Definition: The type of molecule (e.g., DNA, RNA, amino acid). This is a broad concept that refers to the general physical composition of the molecule, intended to facilitate searching and to provide domain context for profiles and instances. The terminology binding may be expanded to support additional types of molecules in the future (e.g., peptide nucleic acids, oligosaccharides).

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.type

Classification of the molecule into types other than those defined by moleculeType

Definition: Classifications of an instance of the resource into arbitrary types, based on domain semantics. For example, this element could indicate that an instance of moleculeType 'RNA' could have a type of 'mRNA' or 'siRNA'.

Cardinality: 0..*

Type: CodeableConcept

Summary: true

MolecularDefinition.topology

The structural topology of the molecular entity (e.g., linear, circular)

Definition: The structural topology of the molecular entity. For sequences (e.g., DNA), this could specify 'linear' and 'circular'. More complex entities might be branched or have a quaternary structure.

Cardinality: 0..*

Type: CodeableConcept

Summary: true

MolecularDefinition.member

Constituents of an aggregate molecular concept (e.g., haplotype, genotype)

Definition: Constituents of an aggregate molecular concept (e.g., haplotype, genotype).

Cardinality: 0..*

Type: Reference(MolecularDefinition)

Summary: true

MolecularDefinition.location

A defined location on a molecular entity

Definition: A defined location on a molecular entity. Location definitions may vary with respect to coordinate space and precision or level of granularity.

Cardinality: 0..*

Type: BackboneElement

Summary: true

MolecularDefinition.location.sequenceLocation

A coordinate-based location on a sequence

Definition: A location on a sequence, defined using a nucleotide coordinate system.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.sequenceLocation.sequenceContext

The sequence on which the location is defined

Definition: A reference to a sequence on which the location is defined.

Cardinality: 1..1

Type: Reference(MolecularDefinition)

Summary: true

MolecularDefinition.location.sequenceLocation.coordinateInterval

An interval on a sequence

Definition: An interval on a sequence, defined by coordinate-based start and end coordinates.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem

The coordinate system used to define the location

Definition: A definition of the coordinate system. Examples include 1-based character counting, and 0-based interval counting.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.system

The type of coordinate system used

Definition: A definition of the coordinate system. Examples include 1-based character counting, and 0-based interval counting.

Cardinality: 0..1

Type: CodeableConcept

Binding: extensible:LL5323-2

Summary: true

MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.origin

The location of the origin of the coordinate system

Definition: The location of the origin (0 or 1, depending on the coordinate system). For example, this could specify the origin is at the start of the sequence (e.g., 5’ end or N-terminus), the beginning of a designated feature (e.g., A in the ATG translation initiation codon), or the end of a designated feature (e.g., 3’ end of an exon, from which an offset is calculated into the following intron).

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.location.sequenceLocation.coordinateInterval.coordinateSystem.normalizationMethod

The normalization method used for determining a location within the coordinate system

Definition: The normalization method used for determining a location within the coordinate system. Examples include left shift (e.g., VCF), right shift (e.g., HGVS), or fully justified (e.g., VOCA).

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.location.sequenceLocation.coordinateInterval.start[x]

The start location of the interval

Definition: The start location of the interval expressed as a precise coordinate (Quantity) or expressed as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported.

Cardinality: 0..1

Type: Quantity, Range

Summary: true

MolecularDefinition.location.sequenceLocation.coordinateInterval.end[x]

The end location of the interval

Definition: The end location of the interval expressed as a precise coordinate (Quantity) or as a range (Range) that is defined by low (range start) and high (range end). Open-ended ranges, where one end is unbounded, may be supported..

Cardinality: 0..1

Type: Quantity, Range

Summary: true

MolecularDefinition.location.sequenceLocation.strand

The strand at the coordinateInterval

Definition: The specific strand at the coordinateInterval, when the interval alone is not sufficient to define a location (e.g., double stranded DNA). Example values include 'forward' and 'reverse'.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation

A cytoband-based location on a sequence

Definition: A location on a sequence, defined using cytobands.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.cytobandLocation.genomeAssembly

Reference Genome

Definition: The reference genome assemble.

Cardinality: 1..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.cytobandLocation.genomeAssembly.organism

Species of the organism

Definition: Species of the organism.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.genomeAssembly.build

Build number

Definition: The build number of this genome assemble.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.genomeAssembly.accession

Accession

Definition: The accession of this genome assemble.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.genomeAssembly.description[x]

Genome assembly description

Definition: The description of this genome assembly.

Cardinality: 0..1

Type: markdown, string

Summary: false

MolecularDefinition.location.cytobandLocation.cytobandInterval

Cytoband Interval

Definition: The Cytoband Interval.

Cardinality: 1..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.cytobandLocation.cytobandInterval.chromosome

Chromosome

Definition: The chromosome where this cytoband interval occurs.

Cardinality: 1..1

Type: CodeableConcept

Summary: true

MolecularDefinition.location.cytobandLocation.cytobandInterval.simpleCytoband

SimpleCytoband

Definition: The cytoband Interval expressed as start and end code.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.cytobandLocation.cytobandInterval.simpleCytoband.start

Start

Definition: The start of this cytoband Interval expressed as a single code.

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.location.cytobandLocation.cytobandInterval.simpleCytoband.end

End

Definition: The end of this cytoband Interval expressed as a single code.

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband

StructuredCytoband

Definition: The cytoband Interval expressed as a set of discrete codes.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.start

Start

Definition: The start of this cytoband Interval.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.start.arm

Arm

Definition: The arm of this start interval.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.start.region

Region

Definition: The region of this start interval.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.start.band

Band

Definition: The band of this start interval.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.start.subBand

Sub-band

Definition: The sub-band of this start interval.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.end

End

Definition: The end of this cytoband Interval.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.end.arm

Arm

Definition: The arm of this end interval.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.end.region

Region

Definition: The region of this end interval.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.end.band

Band

Definition: The band of this end interval.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.location.cytobandLocation.cytobandInterval.structuredCytoband.end.subBand

Sub-band

Definition: The sub-band of this end interval.

Cardinality: 0..1

Type: CodeableConcept

Summary: false

MolecularDefinition.representation

A representation of a molecular entity

Definition: A representation of a molecular entity, specifically including sequence. Note this element is intended to define the entity primarily through computable, discrete elements that express domain semantics rather than replicating a particular file format or relational schema.

Cardinality: 0..*

Type: BackboneElement

Summary: true

MolecularDefinition.representation.focus

The domain concept that is the focus of a given instance of the representation

Definition: The domain concept that is the focus of the representation. This element is used to disambiguate the representations of the “reference” and the “alternate” alleles at a given location, for example.

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.representation.code

A code (e.g., sequence accession number) used to represent a molecular entity

Definition: A code (e.g., sequence accession number) used to represent a molecular entity.

Cardinality: 0..*

Type: CodeableConcept

Summary: true

MolecularDefinition.representation.literal

A molecular entity defined as a string literal

Definition: A molecular entity defined as a string literal.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.representation.literal.encoding

The encoding used in the value

Definition: The encoding used for the expression of the entity. For a primary sequence, this element represents the alphabet used (e.g., 1 character DNA without ambiguity codes, 3 character amino acid codes).

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.representation.literal.value

A string literal representation of the molecular entity, using the encoding specified in encoding

Definition: A string literal representation of the molecular entity, using a specific encoding. For example, this may be the primary sequence of a strand of DNA.

Cardinality: 1..1

Type: string

Summary: true

MolecularDefinition.representation.resolvable

A resolvable representation of a molecular entity (e.g., URI, attached and formatted file)

Definition: A resolvable representation of a molecular entity, which may be specified as a URI and/or attached document (in a defined format).

Cardinality: 0..1

Type: Reference(DocumentReference)

Summary: true

MolecularDefinition.representation.extracted

A molecular entity that is represented as a portion of a different entity

Definition: A molecular entity that is represented as a portion of a different entity. For example, this element can represent a subsequence (e.g., genetic region) that is part of and conceptually extracted from a longer sequence (e.g., chromosome sequence). The “parent” entity is specified in startingMolecule and the location of the intended molecular entity on the parent entity is defined by coordinateInterval.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.representation.extracted.startingMolecule

The molecular entity that serves as the conceptual 'parent' from which the intended entity is derived

Definition: A reference to the molecular entity that serves as the conceptual 'parent' from which the intended entity is derived. For example, this could be a chromosome sequence on which a coordinateInterval is defined.

Cardinality: 1..1

Type: Reference(MolecularDefinition)

Summary: true

MolecularDefinition.representation.extracted.coordinateInterval

The interval on startingMolecule that defines the portion to be extracted to produce the intended entity

Definition: The interval on startingMolecule that defines the portion to be extracted in order to create the intended entity.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem

The coordinate system used to define the location

Definition: The coordinate system used to define the location, which may vary depending on application or context of use.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.system

The type of coordinate system used

Definition: A definition of the coordinate system. Examples include 1-based character counting, and 0-based interval counting.

Cardinality: 0..1

Type: CodeableConcept

Binding: extensible:LL5323-2

Summary: true

MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.origin

The location of the origin of the coordinate system

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.representation.extracted.coordinateInterval.coordinateSystem.normalizationMethod

The normalization method used for determining a location within the coordinate system

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.representation.extracted.coordinateInterval.start[x]

The start location of the interval

Cardinality: 0..1

Type: Quantity, Range

Summary: true

MolecularDefinition.representation.extracted.coordinateInterval.end[x]

The end location of the interval

Cardinality: 0..1

Type: Quantity, Range

Summary: true

MolecularDefinition.representation.extracted.reverseComplement

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

Definition: A flag that indicates whether the extracted sequence should be reverse complemented in order to produce the intended entity. This element is only relevant to molecular entities that support the concept of reverse complement (e.g., double stranded DNA).

Cardinality: 0..1

Type: boolean

Summary: true

MolecularDefinition.representation.repeated

A representation as a repeated motif

Definition: A representation of a molecular entity that is expressed as a number of copies of a repeated motif.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.representation.repeated.sequenceMotif

The motif that is repeated

Definition: The motif that is repeated in tandem, which ultimately defines the intended molecular entity.

Cardinality: 1..1

Type: Reference(MolecularDefinition)

Summary: true

MolecularDefinition.representation.repeated.copyCount

The number of copies of the motif

Definition: The number of times the motif is repeated to create the intended molecular entity.

Cardinality: 1..1

Type: integer

Summary: true

MolecularDefinition.representation.concatenated

An ordered concatenation of molecular entities

Definition: A representation comprised of an ordered concatenation of two or more molecular entities.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.representation.concatenated.sequenceElement

One of the concatenated entities

Definition: One of the concatenated entities within the concatenated representation.

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

Cardinality: 1..*

Type: BackboneElement

Summary: true

MolecularDefinition.representation.concatenated.sequenceElement.sequence

A reference to the sequence that defines this specific concatenated element

Definition: A reference to the sequence that defines this specific concatenated element.

Cardinality: 1..1

Type: Reference(MolecularDefinition)

Summary: true

MolecularDefinition.representation.concatenated.sequenceElement.ordinalIndex

The ordinal index of the element within the concatenated representation

Definition: The ordinal index of the element within the concatenated representation.

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

Cardinality: 1..1

Type: integer

Summary: true

MolecularDefinition.representation.relative

A molecular entity represented as an ordered series of edits on a specified starting entity

Definition: A molecular entity represented as an ordered series of edits on a specified starting entity. This representation can be used to define one entity relative to another.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.representation.relative.startingMolecule

The molecular entity on which edits will be applied

Definition: The molecular entity that serves as the starting point, on which edits will be applied.

Cardinality: 1..1

Type: Reference(MolecularDefinition)

Summary: true

MolecularDefinition.representation.relative.edit

A defined edit (change) to be applied

Definition: A defined edit (change) to be applied to the molecular entity.

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

Cardinality: 0..*

Type: BackboneElement

Summary: true

MolecularDefinition.representation.relative.edit.editOrder

Defines the order of edits when multiple edits are to be applied to the startingMolecule

Definition: Defines the order of edits when multiple edits are to be applied to the startingMolecule. This is important when edits may overlap (intervals) or when edits change the length of the entity.

Cardinality: 0..1

Type: integer

Summary: false

MolecularDefinition.representation.relative.edit.coordinateInterval

The interval on startingMolecule that defines the portion to be extracted to produce the intended entity

Definition: The interval on startingMolecule that defines the portion to be extracted in order to create the intended entity.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem

The coordinate system used to define the location

Definition: The coordinate system used to define the location, which may vary depending on application or context of use.

Cardinality: 0..1

Type: BackboneElement

Summary: true

MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.system

The type of coordinate system used

Definition: A definition of the coordinate system. Examples include 1-based character counting, and 0-based interval counting.

Cardinality: 0..1

Type: CodeableConcept

Binding: extensible:LL5323-2

Summary: true

MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.origin

The location of the origin of the coordinate system

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.representation.relative.edit.coordinateInterval.coordinateSystem.normalizationMethod

The normalization method used for determining a location within the coordinate system

Cardinality: 0..1

Type: CodeableConcept

Summary: true

MolecularDefinition.representation.relative.edit.coordinateInterval.start[x]

The start location of the interval

Cardinality: 0..1

Type: Quantity, Range

Summary: true

MolecularDefinition.representation.relative.edit.coordinateInterval.end[x]

The end location of the interval

Cardinality: 0..1

Type: Quantity, Range

Summary: true

MolecularDefinition.representation.relative.edit.replacementMolecule

The molecular entity that serves as the replacement in the edit operation

Definition: The molecular entity that serves as the replacement in the edit operation. After the edit has been applied, the state of the entity at the specified coordinateInterval is defined by the state of the replacementMolecule.

Cardinality: 1..1

Type: Reference(MolecularDefinition)

Summary: true

MolecularDefinition.representation.relative.edit.replacedMolecule

The portion of the molecular entity that is replaced by the replacementMolecule

Definition: The portion of the molecular entity that is replaced by the replacementMolecule as a result of the edit. The value of this element can be derived as the state of the entity at the specified coordinateInterval, prior to the edit being applied. It is provided for convenience.

Cardinality: 0..1

Type: Reference(MolecularDefinition)

Summary: true