Cat-VRS Constraints

[DanielPuthawala]

Submitter Name

Daniel Puthawala

Submitter Affiliation

NCH / GA4GH

Project Details

The Cat-VRS is the newest product (still under development) under the GKS workstream. Cat-VRS is built on top of existing GKS standards such as VRS, and is itself destined to be a component part of other GKS efforts such as the VA-Spec.

This proposed session at the unconference focuses on pushing forward the development of Constraints and Profiles in the Cat-VRS. Possible topics include reviewing recently proposed changes to the DefiningContextConstraint, building out the LocationConstraint with an eye towards handing Fusions and Rearrangement Variants, and brainstorming new relation functions necessary to address currently unserviced implementor use cases.

Required Skills

No minimum skillset required (and we encourage participation from a broad diversity of perspectives!), though any of the following would be particularly helpful:

• Experience in Clinical genomics, variant analysis, or genomics bioinformatics pipelines
• Experience in python, JSON schema, or other technical tools for building and querying databases
• Familiarity with set theory, logic, or the fundamentals of computer science

[DanielPuthawala]

Current mock-up

[korikuzma]

Morning session

[ahwagner]

https://lucid.app/lucidchart/41566bc0-bb68-47c5-a212-b04c7d361bef/edit?invitationId=inv_8c80df88-7f5e-490e-aa9c-d60a78a6ceca

[ahwagner]

@larrybabb and @ahwagner continued this discussion during the afternoon session, and came up with the following additional decisions:

1. Drop molecularContextConstraint

2. Clarified the relations to be used in defining context constraints:
   translates_from
   translates_from_reading_frame
   liftover_to
   transcribes_to
   translates_to
   translates_through

3. Clarified that constraints are filter functions that return T/F for membership, e.g.

def definingAlleleContext(query allele, defining allele, relations[]) -> bool:
"""Returns if query allele is related to defining allele by a specified relation"""