molecular sequences

Create Molecular Sequence

post
/organizations/{organizationId}/fhir/4/MolecularSequence

Raw data describing a biological sequence.

Request

Headers

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

Params

organizationId*string|stringid|slug

Body

resourceType*This is a MolecularSequence resource
ididThe logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
metaMetaThe 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.
implicitRulesuriA 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.
languagecodeThe base language in which the resource is written.
textNarrativeA 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.
containedarray(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.
extensionarray(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.
modifierExtensionarray(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).
identifierarray(Identifier)A unique identifier for this particular sequence instance. This is a FHIR-defined id.
typeaa|dna|rnaAmino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystemintegerWhether 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 sequence of interest. (RNASeq).
referenceSeqMolecularSequence_ReferenceSeqA sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variantarray(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.
observedSeqstringSequence 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.
qualityarray(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)).
readCoverageintegerCoverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repositoryarray(MolecularSequence_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.
structureVariantarray(MolecularSequence_StructureVariant)Information about chromosome structure variation.

Response

Patch Molecular Sequence

patch
/organizations/{organizationId}/fhir/4/MolecularSequence/{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*This is a MolecularSequence resource
ididThe logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
metaMetaThe 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.
implicitRulesuriA 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.
languagecodeThe base language in which the resource is written.
textNarrativeA 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.
containedarray(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.
extensionarray(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.
modifierExtensionarray(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).
identifierarray(Identifier)A unique identifier for this particular sequence instance. This is a FHIR-defined id.
typeaa|dna|rnaAmino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystemintegerWhether 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 sequence of interest. (RNASeq).
referenceSeqMolecularSequence_ReferenceSeqA sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variantarray(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.
observedSeqstringSequence 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.
qualityarray(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)).
readCoverageintegerCoverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repositoryarray(MolecularSequence_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.
structureVariantarray(MolecularSequence_StructureVariant)Information about chromosome structure variation.

Response

Read Molecular Sequence

get
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}

Request

Headers

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

Params

organizationId*string|stringid|slug
resourceId*

Response

Read History Molecular Sequence

get
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}/_history

Request

Headers

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

Query params

_countstring
_sincestring

Params

organizationId*string|stringid|slug
resourceId*

Response

Read Version Molecular Sequence

get
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}/_history/{versionId}

Request

Headers

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

Params

organizationId*string|stringid|slug
resourceId*
versionId*

Response

Remove Molecular Sequence

delete
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}

Request

Headers

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

Params

organizationId*string|stringid|slug
resourceId*

Response

Search Get Molecular Sequence

get
/organizations/{organizationId}/fhir/4/MolecularSequence

Request

Headers

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

Query params

_idstring
_languagestring
chromosomestring
chromosome-variant-coordinatestring
chromosome-window-coordinatestring
identifierstring
patientstring
referenceseqidstring
referenceseqid-variant-coordinatestring
referenceseqid-window-coordinatestring
typestring
variant-endstring
variant-startstring
window-endstring
window-startstring

Params

organizationId*string|stringid|slug

Response

Search History Molecular Sequence

get
/organizations/{organizationId}/fhir/4/MolecularSequence/_history

Request

Headers

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

Query params

_countstring
_sincestring

Params

organizationId*string|stringid|slug

Response

Search Post Molecular Sequence

post
/organizations/{organizationId}/fhir/4/MolecularSequence/_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
chromosome-variant-coordinatestring
chromosome-window-coordinatestring
identifierstring
patientstring
referenceseqidstring
referenceseqid-variant-coordinatestring
referenceseqid-window-coordinatestring
typestring
variant-endstring
variant-startstring
window-endstring
window-startstring

Params

organizationId*string|stringid|slug

Body

resourceType*This is a MolecularSequence resource
ididThe logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
metaMetaThe 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.
implicitRulesuriA 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.
languagecodeThe base language in which the resource is written.
textNarrativeA 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.
containedarray(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.
extensionarray(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.
modifierExtensionarray(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).
identifierarray(Identifier)A unique identifier for this particular sequence instance. This is a FHIR-defined id.
typeaa|dna|rnaAmino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystemintegerWhether 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 sequence of interest. (RNASeq).
referenceSeqMolecularSequence_ReferenceSeqA sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variantarray(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.
observedSeqstringSequence 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.
qualityarray(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)).
readCoverageintegerCoverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repositoryarray(MolecularSequence_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.
structureVariantarray(MolecularSequence_StructureVariant)Information about chromosome structure variation.

Response

Update Molecular Sequence

put
/organizations/{organizationId}/fhir/4/MolecularSequence/{resourceId}

Raw data describing a biological sequence.

Request

Headers

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

Params

organizationId*string|stringid|slug
resourceId*

Body

resourceType*This is a MolecularSequence resource
ididThe logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
metaMetaThe 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.
implicitRulesuriA 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.
languagecodeThe base language in which the resource is written.
textNarrativeA 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.
containedarray(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.
extensionarray(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.
modifierExtensionarray(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).
identifierarray(Identifier)A unique identifier for this particular sequence instance. This is a FHIR-defined id.
typeaa|dna|rnaAmino Acid Sequence/ DNA Sequence / RNA Sequence.
coordinateSystemintegerWhether 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 sequence of interest. (RNASeq).
referenceSeqMolecularSequence_ReferenceSeqA sequence that is used as a reference to describe variants that are present in a sequence analyzed.
variantarray(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.
observedSeqstringSequence 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.
qualityarray(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)).
readCoverageintegerCoverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
repositoryarray(MolecularSequence_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.
structureVariantarray(MolecularSequence_StructureVariant)Information about chromosome structure variation.

Response