Code Table Request - new part preparation method: ethanol precipitation

[Jegelewicz]

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.

Apply methods for DNA extraction consistently

Context

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

populate the new code table created in https://github.com/ArctosDB/arctos/issues/6802

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=ctpreparation_method

Proposed Value

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

ethanol precipitation

Proposed Definition

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

DNA was extracted using a non kit-based ethanol precipitation. https://en.wikipedia.org/wiki/Ethanol_precipitation

Collection type

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

N/A

Attribute Extras

Attribute data type

If the request is for an attribute, what values will be allowed? free-text, categorical, or number+units depending upon the attribute (TBA)

N/A

Attribute controlled values

If the values are categorical (to be controlled by a code table), add a link to the appropriate code table. If a new table or set of values is needed, please elaborate.

N/A

Attribute units

if numerical values should be accompanied by units, provide a link to the appropriate units table.

N/A

Part preservation attribute affect on "tissueness"

if a new part preservation is requested, please add the affect it would have on "tissueness": No Influence, Allows, or Denies

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.

https://github.com/ArctosDB/data-migration/issues/1517#issuecomment-1747380980

Available for Public View

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

yes

Helpful Actions

• [x] Add the issue to the Code Table Management Project.

• [x] 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 @campmlc @megulbranson

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._

• [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.

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

• [x] 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.

[happiah-madson]

Any questions we can answer about this?

[Jegelewicz]

@dustymc @mkoo @ccicero @campmlc @Nicole-Ridgwell-NMMNHS questions? Check boxes?

[dustymc]

Does this need ' extraction' appended to match https://github.com/ArctosDB/arctos/issues/6867? I'm happy either way....

[Nicole-Ridgwell-NMMNHS]

This looks fine to me.

[happiah-madson]

Does this need ' extraction' appended to match https://github.com/ArctosDB/arctos/issues/6867? I'm happy either way....

No, because the DNA isn't extracted out of say, tissue, it's precipitated out of a solution: e.g., https://pubmed.ncbi.nlm.nih.gov/27934690/ ; https://projects.iq.harvard.edu/files/hlalab/files/ethanol-precipitation-of-rna_hla.pdf ; https://cshprotocols.cshlp.org/content/2016/12/pdb.prot093377.full

My quick google search says that most language is "Ethanol precipitation of DNA/RNA" . IDK if anyone else would use 'ethanol precipitation' so I'm ok with adding the 'of DNA/RNA' to the end if it helps with clarity.

[campmlc]

I checked a box.

[Jegelewicz]

Does this need ' extraction' appended to match https://github.com/ArctosDB/arctos/issues/6867? I'm happy either way....

I think that "precipitation" is somewhat the equivalent of "extraction" in the other term.

[Jegelewicz]

added