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
keyboard_arrow_down
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
keyboard_arrow_down
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
keyboard_arrow_down
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
keyboard_arrow_down
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
keyboard_arrow_down
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
keyboard_arrow_down
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
keyboard_arrow_down
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
keyboard_arrow_down
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
keyboard_arrow_down
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
keyboard_arrow_down