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MolecularSequence

Raw data describing a biological sequence.

Properties

NameCardTypeDescription
id0..1stringLogical id of this artifact
meta0..1MetaMetadata about the resource
implicitRules0..1uriA set of rules under which this content was created
language0..1codeLanguage of the resource content
text0..1NarrativeText summary of the resource, for human interpretation
contained0..*ResourceContained, inline Resources
extension0..*ExtensionAdditional content defined by implementations
modifierExtension0..*ExtensionExtensions that cannot be ignored
identifier0..*IdentifierUnique ID for this particular sequence. This is a FHIR-defined id
type0..1codeaa | dna | rna
coordinateSystem1..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 | 0..1 | Reference | Who and/or what this is about | specimen | 0..1 | Reference | Specimen used for sequencing | device | 0..1 | Reference | The method for sequencing | performer | 0..1 | Reference | Who should be responsible for test result | quantity | 0..1 | Quantity | The number of copies of the sequence of interest. (RNASeq) | referenceSeq | 0..1 | BackboneElement | A sequence used as reference | variant | 0.. | BackboneElement | Variant in sequence | observedSeq | 0..1 | string | Sequence that was observed | quality | 0.. | BackboneElement | An set of value as quality of sequence | readCoverage | 0..1 | integer | Average number of reads representing a given nucleotide in the reconstructed sequence | repository | 0.. | BackboneElement | External repository which contains detailed report related with observedSeq in this resource | pointer | 0.. | Reference | Pointer to next atomic sequence | structureVariant | 0..* | BackboneElement | Structural variant

Search Parameters

NameTypeDescriptionExpression
chromosometokenChromosome number of the reference sequenceMolecularSequence.referenceSeq.chromosome
identifiertokenThe unique identity for a particular sequenceMolecularSequence.identifier
patientreferenceThe subject that the observation is aboutMolecularSequence.patient
referenceseqidtokenReference Sequence of the sequenceMolecularSequence.referenceSeq.referenceSeqId
typetokenAmino Acid Sequence/ DNA Sequence / RNA SequenceMolecularSequence.type
variant-endnumberEnd position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant.MolecularSequence.variant.end
variant-startnumberStart position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant.MolecularSequence.variant.start
window-endnumberEnd position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence.MolecularSequence.referenceSeq.windowEnd
window-startnumberStart position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence.MolecularSequence.referenceSeq.windowStart
chromosome-variant-coordinatecompositeSearch parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as chromosome-variant-coordinate=1$lt345$gt123, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.MolecularSequence.variant
chromosome-window-coordinatecompositeSearch parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as chromosome-window-coordinate=1$lt345$gt123, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.MolecularSequence.referenceSeq
referenceseqid-variant-coordinatecompositeSearch parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.MolecularSequence.variant
referenceseqid-window-coordinatecompositeSearch parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.MolecularSequence.referenceSeq