sequences

Create Sequence

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

Raw data describing a biological sequence.

Request

Headers

content-type*stringapplication/jsonapplication/json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Params

organizationId*string|stringid|slug

Body

resourceType*stringSequenceThis is a Sequence resource
identifierarray(Identifier)A unique identifier for this particular sequence instance. This is a FHIR-defined id.
typestringaa|dna|rnaAmino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystemnumberWhether 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).
patientReferenceThe patient whose sequencing results are described by this resource.
specimenReferenceSpecimen used for sequencing.
deviceReferenceThe method for sequencing, for example, chip information.
performerReferenceThe organization or lab that should be responsible for this result.
quantityQuantityThe number of copies of the seqeunce of interest. (RNASeq).
referenceSeqSequence_ReferenceSeqA sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variantarray(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.
observedSeqstringSequence 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.
qualityarray(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)).
readCoveragenumberCoverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repositoryarray(Sequence_Repository)Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
pointerarray(Reference)Pointer to next atomic sequence which at most contains one variant.

Response

Patch Sequence

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

Raw data describing a biological sequence.

Request

Headers

content-type*stringapplication/json-patch+jsonapplication/json-patch+json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Params

organizationId*string|stringid|slug
resourceId*

Body

resourceType*stringSequenceThis is a Sequence resource
identifierarray(Identifier)A unique identifier for this particular sequence instance. This is a FHIR-defined id.
typestringaa|dna|rnaAmino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystemnumberWhether 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).
patientReferenceThe patient whose sequencing results are described by this resource.
specimenReferenceSpecimen used for sequencing.
deviceReferenceThe method for sequencing, for example, chip information.
performerReferenceThe organization or lab that should be responsible for this result.
quantityQuantityThe number of copies of the seqeunce of interest. (RNASeq).
referenceSeqSequence_ReferenceSeqA sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variantarray(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.
observedSeqstringSequence 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.
qualityarray(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)).
readCoveragenumberCoverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repositoryarray(Sequence_Repository)Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
pointerarray(Reference)Pointer to next atomic sequence which at most contains one variant.

Response

Read Sequence

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

Request

Headers

content-type*stringapplication/jsonapplication/json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Params

organizationId*string|stringid|slug
resourceId*

Response

Read History Sequence

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

Request

Headers

content-type*stringapplication/jsonapplication/json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Query params

_countstring
_sincestring

Params

organizationId*string|stringid|slug
resourceId*

Response

Read Version Sequence

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

Request

Headers

content-type*stringapplication/jsonapplication/json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Params

organizationId*string|stringid|slug
resourceId*
versionId*

Response

Remove Sequence

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

Request

Headers

content-type*stringapplication/jsonapplication/json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Params

organizationId*string|stringid|slug
resourceId*

Response

Search Get Sequence

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

Request

Headers

content-type*stringapplication/jsonapplication/json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Query params

_idstring
_languagestring
chromosomestring
coordinatestring
endstring
identifierstring
patientstring
startstring
typestring

Params

organizationId*string|stringid|slug

Response

Search History Sequence

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

Request

Headers

content-type*stringapplication/jsonapplication/json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Query params

_countstring
_sincestring

Params

organizationId*string|stringid|slug

Response

Search Post Sequence

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

Raw data describing a biological sequence.

Request

Headers

content-type*stringapplication/json|application/x-www-form-urlencodedapplication/json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Query params

_idstring
_languagestring
chromosomestring
coordinatestring
endstring
identifierstring
patientstring
startstring
typestring

Params

organizationId*string|stringid|slug

Body

resourceType*stringSequenceThis is a Sequence resource
identifierarray(Identifier)A unique identifier for this particular sequence instance. This is a FHIR-defined id.
typestringaa|dna|rnaAmino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystemnumberWhether 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).
patientReferenceThe patient whose sequencing results are described by this resource.
specimenReferenceSpecimen used for sequencing.
deviceReferenceThe method for sequencing, for example, chip information.
performerReferenceThe organization or lab that should be responsible for this result.
quantityQuantityThe number of copies of the seqeunce of interest. (RNASeq).
referenceSeqSequence_ReferenceSeqA sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variantarray(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.
observedSeqstringSequence 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.
qualityarray(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)).
readCoveragenumberCoverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repositoryarray(Sequence_Repository)Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
pointerarray(Reference)Pointer to next atomic sequence which at most contains one variant.

Response

Update Sequence

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

Raw data describing a biological sequence.

Request

Headers

content-type*stringapplication/jsonapplication/json
log-cdatastring
log-cdata-formatstringkv|jsonkv
AuthorizationstringBearer <token>

Params

organizationId*string|stringid|slug
resourceId*

Body

resourceType*stringSequenceThis is a Sequence resource
identifierarray(Identifier)A unique identifier for this particular sequence instance. This is a FHIR-defined id.
typestringaa|dna|rnaAmino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystemnumberWhether 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).
patientReferenceThe patient whose sequencing results are described by this resource.
specimenReferenceSpecimen used for sequencing.
deviceReferenceThe method for sequencing, for example, chip information.
performerReferenceThe organization or lab that should be responsible for this result.
quantityQuantityThe number of copies of the seqeunce of interest. (RNASeq).
referenceSeqSequence_ReferenceSeqA sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variantarray(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.
observedSeqstringSequence 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.
qualityarray(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)).
readCoveragenumberCoverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repositoryarray(Sequence_Repository)Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.
pointerarray(Reference)Pointer to next atomic sequence which at most contains one variant.

Response