Sequence Location

Note

This data class is at a trial use maturity level and may change in future releases. Maturity levels are described in the GKS Maturity Model.

Computational Definition

A Location defined by an interval on a Sequence Reference.

GA4GH Digest

Prefix	Inherent
SL	[‘end’, ‘sequenceReference’, ‘start’, ‘type’]

Information Model

Some SequenceLocation attributes are inherited from Ga4ghIdentifiableObject.

Field	Flags	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, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
digest		string	0..1	A sha512t24u digest created using the VRS Computed Identifier algorithm.
type		string	1..1	MUST be “SequenceLocation”
sequenceReference		iriReference | Sequence Reference	0..1	A reference to a Sequence Reference 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. For locations on linear sequences, this MUST represent a coordinate or range less than or equal to the value of end. For circular sequences, start is greater than end when the location spans the sequence 0 coordinate.
end		integer | Range	0..1	The end coordinate or range of the SequenceLocation. The minimum value of this coordinate or range is 0. For locations on linear sequences, this MUST represent a coordinate or range greater than or equal to the value of start. For circular sequences, end is less than start when the location spans the sequence 0 coordinate.
sequence		sequenceString	0..1	The literal sequence encoded by the sequenceReference at these coordinates.