GenomicStudy - Trio study - De novo mutation 1

@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:GenomicStudy;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "example"]; #   from Resource: id, meta, implicitRules, and language  
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "additional" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">This is a genomic study that involves a de novo mutation analysis of a proband, mother, and father. The analysis involves the use use of NGS device and a specilized analysis platform.</div>"
  ]; #   from DomainResource: text, contained, extension, and modifierExtension  
  fhir:GenomicStudy.identifier [
     fhir:index 0;
     fhir:Identifier.use [ fhir:value "temp" ];
     fhir:Identifier.system [ fhir:value "http://www.somesystemabc.net/identifiers/genomicstudies" ];
     fhir:Identifier.value [ fhir:value "urn:uuid:1111-1111-1111-1111" ]
  ]; # 
  fhir:GenomicStudy.status [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       fhir:Coding.system [ fhir:value "http://hl7.org/fhir/genomicstudy-status" ];
       fhir:Coding.code [ fhir:value "unknown" ];
       fhir:Coding.display [ fhir:value "Unknown" ]
     ]
  ]; # 
  fhir:GenomicStudy.type [
     fhir:index 0;
     fhir:CodeableConcept.coding [
       fhir:index 0;
       fhir:Coding.system [ fhir:value "http://hl7.org/fhir/genomicstudy-type" ];
       fhir:Coding.code [ fhir:value "fam-var-segr" ];
       fhir:Coding.display [ fhir:value "Familial variant segregation" ]
     ]
  ]; # 
  fhir:GenomicStudy.subject [
     fhir:Reference.reference [ fhir:value "Patient/denovoChild" ]
  ]; # 
  fhir:GenomicStudy.encounter [
     fhir:Reference.reference [ fhir:value "Encounter/denovoEncounter" ]
  ]; # 
  fhir:GenomicStudy.startDate [ fhir:value "2021-01-01"^^xsd:date]; # 
  fhir:GenomicStudy.basedOn [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "ServiceRequest/genomicServiceRequest" ]
  ]; # 
  fhir:GenomicStudy.referrer [
     fhir:Reference.reference [ fhir:value "Practitioner/practitioner01" ]
  ]; # 
  fhir:GenomicStudy.interpreter [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Practitioner/practitioner02" ]
  ]; # 
  fhir:GenomicStudy.reason [
     fhir:index 0;
     fhir:CodeableReference.concept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a sct:267431006;
         fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
         fhir:Coding.code [ fhir:value "267431006" ];
         fhir:Coding.display [ fhir:value "Disorder of lipid metabolism (disorder)" ]
       ]
     ]
  ]; # 
  fhir:GenomicStudy.note [
     fhir:index 0;
     fhir:Annotation.text [ fhir:value "This de novo mutation is urgent and important for establishing the treatment plan." ]
  ]; # 
  fhir:GenomicStudy.description [ fhir:value "De novo mutation study of the patient."]; # 
  fhir:GenomicStudy.analysis [
     fhir:index 0;
     fhir:GenomicStudy.analysis.identifier [
       fhir:index 0;
       fhir:Identifier.use [ fhir:value "temp" ];
       fhir:Identifier.system [ fhir:value "http://www.somesystemabc.net/identifiers/genomicAnalyses" ];
       fhir:Identifier.value [ fhir:value "urn:uuid:1111-1111-1111-1111" ]
     ]; #   0..* Genomic Analysis Event of proband  
     fhir:GenomicStudy.analysis.instantiatesUri [ fhir:value "https://pubmed.ncbi.nlm.nih.gov/33927380/" ]; #   <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis<\/instantiatesCanonical>  
     fhir:GenomicStudy.analysis.title [ fhir:value "Proband Sequence Variation Detection Using Next Generation Sequencing" ];
     fhir:GenomicStudy.analysis.subject [
       fhir:Reference.reference [ fhir:value "Patient/denovoChild" ]
     ];
     fhir:GenomicStudy.analysis.specimen [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "Specimen/denovo-1" ]
     ];
     fhir:GenomicStudy.analysis.date [ fhir:value "2021-01-01T01:01:10-06:00"^^xsd:dateTime ];
     fhir:GenomicStudy.analysis.note [
       fhir:index 0;
       fhir:Annotation.text [ fhir:value "This is a next generation sequencing analysis of a proband." ]
     ]; #   0..1 The date of the analysis event  
     fhir:GenomicStudy.analysis.input [
       fhir:index 0;
       fhir:GenomicStudy.analysis.input.file [
         fhir:Reference.reference [ fhir:value "DocumentReference/genomicFile1" ]
       ]; #   0..* Inputs for the analysis event of Child 
       fhir:GenomicStudy.analysis.input.type [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.code [ fhir:value "vcf" ];
           fhir:Coding.display [ fhir:value "VCF" ]
         ]
       ]
     ]; #   <protocolPerformed>0..1 Reference(Procedure|Task) The protocol that was performed for the analysis event<\/protocolPerformed>  ,   <regionsCalled>0..1 Reference(DocumentReference) Genomic regions actually called in the analysis event (BED file)<\/regionsCalled>  ,   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file<\/generatedBy[x]>  
     fhir:GenomicStudy.analysis.performer [
       fhir:index 0;
       fhir:GenomicStudy.analysis.performer.actor [
         fhir:Reference.reference [ fhir:value "Practitioner/practitioner02" ]
       ]; #   0..* Performer for the analysis event  
       fhir:GenomicStudy.analysis.performer.role [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html" ];
           fhir:Coding.code [ fhir:value "PRF" ];
           fhir:Coding.display [ fhir:value "Performer" ]
         ]
       ]
     ];
     fhir:GenomicStudy.analysis.device [
       fhir:index 0;
       fhir:GenomicStudy.analysis.device.device [
         fhir:Reference.reference [ fhir:value "Device/NGS-device" ]
       ]; #   0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters  
       fhir:GenomicStudy.analysis.device.function [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.display [ fhir:value "Next Generation Sequencing" ]
         ]
       ]
     ]
  ], [
     fhir:index 1;
     fhir:GenomicStudy.analysis.identifier [
       fhir:index 0;
       fhir:Identifier.use [ fhir:value "temp" ];
       fhir:Identifier.system [ fhir:value "http://www.somesystemabc.net/identifiers/genomicAnalyses" ];
       fhir:Identifier.value [ fhir:value "urn:uuid:1111-1111-1111-1112" ]
     ]; #   0..* Genomic Analysis Event of mother  
     fhir:GenomicStudy.analysis.instantiatesUri [ fhir:value "https://pubmed.ncbi.nlm.nih.gov/33927380/" ]; #   <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis<\/instantiatesCanonical>  
     fhir:GenomicStudy.analysis.title [ fhir:value "Maternal Sequence Variation Detection Using Next Generation Sequencing" ];
     fhir:GenomicStudy.analysis.subject [
       fhir:Reference.reference [ fhir:value "Patient/denovoMother" ]
     ]; #   0..1 Name of the analysis event (human friendly)  
     fhir:GenomicStudy.analysis.specimen [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "Specimen/denovo-2" ]
     ];
     fhir:GenomicStudy.analysis.date [ fhir:value "2021-01-01T01:01:10-06:00"^^xsd:dateTime ];
     fhir:GenomicStudy.analysis.note [
       fhir:index 0;
       fhir:Annotation.text [ fhir:value "This is a next generation sequencing analysis of a mother of a proband." ]
     ]; #   0..1 The date of the analysis event  
     fhir:GenomicStudy.analysis.input [
       fhir:index 0;
       fhir:GenomicStudy.analysis.input.file [
         fhir:Reference.reference [ fhir:value "DocumentReference/genomicFile2" ]
       ]; #   0..* Inputs for the analysis event of Mother 
       fhir:GenomicStudy.analysis.input.type [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.code [ fhir:value "vcf" ];
           fhir:Coding.display [ fhir:value "VCF" ]
         ]
       ]
     ]; #   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file<\/generatedBy[x]>  
     fhir:GenomicStudy.analysis.performer [
       fhir:index 0;
       fhir:GenomicStudy.analysis.performer.actor [
         fhir:Reference.reference [ fhir:value "Practitioner/practitioner02" ]
       ]; #   0..* Performer for the analysis event  
       fhir:GenomicStudy.analysis.performer.role [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html" ];
           fhir:Coding.code [ fhir:value "PRF" ];
           fhir:Coding.display [ fhir:value "Performer" ]
         ]
       ]
     ];
     fhir:GenomicStudy.analysis.device [
       fhir:index 0;
       fhir:GenomicStudy.analysis.device.device [
         fhir:Reference.reference [ fhir:value "Device/NGS-device" ]
       ] #   0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters  
     ] #   <function>0..1 CodeableConcept Specific function for the device used for the analysis<\/function>  
  ], [
     fhir:index 2;
     fhir:GenomicStudy.analysis.identifier [
       fhir:index 0;
       fhir:Identifier.use [ fhir:value "temp" ];
       fhir:Identifier.system [ fhir:value "http://www.somesystemabc.net/identifiers/genomicAnalyses" ];
       fhir:Identifier.value [ fhir:value "urn:uuid:1111-1111-1111-1113" ]
     ]; #   0..* Genomic Analysis Event of father  
     fhir:GenomicStudy.analysis.instantiatesUri [ fhir:value "https://pubmed.ncbi.nlm.nih.gov/33927380/" ]; #   <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis<\/instantiatesCanonical>  
     fhir:GenomicStudy.analysis.title [ fhir:value "Paternal Sequence Variation Detection Using Next Generation Sequencing" ];
     fhir:GenomicStudy.analysis.subject [
       fhir:Reference.reference [ fhir:value "Patient/denovoFather" ]
     ];
     fhir:GenomicStudy.analysis.specimen [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "Specimen/denovo-3" ]
     ];
     fhir:GenomicStudy.analysis.date [ fhir:value "2021-01-01T01:01:10-06:00"^^xsd:dateTime ];
     fhir:GenomicStudy.analysis.note [
       fhir:index 0;
       fhir:Annotation.text [ fhir:value "This is a next generation sequencing analysis of a father of a proband." ]
     ]; #   0..1 The date of the analysis event  
     fhir:GenomicStudy.analysis.input [
       fhir:index 0;
       fhir:GenomicStudy.analysis.input.file [
         fhir:Reference.reference [ fhir:value "DocumentReference/genomicFile3" ]
       ]; #   0..* Inputs for the analysis event  
       fhir:GenomicStudy.analysis.input.type [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.code [ fhir:value "vcf" ];
           fhir:Coding.display [ fhir:value "VCF" ]
         ]
       ]
     ]; #   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file<\/generatedBy[x]>  
     fhir:GenomicStudy.analysis.performer [
       fhir:index 0;
       fhir:GenomicStudy.analysis.performer.actor [
         fhir:Reference.reference [ fhir:value "Practitioner/practitioner02" ]
       ]; #   0..* Performer for the analysis event  
       fhir:GenomicStudy.analysis.performer.role [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html" ];
           fhir:Coding.code [ fhir:value "PRF" ];
           fhir:Coding.display [ fhir:value "Performer" ]
         ]
       ]
     ];
     fhir:GenomicStudy.analysis.device [
       fhir:index 0;
       fhir:GenomicStudy.analysis.device.device [
         fhir:Reference.reference [ fhir:value "Device/NGS-device" ]
       ] #   0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters  
     ] #   <function>0..1 CodeableConcept Specific function for the device used for the analysis<\/function>  
  ], [
     fhir:index 3;
     fhir:GenomicStudy.analysis.identifier [
       fhir:index 0;
       fhir:Identifier.use [ fhir:value "temp" ];
       fhir:Identifier.system [ fhir:value "http://www.somesystemabc.net/identifiers/genomicAnalyses" ];
       fhir:Identifier.value [ fhir:value "urn:uuid:1111-1111-1111-1114" ]
     ]; #   0..* De Novo Mutation Analysis  
     fhir:GenomicStudy.analysis.instantiatesUri [ fhir:value "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885382/" ]; #   <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis<\/instantiatesCanonical>  
     fhir:GenomicStudy.analysis.title [ fhir:value "De Novo Mutation Detection and Interpretation" ];
     fhir:GenomicStudy.analysis.subject [
       fhir:Reference.reference [ fhir:value "Patient/denovoChild" ]
     ];
     fhir:GenomicStudy.analysis.date [ fhir:value "2021-01-01T03:01:10-06:00"^^xsd:dateTime ]; #   <specimen> 0..1 Reference(Specimen) The specimen used in the analysis event<\/specimen>  
     fhir:GenomicStudy.analysis.note [
       fhir:index 0;
       fhir:Annotation.text [ fhir:value "This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences." ]
     ]; #   0..1 The date of the analysis event  
     fhir:GenomicStudy.analysis.input [
       fhir:index 0;
       fhir:GenomicStudy.analysis.input.file [
         fhir:Reference.reference [ fhir:value "DocumentReference/genomicFile1" ]
       ]; #   0..* Inputs for the analysis event of Child 
       fhir:GenomicStudy.analysis.input.type [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.code [ fhir:value "vcf" ];
           fhir:Coding.display [ fhir:value "VCF" ]
         ]
       ]
     ], [
       fhir:index 1;
       fhir:GenomicStudy.analysis.input.file [
         fhir:Reference.reference [ fhir:value "DocumentReference/genomicFile2" ]
       ]; #   0..* Inputs for the analysis event of Mother 
       fhir:GenomicStudy.analysis.input.type [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.code [ fhir:value "vcf" ];
           fhir:Coding.display [ fhir:value "VCF" ]
         ]
       ]
     ], [
       fhir:index 2;
       fhir:GenomicStudy.analysis.input.file [
         fhir:Reference.reference [ fhir:value "DocumentReference/genomicFile3" ]
       ]; #   0..* Inputs for the analysis event of Father  
       fhir:GenomicStudy.analysis.input.type [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.code [ fhir:value "vcf" ];
           fhir:Coding.display [ fhir:value "VCF" ]
         ]
       ]
     ]; #   <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file<\/generatedBy[x]>  
     fhir:GenomicStudy.analysis.performer [
       fhir:index 0;
       fhir:GenomicStudy.analysis.performer.actor [
         fhir:Reference.reference [ fhir:value "Practitioner/practitioner02" ]
       ]; #   0..* Performer for the analysis event  
       fhir:GenomicStudy.analysis.performer.role [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html" ];
           fhir:Coding.code [ fhir:value "PRF" ];
           fhir:Coding.display [ fhir:value "Performer" ]
         ]
       ]
     ];
     fhir:GenomicStudy.analysis.device [
       fhir:index 0;
       fhir:GenomicStudy.analysis.device.device [
         fhir:Reference.reference [ fhir:value "Device/Triodenovo-SW" ]
       ] #   0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters  
     ] #   <function>0..1 CodeableConcept Specific function for the device used for the analysis<\/function>  
  ]] . # 

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

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

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