Code Table Request - Add bacteria: Mycobacterium to the Examined_Detected code table

[campmlc]

Initial Request

Goal

Add the term "bacteria: Mycobacterium" to the Examined_Detected code table

Proposed Value:

bacteria: Mycobacterium

Proposed Definition:

Mycobacterium is a genus of over 190 species in the phylum Actinomycetota, assigned its own family, Mycobacteriaceae. This genus includes pathogens known to cause serious diseases in mammals, including tuberculosis (M. tuberculosis) and leprosy (M. leprae) in humans. https://en.wikipedia.org/wiki/Mycobacterium

Context:

This is a new attribute value to capture data currently being evaluated in museum specimens through active loans. Preliminary results are already available.

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

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
• [ ] 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
• [ ] DBA - The request is functionally acceptable. The term is not a functional duplicate, and is compatible with existing data and code.
• [ ] 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]

Do we need the generic term or the more specific ones? Are the tests for any Mycobacterium or for specific pathogenic species?

[campmlc]

We could include M. tuberculosis M. leprae as separate values. But given that tests and results may differ in their level of specificity, and frequently researchers discover there are actually more species than previously know involved with these microrganisms once they start doing genetic tests, I started with the broader term. The data I have is only for M. leprae, however.

[Jegelewicz]

The data I have is only for M. leprae, however.

For my own understanding - no matter what the organism of interest, should I expect examined for and detected to use bacteria: Mycobacterium as the value, with the details (Mycobacterium leprae) in the remark OR will we end up also adding bacteria: Mycobacterium leprae to the code table? Was the examination specifically for Mycobacterium leprae or was it more general and Mycobacterium leprae was found?

I am asking so that I can try to formulate some rules about this code table and the creation and use of terms with the respective values "examined for, not examined for, detected, and not detected".

[campmlc]

This may need to be a case by case basis, as in many taxa, there is only one pathogenic or parasitic species, in which case the specific pathogen should be referenced, whereas in others, there may be many, and using a higher level or more generic term or common name may be appropriate. I've been grappling with this too - when do we use common names that are readily searchable vs taxonomic names that obscure, used for different taxa, or may change, (Siphonaptera, for example). In this case, I'd like to request to use just Mycobacterium in the event they discover new "species".

[campmlc]

During code table meeting today, we discussed assessing these on a taxon by taxon basis but keeping these as general as possible, and using relationships to specific identified taxa whenever feasible. So my understanding is that bacteria: Mycobacterium would be correct in this case, with M. leprae in methods/remarks. We would need to further discuss some way to catalog bacteria, pathogenic fungi, protozoa and viruses as Arctos:Pathogen or MSB:Pathogen or some other means of cataloging relationships. Another option is using the A:string for the host record but that may be problematic to implement because of access, timing, or workflow concerns.

[Jegelewicz]

using the A:string for the host record but that may be problematic to implement because of access, timing, or workflow concerns.

Why A {string}? Just use the identification! A record can have multiple identifications that are ranked. Both the mammal and it's associated bacteria could be identifications on a single record until such time that you want to catalog the bacterium separately.

[Jegelewicz]

Suggest simplifying the definition.

Mycobacterium is a genus that includes pathogens known to cause serious diseases in mammals, including tuberculosis (M. tuberculosis) and leprosy (M. leprae) in humans. https://en.wikipedia.org/wiki/Mycobacterium

If we are being as general as possible, then should this be Mycobacteriaceae?

[dustymc]

should this be Mycobacteriaceae

Seems reasonable to me, and a great example of why anything very specific needs more structure than this can carry:

Members of Mycolicibacillus were demarcated from the larger genus Mycobacterium in 2018 by Gupta ....

These attribute values just do not have the capacity to effectively deal with 'taxon concepts' (however rough).

[mkoo]

is the new proposal: bacteria_Mycobacteriaceae

and thus following our new rules of punctuation? if so, I will check a box