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

Generated Narrative

Resource "fda-vcfeval-comparison"

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

quality
type: indel
standardSequence: file-BkZxBZ00bpJVk2q6x43b1YBx (#file-BkZxBZ00bpJVk2q6x43b1YBx)
start: 10453
end: 101770080
method: Vcfeval + Hap.py Comparison (#app-BxfGF8j02pBZzZxbzZxP725P)
truthTP: 7749
truthFN: 2554
queryFP: 10670
gtFP: 2186
precision: 0.428005
recall: 0.752111

quality
type: snp
standardSequence: file-BkZxBZ00bpJVk2q6x43b1YBx (#file-BkZxBZ00bpJVk2q6x43b1YBx)
start: 10453
end: 101770080
method: Vcfeval + Hap.py Comparison (#app-BxfGF8j02pBZzZxbzZxP725P)
truthTP: 92106
truthFN: 1247
queryFP: 21744
gtFP: 493
precision: 0.808602
recall: 0.986642

Repositories

-	Type	Url	Name
*	login	https://precision.fda.gov/jobs/job-ByxYPx809jFVy21KJG74Jg3Y	FDA

" ]; 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 "indel" ]; 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-BkZxBZ00bpJVk2q6x43b1YBx" ] ] ]; 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/apps/" ]; fhir:Coding.code [ fhir:value "app-BxfGF8j02pBZzZxbzZxP725P" ] ]; fhir:CodeableConcept.text [ fhir:value "Vcfeval + Hap.py Comparison" ] ]; fhir:MolecularSequence.quality.truthTP [ fhir:value "7749"^^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:index 1; 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-BkZxBZ00bpJVk2q6x43b1YBx" ] ] ]; 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/apps/" ]; fhir:Coding.code [ fhir:value "app-BxfGF8j02pBZzZxbzZxP725P" ] ]; fhir:CodeableConcept.text [ fhir:value "Vcfeval + Hap.py Comparison" ] ]; fhir:MolecularSequence.quality.truthTP [ fhir:value "92106"^^xsd:decimal ]; fhir:MolecularSequence.quality.truthFN [ fhir:value "1247"^^xsd:decimal ]; fhir:MolecularSequence.quality.queryFP [ fhir:value "21744"^^xsd:decimal ]; fhir:MolecularSequence.quality.gtFP [ fhir:value "493"^^xsd:decimal ]; fhir:MolecularSequence.quality.precision [ fhir:value "0.808602"^^xsd:decimal ]; fhir:MolecularSequence.quality.recall [ fhir:value "0.986642"^^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/jobs/job-ByxYPx809jFVy21KJG74Jg3Y" ]; fhir:MolecularSequence.repository.name [ fhir:value "FDA" ] ] . a fhir:Patient . # - ontology header ------------------------------------------------------------ a owl:Ontology; owl:imports fhir:fhir.ttl; owl:versionIRI . # -------------------------------------------------------------------------------------