VRS 2.0.0 Community Review Ballot

[ahwagner]

This is the ballot pre-release of the VRS 2.0 specification, open for community review following the GA4GH Product Development and Approval process.

Important Links

Documentation: https://vrs.ga4gh.org/en/2.0.0-ballot.2024-11/
Release log: https://vrs.ga4gh.org/en/2.0.0-ballot.2024-11/releases/2.0.html
Schemas: https://github.com/ga4gh/vrs/tree/2.0.0-ballot.2024-11.1/schema/vrs/json
Discussion: this page!

Full Changelog: 1.3.0...2.0.0-ballot.2024-11.1

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This discussion was created from the release VRS 2.0.0 Community Review Ballot.

[korikuzma]

VRS Roadmap in https://vrs.ga4gh.org/en/2.0.0-ballot.2024-11/releases/index.html gives 404. Should it point to project 12 instead?

[monicacecilia]

This was fixed.

[korikuzma]

https://vrs.ga4gh.org/en/2.0.0-ballot.2024-11/appendices/class_diagram.html

1. I believe vrs in sequenceString and residue should be blue
2. Is it necessary to include Normative in the legend if no classes in the diagram have this maturity level?
3. SequenceExpression inherits from Entity, but this is not expressed in the diagram. Is there a reason for this?

[monicacecilia]

Points 1. and 2. were addressed. I don't see an update for point 3.

[korikuzma]

CopyNumberCount and CopyNumberChange no longer inherit from CopyNumber. However, the RTD does not reflect this change to inherit from SystemicVariation directly.

Additionally, it would be nice to have the organization follow the other classes, where Definition and Information Model and Examples are in the expanded section.

[monicacecilia]

Has not been fixed. 👀

[korikuzma]

I have PR out for some of these! #623

[korikuzma]

The Primitive Types section includes Range, which is not correct.

The class diagram correctly puts Range in the General Purpose Data Classes

[korikuzma]

https://vrs.ga4gh.org/en/2.0.0-ballot.2024-11/appendices/ga4gh_identifiers.html#ga4gh-digest-keys

I'm not sure the thought is complete.

Also, this is minor and just an example, but the brackets not being closed bothers me.

[monicacecilia]

Just here to let you know that said bracket offense hasn't been fixed. 😉 ... and in all seriousness, that the thought still appears incomplete.

[korikuzma]

GKS Core references are not working because it's using targets that aren't defined, such as

:ref:`gks-core:Entity`

when it should be using (no gks-core: prefix)

:ref:`Entity`

When changing the reference, this links correctly to https://vrs.ga4gh.org/en/2.0.0-ballot.2024-11/concepts/AdditionalDataTypes/Element.html

By the way, I'm not sure if I should be creating issues for these. We can convert to issues if leads agree.

[korikuzma]

Currently Location is an ABC, but SequenceLocation is currently the only kind of Location. This comment leads me to believe it will be removed in the future. Is there a reason for this, such as potentially adding more types of Locations in the future? From a dev standpoint, this feels like a potential case for YAGNI

Given that the CopyNumber ABC was removed and CopyNumberCount and CopyNumberChange directly inherit from SystemicVariation (as seen in #600), I would assume that we'd have SequenceLocation directly inherit from Ga4ghIdentifiableObject too. But I might be missing why CN was removed.

[andrewpatto]

The intro paragraph for Systemic Variation is identical to the intro paragraph of Molecular Variation - which is probably an editing oversight

[korikuzma]

@ahwagner @larrybabb This should probably get resolved before 2.0 product review, right?

[korikuzma]

code is missing in imported classes: https://vrs.ga4gh.org/en/2.0.0-ballot.2024-11/concepts/AdditionalDataTypes/index.html#imported-classes

This can be fixed by fixing the case of code RST file (or references). It'll probably be good to have this updated in gks-core with proper lowercase now (since iriReference files have correct case)