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

Draft

May change significantly in future releases. See 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.
type		string	1..1	MUST be “Terminus”.
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
location		iriReference | Location	1..1	The location of the terminus.

Inherits: Molecular Variation

Used in: Derivative Molecule

Example

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