Code Table Request - new part preservation: buffer TE

[Jegelewicz]

Context

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

Needed for incoming collection to record DNA preservation

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=ctpart_preservation

Proposed Value

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

buffer TE

Proposed Definition

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

10 mM Tris-Cl, 1 mM EDTA, pH 8.0

Part preservation attribute affect on "tissueness"

allows

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.

Example Data

Requests with clarifying sample data are generally much easier to understand and prioritize. Please attach or link to any representative data, in any form or format, which might help clarify the request.

Available for Public View

Most data are by default publicly available. Describe any necessary access restrictions.

Helpful Actions

• Add the issue to the Code Table Management Project.

• 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 @happiah-madson @falco-rk - please address the "tissueness" question.

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). No person should act in multiple roles; the submitter cannot also serve as a Code Table Administrator, for example.

• 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 - Code Table Request - new part preservation: buffer TE #6792 (comment)
• 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.

• Add or revise the code table term/definition as described above. Ensure the URL of this Issue is included in the definition. URLs should be included as text, separated by spaced pipes. Do not include HTML in definitions.

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.

[campmlc]

I support this.

[happiah-madson]

I think Tissueness is allows or no effect? But my understanding of tissueness is a bit wonky? IDK why someone would collected tissues into TE? But the DNA in TE is definitely GGBN-able?

[campmlc]

The preservation history of a part as captured in the preservation attribute affects tissueness. So even if a part is currently in 95% ethanol in -80C, if it was originally collected into formalin, that disqualifies it for "tissueness". We have whole animals stored in ethanol and stored at room temperature- and technically they can be a source of tissue as long as they weren't fixed in formalin on collection. This may of course change as technology advances, but currently this is how we determine what gets published as "tissue" to GGBN.

[campmlc]

BN-able?

I think Tissueness is allows or no effect? But my understanding of tissueness is a bit wonky? IDK why someone would collected tissues into TE? But the DNA in TE is definitely GGBN-able?

So my understanding of these proposed preservation part attribute code table values is that they would be used for part = DNA specifically.

[happiah-madson]

So my understanding of these proposed preservation part attribute code table values is that they would be used for part = DNA specifically.

In my opinion, yes.

[campmlc]

You are lucky you get all the DNA quality metadata - usually when I get samples returned, they are coming from PIs and student labs in an Eppendorf tube hopefully marked with something more informative than "A1", and I have to beg and plead for any extraction methodology, absorbance ratios, ng etc.
Most of what we have is actual "tissue" = samples of liver, heart, muscle, spleen etc that are flash frozen in LN2, and we subsample these in 25mg increments for loan to researchers. It is a challenge to get usable extractions returned, and the data are usually dubious.

[dustymc]

edited to follow #6791

[happiah-madson]

You are lucky you get all the DNA quality metadata

This is a direct effect of our lab doing most of the extractions!

[Jegelewicz]

@campmlc please check a box.

[Nicole-Ridgwell-NMMNHS]

sounds good, box checked

[Jegelewicz]

added