MolecularSequence - FHIR Resource (r4)


This MolecularSequence Resource uses the FHIR API standard for access and structure.

Validate an MolecularSequence FHIR Resource (r4)



Resource Attributes

AttributeField is listTypeDescription
coordinateSystemfalseinteger# 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)
devicefalseReference# The method for sequencing
identifiertrueIdentifier# Unique ID for this particular sequence. This is a FHIR-defined id
observedSeqfalsestring# Sequence that was observed
patientfalseReference# Who and/or what this is about
performerfalseReference# Who should be responsible for test result
pointertrueReference# Pointer to next atomic sequence
qualitytrueData Type# An set of value as quality of sequence
quantityfalseQuantity# The number of copies of the sequence of interest. (RNASeq)
readCoveragefalseinteger# Average number of reads representing a given nucleotide in the reconstructed sequence
referenceSeqfalseData Type# A sequence used as reference
repositorytrueData Type# External repository which contains detailed report related with observedSeq in this resource
specimenfalseReference# Specimen used for sequencing
structureVarianttrueData Type# Structural variant
typefalsecode# aa | dna | rna
varianttrueData Type# Variant in sequence

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 ParameterField TypeResource Fields Searched
chromosometextreferenceSeq.chromosome
chromosome-variant-coordinatecompositevariant
chromosome-window-coordinatecompositereferenceSeq
identifiertextidentifier
patientreferencepatient
referenceseqidtextreferenceSeq.referenceSeqId
referenceseqid-variant-coordinatecompositevariant
referenceseqid-window-coordinatecompositereferenceSeq
typetexttype
variant-endnumbervariant.end
variant-startnumbervariant.start
window-endnumberreferenceSeq.windowEnd
window-startnumberreferenceSeq.windowStart