SequenceLocation

The sequence location class is a fundamental concept in VRS, and is used to describe every form of Variation, and has stand-alone utility for describing sequence locations in other (non-variation) contexts. This class is used to represent a subsequence of a specified SequenceReference. The reference is typically a chromosome, transcript, or protein sequence.

Definition and Information Model

Computational Definition

A Location defined by an interval on a referenced Sequence.

Information Model

Some SequenceLocation attributes are inherited from Ga4ghIdentifiableObject.

Field	Type	Limits	Description
id	string	0..1	The ‘logical’ identifier of the entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system. The identified entity may have a different ‘id’ in a different system, or may refer to an ‘id’ for the shared concept in another system (e.g. a CURIE).
label	string	0..1	A primary label for the entity.
description	string	0..1	A free-text description of the entity.
extensions	Extension	0..m
type	string	0..1	MUST be “SequenceLocation”
digest	string	0..1	A sha512t24u digest created using the VRS Computed Identifier algorithm.
sequenceReference	IRI | SequenceReference	0..1	A reference to a Sequence on which the location is defined.
start	integer | Range	0..1	The start coordinate or range of the SequenceLocation. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range less than or equal to the value of end.
end	integer | Range	0..1	The end coordinate or range of the SequenceLocation. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range greater than or equal to the value of start.

Implementation Guidance

Start, End, and Ranges

At least one of the start and end properties MUST be specified in any SequenceLocation instance. When only one of these properties is specified, this represents an open interval beginning at the specified coordinate and extending left (when start is null) or right (when end is null).

When there is ambiguity at a coordinate (e.g., when using a SequenceLocation to describe the confidence boundary of a copy number segment), this is specified using the Range class for that coordinate.

New in v2

In VRS v1.x, the SequenceLocation class had an interval property which contained start and end attributes. This intermediate object layer has been removed in v2.0, making start and end top-level properties of the SequenceLocation.

Linear and Circular Sequence Coordinates

When representing a linear sequence, it is expected that for a Sequence of length n, 0 ≤ start ≤ end ≤ n

For a circular sequence, 0 ≤ end ≤ start ≤ n is also allowed. In cases where end < start, this represents a location that spans the circular sequence origin coordinate.

New in v2

The v2 SequenceLocation now also supports circular sequences. The optional circular property of the SequenceReference class may be set to True or False to explicitly indicate if a reference is circular, and therefore if 0 ≤ end ≤ start ≤ n is also allowed.

Implied Sequence Coordinates

The Sequence Location class refers to coordinates on a SequenceReference; if that sequence represents a coding transcript, then the coordinates refer to the coding transcript, and not a chromosome sequence to which it aligns. VRS intentionally does not allow for start or end values that use an offset system to represent sequence not found on the SequenceReference.

Todo

Describe and add a ref to an intronic variant profile