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Clinical Genomics icon Work GroupMaturity Level: 1 Trial UseSecurity Category: N/A Compartments: No defined compartments

Detailed Descriptions for the elements in the MolecularSequence resource.

MolecularSequence
Element Id MolecularSequence
Definition

Representation of a molecular sequence.

Short Display Representation of a molecular sequence
Cardinality 0..*
Type DomainResource
Summary false
MolecularSequence.identifier
Element Id MolecularSequence.identifier
Definition

A unique identifier for this particular sequence instance.

Short Display Unique ID for this particular sequence
Note This is a business identifier, not a resource identifier (see discussion)
Cardinality 0..*
Type Identifier
Requirements

Allows sequences to be distinguished and referenced.

Summary true
MolecularSequence.type
Element Id MolecularSequence.type
Definition

The type of the Molecular Sequence (Amino Acid Sequence, DNA Sequence, RNA Sequence).

Short Display aa | dna | rna
Cardinality 0..1
Terminology Binding sequence Type (Required)
Type code
Summary true
MolecularSequence.literal
Element Id MolecularSequence.literal
Definition

A literal representation of a Molecular Sequence.

Short Display A literal representation of a Molecular Sequence
Cardinality 0..*
Summary true
MolecularSequence.literal.sequenceValue
Element Id MolecularSequence.literal.sequenceValue
Definition

The primary (linear) sequence, expressed as a literal string.

Short Display The primary (linear) sequence, expressed as a literal string
Cardinality 1..1
Type string
Summary true
MolecularSequence.file
Element Id MolecularSequence.file
Definition

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

Short Display Embedded file or a link (URL) which contains content to represent the sequence
Cardinality 0..*
Type Attachment
Summary true
MolecularSequence.relative
Element Id MolecularSequence.relative
Definition

A Molecular Sequence that is represented as an ordered series of edits on a specified starting sequence.

Short Display A Molecular Sequence that is represented as an ordered series of edits on a specified starting sequence
Cardinality 0..*
Summary true
MolecularSequence.relative.startingSequence
Element Id MolecularSequence.relative.startingSequence
Definition

The Molecular Sequence that serves as the starting sequence, on which edits will be applied.

Short Display The Molecular Sequence that serves as the starting sequence, on which edits will be applied
Cardinality 1..1
Type Reference(MolecularSequence)
Summary true
MolecularSequence.relative.edit
Element Id MolecularSequence.relative.edit
Definition

An edit (change) made to a sequence.

Short Display An edit (change) made to a sequence
Cardinality 0..*
Summary true
Comments

Edits are applied sequentially. The sequence that results from one edit operation is used as the 'starting' sequence of the next edit operation.

MolecularSequence.relative.edit.editOrder
Element Id MolecularSequence.relative.edit.editOrder
Definition

The order of this edit, relative to other edits on the starting sequence.

Short Display The order of this edit, relative to other edits on the starting sequence
Cardinality 0..1
Type integer
Summary false
MolecularSequence.relative.edit.coordinateSystem
Element Id MolecularSequence.relative.edit.coordinateSystem
Definition

The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based.

Short Display The coordinate system used to define the edited intervals on the starting sequence. Coordinate systems are usually 0- or 1-based
Cardinality 1..1
Terminology Binding LL5323-2 icon:
Type CodeableConcept
Summary true
MolecularSequence.relative.edit.start
Element Id MolecularSequence.relative.edit.start
Definition

The start coordinate of the interval that will be edited.

Short Display The start coordinate of the interval that will be edited
Cardinality 1..1
Type integer
Summary true
MolecularSequence.relative.edit.end
Element Id MolecularSequence.relative.edit.end
Definition

The end coordinate of the interval that will be edited.

Short Display The end coordinate of the interval that will be edited
Cardinality 1..1
Type integer
Summary true
MolecularSequence.relative.edit.replacementSequence
Element Id MolecularSequence.relative.edit.replacementSequence
Definition

The sequence that defines the replacement sequence used in the edit operation.

Short Display The sequence that defines the replacement sequence used in the edit operation
Cardinality 1..1
Type Reference(MolecularSequence)
Summary true
MolecularSequence.relative.edit.replacedSequence
Element Id MolecularSequence.relative.edit.replacedSequence
Definition

The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit.

Short Display The sequence on the 'starting' sequence for the edit operation, defined by the specified interval, that will be replaced during the edit
Cardinality 0..1
Type Reference(MolecularSequence)
Summary true
MolecularSequence.extracted
Element Id MolecularSequence.extracted
Definition

A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence.

Short Display A Molecular Sequence that is represented as an extracted portion of a different Molecular Sequence
Cardinality 0..*
Summary true
MolecularSequence.extracted.startingSequence
Element Id MolecularSequence.extracted.startingSequence
Definition

The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted.

Short Display The Molecular Sequence that serves as the parent sequence, from which the intended sequence will be extracted
Cardinality 1..1
Type Reference(MolecularSequence)
Summary true
MolecularSequence.extracted.start
Element Id MolecularSequence.extracted.start
Definition

The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted.

Short Display The start coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
Cardinality 1..1
Type integer
Summary true
MolecularSequence.extracted.end
Element Id MolecularSequence.extracted.end
Definition

The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted.

Short Display The end coordinate (on the parent sequence) of the interval that defines the subsequence to be extracted
Cardinality 1..1
Type integer
Summary true
MolecularSequence.extracted.coordinateSystem
Element Id MolecularSequence.extracted.coordinateSystem
Definition

The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based.

Short Display The coordinate system used to define the interval that defines the subsequence to be extracted. Coordinate systems are usually 0- or 1-based
Cardinality 1..1
Type CodeableConcept
Summary true
MolecularSequence.extracted.reverseComplement
Element Id MolecularSequence.extracted.reverseComplement
Definition

A flag that indicates whether the extracted sequence should be reverse complemented.

Short Display A flag that indicates whether the extracted sequence should be reverse complemented
Cardinality 0..1
Type boolean
Summary true
Comments

This attribute might be needed in all sequence representation classes, so that any sequence representation could be reverseComplemented.

MolecularSequence.repeated
Element Id MolecularSequence.repeated
Definition

A Molecular Sequence that is represented as a repeated sequence motif.

Short Display A Molecular Sequence that is represented as a repeated sequence motif
Cardinality 0..*
Summary true
Comments

This class represents motifs that occur in tandem (immediately adjacent to each other) and without edits (each copy of the motif is identical).

MolecularSequence.repeated.sequenceMotif
Element Id MolecularSequence.repeated.sequenceMotif
Definition

The sequence that defines the repeated motif.

Short Display The sequence that defines the repeated motif
Cardinality 1..1
Type Reference(MolecularSequence)
Summary true
MolecularSequence.repeated.copyCount
Element Id MolecularSequence.repeated.copyCount
Definition

The number of repeats (copies) of the sequence motif.

Short Display The number of repeats (copies) of the sequence motif
Cardinality 1..1
Type integer
Summary true
MolecularSequence.concatenated
Element Id MolecularSequence.concatenated
Definition

A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences.

Short Display A Molecular Sequence that is represented as an ordered concatenation of two or more Molecular Sequences
Cardinality 0..1
Summary true
MolecularSequence.concatenated.sequenceElement
Element Id MolecularSequence.concatenated.sequenceElement
Definition

One element of a concatenated Molecular Sequence.

Short Display One element of a concatenated Molecular Sequence
Cardinality 1..*
Summary true
Comments

At least two sequenceElement elements are required to represent a concatenated sequence.

MolecularSequence.concatenated.sequenceElement.sequence
Element Id MolecularSequence.concatenated.sequenceElement.sequence
Definition

The Molecular Sequence corresponding to this element.

Short Display The Molecular Sequence corresponding to this element
Cardinality 1..1
Type Reference(MolecularSequence)
Summary true
MolecularSequence.concatenated.sequenceElement.ordinalIndex
Element Id MolecularSequence.concatenated.sequenceElement.ordinalIndex
Definition

The ordinal position of this sequence element within the concatenated Molecular Sequence.

Short Display The ordinal position of this sequence element within the concatenated Molecular Sequence
Cardinality 1..1
Type integer
Summary true
Comments

0 or 1 based indices are possible, could potentially skip numbers in the sequence, suggest implementers sort numerically prior to concatenating