Separate attribution from descriptions in extension documentation

[cmungall]

https://genomicsstandardsconsortium.github.io/mixs/0016012/

A collection of terms appropriate when collecting samples and sequencing samples obtained from the uppermost layer of Earth's crust, contributed by the Terragenome Consortium

This is an odd description. It makes it seem like this when samples are contributed by the Terragenome Consortium.

I recommend separating source from description. The source field can be used with a link to the paper https://www.nature.com/articles/nrmicro2119

And the description could be made more informative to an end user

[only1chunts]

I like your suggestion, thanks.

[mslarae13]

@cmungall @turbomam Do you imagine this being

"A collection of terms appropriate when collecting samples and sequencing samples obtained from the uppermost layer of Earth's crust. Extension contributed by the Terragenome Consortium"

Or, is there a separate linkML attribute we should put the contributed team?

[turbomam]

Soil (and all LinkML Extensions) are modeled as LinkML classes. We can (and should) use any metaslots applicable to ClassDefinition to independently capture those two different concepts:

• a textual description of a MIxS Soil instance's fundamental/distinctive characteristics
• who should get credit for contributing that work

Of course we will want to

• apply whatever attribution decisions we make for Soil as broadly as possible... all Extensions? All classes? All elements including slots?
• introduce as few new LinkML metaslots as possible

[turbomam]

Most of the LinkML metaslots that are jumping out to me require a URI value:

• contributors
• created_by
• see_also
• source

Does the Terragenome Consortium have a URL, or a stable identifier for soil sample in their system?

@cmungall already suggested linking to their paper.

I agree with @cmungall that we should add some links, like source to the ClassDefinition. I also think we should remove "...contributed by the Terragenome Consortium..." from the description. But adding links alone won't make the "Terragenome Consortium" text appear on the MIxS documentation page, without some additional development.

It seems like we need a textual (string range) slot for attribution. The closest thing I've though of so far is conforms_to

Others are welcome to look at the ClassDefinition slots list page and make suggestions!

[lschriml]

Keep the : "..contributed by the Terragenome Consortium"

--> this should not be changed, as this was agreed upon with the developers of this package/extension.

We should not be editing the content of the MIxS fields ad hoc. That is not within the work of the CIG, not after the standard has been created. The changes we do are minor: such as formatting, grammar, or slight editing is permissible. I can see this being a slippery slope that would derail our efforts to develop new standards. This type of review was done when the checklist/extension was created.

Changes are not to be made without a full review by CIG and the originating group.

This is GSC policy.

Rather than focusing on the content of terms already in place, I would like to see the CIG move to focusing primarily on putting together the new standards. Currently this would be working on the eDNA checklist.

Cheers, Lynn

On Thu, Jul 18, 2024 at 10:03 AM Mark Andrew Miller < @.***> wrote:

Most of the LinkML metaslots that are jumping out to me require a URI value:

• contributors
• created_by
• see_also
• source

Does the Terragenome Consortium have a URL, or a stable identifier for soil sample in their system?

@cmungall https://github.com/cmungall already suggested linking to their paper.

I agree with @cmungall https://github.com/cmungall that we should add some links, like source to the ClassDefinition. I also think we should remove t...contributed by the Terragenome Consortium..." from the description. But adding links alone won't make the "Terragenome Consortium" text appear on the MIxS documentation page, without some additional development.

— Reply to this email directly, view it on GitHub https://github.com/GenomicsStandardsConsortium/mixs/issues/797#issuecomment-2236618796, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DNN3VHRXWBELEF5EV3ZM7DLDAVCNFSM6AAAAABHZHGA2CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGYYTQNZZGY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[lschriml]

It would also be quite helpful for the CIG and TWG to finalize the documentation, for putting out the next release.

Are the protocols and their documentation in place for how we add new updates, what are the steps, starting with the excel or YAML provided to the CIG, to getting that integrated into LinkML, going through QC and trouble shooting.

This would be great to have as a focus, moving forward.

Cheers, Lynn

On Thu, Jul 18, 2024 at 10:33 AM Lynn Schriml @.***> wrote:

Keep the : "..contributed by the Terragenome Consortium"

--> this should not be changed, as this was agreed upon with the developers of this package/extension.

We should not be editing the content of the MIxS fields ad hoc. That is not within the work of the CIG, not after the standard has been created. The changes we do are minor: such as formatting, grammar, or slight editing is permissible. I can see this being a slippery slope that would derail our efforts to develop new standards. This type of review was done when the checklist/extension was created.

Changes are not to be made without a full review by CIG and the originating group.

This is GSC policy.

Rather than focusing on the content of terms already in place, I would like to see the CIG move to focusing primarily on putting together the new standards. Currently this would be working on the eDNA checklist.

Cheers, Lynn

On Thu, Jul 18, 2024 at 10:03 AM Mark Andrew Miller < @.***> wrote:

Most of the LinkML metaslots that are jumping out to me require a URI value:

• contributors
• created_by
• see_also
• source

Does the Terragenome Consortium have a URL, or a stable identifier for soil sample in their system?

@cmungall https://github.com/cmungall already suggested linking to their paper.

I agree with @cmungall https://github.com/cmungall that we should add some links, like source to the ClassDefinition. I also think we should remove t...contributed by the Terragenome Consortium..." from the description. But adding links alone won't make the "Terragenome Consortium" text appear on the MIxS documentation page, without some additional development.

— Reply to this email directly, view it on GitHub https://github.com/GenomicsStandardsConsortium/mixs/issues/797#issuecomment-2236618796, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DNN3VHRXWBELEF5EV3ZM7DLDAVCNFSM6AAAAABHZHGA2CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWGYYTQNZZGY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[turbomam]

@lschriml we will keep "..contributed by the Terragenome Consortium", but put it into a more appropriate slot, as described in the comments above.

[lschriml]

As I was saying, We should not be editing the definitions as part of this work.

I would not want this moved to another slot.

On Thu, Jul 18, 2024 at 10:48 AM Mark Andrew Miller < @.***> wrote:

@lschriml https://github.com/lschriml we will keep "..contributed by the Terragenome Consortium", but put it into a more appropriate slot, as described in the comments above.

— Reply to this email directly, view it on GitHub https://github.com/GenomicsStandardsConsortium/mixs/issues/797#issuecomment-2236770607, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DOP3KOAHVNVM3FMJH3ZM7ISXAVCNFSM6AAAAABHZHGA2CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZWG43TANRQG4 . You are receiving this because you were mentioned.Message ID: @.***>

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[turbomam]

Please provide a specification for what should and should not go into the description slot. (Or suggest a way we can work together to get to that point)

[mslarae13]

@turbomam I just found https://linkml.io/linkml-model/latest/docs/contributors/

It requires a URI, but maybe we could investigate the ability to use this slit & still display it in the docs?

[turbomam]

@turbomam I just found https://linkml.io/linkml-model/latest/docs/contributors/

It requires a URI, but maybe we could investigate the ability to use this slit & still display it in the docs?

I agree 100% and suggested this earlier in

• https://github.com/GenomicsStandardsConsortium/mixs/issues/797#issuecomment-2236618796

But @lschriml's comment

• https://github.com/GenomicsStandardsConsortium/mixs/issues/797#issuecomment-2236782426

seems to be incompatible with our more modular vision