Terminus

New in v2

The Terminus class was added in v2 to describe molecules resulting from structural variation.

Terminus is a data class for describing the termination of a molecule, typically resulting from genomic rearrangements such as inversions or translocations.

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

The Terminus data class provides a structure for describing the end (terminus) of a molecule. Structurally similar to Adjacency, but used for describing where a molecule terminates (instead of adjoining another molecule).

GA4GH Digest

Prefix	Inherent
TM	[‘location’, ‘type’]

Information Model

Some Terminus 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 “Terminus”.
location		iriReference | Location	1..1	The location of the terminus.

Example

{
   "id": "ga4gh:TM.8xpg7Q826fQJJ_6rImuqufhTXj0mh5gV",
   "type": "Terminus"
   "location": {
      "end": 44908822,
      "start": 44908821,
      "sequenceReference": {
         "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
         "type": "SequenceReference"
      },
      "type": "SequenceLocation"
   }
}