Name | Flags | Card. | Type | Description & Constraints |
---|---|---|---|---|
MolecularSequence | TU | DomainResource | Representation of a molecular sequence Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension | |
identifier | Σ | 0..* | Identifier | Unique ID for this particular sequence |
type | Σ | 0..1 | code | aa | dna | rna Binding: sequence Type (Required) |
subject | Σ | 0..1 | Reference(Patient | Group | Substance | BiologicallyDerivedProduct | NutritionProduct) | Subject this sequence is associated too |
focus | Σ | 0..* | Reference(Any) | What the molecular sequence is about, when it is not about the subject of record |
specimen | Σ | 0..1 | Reference(Specimen) | Specimen used for sequencing |
device | Σ | 0..1 | Reference(Device) | The method for sequencing |
performer | Σ | 0..1 | Reference(Organization) | Who should be responsible for test result |
literal | Σ | 0..1 | string | Sequence that was observed |
formatted | Σ | 0..* | Attachment | Embedded file or a link (URL) which contains content to represent the sequence |
relative | Σ | 0..* | BackboneElement | A sequence defined relative to another sequence |
coordinateSystem | Σ | 1..1 | CodeableConcept | Ways of identifying nucleotides or amino acids within a sequence Binding: LL5323-2 (Extensible) |
ordinalPosition | 0..1 | integer | Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together | |
sequenceRange | 0..1 | Range | Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together | |
startingSequence | ΣC | 0..1 | BackboneElement | A sequence used as starting sequence + Rule: Both genomeAssembly and chromosome must be both contained if either one of them is contained + Rule: Have and only have one of the following elements in startingSequence: 1. genomeAssembly; 2 sequence |
genomeAssembly | ΣC | 0..1 | CodeableConcept | The genome assembly used for starting sequence, e.g. GRCh38 Binding: LL1040-6 (Extensible) |
chromosome | ΣC | 0..1 | CodeableConcept | Chromosome Identifier Binding: LL2938-0 (Required) |
sequence[x] | ΣC | 0..1 | The reference sequence that represents the starting sequence Binding: Multiple bindings acceptable (NCBI or LRG) (Example) | |
sequenceCodeableConcept | CodeableConcept | |||
sequenceString | string | |||
sequenceReference | Reference(MolecularSequence) | |||
windowStart | Σ | 0..1 | integer | Start position of the window on the starting sequence |
windowEnd | Σ | 0..1 | integer | End position of the window on the starting sequence |
orientation | Σ | 0..1 | code | sense | antisense Binding: orientation Type (Required) |
strand | Σ | 0..1 | code | watson | crick Binding: strand Type (Required) |
edit | Σ | 0..* | BackboneElement | Changes in sequence from the starting sequence |
start | Σ | 0..1 | integer | Start position of the edit on the starting sequence |
end | Σ | 0..1 | integer | End position of the edit on the starting sequence |
replacementSequence | Σ | 0..1 | string | Allele that was observed |
replacedSequence | Σ | 0..1 | string | Allele in the starting sequence |
Documentation for this format |