><p><b>dose</b></p><blockquote><p><b>dosageInstruction</b></p><p><b>sequence</b>: 1</p><p><b>text</b>: Insert one suppository rectally twice daily as needed for fever to a maximim of 3 per day</p><p><b>additionalInstruction</b>: Do not take with any other paracetamol products (qualifier value) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#418637003)</span></p><p><b>timing</b>: 2 per 1 days</p><p><b>asNeededFor</b>: Fever (finding) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#386661006)</span></p><p><b>maxDosePerPeriod</b>: 720 mg<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code mg = 'mg')</span>/1 d<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code d = 'd')</span></p></blockquote></blockquote><blockquote><p><b>dispenseRequest</b></p><p><b>validityPeriod</b>: 2015-01-15 --&gt; 2016-01-15</p><p><b>numberOfRepeatsAllowed</b>: 3</p><p><b>quantity</b>: 30 RECSUPP<span style=\"background: LightGoldenRodYellow\"> (Details: http://terminology.hl7.org/CodeSystem/v3-orderableDrugForm code RECSUPP = 'Rectal Suppository')</span></p><h3>ExpectedSupplyDurations</h3><table class=\"grid\"><tr><td>-</td><td><b>Value</b></td><td><b>Unit</b></td><td><b>System</b></td><td><b>Code</b></td></tr><tr><td>*</td><td>10</td><td>days</td><td><a href=\"http://terminology.hl7.org/4.0.0/CodeSystem-v3-ucum.html\">Unified Code for Units of Measure (UCUM)</a></td><td>d</td></tr></table></blockquote><h3>Substitutions</h3><table class=\"grid\"><tr><td>-</td><td><b>Allowed[x]</b></td><td><b>Reason</b></td></tr><tr><td>*</td><td>true</td><td>formulary policy <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/4.0.0/CodeSystem-v3-ActReason.html\">ActReason</a>#FP)</span></td></tr></table></div>"
  ]; # 
  fhir:MedicationRequest.identifier [
     fhir:index 0;
     fhir:Identifier.use [ fhir:value "official" ];
     fhir:Identifier.system [ fhir:value "http://www.bmc.nl/portal/prescriptions" ];
     fhir:Identifier.value [ fhir:value "12345689" ]
  ]; # 
  fhir:MedicationRequest.status [ fhir:value "completed"]; # 
  fhir:MedicationRequest.intent [ fhir:value "order"]; # 
  fhir:MedicationRequest.medication [
     fhir:CodeableReference.concept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a sct:322254008;
         fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
         fhir:Coding.code [ fhir:value "322254008" ];
         fhir:Coding.display [ fhir:value "Paracetamol 240mg suppository (product)" ]
       ]
     ]
  ]; # 
  fhir:MedicationRequest.subject [
     fhir:Reference.reference [ fhir:value "Patient/pat1" ]; #    Linked to the resource patient who needs the medication   
     fhir:Reference.display [ fhir:value "Donald Duck" ]
  ]; # 
  fhir:MedicationRequest.authoredOn [ fhir:value "2015-01-15"^^xsd:date]; # 
  fhir:MedicationRequest.requester [
     fhir:Reference.reference [ fhir:value "Practitioner/f007" ];
     fhir:Reference.display [ fhir:value "Patrick Pump" ]
  ]; # 
  fhir:MedicationRequest.reason [
     fhir:index 0;
     fhir:CodeableReference.concept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a sct:30242009;
         fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
         fhir:Coding.code [ fhir:value "30242009" ];
         fhir:Coding.display [ fhir:value "Scarlet Fever (disorder)" ]
       ]
     ]
  ]; # 
  fhir:MedicationRequest.dose [
     fhir:MedicationRequest.dose.dosageInstruction [
       fhir:index 0;
       fhir:Dosage.sequence [ fhir:value "1"^^xsd:integer ];
       fhir:Dosage.text [ fhir:value "Insert one suppository rectally twice daily as needed for fever to a maximim of 3 per day" ];
       fhir:Dosage.additionalInstruction [
         fhir:index 0;
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a sct:418637003;
           fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
           fhir:Coding.code [ fhir:value "418637003" ];
           fhir:Coding.display [ fhir:value "Do not take with any other paracetamol products (qualifier value)" ]
         ]
       ];
       fhir:Dosage.timing [
         fhir:Timing.repeat [
           fhir:Timing.repeat.frequency [ fhir:value "2"^^xsd:positiveInteger ];
           fhir:Timing.repeat.period [ fhir:value "1"^^xsd:decimal ];
           fhir:Timing.repeat.periodUnit [ fhir:value "d" ]
         ]
       ];
       fhir:Dosage.asNeededFor [
         fhir:index 0;
         fhir:CodeableConcept.coding [
           fhir:index 0;
           a sct:386661006;
           fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
           fhir:Coding.code [ fhir:value "386661006" ];
           fhir:Coding.display [ fhir:value "Fever (finding)" ]
         ]
       ];
       fhir:Dosage.doseAndRate [
         fhir:index 0;
         fhir:Dosage.doseAndRate.type [
           fhir:CodeableConcept.coding [
             fhir:index 0;
             fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/dose-rate-type" ];
             fhir:Coding.code [ fhir:value "ordered" ];
             fhir:Coding.display [ fhir:value "Ordered" ]
           ]
         ];
         fhir:Dosage.doseAndRate.doseQuantity [
           fhir:Quantity.value [ fhir:value "240"^^xsd:decimal ];
           fhir:Quantity.unit [ fhir:value "mg" ];
           fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
           fhir:Quantity.code [ fhir:value "mg" ]
         ]
       ];
       fhir:Dosage.maxDosePerPeriod [
         fhir:index 0;
         fhir:Ratio.numerator [
           fhir:Quantity.value [ fhir:value "720"^^xsd:decimal ];
           fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
           fhir:Quantity.code [ fhir:value "mg" ]
         ];
         fhir:Ratio.denominator [
           fhir:Quantity.value [ fhir:value "1"^^xsd:decimal ];
           fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
           fhir:Quantity.code [ fhir:value "d" ]
         ]
       ]
     ]
  ]; # 
  fhir:MedicationRequest.dispenseRequest [
     fhir:MedicationRequest.dispenseRequest.validityPeriod [
       fhir:Period.start [ fhir:value "2015-01-15"^^xsd:date ];
       fhir:Period.end [ fhir:value "2016-01-15"^^xsd:date ]
     ];
     fhir:MedicationRequest.dispenseRequest.numberOfRepeatsAllowed [ fhir:value "3"^^xsd:nonNegativeInteger ];
     fhir:MedicationRequest.dispenseRequest.quantity [
       fhir:Quantity.value [ fhir:value "30"^^xsd:decimal ];
       fhir:Quantity.unit [ fhir:value "RECSUPP" ];
       fhir:Quantity.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v3-orderableDrugForm" ];
       fhir:Quantity.code [ fhir:value "RECSUPP" ]
     ];
     fhir:MedicationRequest.dispenseRequest.expectedSupplyDuration [
       fhir:Quantity.value [ fhir:value "10"^^xsd:decimal ];
       fhir:Quantity.unit [ fhir:value "days" ];
       fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
       fhir:Quantity.code [ fhir:value "d" ]
     ]
  ]; # 
  fhir:MedicationRequest.substitution [
     fhir:MedicationRequest.substitution.allowedBoolean [ fhir:value "true"^^xsd:boolean ];
     fhir:MedicationRequest.substitution.reason [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v3-ActReason" ];
         fhir:Coding.code [ fhir:value "FP" ];
         fhir:Coding.display [ fhir:value "formulary policy" ]
       ]
     ]
  ]] . # 

# - ontology header ------------------------------------------------------------

[a owl:Ontology;
  owl:imports fhir:fhir.ttl] .

# -------------------------------------------------------------------------------------

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.