Code Table Request - new part preparation method: Qiagen BioSprint96 DNA Blood Kit

[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.

Qiagen BioSprint96

Qiagen BioSprint96 DNA Blood Kit

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 Qiagen BioSprint96 DNA Blood Kit https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/dna-purification/genomic-dna/biosprint-dna-blood-kits

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.

[Jegelewicz]

@happiah-madson @falco-rk is this really a thing or is it some combination of things?

https://www.qiagen.com/us/search/products?query=Biosprint%2096

[falco-rk]

Biosprint96 is a machine to automate extractions that could be used with a couple different extraction kits. We used it with the biosprint DNA blood kit . So we should maybe make the definition more specific or add an additional part preparation method that is the biosprint DNA blood kit and we would have 2 attributes on our samples extracted using biosprint.

[falco-rk]

Or we could just put the biosprint DNA blood kit as the part preparation method attribute and write "Biosprint96" in the methods place. That has the downside of being terrible and requiring us to remember, but its mostly legacy data, so I'm not too worried about it.

[Jegelewicz]

Or we could just put the biosprint DNA blood kit as the part preparation method attribute and write "Biosprint96" in the methods place.

I think this makes more sense?

[happiah-madson]

If we do that, then we need to add Biosprint DNA Blood Kit as a new preparation method.

[Jegelewicz]

Biosprint DNA Blood Kit as a new preparation method.

file an issue!

[happiah-madson]

yes ma'am!

[Jegelewicz]

@dustymc OK?

[dustymc]

Is 96 just the size??

https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/dna-purification/genomic-dna/biosprint-dna-blood-kits

[mkoo]

I adjusted the term and added the link to the definition-- this is proprietary so keep the company name associated with it. (and yes, @dustymc it's the size/number of wells). Otherwise I checked a box

[dustymc]

So value should be "Qiagen BioSprint" - right??

[mkoo]

Yes I suppose you are right in some sense but 96 is the standard size most would get and it is a separate product line so I am inclined to be as specific as possible and include the 96

However rereading this maybe the term should be Qiagen BioSprint96 DNA Blood Kit to be specific and complete Anyway, I would be ok with or without 96 so @happiah-madson maybe weigh in if you guys ever buy the smaller kits

[falco-rk]

We are happy with Qiagen BioSprint96 DNA Blood Kit.

BioSprint 96 is a specific instrument. There is also a BioSprint 15.

[Jegelewicz]

edits made - @dustymc are we happy?

[dustymc]

I'm still lost, sorry!

I think this is something like Qiagen BioSprint DNA Blood Kit and one could purchase 96, 15, or maybe other amounts of the same thing packaged for usage in various machines. If that's correct then including the number of wells-er-whatever here just makes it impossible to find everything with a single query - we'll end up with a bunch of the same things but in different sizes. If that's not correct then please set me straight!

The same thing will need addressed on the machine, but in that case it seems more likely that eg the 15-well models have a reputation for whatevering and there might be some reason to keep them separate (or not, whatever, I'm asking - and I suppose that could be true here too).

?????

[happiah-madson]

So my understanding is our BioSprint can exclusively handle 96-well plates and we would never be able to use a 15 kit because of reasons. I totally get what you mean about searchability, though. If it helps, we only have BioSprint96.

I don't think we're interested on dying on this hill, though, so...

[dustymc]

dying on this hill,

Yea, that hill's definitely not getting fertilized today...

The concerns are laid out here, this is part of the definition, if someone shows up with a 23½-well kit and wants to argue it's the same then we can merge. Concerns addressed, @Jegelewicz you're up.

[happiah-madson]

Yea, that hill's definitely not getting fertilized today...

💀💀💀💀💀💀💀💀

[Jegelewicz]

added