molecular sequences
Create Molecular Sequence
post
/organizations/{organizationId}/fhir/4/MolecularSequence
Raw data describing a biological sequence.
Request
Headers
content-type* | string | application/json|application/json+fhir | application/json |
log-cdata | string | ||
log-cdata-format | string | kv|json | kv |
Authorization | string | Bearer <token> |
Params
organizationId* | string|string | id|slug |
Body
resourceType* | This is a MolecularSequence resource | ||
id | id | The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. | |
meta | Meta | The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource. | |
implicitRules | uri | A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. | |
language | code | The base language in which the resource is written. | |
text | Narrative | A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety. | |
contained | array(ResourceList) | These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. | |
extension | array(Extension) | May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. | |
modifierExtension | array(Extension) | May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). | |
identifier | array(Identifier) | A unique identifier for this particular sequence instance. This is a FHIR-defined id. | |
type | aa|dna|rna | Amino Acid Sequence/ DNA Sequence / RNA Sequence. | |
coordinateSystem | integer | 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 sequence of interest. (RNASeq). | |
referenceSeq | MolecularSequence_ReferenceSeq | A sequence that is used as a reference to describe variants that are present in a sequence analyzed. | |
variant | array(MolecularSequence_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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd. | |
quality | array(MolecularSequence_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 | integer | Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. | |
repository | array(MolecularSequence_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. | |
structureVariant | array(MolecularSequence_StructureVariant) | Information about chromosome structure variation. |
Response
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Patch Molecular Sequence
patch
/organizations/{organizationId}/fhir/4/MolecularSequence/{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* | This is a MolecularSequence resource | ||
id | id | The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. | |
meta | Meta | The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource. | |
implicitRules | uri | A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. | |
language | code | The base language in which the resource is written. | |
text | Narrative | A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety. | |
contained | array(ResourceList) | These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. | |
extension | array(Extension) | May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. | |
modifierExtension | array(Extension) | May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). | |
identifier | array(Identifier) | A unique identifier for this particular sequence instance. This is a FHIR-defined id. | |
type | aa|dna|rna | Amino Acid Sequence/ DNA Sequence / RNA Sequence. | |
coordinateSystem | integer | 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 sequence of interest. (RNASeq). | |
referenceSeq | MolecularSequence_ReferenceSeq | A sequence that is used as a reference to describe variants that are present in a sequence analyzed. | |
variant | array(MolecularSequence_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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd. | |
quality | array(MolecularSequence_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 | integer | Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. | |
repository | array(MolecularSequence_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. | |
structureVariant | array(MolecularSequence_StructureVariant) | Information about chromosome structure variation. |
Response
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Read Molecular Sequence
get
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}
Request
Headers
content-type* | string | application/json|application/json+fhir | application/json |
log-cdata | string | ||
log-cdata-format | string | kv|json | kv |
Authorization | string | Bearer <token> |
Params
organizationId* | string|string | id|slug | |
resourceId* |
Response
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Read History Molecular Sequence
get
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}/_history
Request
Headers
content-type* | string | application/json|application/json+fhir | 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
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Read Version Molecular Sequence
get
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}/_history/{versionId}
Request
Headers
content-type* | string | application/json|application/json+fhir | 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
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Remove Molecular Sequence
delete
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}
Request
Headers
content-type* | string | application/json|application/json+fhir | application/json |
log-cdata | string | ||
log-cdata-format | string | kv|json | kv |
Authorization | string | Bearer <token> |
Params
organizationId* | string|string | id|slug | |
resourceId* |
Response
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Search Get Molecular Sequence
get
/organizations/{organizationId}/fhir/4/MolecularSequence
Request
Headers
content-type* | string | application/json|application/json+fhir | application/json |
log-cdata | string | ||
log-cdata-format | string | kv|json | kv |
Authorization | string | Bearer <token> |
Query params
_id | string | ||
_language | string | ||
chromosome | string | ||
chromosome-variant-coordinate | string | ||
chromosome-window-coordinate | string | ||
identifier | string | ||
patient | string | ||
referenceseqid | string | ||
referenceseqid-variant-coordinate | string | ||
referenceseqid-window-coordinate | string | ||
type | string | ||
variant-end | string | ||
variant-start | string | ||
window-end | string | ||
window-start | string |
Params
organizationId* | string|string | id|slug |
Response
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Search History Molecular Sequence
get
/organizations/{organizationId}/fhir/4/MolecularSequence/_history
Request
Headers
content-type* | string | application/json|application/json+fhir | 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
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Search Post Molecular Sequence
post
/organizations/{organizationId}/fhir/4/MolecularSequence/_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 | ||
chromosome-variant-coordinate | string | ||
chromosome-window-coordinate | string | ||
identifier | string | ||
patient | string | ||
referenceseqid | string | ||
referenceseqid-variant-coordinate | string | ||
referenceseqid-window-coordinate | string | ||
type | string | ||
variant-end | string | ||
variant-start | string | ||
window-end | string | ||
window-start | string |
Params
organizationId* | string|string | id|slug |
Body
resourceType* | This is a MolecularSequence resource | ||
id | id | The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. | |
meta | Meta | The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource. | |
implicitRules | uri | A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. | |
language | code | The base language in which the resource is written. | |
text | Narrative | A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety. | |
contained | array(ResourceList) | These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. | |
extension | array(Extension) | May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. | |
modifierExtension | array(Extension) | May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). | |
identifier | array(Identifier) | A unique identifier for this particular sequence instance. This is a FHIR-defined id. | |
type | aa|dna|rna | Amino Acid Sequence/ DNA Sequence / RNA Sequence. | |
coordinateSystem | integer | 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 sequence of interest. (RNASeq). | |
referenceSeq | MolecularSequence_ReferenceSeq | A sequence that is used as a reference to describe variants that are present in a sequence analyzed. | |
variant | array(MolecularSequence_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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd. | |
quality | array(MolecularSequence_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 | integer | Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. | |
repository | array(MolecularSequence_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. | |
structureVariant | array(MolecularSequence_StructureVariant) | Information about chromosome structure variation. |
Response
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Update Molecular Sequence
put
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}
Raw data describing a biological sequence.
Request
Headers
content-type* | string | application/json|application/json+fhir | 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* | This is a MolecularSequence resource | ||
id | id | The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. | |
meta | Meta | The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource. | |
implicitRules | uri | A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. | |
language | code | The base language in which the resource is written. | |
text | Narrative | A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety. | |
contained | array(ResourceList) | These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. | |
extension | array(Extension) | May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. | |
modifierExtension | array(Extension) | May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). | |
identifier | array(Identifier) | A unique identifier for this particular sequence instance. This is a FHIR-defined id. | |
type | aa|dna|rna | Amino Acid Sequence/ DNA Sequence / RNA Sequence. | |
coordinateSystem | integer | 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 sequence of interest. (RNASeq). | |
referenceSeq | MolecularSequence_ReferenceSeq | A sequence that is used as a reference to describe variants that are present in a sequence analyzed. | |
variant | array(MolecularSequence_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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd. | |
quality | array(MolecularSequence_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 | integer | Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. | |
repository | array(MolecularSequence_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. | |
structureVariant | array(MolecularSequence_StructureVariant) | Information about chromosome structure variation. |
Response
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