Sequence Offset Location

Definition and Information Model

Warning

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

Computational Definition

A location defined by an offset relative to an anchor on a mapped sequence reference.

GA4GH Digest

Prefix	Inherent
None	[‘type’, ‘sequenceReference’, ‘anchor’, ‘anchorOrientation’, ‘offsetStart’, ‘offsetEnd’]

Information Model

Some SequenceOffsetLocation attributes are inherited from Entity.

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.
type		string	1..1	MUST be “SequenceOffsetLocation”
sequenceReference		Sequence Reference | iriReference	1..1	A sequence reference that has been mapped from which a relative location is defined.
anchor		integer	1..1	The inter-residue position on the sequence reference from which the relative location offset is calculated.
anchorOrientation		string	1..1	Indicates which side of a discontinuous anchor on the sequenceReference is used as the reference point for interpreting offsetStart/offsetEnd. The anchor is an inter-residue coordinate on the sequenceReference. When that anchor corresponds to a boundary whose realization on a base sequence yields two distinct locations (e.g., an exon junction), this property disambiguates which anchor side on the sequenceReference is intended. left denotes the side immediately preceding the anchor in sequenceReference coordinate order; right denotes the side immediately following the anchor in sequenceReference coordinate order.
offsetStart		integer | Range	0..1	The start offset, in inter-residue coordinates, from the anchor realization selected by anchorOrientation on the sequenceReference.
offsetEnd		integer | Range	0..1	The end offset, in inter-residue coordinates, from the anchor realization selected by anchorOrientation on the sequenceReference.