sequences

Create Sequence

post

/organizations/{organizationId}/fhir/3/Sequence

Raw data describing a biological sequence.

Request

Headers


content-type*	string	application/json	application/json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Params


organizationId*	string\|string		id\|slug

Body


resourceType*	string	Sequence	This is a Sequence resource
identifier	array(Identifier)		A unique identifier for this particular sequence instance. This is a FHIR-defined id.
type	string	aa\|dna\|rna	Amino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystem	number		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).
patient	Reference		The patient whose sequencing results are described by this resource.
specimen	Reference		Specimen used for sequencing.
device	Reference		The method for sequencing, for example, chip information.
performer	Reference		The organization or lab that should be responsible for this result.
quantity	Quantity		The number of copies of the seqeunce of interest. (RNASeq).
referenceSeq	Sequence_ReferenceSeq		A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variant	array(Sequence_Variant)		The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.
observedSeq	string		Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.
quality	array(Sequence_Quality)		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)).
readCoverage	number		Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repository	array(Sequence_Repository)		Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
pointer	array(Reference)		Pointer to next atomic sequence which at most contains one variant.

Response

201 400 401 404

Patch Sequence

patch

/organizations/{organizationId}/fhir/3/Sequence/{resourceId}

Raw data describing a biological sequence.

Request

Headers


content-type*	string	application/json-patch+json	application/json-patch+json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Params


organizationId*	string\|string		id\|slug
resourceId*

Body


resourceType*	string	Sequence	This is a Sequence resource
identifier	array(Identifier)		A unique identifier for this particular sequence instance. This is a FHIR-defined id.
type	string	aa\|dna\|rna	Amino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystem	number		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).
patient	Reference		The patient whose sequencing results are described by this resource.
specimen	Reference		Specimen used for sequencing.
device	Reference		The method for sequencing, for example, chip information.
performer	Reference		The organization or lab that should be responsible for this result.
quantity	Quantity		The number of copies of the seqeunce of interest. (RNASeq).
referenceSeq	Sequence_ReferenceSeq		A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variant	array(Sequence_Variant)		The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.
observedSeq	string		Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.
quality	array(Sequence_Quality)		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)).
readCoverage	number		Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repository	array(Sequence_Repository)		Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
pointer	array(Reference)		Pointer to next atomic sequence which at most contains one variant.

Response

200 201 400 401 404 409

Read Sequence

get

/organizations/{organizationId}/fhir/3/Sequence/{resourceId}

Request

Headers


content-type*	string	application/json	application/json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Params


organizationId*	string\|string		id\|slug
resourceId*

Response

200 401 404

Read History Sequence

get

/organizations/{organizationId}/fhir/3/Sequence/{resourceId}/_history

Request

Headers


content-type*	string	application/json	application/json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Query params


_count	string
_since	string

Params


organizationId*	string\|string		id\|slug
resourceId*

Response

200 401 404

Read Version Sequence

get

/organizations/{organizationId}/fhir/3/Sequence/{resourceId}/_history/{versionId}

Request

Headers


content-type*	string	application/json	application/json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Params


organizationId*	string\|string	id\|slug
resourceId*
versionId*

Response

200 400 401 404

Remove Sequence

delete

/organizations/{organizationId}/fhir/3/Sequence/{resourceId}

Request

Headers


content-type*	string	application/json	application/json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Params


organizationId*	string\|string		id\|slug
resourceId*

Response

200 204 400 401 404 409

Search Get Sequence

get

/organizations/{organizationId}/fhir/3/Sequence

Request

Headers


content-type*	string	application/json	application/json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Query params


_id	string
_language	string
chromosome	string
coordinate	string
end	string
identifier	string
patient	string
start	string
type	string

Params


organizationId*	string\|string		id\|slug

Response

200 401 404

Search History Sequence

get

/organizations/{organizationId}/fhir/3/Sequence/_history

Request

Headers


content-type*	string	application/json	application/json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Query params


_count	string
_since	string

Params


organizationId*	string\|string		id\|slug

Response

200 401 404

Search Post Sequence

post

/organizations/{organizationId}/fhir/3/Sequence/_search

Raw data describing a biological sequence.

Request

Headers


content-type*	string	application/json\|application/x-www-form-urlencoded	application/json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Query params


_id	string
_language	string
chromosome	string
coordinate	string
end	string
identifier	string
patient	string
start	string
type	string

Params


organizationId*	string\|string		id\|slug

Body


resourceType*	string	Sequence	This is a Sequence resource
identifier	array(Identifier)		A unique identifier for this particular sequence instance. This is a FHIR-defined id.
type	string	aa\|dna\|rna	Amino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystem	number		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).
patient	Reference		The patient whose sequencing results are described by this resource.
specimen	Reference		Specimen used for sequencing.
device	Reference		The method for sequencing, for example, chip information.
performer	Reference		The organization or lab that should be responsible for this result.
quantity	Quantity		The number of copies of the seqeunce of interest. (RNASeq).
referenceSeq	Sequence_ReferenceSeq		A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variant	array(Sequence_Variant)		The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.
observedSeq	string		Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.
quality	array(Sequence_Quality)		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)).
readCoverage	number		Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repository	array(Sequence_Repository)		Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
pointer	array(Reference)		Pointer to next atomic sequence which at most contains one variant.

Response

200 401 404

Update Sequence

put

/organizations/{organizationId}/fhir/3/Sequence/{resourceId}

Raw data describing a biological sequence.

Request

Headers


content-type*	string	application/json	application/json
log-cdata	string
log-cdata-format	string	kv\|json	kv
Authorization	string	Bearer <token>

Params


organizationId*	string\|string		id\|slug
resourceId*

Body


resourceType*	string	Sequence	This is a Sequence resource
identifier	array(Identifier)		A unique identifier for this particular sequence instance. This is a FHIR-defined id.
type	string	aa\|dna\|rna	Amino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystem	number		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).
patient	Reference		The patient whose sequencing results are described by this resource.
specimen	Reference		Specimen used for sequencing.
device	Reference		The method for sequencing, for example, chip information.
performer	Reference		The organization or lab that should be responsible for this result.
quantity	Quantity		The number of copies of the seqeunce of interest. (RNASeq).
referenceSeq	Sequence_ReferenceSeq		A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variant	array(Sequence_Variant)		The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.
observedSeq	string		Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.
quality	array(Sequence_Quality)		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)).
readCoverage	number		Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repository	array(Sequence_Repository)		Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
pointer	array(Reference)		Pointer to next atomic sequence which at most contains one variant.

Response

200 201 400 401 404 409