Adjacency

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

The Adjacency class represents the adjoining of the end of a sequence with the beginning of an adjacent sequence, potentially with an intervening linker sequence.

GA4GH Digest

Prefix	Inherent
AJ	[‘adjoinedSequences’, ‘linker’, ‘type’]

Information Model

Some Adjacency attributes are inherited from Variation.

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.
expressions	⋮	Expression	0..m
type		string	1..1	MUST be “Adjacency”.
adjoinedSequences	↓	iriReference | Location	2..2	The terminal sequence or pair of adjoined sequences that defines in the adjacency.
linker		Sequence Expression	0..1	The sequence found between adjoined sequences.
homology	D	boolean	0..1	A flag indicating if coordinate ambiguity in the adjoined sequences is from sequence homology (true) or other uncertainty, such as instrument ambiguity (false).