Representation of a molecular definition.

A unique identifier for this particular resource instance.

Allows MolecularDefinition to be distinguished and referenced.

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

The molecular location of this molecule.

The Location of this molecule in context of a sequence.

The reference Sequence that contains this location.

The coordinate interval for this location.

The coordinate system of this interval.

The start of this interval.

The end of this interval.

The identification of the strand direction, i.e, forward vs reverse strand.

The location of this molecule in context of a cytoband.

The reference genome assemble.

Species of the organism.

The build number of this genome assemble.

The accession of this genome assemble.

The description of this genome assemble.

The Cytoband Interval.

The chromosome where this cytoband interval occurs.

The start of this cytoband Interval.

The arm of this start interval.

The region of this start interval.

The band of this start interval.

The sub-band of this start interval.

The end of this cytoband Interval.

The arm of this end interval.

The region of this end interval.

The band of this end interval.

The sub-band of this end interval.

The location of this molecule in context of a feature.

The gene Id where this molecule occurs.

A member or part of this molecule.

The representation of this molecular definition, e.g., as a literal or repeated elements.

A representation focus, e.g., reference or alternative state.

A representation code.

A literal representation.

The encoding used for the expression of the primary sequence. This defines the characters that may be used in the primary sequence and it permits the explicit inclusion/exclusion of IUPAC ambiguity codes.

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

A resolvable representation of a molecule that optionally contains formatting in addition to the specification of the primary sequence itself. The sequence may be provided inline as an attached document or through a resolvable URI.

Attachment.data for inline, .url for resolvable, optionally with .contentType for format.

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

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

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

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

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

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

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

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

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

The sequence that defines the repeated motif.

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

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

One element of a concatenated Molecular Sequence.

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

The Molecular Sequence corresponding to this element.

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

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

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

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

An edit (change) made to a sequence.

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

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

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

The start coordinate of the interval that will be edited.

The end coordinate of the interval that will be edited.

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

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