Code Table Request - Add microbiome to the Examined_Detected code table

[campmlc]

Initial Request Add the term "microbiome" to the Examined_Detected code table to aid in the migration of legacy data.

_Proposed Value: microbiome

_Proposed Definition: The microbiome is a community of microorganisms (microbiota) that can usually be found living together in any given habitat, such as in the digestive tract, on the skin, or in a cave deposit; includes bacteria, archaea, fungi, algae, small protists and potentially viruses and other genetic elements. For specific communities, such as fungal mycobiomes, include detail in Methods. https://en.wikipedia.org/wiki/Microbiome

_Context: This is a new attribute value to capture current research results and pathogen studies using museum specimens. Data are available in publications referencing voucher specimens.

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

_Priority: High

_Available for Public View: 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.

@jldunnum @jtgiermakowski https://github.com/orgs/ArctosDB/teams/arctos-code-table-administrators

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
• [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]

Why is the proposed value fungi: microbiome but the definition clearly indicates that more than fungi are involved? Should we also have:

bacteria: microbiome virus: microbiome etc.

or should this just be microbiome (probably ONLY used in examined for) and whatever is detected gets a more detailed attribute value?

[campmlc]

My bad - I was originally going to request fungi: mycobiome, but it makes more sense to me to use the broader term and use methods to distinguish. I'll fix the typos.

On Wed, May 10, 2023, 7:54 AM Teresa Mayfield-Meyer < @.***> wrote:

• [EXTERNAL]*

Why is the proposed value fungi: microbiome but the definition clearly indicates that more than fungi are involved? Should we also have:

bacteria: microbiome virus: microbiome etc.

or should this just be microbiome (probably ONLY used in examined for) and whatever is detected gets a more detailed attribute value?

— Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/6269#issuecomment-1542258891, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADQ7JBF673YR3NGQIAGAKA3XFOMXTANCNFSM6AAAAAAX3ZZ4M4 . You are receiving this because you were assigned.Message ID: @.***>

[campmlc]

And I agree that for these types of broad screenings the more general terms should be used in examined for and whatever is detected gets a more detailed attribute value.

For specific screenings, eg for a specific virus, the examined for and detected will be the same.

[campmlc]

Approved by code table committee 5 May 2023.