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

201 400 401 404

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

200 201 400 401 404 409

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

200 401 404

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

200 401 404

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

200 400 401 404

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

200 204 400 401 404 409

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

200 401 404

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

200 401 404

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

200 401 404

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

200 201 400 401 404 409