Name | Flags | Card. | Type | Description & Constraints![]() |
---|---|---|---|---|
ΣI | DomainResource | Information about a biological sequence + Only 0 and 1 are valid for coordinateSystem Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension | ||
Σ | 0..* | Identifier | Unique ID for this particular sequence. This is a FHIR-defined id | |
Σ | 0..1 | code | aa | dna | rna sequenceType (Example) | |
Σ | 1..1 | integer | Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end) | |
Σ | 0..1 | Reference(Patient) | Who and/or what this is about | |
Σ | 0..1 | Reference(Specimen) | Specimen used for sequencing | |
Σ | 0..1 | Reference(Device) | The method for sequencing | |
Σ | 0..1 | Reference(Organization) | Who should be responsible for test result | |
Σ | 0..1 | Quantity | The number of copies of the seqeunce of interest. (RNASeq) | |
ΣI | 0..1 | BackboneElement | A 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; | |
Σ | 0..1 | CodeableConcept | Chromosome containing genetic finding chromosome-human (Example) | |
Σ | 0..1 | string | The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37' | |
Σ | 0..1 | CodeableConcept | Reference identifier ENSEMBL (Example) | |
Σ | 0..1 | Reference(Sequence) | A Pointer to another Sequence entity as reference sequence | |
Σ | 0..1 | string | A string to represent reference sequence | |
Σ | 0..1 | integer | Directionality of DNA ( +1/-1) | |
Σ | 1..1 | integer | Start position of the window on the reference sequence | |
Σ | 1..1 | integer | End position of the window on the reference sequence | |
Σ | 0..* | BackboneElement | Variant in sequence | |
Σ | 0..1 | integer | Start position of the variant on the reference sequence | |
Σ | 0..1 | integer | End position of the variant on the reference sequence | |
Σ | 0..1 | string | Allele that was observed | |
Σ | 0..1 | string | Allele in the reference sequence | |
Σ | 0..1 | string | Extended CIGAR string for aligning the sequence with reference bases | |
Σ | 0..1 | Reference(Observation) | Pointer to observed variant information | |
Σ | 0..1 | string | Sequence that was observed | |
Σ | 0..* | BackboneElement | An set of value as quality of sequence | |
Σ | 1..1 | code | indel | snp | unknown qualityType (Required) | |
Σ | 0..1 | CodeableConcept | Standard sequence for comparison FDA-StandardSequence (Example) | |
Σ | 0..1 | integer | Start position of the sequence | |
Σ | 0..1 | integer | End position of the sequence | |
Σ | 0..1 | Quantity | Quality score for the comparison | |
Σ | 0..1 | CodeableConcept | Method to get quality FDA-Method (Example) | |
Σ | 0..1 | decimal | True positives from the perspective of the truth data | |
Σ | 0..1 | decimal | True positives from the perspective of the query data | |
Σ | 0..1 | decimal | False negatives | |
Σ | 0..1 | decimal | False positives | |
Σ | 0..1 | decimal | False positives where the non-REF alleles in the Truth and Query Call Sets match | |
Σ | 0..1 | decimal | Precision of comparison | |
Σ | 0..1 | decimal | Recall of comparison | |
Σ | 0..1 | decimal | F-score | |
Σ | 0..1 | integer | Average number of reads representing a given nucleotide in the reconstructed sequence | |
Σ | 0..* | BackboneElement | External repository which contains detailed report related with observedSeq in this resource | |
Σ | 1..1 | code | directlink | openapi | login | oauth | other repositoryType (Required) | |
Σ | 0..1 | uri | URI of the repository | |
Σ | 0..1 | string | Repository's name | |
Σ | 0..1 | string | Id of the dataset that used to call for dataset in repository | |
Σ | 0..1 | string | Id of the variantset that used to call for variantset in repository | |
Σ | 0..1 | string | Id of the read | |
Σ | 0..* | Reference(Sequence) | Pointer to next atomic sequence | |
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