MolecularSequence

Raw data describing a biological sequence.

These interaction paths describe standard FHIR R4 patterns. Availability can depend on the API capabilities enabled for your Ovok project.

Interaction	Method	Path
Read	GET	/fhir/R4/MolecularSequence/[id]
Vread	GET	/fhir/R4/MolecularSequence/[id]/_history/[vid]
Update	PUT	/fhir/R4/MolecularSequence/[id]
Patch	PATCH	/fhir/R4/MolecularSequence/[id]
Delete	DELETE	/fhir/R4/MolecularSequence/[id]
Create	POST	/fhir/R4/MolecularSequence
Search	GET	/fhir/R4/MolecularSequence
History	GET	/fhir/R4/MolecularSequence/[id]/_history

Top-level elements

Element	Type	Cardinality	Description
id	string	0..1	Logical id of this artifact
meta	Meta	0..1	Metadata about the resource
implicitRules	uri	0..1	A set of rules under which this content was created
language	code	0..1	Language of the resource content
text	Narrative	0..1	Text summary of the resource, for human interpretation
contained	Resource	0..*	Contained, inline Resources
extension	Extension	0..*	Additional content defined by implementations
modifierExtension	Extension	0..*	Extensions that cannot be ignored
identifier	Identifier	0..*	Unique ID for this particular sequence. This is a FHIR-defined id
type	code	0..1	aa | dna | rna
coordinateSystem	integer	1..1	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)
patient	Reference	0..1	Who and/or what this is about
specimen	Reference	0..1	Specimen used for sequencing
device	Reference	0..1	The method for sequencing
performer	Reference	0..1	Who should be responsible for test result
quantity	Quantity	0..1	The number of copies of the sequence of interest. (RNASeq)
referenceSeq	BackboneElement	0..1	A sequence used as reference
variant	BackboneElement	0..*	Variant in sequence
observedSeq	string	0..1	Sequence that was observed
quality	BackboneElement	0..*	An set of value as quality of sequence
readCoverage	integer	0..1	Average number of reads representing a given nucleotide in the reconstructed sequence
repository	BackboneElement	0..*	External repository which contains detailed report related with observedSeq in this resource
pointer	Reference	0..*	Pointer to next atomic sequence
structureVariant	BackboneElement	0..*	Structural variant

Resource-specific search parameters

Parameter	Type	Description
chromosome	token	Chromosome number of the reference sequence
chromosome-variant-coordinate	composite	Search 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.
chromosome-window-coordinate	composite	Search 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.
identifier	token	The unique identity for a particular sequence
patient	reference	The subject that the observation is about
referenceseqid	token	Reference Sequence of the sequence
referenceseqid-variant-coordinate	composite	Search 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.
referenceseqid-window-coordinate	composite	Search 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.
type	token	Amino Acid Sequence/ DNA Sequence / RNA Sequence
variant-end	number	End 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.
variant-start	number	Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant.
window-end	number	End 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.
window-start	number	Start 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.

Reference

Official FHIR R4 spec: MolecularSequence.
Maturity: Trial Use 1 (FMM 1).