Code Table Request - new examined_detected value = virus: SARS-CoV-2

[Jegelewicz]

Instructions

This is a template to facilitate communication with the Arctos Code Table Committee. Submit a separate request for each relevant value. This form is appropriate for exploring how data may best be stored, for adding vocabulary, or for updating existing definitions.

Reviewing documentation before proceeding will result in a more enjoyable experience.

• Issue Documentation
• Code Table Documentation
• Video Tutorial - Submit a Code Table Request

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Initial Request

Goal: Describe what you're trying to accomplish. This is the only necessary step to start this process. The Committee is available to assist with all other steps. Please clearly indicate any uncertainty or desired guidance if you proceed beyond this step.

Proposed Value: Proposed new value. This should be clear and compatible with similar values in the relevant table and across Arctos.

virus: SARS-CoV-2

Proposed Definition: Clear, complete, non-collection-type-specific functional definition of the value. Avoid discipline-specific terminology if possible, include parenthetically if unavoidable.

Severe acute respiratory syndrome coronavirus 2. A strain of coronavirus that causes COVID-19 (coronavirus disease 2019). ICTV Taxon details

Context: Describe why this new value is necessary and existing values are not.

There are other pathogens we test for though, including COVID and EHD (epizootic hemorrhagic disease) See addition comments in https://github.com/ArctosDB/data-migration/issues/889

Table: Code Tables are http://arctos.database.museum/info/ctDocumentation.cfm. Link to the specific table or value. This may involve multiple tables and will control datatype for Attributes. OtherID requests require BaseURL (and example) or explanation. Please ask for assistance if unsure.

https://arctos.database.museum/info/ctDocumentation.cfm?table=ctexamined_detected

_Collection type: Some code tables contain collection-type-specific values. collection_cde may be found from https://arctos.database.museum/home.cfm_

Mamm Teach

Priority: Please describe the urgency and/or choose a priority-label to the right. You should expect a response within two working days, and may utilize Arctos Contacts if you feel response is lacking.

Available for Public View: Most data are by default publicly available. Describe any necessary access restrictions.

yes

Project: Add the issue to the Code Table Management Project.

Discussion: Please reach out to anyone who might be affected by this change. Leave a comment or add this to the Committee agenda if you believe more focused conversation is necessary.

@ArctosDB/arctos-code-table-administrators @hkevans

Approval

All of the following must be checked before this may proceed.

_The How-To Document should be followed. Pay particular attention to terminology (with emphasis on consistency) and documentation (with emphasis on functionality)._

• [x] Code Table Administrator[1] - check and initial, comment, or thumbs-up to indicate that the request complies with the how-to documentation and has your approval (https://github.com/ArctosDB/arctos/issues/6117#issuecomment-1503932791)
• [x] Code Table Administrator[2] - check and initial, comment, or thumbs-up to indicate that the request complies with the how-to documentation and has your approval
• [x] DBA - The request is functionally acceptable. The term is not a functional duplicate, and is compatible with existing data and code.
• [x] DBA - Appropriate code or handlers are in place as necessary. (ID_References, Media Relationships, Encumbrances, etc. require particular attention)

Rejection

If you believe this request should not proceed, explain why here. Suggest any changes that would make the change acceptable, alternate (usually existing) paths to the same goals, etc.

1. Can a suitable solution be found here? If not, proceed to (2)
2. Can a suitable solution be found by Code Table Committee discussion? If not, proceed to (3)
3. Take the discussion to a monthly Arctos Working Group meeting for final resolution.

Implementation

Once all of the Approval Checklist is appropriately checked and there are no Rejection comments, or in special circumstances by decree of the Arctos Working Group, the change may be made.

Review everything one last time. Ensure the How-To has been followed. Ensure all checks have been made by appropriate personnel.

Make changes as described above. Ensure the URL of this Issue is included in the definition.

Close this Issue.

DO NOT modify Arctos Authorities in any way before all points in this Issue have been fully addressed; data loss may result.

Special Exemptions

In very specific cases and by prior approval of The Committee, the approval process may be skipped, and implementation requirements may be slightly altered. Please note here if you are proceeding under one of these use cases.

1. Adding an existing term to additional collection types may proceed immediately and without discussion, but doing so may also subject users to future cleanup efforts. If time allows, please review the term and definition as part of this step.
2. The Committee may grant special access on particular tables to particular users. This should be exercised with great caution only after several smooth test cases, and generally limited to "taxonomy-like" data such as International Commission on Stratigraphy terminology.

[Jegelewicz]

Incoming collection - no available digital data. Needed for data entry.

[campmlc]

I have several loans out of samples that will have these data once the project is complete. I support this

[cjconroy]

Is AWG considering what might happen if data like this are public? It might have implications for regulation. For example, if we add anything on a Select Agents list https://www.selectagents.gov/sat/list.htm, it will likely need to be destroyed. Or at least reported to certain authorities. This list is dynamic and changes over time. Is this an area of the database that could be hidden from casual viewers?

[dustymc]

Excellent point.

I think the intent (and reality) is to record that something was detected at some point during the life of the host, not to suggest anything about "parts" (eg physical things which might present some sort of danger). Many of us have been examined for SARS-CoV-2, a few billion of us have positive detection, that doesn't mean the CDC considers us to be biohazards. That is not clear from the definition, it should be adjusted.

[campmlc]

This was one of the reasons that the SNV attribute was deliberately made unclear when it was originally developed. No public user would know this means "sin nombre hantavirus" positive or negative. However, in either case, these were antibody tests in host tissue, not cultured virus. So we need the ability to encumber. But we also need the ability to make these data available.

[Nicole-Ridgwell-NMMNHS]

Does this need to wait on ability to encumber?

[Jegelewicz]

@hkevans will you need to encumber these data or are you OK with them being public?

[hkevans]

They will be public - there are management zones based around these detections.

Heather K. Evans, Ph.D. Conservation Geneticist

NC Wildlife Resources Commission 11 W. Jones St. Raleigh, NC 27601 Office: 919-707-9285 Mobile:984-480-6408

ncwildlife.org

On May 23, 2023, at 7:28 PM, Teresa Mayfield-Meyer @.***> wrote:

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@hkevanshttps://github.com/hkevans will you need to encumber these data or are you OK with them being public?

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[Jegelewicz]

I think the intent (and reality) is to record that something was detected at some point during the life of the host, not to suggest anything about "parts" (eg physical things which might present some sort of danger). Many of us have been examined for SARS-CoV-2, a few billion of us have positive detection, that doesn't mean the CDC considers us to be biohazards. That is not clear from the definition, it should be adjusted.

Isn't the time/location/intent of sampling "method"? I think the definition is for what was "examined for" or "detected" and is fine as it is.

[campmlc]

I approved.

[Jegelewicz]

@campmlc I had noted that in the first code table approval. We still need a second. @Nicole-Ridgwell-NMMNHS

[campmlc]

Maybe we need to change the form to add the GitHub ID of the person approving and the date?

On Wed, May 24, 2023, 8:15 AM Teresa Mayfield-Meyer < @.***> wrote:

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@campmlc https://github.com/campmlc I had noted that in the first code table approval. We still need a second. @Nicole-Ridgwell-NMMNHS https://github.com/Nicole-Ridgwell-NMMNHS

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[campmlc]

I would also propose that given you are submitting these issues for other institutions, as code table admin and coordinator you should be able to approve them as well as submit.

[Jegelewicz]

Maybe we need to change the form to add the GitHub ID of the person approving and the date?

I did that for yours because you approved, but did not check the box. I think once everyone is used to checking the box, this will be less of an issue.

And one can see all the edits made to an issues using this.

[dustymc]

approve them as well as submit

No. The point is independent review. Without, we have made some impressive messes. (https://docs.google.com/spreadsheets/d/1tlylrcUSn6Nk0lyim2nf84WlBHPSYlSgIqp8lATZ-gU/edit#gid=1450889050) If we can't get the few requested reviews then we need a different process - there's no reason to deal with all this if it's not going to DO STUFF for us.

did not check the box

Suggest editing the template to change the "just do anything" bits to "check the box" - that's obviously causing some unnecessary confusion. (The point is careful review, surely specific instructions can't cause problems?!)

[Jegelewicz]

approve them as well as submit

No. The point is independent review. Without, we have made some impressive messes. (https://docs.google.com/spreadsheets/d/1tlylrcUSn6Nk0lyim2nf84WlBHPSYlSgIqp8lATZ-gU/edit#gid=1450889050) If we can't get the few requested reviews then we need a different process - there's no reason to deal with all this if it's not going to DO STUFF for us.

I agree with @dustymc I probably make more mistakes than anyone! I may have drafted this for someone else, but I still drafted it and it would be nice to know that at least two independent reviews were made.

[Nicole-Ridgwell-NMMNHS]

Approved.

[Jegelewicz]

Added.