MolecularSequence.repository

FHIR attribute (r4)

In the MolecularSequence resource for FHIR r4 , the repository attribute identifies the External repository which contains detailed report related with observedSeq in this resource

repository (MolecularSequence) description

Resource Type: MolecularSequence

Attribute Name: repository

Description: External repository which contains detailed report related with observedSeq in this resource

FHIR Version: r4

Attribute Type :

Required: N/A

Countability: Array

Flags: N/A

Terminology bindings: N/A

Requirements: N/A

Comments: N/A

MolecularSequence.repository Example

"repository": [
  {
    "type": "openapi",
    "url": "http://grch37.rest.ensembl.org/ga4gh/variants/3:rs1333049?content-type=application/json",
    "name": "GA4GH API",
    "variantsetId": "3:rs1333049"
  }
]

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": 0

Learn 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: