NameFlagsCard.TypeDescription & Constraintsdoco
.. Sequence ΣIDomainResourceInformation about a biological sequence
+ Only 0 and 1 are valid for coordinateSystem
Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
... 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..1BackboneElementA sequence used as reference
+ 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 string to represent reference sequence
.... 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..*BackboneElementVariant in sequence
.... 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 in the 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..1stringSequence that was observed
... quality Σ0..*BackboneElementAn set of value as quality of sequence
.... type Σ1..1codeindel | snp | unknown
qualityType (Required)
.... standardSequence Σ0..1CodeableConceptStandard sequence for comparison
FDA-StandardSequence (Example)
.... start Σ0..1integerStart position of the sequence
.... end Σ0..1integerEnd position of the sequence
.... score Σ0..1QuantityQuality score for the comparison
.... method Σ0..1CodeableConceptMethod to get quality
FDA-Method (Example)
.... 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 of comparison
.... recall Σ0..1decimalRecall of comparison
.... 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..1stringRepository's name
.... 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

doco Documentation for this format