@prefix fhir: . @prefix owl: . @prefix rdfs: . @prefix xsd: . # - resource ------------------------------------------------------------------- a fhir:MolecularSequence; fhir:nodeRole fhir:treeRoot; fhir:Resource.id [ fhir:value "fda-example"]; fhir:DomainResource.text [ fhir:Narrative.status [ fhir:value "generated" ]; fhir:Narrative.div "

Generated Narrative

Resource "fda-example"

type: dna

coordinateSystem: 1

patient: Patient/example "Peter CHALMERS"

ReferenceSeqs

-	ReferenceSeqId	Strand	WindowStart	WindowEnd
*	NC_000001.11 (nuccore#NC_000001.11)	watson	10453	101770080

Variants

-	Start	End	ObservedAllele	ReferenceAllele
*	13116	13117	T	G

Qualities

Type

StandardSequence

Start

End

Method

TruthTP

QueryTP

TruthFN

QueryFP

GtFP

Precision

Recall

FScore

snp

file-Bk50V4Q0qVb65P0v2VPbfYPZ (#file-Bk50V4Q0qVb65P0v2VPbfYPZ)

10453

101770080

Vcfeval + Hap.py Comparison (#job-ByxYPx809jFVy21KJG74Jg3Y)

7749

7984

2554

10670

2186

0.428005

0.752111

0.545551

Repositories

-	Type	Url	Name	VariantsetId
*	login	https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38	FDA	file-Bx37ZK009P4bX5g3qjkFZV38

" ]; fhir:MolecularSequence.type [ fhir:value "dna"]; fhir:MolecularSequence.coordinateSystem [ fhir:value "1"^^xsd:integer]; fhir:MolecularSequence.patient [ fhir:link ; fhir:Reference.reference [ fhir:value "Patient/example" ] ]; fhir:MolecularSequence.referenceSeq [ fhir:MolecularSequence.referenceSeq.referenceSeqId [ fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ]; fhir:Coding.code [ fhir:value "NC_000001.11" ] ] ]; fhir:MolecularSequence.referenceSeq.strand [ fhir:value "watson" ]; fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "10453"^^xsd:integer ]; fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "101770080"^^xsd:integer ] ]; fhir:MolecularSequence.variant [ fhir:index 0; fhir:MolecularSequence.variant.start [ fhir:value "13116"^^xsd:integer ]; fhir:MolecularSequence.variant.end [ fhir:value "13117"^^xsd:integer ]; fhir:MolecularSequence.variant.observedAllele [ fhir:value "T" ]; fhir:MolecularSequence.variant.referenceAllele [ fhir:value "G" ] ]; fhir:MolecularSequence.quality [ fhir:index 0; fhir:MolecularSequence.quality.type [ fhir:value "snp" ]; fhir:MolecularSequence.quality.standardSequence [ fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "https://precision.fda.gov/files/" ]; fhir:Coding.code [ fhir:value "file-Bk50V4Q0qVb65P0v2VPbfYPZ" ] ] ]; fhir:MolecularSequence.quality.start [ fhir:value "10453"^^xsd:integer ]; fhir:MolecularSequence.quality.end [ fhir:value "101770080"^^xsd:integer ]; fhir:MolecularSequence.quality.method [ fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "https://precision.fda.gov/jobs/" ]; fhir:Coding.code [ fhir:value "job-ByxYPx809jFVy21KJG74Jg3Y" ] ]; fhir:CodeableConcept.text [ fhir:value "Vcfeval + Hap.py Comparison" ] ]; fhir:MolecularSequence.quality.truthTP [ fhir:value "7749"^^xsd:decimal ]; fhir:MolecularSequence.quality.queryTP [ fhir:value "7984"^^xsd:decimal ]; fhir:MolecularSequence.quality.truthFN [ fhir:value "2554"^^xsd:decimal ]; fhir:MolecularSequence.quality.queryFP [ fhir:value "10670"^^xsd:decimal ]; fhir:MolecularSequence.quality.gtFP [ fhir:value "2186"^^xsd:decimal ]; fhir:MolecularSequence.quality.precision [ fhir:value "0.428005"^^xsd:decimal ]; fhir:MolecularSequence.quality.recall [ fhir:value "0.752111"^^xsd:decimal ]; fhir:MolecularSequence.quality.fScore [ fhir:value "0.545551"^^xsd:decimal ] ]; fhir:MolecularSequence.repository [ fhir:index 0; fhir:MolecularSequence.repository.type [ fhir:value "login" ]; fhir:MolecularSequence.repository.url [ fhir:value "https://precision.fda.gov/files/file-Bx37ZK009P4bX5g3qjkFZV38" ]; fhir:MolecularSequence.repository.name [ fhir:value "FDA" ]; fhir:MolecularSequence.repository.variantsetId [ fhir:value "file-Bx37ZK009P4bX5g3qjkFZV38" ] ] . a fhir:Patient . # - ontology header ------------------------------------------------------------ a owl:Ontology; owl:imports fhir:fhir.ttl; owl:versionIRI . # -------------------------------------------------------------------------------------