fhirtypes
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TypeScript
import { IMolecularSequenceQuality, IMolecularSequenceReferenceSeq, IMolecularSequenceRepository, IMolecularSequenceStructureVariant, IMolecularSequenceVariant } from '../backbones';
import { IDomainResource, IElement } from '../base';
import { IIdentifier, IQuantity, IReference } from '../datatypes';
import { SequenceTypeType } from '../types';
/**
* @name IMolecularSequence
* @description Raw data describing a biological sequence.
* @see <a href="https://hl7.org/fhir/R4/molecularsequence.html">MolecularSequence</a>
* @version R4
* @extends {IDomainResource}
* @author Claudia Alarcón Lazo
*/
export interface IMolecularSequence extends IDomainResource {
/**
* @description A unique identifier for this particular sequence instance. This is a FHIR-defined id.
*/
identifier?: IIdentifier[];
/**
* @description Amino Acid Sequence/ DNA Sequence / RNA Sequence.
* @description aa | dna | rna
* @see <a href="https://hl7.org/fhir/R4/valueset-sequence-type.html">SequenceType</a>
*/
type?: SequenceTypeType;
/**
* @description Extensions for type
*/
_type?: IElement;
/**
* @description Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).
*/
coordinateSystem: number;
/**
* @description Extensions for coordinateSystem
*/
_coordinateSystem?: IElement;
/**
* @description The patient whose sequencing results are described by this resource.
*/
patient?: IReference;
/**
* @description Specimen used for sequencing.
*/
specimen?: IReference;
/**
* @description The method for sequencing, for example, chip information.
*/
device?: IReference;
/**
* @description The organization or lab that should be responsible for this result.
*/
performer?: IReference;
/**
* @description The number of copies of the sequence of interest. (RNASeq).
*/
quantity?: IQuantity;
/**
* @description A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
*/
referenceSeq?: IMolecularSequenceReferenceSeq;
/**
* @description A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
*/
variant?: IMolecularSequenceVariant[];
/**
* @description Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.
*/
observedSeq?: string;
/**
* @description Extensions for observedSeq
*/
_observedSeq?: IElement;
/**
* @description An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
*/
quality?: IMolecularSequenceQuality[];
/**
* @description Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
*/
readCoverage?: number;
/**
* @description Extensions for readCoverage
*/
_readCoverage?: IElement;
/**
* @description Configurations of the external repository. The repository shall store target\u0027s observedSeq or records related with target\u0027s observedSeq.
*/
repository?: IMolecularSequenceRepository[];
/**
* @description Pointer to next atomic sequence which at most contains one variant.
*/
pointer?: IReference[];
/**
* @description Information about chromosome structure variation.
*/
structureVariant?: IMolecularSequenceStructureVariant[];
}