updated fao_class description link and permissible values

[mslarae13]

Updated FaoClassEnum to match available list Updated fao_class description to have updated link & reference for enum source

[mslarae13]

Blocked by https://github.com/GenomicsStandardsConsortium/mixs/pull/805

[mslarae13]

To discuss at TWG:

deprecation protocol in place. However, policy should still be discussed & by that I mean I have tagged these to be deprecated but I'm not sure we've settled on WHEN things get removed from the mixs.yaml and put into the deprecated.yaml?

[lschriml]

Hello Montana,I was not on the last call.Can you please clarify why the allowable values are being changed ?Much appreciated,LynnSent from my iPhoneOn Jul 17, 2024, at 6:08 PM, Montana @.***> wrote: To discuss at TWG: deprecation protocol in place. However, policy should still be discussed & by that I mean I have tagged these to be deprecated but I'm not sure we've settled on WHEN things get removed from the mixs.yaml and put into the deprecated.yaml?

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[lschriml]

Hello Montana,  Another consideration: it would be useful to put a term review / update protocol in place. So that if the TWG/CIG are considering changing the terms of a checklist or package, in a substantial way, that the process of the  review include the original developers/CIG members involved with the development. That way, we are not mistakenly changing what the standards was meant to collect.In the past the CIG did not edit packages/checklists, other than to fix minor edits.We need to consider if this is an area of work we want to do or should be doing as it has been the community developers that have decided what metadata terms they want in their standards.Cheers,LynnSent from my iPhoneOn Jul 17, 2024, at 6:08 PM, Montana @.***> wrote: To discuss at TWG: deprecation protocol in place. However, policy should still be discussed & by that I mean I have tagged these to be deprecated but I'm not sure we've settled on WHEN things get removed from the mixs.yaml and put into the deprecated.yaml?

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[turbomam]

Good point @lschriml . @mslarae13 and Sierra have put together a good, tracable deprecation framework but I don' think we have something equivalent for traceable changes yet.

[turbomam]

Or, specifically in this case, where do deprecated permissible values go? Other schema elements like classes and slots are eventually moved https://github.com/GenomicsStandardsConsortium/mixs/blob/main/src/mixs/schema/deprecated.yaml. Permissible values can't be moved (or searched) in a free standing manner

[lschriml]

There is not yet, a protocol for deprecating elements of a metadata term. Let's discuss at an upcoming call. I think this could fit into a change log, type of reporting.

On Thu, Jul 18, 2024 at 10:53 AM Mark Andrew Miller < @.***> wrote:

Or, specifically in this case, where do deprecated permissible values go? Other schema elements like classes and slots are eventually moved https://github.com/GenomicsStandardsConsortium/mixs/blob/main/src/mixs/schema/deprecated.yaml. Permissible values can't be moved (or searched) in a free standing manner

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[mslarae13]

@lschriml

In the issue linked above. https://github.com/GenomicsStandardsConsortium/mixs/issues/696, and @only1chunts comment https://github.com/GenomicsStandardsConsortium/mixs/issues/696#issuecomment-1790283905

The FAO permissible values have changes & the previously provided link is no longer active. So I updated the enum to match the updated list of values. But yes, we can discuss

[lschriml]

Sound good.Sent from my iPhoneOn Jul 19, 2024, at 6:18 PM, Montana @.***> wrote: @lschriml In the issue linked above. #696, and @only1chunts comment #696 (comment) The FAO permissible values have changes & the previously provided link is no longer active. So I updated the enum to match the updated list of values. But yes, we can discuss

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[mslarae13]

I don't know what the MIxS policy is on removing permissible values - these may have been used in existing projects.

I would instead mark these as deprecated; e.g

   Lithosols:
      deprecated: No longer in FAO as of YYYY-MM-DD / version X

Thanks @cmungall Yes, we did implement the deprecated.yaml.

Based on the workflow proposed by Sierra and approved byt GSC and NMDC, the terms are marked for deprecation for 1 release. And after a release as marked for deprecation, the terms/items marked for deprecation are then moved into the deprecated.yaml.

As such, for this PR, the terms only get marked for deprecation. Then, a version of MIxS will be released. And then an separate PR will move these terms into deprecated.yaml.

Does this satisfy your request?

[mslarae13]

Additional note based on todays discussion, the current deprecation method doesn't not have a way to capture JUST the permissible values within an enum. A LinkML update will be needed to move these deprecated PVs into the deprecated.yaml