Sequence

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    Resource Representation
    Methods
        Get
        Create
        Update
        Search

Resource Representation

A Sequence resource stores data about a patient's DNA or RNA sequences.

Sequence

Field Name

Field Type

Cardinality

Description

genomeBuild1

string

1

Assembly of the sequence

type2

code

1

Type of the sequence. One of dna, rna, or aa.

quantity2

quantity

0..1

Quantity of sequence presented in the sample

referenceSeq2

 

string

0..1

Reference of the sequence (IUPAC format)

observedSeq2

 

string

1

Read string for the sequence (IUPAC format)

cigar1

string

0..1

CIGAR string for the sequence

source2

0..1

Source of the sequence. 

source.sample

code

0..1

Type of the sample of the sequence. One of prenatal, somatic, or germline.

source.lab

Resource (Procedure)

0..1

Procedure in which the sequence is determined.

chromosome1

string

1

Chromosome of the sequence. 

The chromosome containing the genetic finding. e.g. "1" for chromosome 1

startPosition1

(GenomicStart)

integer

1

Start of the sequence.  0-based

endPosition1

(GenomicStop)

integer

1

End of the sequence

species1

CodeableConcept

1

Species identifier (NCBI taxonomy)

patient

Resource (Patient)

1

Genetic lab’s patient ID for this sequence

1 Adopted from SMART into the HL7 Clinical Genomics Standard Profile for Genetics. Where elements were constrained for integration into the observation profile which is limited to genetic information, the FHIR DSTU2 name is in parenthesis.

2 Sequence and Sequencing Lab Resources are undergoing HL7 review for inclusion in FHIR DSTU3.

3 These components are inherited from the FHIR Observation resource.

4 These components focus on HL7 standard reporting findings based on traditional genetic testing technologies.

Methods

Get

Gets a Sequence 

HTTP Request:    GET /Sequence/{Id}

Parameters: 
  Id - ID of Sequence to get

Permission Scope: user/Sequence.read or patient/Sequence.read

Request Body: None

Response Body: If successful, returns the requested Sequence resource

Update

Updates a Sequence

HTTP Request:    PUT /Sequence/{Id}

Parameters: 
  Id - ID of Sequence to update

Permission Scope: user/Sequence.write or patient/Sequence.write

Request Body: Sequence Resource with updated values

Response Body: None

Search

Searches for a Sequence

HTTP Request:    GET /Sequence

Parameters: 
  Coordinate - Coordinate of sequence (Chromosome:Start-End format)
  Source - Source of sequence
  Patient - Patient sequence is coming from
  Type - Type of sequence

Permission Scope: User/Sequence.read or Patient/Sequence.read

Request Body: None

Response: If successful, returns the Sequences that match the search parameters