This draft specification, under development by Driver Projects of the GKS Work Stream, specifies standard data classes for the exchange of common information useful for the description of variation but superfluous to the salient elements necessary for specifying a value object. We describe these classes as Value Object Descriptors (VODs). The VOD specification introduced here is version-controlled and extensible, and envisioned to seed a larger collection of VODs used with other GA4GH standards beyond VRSATILE.
Use of VODs provides a convenience mechanism for passing labels that you As an example, this means that a value object representing a genomic variant in VRS can be conveniently passed alongside human identifiers (e.g. ClinVar IDs), expressions (e.g. HGVS descriptions), and important contexts (e.g. sequence type, gene, transcript) in a standard format. This additional structure is necessary due to the nature of value objects and .
The GA4GH Variation Representation Specification () is a terminology, information model, and schema for the computational representation of variation. VRS also describes useful conventions for the normalization of variation forms for message passing between systems. Objects compliant with VRS are value objects: data objects that are compared by structure and value, in contrast to entities which are compared by registered identifiers. For example, the variants represented by the NM_004415.2:c.8472_8483del and LRG_423t1:c.8472_8483del HGVS descriptions are not found equivalent by comparing these strings, but by comparing the structure of the reference sequence and indicated change underlying the descriptors. Conversely, the meaning of the variant (a specific deletion on a specific residue sequence) is clear without reference to any external naming authority (in this example, the NM and LRG sequence identifiers), and in fact the referenced entities can only be retrieved through lookup on a sequence registry instead of through inspection of the variant itself.
The Extension class provides VODs with a means to extend descriptions with other attributes unique to a content provider. These extensions are not expected to be natively understood under VRSATILE, but may be used for pre-negotiated exchange of message attributes when needed.
| Field | Type | Limits | Description |
|---|---|---|---|
| type | string | 1..1 | MUST be "Extension" |
| name | string | 1..1 | A name for the Extension |
| value | any[] | 0..* | Any primitive or structured object |
The Expression class is designed to enable descriptions based on a specified nomenclature or syntax for representing an object. Common examples of expressions for the description of molecular variation include the HGVS and ISCN nomenclatures.
| Field | Type | Limits | Description |
|---|---|---|---|
| type | string | 1..1 | MUST be "Expression" |
| syntax | CURIE | 1..1 | CURIE referencing the expression syntax |
| value | string | 1..1 | The concept expression as a string |
| version | string | 0..1 | An optional version of the expression syntax |