Release 5 Draft Ballot

This is the Continuous Integration Build of FHIR (will be incorrect/inconsistent at times).
See the Directory of published versions

Clinical Genomics Work GroupMaturity Level: 1 Trial UseSecurity Category: Patient Compartments: Patient

Detailed Descriptions for the elements in the MolecularSequence resource.

MolecularSequence
Element IdMolecularSequence
Definition

Representation of a molecular sequence.

Cardinality0..*
TypeDomainResource
Summaryfalse
MolecularSequence.identifier
Element IdMolecularSequence.identifier
Definition

A unique identifier for this particular sequence instance.

NoteThis is a business identifier, not a resource identifier (see discussion)
Cardinality0..*
TypeIdentifier
Requirements

Allows sequences to be distinguished and referenced.

Summarytrue
MolecularSequence.type
Element IdMolecularSequence.type
Definition

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

Cardinality0..1
Terminology BindingsequenceType (Required)
Typecode
Summarytrue
MolecularSequence.patient
Element IdMolecularSequence.patient
Definition

Indicates the patient this sequence is associated too.

Cardinality0..1
TypeReference(Patient)
Summarytrue
MolecularSequence.specimen
Element IdMolecularSequence.specimen
Definition

Specimen used for sequencing.

Cardinality0..1
TypeReference(Specimen)
Summarytrue
MolecularSequence.device
Element IdMolecularSequence.device
Definition

The method for sequencing, for example, chip information.

Cardinality0..1
TypeReference(Device)
Summarytrue
MolecularSequence.performer
Element IdMolecularSequence.performer
Definition

The organization or lab that should be responsible for this result.

Cardinality0..1
TypeReference(Organization)
Summarytrue
MolecularSequence.literal
Element IdMolecularSequence.literal
Definition

Sequence that was observed.

Cardinality0..1
Typestring
Summarytrue
MolecularSequence.formatted
Element IdMolecularSequence.formatted
Definition

Sequence that was observed as file content. Can be an actual file contents, or referenced by a URL to an external system.

Cardinality0..*
TypeAttachment
Summarytrue
MolecularSequence.relative
Element IdMolecularSequence.relative
Definition

A sequence defined relative to another sequence.

Cardinality0..*
Summarytrue
MolecularSequence.relative.coordinateSystem
Element IdMolecularSequence.relative.coordinateSystem
Definition

These are different ways of identifying nucleotides or amino acids within a sequence. Different databases and file types may use different systems. For detail definitions, see https://loinc.org/92822-6/ for more detail.

Cardinality1..1
Terminology BindingLL5323-2 :
TypeCodeableConcept
Summarytrue
MolecularSequence.relative.reference
Element IdMolecularSequence.relative.reference
Definition

A sequence that is used as a reference to describe variants that are present in a sequence analyzed.

Cardinality0..1
Summarytrue
Invariants
Defined on this element
msq-5Rule Both referenceSequenceAssembly and chromosome must be both contained if either one of them is contained(chromosome.empty() and referenceSequenceAssembly.empty()) or (chromosome.exists() and referenceSequenceAssembly.exists())
msq-6Rule Have and only have one of the following elements in referenceSeq : 1. referenceSequenceAssembly ; 2 referenceSequence(referenceSequenceAssembly.count()+referenceSequenceCodeableConcept.count()+ referenceSequenceReference.count()+ referenceSequenceString.count()) = 1
MolecularSequence.relative.reference.referenceSequenceAssembly
Element IdMolecularSequence.relative.reference.referenceSequenceAssembly
Definition

The reference assembly used for reference, e.g. GRCh38.

Cardinality0..1
Terminology BindingLL1040-6 :
TypeCodeableConcept
Summarytrue
MolecularSequence.relative.reference.chromosome
Element IdMolecularSequence.relative.reference.chromosome
Definition

Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication (SO:0000340 ).

Cardinality0..1
Terminology BindingLL2938-0 :
TypeCodeableConcept
Summarytrue
MolecularSequence.relative.reference.referenceSequence[x]
Element IdMolecularSequence.relative.reference.referenceSequence[x]
Definition

The reference sequence that represents the starting sequence.

Cardinality0..1
Terminology BindingMultiple bindings acceptable (NCBI or LRG):
TypeCodeableConcept|string|Reference(MolecularSequence)
[x] NoteSee Choice of Data Types for further information about how to use [x]
Summarytrue
Comments

A reference sequnce may be represented in one of three ways:

  1. CodeableConcept, using NCBI, LRG or other appropriate code systems
  2. a simple string of IUPAC codes
  3. a reference to another MolecularSequence resource.
MolecularSequence.relative.reference.windowStart
Element IdMolecularSequence.relative.reference.windowStart
Definition

Start position of the window on the reference sequence. This value should honor the rules of the coordinateSystem.

Cardinality0..1
Typeinteger
Summarytrue
MolecularSequence.relative.reference.windowEnd
Element IdMolecularSequence.relative.reference.windowEnd
Definition

End position of the window on the reference sequence. This value should honor the rules of the coordinateSystem.

Cardinality0..1
Typeinteger
Summarytrue
MolecularSequence.relative.reference.orientation
Element IdMolecularSequence.relative.reference.orientation
Definition

A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand.

Cardinality0..1
Terminology BindingorientationType (Required)
Typecode
Summarytrue
MolecularSequence.relative.reference.strand
Element IdMolecularSequence.relative.reference.strand
Definition

An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm.

Cardinality0..1
Terminology BindingstrandType (Required)
Typecode
Summarytrue
MolecularSequence.relative.edit
Element IdMolecularSequence.relative.edit
Definition

Changes in sequence from the reference.

Cardinality0..*
Summarytrue
MolecularSequence.relative.edit.start
Element IdMolecularSequence.relative.edit.start
Definition

Start position of the edit on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.

Cardinality0..1
Typeinteger
Summarytrue
MolecularSequence.relative.edit.end
Element IdMolecularSequence.relative.edit.end
Definition

End position of the edit on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

Cardinality0..1
Typeinteger
Summarytrue
MolecularSequence.relative.edit.observedAllele
Element IdMolecularSequence.relative.edit.observedAllele
Definition

Allele that was observed. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

Cardinality0..1
Typestring
Summarytrue
MolecularSequence.relative.edit.referenceAllele
Element IdMolecularSequence.relative.edit.referenceAllele
Definition

Allele in the reference sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

Cardinality0..1
Typestring
Summarytrue