Proposal for GA4GH-wide Computed Identifier Standard

This appendix describes a proposal for creating a GA4GH-wide standard for serializing data, computing digests on serialized data, and constructing CURIE identifiers from the digests. Essentially, it is a generalization of the Computed Identifiers section.

This standard is proposed now because VRS needs a well-defined mechanism for generating identifiers. Changing the identifier mechanism later will create significant issues for VR adopters.

Background

The GA4GH mission entails structuring, connecting, and sharing data reliably. A key component of this effort is to be able to identify entities, that is, to associate identifiers with entities. Ideally, there will be exactly one identifier for each entity, and one entity for each identifier. Traditionally, identifiers are assigned to entities, which means that disconnected groups must coordinate on identifier assignment.

The computed identifier scheme proposed in VRS computes identifiers from the data itself. Because identifers depend on the data, groups that independently generate the same variation will generate the same computed identifier for that entity, thereby obviating centralized identifier systems and enabling identifiers to be used in isolated settings such as clinical labs.

The computed identifier mechanism is broadly applicable and useful to the entire GA4GH ecosystem. Adopting a common identifier scheme will make interoperability of GA4GH entities more obvious to consumers, will enable the entire organization to share common entity definitions (such as sequence identifiers), and will enable all GA4GH products to share tooling that manipulate identified data. In short, it provides an important consistency within the GA4GH ecosystem.

As a result, we are proposing that the computed identifier scheme described in VRS be considered for adoption as a GA4GH-wide standard. If the proposal is accepted by the GA4GH executive committee, the current VRS proposal will stand as-is; if the proposal is rejected, the VRS proposal will be modified to rescope the computed identifier mechanism to VRS and under admininstration of the VR team.

Proposal

The following algorithmic processes, described in depth in the VRS Computed Identifiers proposal, are included in this proposal by reference:

  • GA4GH Digest Serialization is the process of converting an object to a canonical binary form based on JSON and inspired by similar (but unratified) JSON standards. This serialization for is used only for the purposes of computing a digest.
  • GA4GH Truncated Digest is a convention for using SHA-512, truncated to 24 bytes, and encoding using base64url.
  • GA4GH Identification is the CURIE-based syntax for constructing a namespaced and typed identifier for an object.

Type Prefixes

A GA4GH identifier is proposed to be constructed according to this syntax:

"ga4gh" ":" type_prefix "." digest

The digest is computed as described above. The type_prefix is a short alphanumeric code that corresponds to the type of object being represented. If this propsal is accepted, this “type prefix map” would be administered by GA4GH. (Currently, this map is maintained in a YAML file within the VRS repository, but it would be relocated on approval of this proposal.)

We propose the following guidelines for type prefixes:

  • Prefixes SHOULD be short, approximately 2-4 characters.
  • Prefixes SHOULD be for concrete types, not polymorphic parent classes.
  • A prefix MUST map 1:1 with a schema type.
  • Variation Representation types SHOULD start with V.
  • Variation Annotation types SHOULD start with A.

Administration

If accepted, administration of these guidelines should be transferred to a technical steering committee. If not accepted, the VR team will assume administration of the existing prefixes.