Equivalence Between Concepts

VRS allows for the expressive representation of variation concepts. Sometimes this allows for forms that can be reduced from one to another, and sometimes bi-directionally. Examples of this include the bi-directional translation of chromosomal bands to sequence coordinates via a sequence-band mapping, the uni-directional translation of a gene to one or more sequence location(s), and the use of different Sequence Expression instances that would resolve to the same sequence. Similarly, authority-based concepts such as Gene are entirely dependent on the definition of the concept by that authority–we provide no guidance on how to translate or relate such concepts to one another.

We provide no guidance or mechanism to enforce “equivalence” between these concepts, because the semantics of one representation to another are distinct, even when there exists functions that equate or translate between two distinct concepts. Instead, we encourage communities to adopt policies about how and when to use the various concepts provided by VRS to represent different forms of variation. To assist in that effort, the GA4GH Genomic Knowledge Standards Work Stream is developing a specification for resource-defined Variation Concept Origination Policies (VCOPs). You can learn more about VCOPs in the VRSATILE framework.