NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣIDomainResourceInformation about a biological sequence
Only 0 and 1 are valid for coordinateSystem
... identifier Σ0..*IdentifierUnique ID for this particular sequence. This is a FHIR-defined id
... type Σ0..1codeAA | DNA | RNA
sequenceType (Example)
... coordinateSystem Σ1..1integerBase number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
... patient Σ0..1Reference(Patient)Who and/or what this is about
... specimen Σ0..1Reference(Specimen)Specimen used for sequencing
... device Σ0..1Reference(Device)The method for sequencing
... performer Σ0..1Reference(Organization)Who should be responsible for test result
... quantity Σ0..1QuantityThe number of copies of the seqeunce of interest. (RNASeq)
... referenceSeq ΣI0..1BackboneElementReference sequence
Only +1 and -1 are valid for strand
GenomeBuild and chromosome must be both contained if either one of them is contained
Have and only have one of the following elements in referenceSeq : 1. genomeBuild ; 2 referenceSeqId; 3. referenceSeqPointer; 4. referenceSeqString;
.... chromosome Σ0..1CodeableConceptChromosome containing genetic finding
chromosome-human (Example)
.... genomeBuild Σ0..1stringThe Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
.... referenceSeqId Σ0..1CodeableConceptReference identifier
ENSEMBL (Example)
.... referenceSeqPointer Σ0..1Reference(Sequence)A Pointer to another Sequence entity as reference sequence
.... referenceSeqString Σ0..1stringA Reference Sequence string
.... strand Σ0..1integerDirectionality of DNA ( +1/-1)
.... windowStart Σ1..1integerStart position of the window on the reference sequence
.... windowEnd Σ1..1integerEnd position of the window on the reference sequence
... variant Σ0..*BackboneElementSequence variant
.... start Σ0..1integerStart position of the variant on the reference sequence
.... end Σ0..1integerEnd position of the variant on the reference sequence
.... observedAllele Σ0..1stringAllele that was observed
.... referenceAllele Σ0..1stringAllele of reference sequence
.... cigar Σ0..1stringExtended CIGAR string for aligning the sequence with reference bases
.... variantPointer Σ0..1Reference(Observation)Pointer to observed variant information
... observedSeq Σ0..1stringObserved sequence
... quality Σ0..*BackboneElementSequence quality
.... type Σ1..1codeINDEL | SNP | UNKNOWN
qualityType (Required)
.... standardSequence Σ0..1CodeableConceptStandard sequence for comparison
.... start Σ0..1integerStart position of the sequence
.... end Σ0..1integerEnd position of the sequence
.... score Σ0..1QuantityQuality score
.... method Σ0..1CodeableConceptMethod for quality
.... truthTP Σ0..1decimalTrue positives from the perspective of the truth data
.... queryTP Σ0..1decimalTrue positives from the perspective of the query data
.... truthFN Σ0..1decimalFalse negatives
.... queryFP Σ0..1decimalFalse positives
.... gtFP Σ0..1decimalFalse positives where the non-REF alleles in the Truth and Query Call Sets match
.... precision Σ0..1decimalPrecision
.... recall Σ0..1decimalRecall
.... fScore Σ0..1decimalF-score
... readCoverage Σ0..1integerAverage number of reads representing a given nucleotide in the reconstructed sequence
... repository Σ0..*BackboneElementExternal repository which contains detailed report related with observedSeq in this resource
.... type Σ1..1codedirectlink | openapi | login | oauth | other
repositoryType (Required)
.... url Σ0..1uriURI of the repository
.... name Σ0..1stringName of the repository
.... datasetId Σ0..1stringId of the dataset that used to call for dataset in repository
.... variantsetId Σ0..1stringId of the variantset that used to call for variantset in repository
.... readsetId Σ0..1stringId of the read
... pointer Σ0..*Reference(Sequence)Pointer to next atomic sequence
... structureVariant Σ0..*BackboneElementStructural variant
.... precisionOfBoundaries Σ0..1stringPrecision of boundaries
.... reportedaCGHRatio Σ0..1decimalStructural Variant reported aCGH ratio
.... length Σ0..1integerStructural Variant Length
.... outer Σ0..1BackboneElementStructural variant outer
..... start Σ0..1integerStructural Variant Outer Start
..... end Σ0..1integerStructural Variant Outer End
.... inner Σ0..1BackboneElementStructural variant inner
..... start Σ0..1integerStructural Variant Inner Start
..... end Σ0..1integerStructural Variant Inner End

doco Documentation for this format