Major Changes

  • New classification of variation types.

    • Molecular Variation refers to variation within or of a contiguous molecule

    • Systemic Variation refers to variation in the context of a system, such as a genome, sample, or homologous chromosomes

    • Utility Variation classes provide useful representations for certain technical operations

  • New SequenceExpressions subclasses replace SequenceState. Subtypes are:

  • CopyNumberCount, a form of SystemicVariation, represents the copies of a molecule within a genome, and can be used to express concepts such as amplification and copy loss.

  • Gene enables reference to an external definition of a gene, particularly for useas a subject of copy number expressions.

  • DefiniteRange and IndefiniteRange represent bounded and half-bounded ranges respectively. A new Number type wraps integers so that some attributes may assume values of any of these three types.

Minor Changes

  • Sequence strings are now formally defined by a Sequence type, which is fundamentally also a string. This change aids documentation but has no technical impact.