Best practice to handle destructive sample(s) on a preparation?

Discipline Hangouts Botany
1

Specify Spotlight from RGBE (16/11/2022) showed that some of you (E, DAO, RJB) are using additional preparations to keep track of destructive samples on existing preparations attached to a collection object.

I’m in the process of migrating the CAY (French Guiana) legacy database into Specify so I’d been thinking on how to handle specimen sampling, and these feedback are timely, thanks!

I’d like to dig a bit deeper though, and make sure I’m making the right decision.

Scenarii of sampling : (i) commonly, a scientist comes to the herbarium, request a sample of a part of a specimen (piece of leaf, flower, etc.), and leaves with the sample, (ii) sometimes, a preparation is loaned and the recipient will ask for permission to sample the loaned preparation, (iii) rarely, someone from a distance will ask for a sample that is prepared and shipped by the herbarium.

No matter which scenario, it looks to me that we are in the scope of “interactions” at the level of a preparation. Uncertainty is (1) whether I should apply an interaction directly on the preparation (and designate somehow this interaction as a sampling) or (2) create an additional preparation specifically for the sampling (and eventually apply an interaction on this new preparation to detail who is it for, where as it been sent, etc.).

Option (1) Playing a bit with Gift in SP6, I realize that I have to increment preparation count every time I want to register a sampling so there is always an available item for creating a new gift/exchange out, not sure that is quite orthodox ?..

Option (2) Draw back for creating new “Destructive sample” preparation is that preparations aren’t related to each other individually, as far as I understand. Let me take an example : one collection object, several preparations (a few dried ones, an alcohol, etc.). Someone makes a sample of one dried preparation. One creates a new “Destructive sample” preparation to keep track of it, but how do you relate this new sampling prep to the dried prep ? With a free field?

Last, I’ve noticed there is a //Material Sample// table in the schema, very much oriented DNA, but neither SP6 nor SP7 seems to provide any default UI/forms for using this table. Conceptually speaking, it seemed to me, at first sight, the right table to use, but I’ve found very little information on the forum or the documentation, and looking more closely at the table and its relationships, it is outside the “interactions” so it doesn’t really do the job. Could Specify team briefly reminds how is it intended to be used and whether it could or should be Option (3) ?

Thanks in advance for sharing your views,
Philippe

2

@pverley Have you considered using the Material Sample table that vertebrate collections traditionally use for tissue samples? This is related to individual preparations so that you can indicate which preparation the material sample was taken from and would satisfy your need in that respect. However you cannot loan/gift material samples so you would still need to create a loan or gift of the preparation to indicate who used it and why.

3

@pverley to answer the question of how we you can link DS preparations back to the source preparation if you decide to go the preparations route - you are correct there’s no inbuilt mechanism for that. what we do is we’ve added a new field which identifies the source preparation that the DS came from - we just enter the appropriate barcode in this field.
Thanks
Ben
RBGE

4

One part of the process that has given us a lot of discussion is how to record samples that were not approved for various reasons. Options for these would be:

  1. Sampling not permitted under specimen permit restrictions.

  2. Material not suitable for sampling request at this time (ie, methodologies not yet developed sufficiently to expect good results from the small amount of older material available). These may be approved in the future.

  3. Material has already been sampled.

  4. Requester not sufficiently experienced or associated with recognised institution.

Following substantial discussion with the curators at RBGE who undertake the destructive sampling, we are looking at protocols that allow us to record the reasons for a sampling event not being approved so that this information is available to assess future request. We are about to do some testing of some options to see how they work in practice.

We’d also be interested to know if/how other institutions record this information.