MolecularSequence - FHIR Resource (r4)
This MolecularSequence Resource uses the FHIR API standard for access and structure.
Validate an MolecularSequence FHIR Resource (r4)
MolecularSequence Attributes
AttributeField is listTypeDescription
Description: Unique ID for this particular sequence. This is a FHIR-defined id
FHIR Version: r4
Attribute Type : Identifier
Required: N/A
Countability: Array
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"identifier": Learn more about the (MolecularSequence) identifier FHIR attribute
Description: aa | dna | rna
FHIR Version: r4
Attribute Type : code
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"type": "dna"Learn more about the (MolecularSequence) type FHIR attribute
Description: Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
FHIR Version: r4
Attribute Type : integer
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"coordinateSystem": 0Learn more about the (MolecularSequence) coordinateSystem FHIR attribute
Description: Who and/or what this is about
FHIR Version: r4
Attribute Type : Reference
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"patient": {
"reference": "Patient/example"
}Learn more about the (MolecularSequence) patient FHIR attribute
Description: Specimen used for sequencing
FHIR Version: r4
Attribute Type : Reference
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"specimen": Learn more about the (MolecularSequence) specimen FHIR attribute
Description: The method for sequencing
FHIR Version: r4
Attribute Type : Reference
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"device": Learn more about the (MolecularSequence) device FHIR attribute
Description: Who should be responsible for test result
FHIR Version: r4
Attribute Type : Reference
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"performer": Learn more about the (MolecularSequence) performer FHIR attribute
Description: The number of copies of the sequence of interest. (RNASeq)
FHIR Version: r4
Attribute Type : Quantity
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"quantity": Learn more about the (MolecularSequence) quantity FHIR attribute
Description: A sequence used as reference
FHIR Version: r4
Attribute Type : Data Type
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"referenceSeq": {
"referenceSeqId": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/nuccore",
"code": "NC_000009.11"
}
]
},
"strand": "watson",
"windowStart": 22125500,
"windowEnd": 22125510
}Learn more about the (MolecularSequence) referenceSeq FHIR attribute
Description: Variant in sequence
FHIR Version: r4
Attribute Type : Data Type
Required: N/A
Countability: Array
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"variant": [
{
"start": 22125503,
"end": 22125504,
"observedAllele": "C",
"referenceAllele": "G"
}
]Learn more about the (MolecularSequence) variant FHIR attribute
Description: Sequence that was observed
FHIR Version: r4
Attribute Type : string
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"observedSeq": Learn more about the (MolecularSequence) observedSeq FHIR attribute
Description: An set of value as quality of sequence
FHIR Version: r4
Attribute Type : Data Type
Required: N/A
Countability: Array
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"quality": Learn more about the (MolecularSequence) quality FHIR attribute
Description: Average number of reads representing a given nucleotide in the reconstructed sequence
FHIR Version: r4
Attribute Type : integer
Required: N/A
Countability: Singleton
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"readCoverage": Learn more about the (MolecularSequence) readCoverage FHIR attribute
Description: External repository which contains detailed report related with observedSeq in this resource
FHIR Version: r4
Attribute Type : Data Type
Required: N/A
Countability: Array
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"repository": [
{
"type": "openapi",
"url": "http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-type=application/json",
"name": "GA4GH API",
"variantsetId": "3:rs1333049"
}
]Learn more about the (MolecularSequence) repository FHIR attribute
Description: Pointer to next atomic sequence
FHIR Version: r4
Attribute Type : Reference
Required: N/A
Countability: Array
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"pointer": Learn more about the (MolecularSequence) pointer FHIR attribute
Description: Structural variant
FHIR Version: r4
Attribute Type : Data Type
Required: N/A
Countability: Array
Flags: N/A
Terminology bindings: N/A
Requirements: N/A
Comments: N/A
Example:
"structureVariant": Learn more about the (MolecularSequence) structureVariant FHIR attribute
MolecularSequence Example
{
"resourceType": "MolecularSequence",
"id": "example",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example</p><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><p><b>patient</b>: <a>Patient/example</a></p><h3>ReferenceSeqs</h3><table><tr><td>-</td><td><b>ReferenceSeqId</b></td><td><b>Strand</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>NC_000009.11 <span>(Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000009.11' = 'NC_000009.11)</span></td><td>watson</td><td>22125500</td><td>22125510</td></tr></table><h3>Variants</h3><table><tr><td>-</td><td><b>Start</b></td><td><b>End</b></td><td><b>ObservedAllele</b></td><td><b>ReferenceAllele</b></td></tr><tr><td>*</td><td>22125503</td><td>22125504</td><td>C</td><td>G</td></tr></table><h3>Repositories</h3><table><tr><td>-</td><td><b>Type</b></td><td><b>Url</b></td><td><b>Name</b></td><td><b>VariantsetId</b></td></tr><tr><td>*</td><td>openapi</td><td><a>http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-type=application/json</a></td><td>GA4GH API</td><td>3:rs1333049</td></tr></table></div>"
},
"type": "dna",
"coordinateSystem": 0,
"patient": {
"reference": "Patient/example"
},
"referenceSeq": {
"referenceSeqId": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/nuccore",
"code": "NC_000009.11"
}
]
},
"strand": "watson",
"windowStart": 22125500,
"windowEnd": 22125510
},
"variant": [
{
"start": 22125503,
"end": 22125504,
"observedAllele": "C",
"referenceAllele": "G"
}
],
"repository": [
{
"type": "openapi",
"url": "http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-type=application/json",
"name": "GA4GH API",
"variantsetId": "3:rs1333049"
}
]
}MolecularSequence Structure
{
"resourceType" : "MolecularSequence",
// from Resource: id, meta, implicitRules, and language
// from DomainResource: text, contained, extension, and modifierExtension
"identifier" : [{ Identifier }], // Unique ID for this particular sequence. This is a FHIR-defined id
"type" : "<code>", // aa | dna | rna
"coordinateSystem" : <integer>, // R! Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)
"patient" : { Reference(Patient) }, // Who and/or what this is about
"specimen" : { Reference(Specimen) }, // Specimen used for sequencing
"device" : { Reference(Device) }, // The method for sequencing
"performer" : { Reference(Organization) }, // Who should be responsible for test result
"quantity" : { Quantity }, // The number of copies of the sequence of interest. (RNASeq)
"referenceSeq" : { // A sequence used as reference
"chromosome" : { CodeableConcept }, // Chromosome containing genetic finding
"genomeBuild" : "<string>", // The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'
"orientation" : "<code>", // sense | antisense
"referenceSeqId" : { CodeableConcept }, // Reference identifier
"referenceSeqPointer" : { Reference(MolecularSequence) }, // A pointer to another MolecularSequence entity as reference sequence
"referenceSeqString" : "<string>", // A string to represent reference sequence
"strand" : "<code>", // watson | crick
"windowStart" : <integer>, // Start position of the window on the reference sequence
"windowEnd" : <integer> // End position of the window on the reference sequence
},
"variant" : [{ // Variant in sequence
"start" : <integer>, // Start position of the variant on the reference sequence
"end" : <integer>, // End position of the variant on the reference sequence
"observedAllele" : "<string>", // Allele that was observed
"referenceAllele" : "<string>", // Allele in the reference sequence
"cigar" : "<string>", // Extended CIGAR string for aligning the sequence with reference bases
"variantPointer" : { Reference(Observation) } // Pointer to observed variant information
}],
"observedSeq" : "<string>", // Sequence that was observed
"quality" : [{ // An set of value as quality of sequence
"type" : "<code>", // R! indel | snp | unknown
"standardSequence" : { CodeableConcept }, // Standard sequence for comparison
"start" : <integer>, // Start position of the sequence
"end" : <integer>, // End position of the sequence
"score" : { Quantity }, // Quality score for the comparison
"method" : { CodeableConcept }, // Method to get quality
"truthTP" : <decimal>, // True positives from the perspective of the truth data
"queryTP" : <decimal>, // True positives from the perspective of the query data
"truthFN" : <decimal>, // False negatives
"queryFP" : <decimal>, // False positives
"gtFP" : <decimal>, // False positives where the non-REF alleles in the Truth and Query Call Sets match
"precision" : <decimal>, // Precision of comparison
"recall" : <decimal>, // Recall of comparison
"fScore" : <decimal>, // F-score
"roc" : { // Receiver Operator Characteristic (ROC) Curve
"score" : [<integer>], // Genotype quality score
"numTP" : [<integer>], // Roc score true positive numbers
"numFP" : [<integer>], // Roc score false positive numbers
"numFN" : [<integer>], // Roc score false negative numbers
"precision" : [<decimal>], // Precision of the GQ score
"sensitivity" : [<decimal>], // Sensitivity of the GQ score
"fMeasure" : [<decimal>] // FScore of the GQ score
}
}],
"readCoverage" : <integer>, // Average number of reads representing a given nucleotide in the reconstructed sequence
"repository" : [{ // External repository which contains detailed report related with observedSeq in this resource
"type" : "<code>", // R! directlink | openapi | login | oauth | other
"url" : "<uri>", // URI of the repository
"name" : "<string>", // Repository's name
"datasetId" : "<string>", // Id of the dataset that used to call for dataset in repository
"variantsetId" : "<string>", // Id of the variantset that used to call for variantset in repository
"readsetId" : "<string>" // Id of the read
}],
"pointer" : [{ Reference(MolecularSequence) }], // Pointer to next atomic sequence
"structureVariant" : [{ // Structural variant
"variantType" : { CodeableConcept }, // Structural variant change type
"exact" : <boolean>, // Does the structural variant have base pair resolution breakpoints?
"length" : <integer>, // Structural variant length
"outer" : { // Structural variant outer
"start" : <integer>, // Structural variant outer start
"end" : <integer> // Structural variant outer end
},
"inner" : { // Structural variant inner
"start" : <integer>, // Structural variant inner start
"end" : <integer> // Structural variant inner end
}
}]
}
MolecularSequence Search Parameters
The following search parameters can be used to query MolecularSequence resources. Just submit them like so:
https://api.1up.health/fhir/r4/MolecularSequence?query-param=queryvalue| Search Parameter | Field Type | Resource Fields Searched |
|---|---|---|
chromosome | text | referenceSeq.chromosome |
chromosome-variant-coordinate | composite | variant |
chromosome-window-coordinate | composite | referenceSeq |
identifier | text | identifier |
patient | reference | patient |
referenceseqid | text | referenceSeq.referenceSeqId |
referenceseqid-variant-coordinate | composite | variant |
referenceseqid-window-coordinate | composite | referenceSeq |
type | text | type |
variant-end | number | variant.end |
variant-start | number | variant.start |
window-end | number | referenceSeq.windowEnd |
window-start | number | referenceSeq.windowStart |
