Sequence - FHIR Resource (stu3)


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

Validate an Sequence FHIR Resource (stu3)



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 seqeunce 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
typefalsecode aa | dna | rna
varianttrueData Type Variant in sequence

Sequence Example

{
  "referenceSeq": {
    "windowEnd": 22125510,
    "windowStart": 22125500,
    "referenceSeqId": {
      "coding": [
        {
          "code": "NC_000009.11",
          "system": "http://www.ncbi.nlm.nih.gov/nuccore"
        }
      ]
    },
    "strand": 1
  },
  "patient": {
    "reference": "Patient/example"
  },
  "repository": [
    {
      "url": "http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-type=application/json",
      "variantsetId": "3:rs1333049",
      "type": "openapi",
      "name": "GA4GH API"
    }
  ],
  "resourceType": "Sequence",
  "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>1</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>"
  },
  "variant": [
    {
      "start": 22125503,
      "referenceAllele": "G",
      "end": 22125504,
      "observedAllele": "C"
    }
  ],
  "coordinateSystem": 0,
  "type": "dna",
  "id": "example"
}

Sequence Structure


  
{
  "resourceType" : "Sequence",
  // 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 seqeunce 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'
    "referenceSeqId" : { CodeableConcept }, // Reference identifier
    "referenceSeqPointer" : { Reference(Sequence) }, // A Pointer to another Sequence entity as reference sequence
    "referenceSeqString" : "<string>", // A string to represent reference sequence
    "strand" : <integer>, // Directionality of DNA ( +1/-1)
    "windowStart" : <integer>, // R!  Start position of the window on the  reference sequence
    "windowEnd" : <integer> // R!  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
  }],
  "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(Sequence) }] // Pointer to next atomic sequence
}


 

Sequence Search Parameters

The following search parameters can be used to query Sequence resources. Just submit the like so:

https://api.1up.health/fhir/stu3/Sequence?query-param=queryvalue
Search ParameterField TypeResource Fields Searched
chromosometextreferenceSeq.chromosome
coordinatecompositevariant
endnumberreferenceSeq.windowEnd
identifiertextidentifier
patientreferencepatient
startnumberreferenceSeq.windowStart
typetexttype