FHIR CI-Build

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

Clinical Genomics icon 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.

Short DisplayRepresentation of a molecular sequence
Cardinality0..*
TypeDomainResource
Summaryfalse
MolecularSequence.identifier
Element IdMolecularSequence.identifier
Definition

A unique identifier for this particular sequence instance.

Short DisplayUnique ID for this particular sequence
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.

Short Displayaa | dna | rna
Cardinality0..1
Terminology BindingsequenceType (Required)
Typecode
Summarytrue
MolecularSequence.subject
Element IdMolecularSequence.subject
Definition

Indicates the subject this sequence is associated too.

Short DisplaySubject this sequence is associated too
Cardinality0..1
TypeReference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct)
Summarytrue
MolecularSequence.specimen
Element IdMolecularSequence.specimen
Definition

Specimen used for sequencing.

Short DisplaySpecimen used for sequencing
Cardinality0..1
TypeReference(Specimen)
Summarytrue
MolecularSequence.device
Element IdMolecularSequence.device
Definition

The method for sequencing, for example, chip information.

Short DisplayThe method for sequencing
Cardinality0..1
TypeReference(Device)
Summarytrue
MolecularSequence.performer
Element IdMolecularSequence.performer
Definition

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

Short DisplayWho should be responsible for test result
Cardinality0..1
TypeReference(Organization)
Summarytrue
MolecularSequence.literal
Element IdMolecularSequence.literal
Definition

Sequence that was observed.

Short DisplaySequence 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.

Short DisplayEmbedded file or a link (URL) which contains content to represent the sequence
Cardinality0..*
TypeAttachment
Summarytrue
MolecularSequence.relative
Element IdMolecularSequence.relative
Definition

A sequence defined relative to another sequence.

Short DisplayA 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.

Short DisplayWays of identifying nucleotides or amino acids within a sequence
Cardinality1..1
Terminology BindingLL5323-2 icon:
TypeCodeableConcept
Summarytrue
MolecularSequence.relative.ordinalPosition
Element IdMolecularSequence.relative.ordinalPosition
Definition

Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together.

Short DisplayIndicates the order in which the sequence should be considered when putting multiple 'relative' elements together
Cardinality0..1
Typeinteger
Summaryfalse
MolecularSequence.relative.sequenceRange
Element IdMolecularSequence.relative.sequenceRange
Definition

Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together.

Short DisplayIndicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together
Cardinality0..1
TypeRange
Summaryfalse
MolecularSequence.relative.startingSequence
Element IdMolecularSequence.relative.startingSequence
Definition

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

Short DisplayA sequence used as starting sequence
Cardinality0..1
Summarytrue
Invariants
Defined on this element
msq-5Rule Both genomeAssembly and chromosome must be both contained if either one of them is contained(chromosome.empty() and genomeAssembly.empty()) or (chromosome.exists() and genomeAssembly.exists())
msq-6Rule Have and only have one of the following elements in startingSequence: 1. genomeAssembly; 2 sequence(genomeAssembly.count()+sequenceCodeableConcept.count()+ sequenceReference.count()+ sequenceString.count()) = 1
MolecularSequence.relative.startingSequence.genomeAssembly
Element IdMolecularSequence.relative.startingSequence.genomeAssembly
Definition

The genome assembly used for starting sequence, e.g. GRCh38.

Short DisplayThe genome assembly used for starting sequence, e.g. GRCh38
Cardinality0..1
Terminology BindingLL1040-6 icon:
TypeCodeableConcept
Summarytrue
MolecularSequence.relative.startingSequence.chromosome
Element IdMolecularSequence.relative.startingSequence.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 icon).

Short DisplayChromosome Identifier
Cardinality0..1
Terminology BindingLL2938-0 icon:
TypeCodeableConcept
Summarytrue
MolecularSequence.relative.startingSequence.sequence[x]
Element IdMolecularSequence.relative.startingSequence.sequence[x]
Definition

The reference sequence that represents the starting sequence.

Short DisplayThe reference sequence that represents the starting sequence
Cardinality0..1
Terminology BindingMultiple bindings acceptable (NCBI or LRG):
TypeCodeableConcept|string|Reference(MolecularSequence)
[x] NoteSee Choice of Datatypes for further information about how to use [x]
Summarytrue
Comments

A starting sequence 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.startingSequence.windowStart
Element IdMolecularSequence.relative.startingSequence.windowStart
Definition

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

Short DisplayStart position of the window on the starting sequence
Cardinality0..1
Typeinteger
Summarytrue
MolecularSequence.relative.startingSequence.windowEnd
Element IdMolecularSequence.relative.startingSequence.windowEnd
Definition

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

Short DisplayEnd position of the window on the starting sequence
Cardinality0..1
Typeinteger
Summarytrue
MolecularSequence.relative.startingSequence.orientation
Element IdMolecularSequence.relative.startingSequence.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.

Short Displaysense | antisense
Cardinality0..1
Terminology BindingorientationType (Required)
Typecode
Summarytrue
MolecularSequence.relative.startingSequence.strand
Element IdMolecularSequence.relative.startingSequence.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.

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

Changes in sequence from the starting sequence.

Short DisplayChanges in sequence from the starting sequence
Cardinality0..*
Summarytrue
MolecularSequence.relative.edit.start
Element IdMolecularSequence.relative.edit.start
Definition

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

Short DisplayStart position of the edit on the starting sequence
Cardinality0..1
Typeinteger
Summarytrue
MolecularSequence.relative.edit.end
Element IdMolecularSequence.relative.edit.end
Definition

End position of the edit on the starting 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.

Short DisplayEnd position of the edit on the starting sequence
Cardinality0..1
Typeinteger
Summarytrue
MolecularSequence.relative.edit.replacementSequence
Element IdMolecularSequence.relative.edit.replacementSequence
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.

Short DisplayAllele that was observed
Cardinality0..1
Typestring
Summarytrue
MolecularSequence.relative.edit.replacedSequence
Element IdMolecularSequence.relative.edit.replacedSequence
Definition

Allele in the starting sequence. Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the starting 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.

Short DisplayAllele in the starting sequence
Cardinality0..1
Typestring
Summarytrue