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VRS references from 1.2 => 1.3 #186

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@mbaudis mbaudis commented Nov 16, 2024

This is an addition to the VRS schema link fix, bumping the version. Reasoning:

The Beacon schema for genomic allows 3 options:

  • VRS MolecularVariation
  • VRS SystemicVariation
  • Beacon LegacyVariation (which adopts the VRS location object but uses separate definitions otherwise)

Unfortunately, during Beacon v2 approval only VRS 1.2. was available and then explicitly referenced in the schema. It fast superseded by 1.3 which allows a much better definition of "Systemic Variations" such as CNV.

This PR changes all VRS references from 1.2 => 1.3 and should be very welcome to implementers (1.3. has been the longstanding standard now until the future 2.x is out; in fact, the bycon based implementations such as progenetix.org have been using it for their Beacons for ~2years).

The Beacon schema for genomic allows 3 options:

* VRS MolecularVariation
* VRS SystemicVariation
* Beacon LegacyVariation (which adopts the VRS location object but uses separate definitions otherwise)

Unfortunately, during Beacon v2 approval only VRS 1.2. was available and then explicitly referenced in the schema. It fast superseded by 1.3 which allows a *much* better definition of "Systemic Variations" such as CNV.

This PR changes all VRS references from 1.2 => 1.3 and should be very welcome to implementers (1.3. has been the longstanding standard now until the future 2.x is out; in fact, the `bycon` based implementations such as progenetix.org have been using it for their Beacons for ~2years).
The `beacon_yaml2md.pl` doc generator contains hard coded definitions to VRS 1.2 `CopyNumber` which doesn't exist in 1.3.

This should be fixed separately, possibly w/ revision of the schema documentation method/engine.
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Yes, I think these are the only places where the version for vrs appears and this is ok for me. Nevertheless, I don't know if there is any difference between 1.3 or 1.3.0 as I remember @ahwagner telling us to choose 1.3.0 but nevermind, 1.3 works and redirects you to the same page as 1.3.0. If this doesn't change...

@costero-e costero-e mentioned this pull request Nov 22, 2024
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You can use either! VRS 1.3 might be the better choice, since you will get (non-breaking) patch enhancements to the spec that way (e.g. fixing typos, clarifying definitions). 1.3.0 will be completely static.

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4 participants