Material Sample: Preparation Type

[dshorthouse]

GIVEN I have accessed DINA as a user

WHEN I access/edit a material sample

THEN I should be able to declare its preparation type

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Here, preparation type is defined as the physical presentation of the organism(s) that constitute the material sample, not the verb-based methods or protocols that were executed to generate it nor its medium/media or fixative(s) used to preserve it.

Terms:

• fossil
• cast
• skin
• skull
• skeleton
• genitalia
• leg
• whole organism
• tissue
• DNA
• leaf
• flower
• virus

[dshorthouse]

Can there be more than one Preparation Type as defined here per Material Sample? Examples please. The reason here is to narrow-in on whether or not we must/should split a Material Sample according some criteria, if necessary, such that downstream details like determinations are appropriately tracked.

[michellelocke]

I can't think of an example where the CNC would need to do that. If we have a wing from a specimen that is slide mounted we would simply give the wing a different unique number, but we would want to associate the two numbers together.

For genitalia dissections, we want to indicate their preparation type (the what and the how it is stored) but those should have a dissection number with info about that dissection, which is separate from the whole organism that the genitalia was dissected from (at least in the way I'd like to see this info tracked). So for the main specimen we would want to say it is a whole organism that is pinned, but then have a dissection that is genitalia and slide mounted, more of a subsample relationship than two preparations for one organism.

[dshorthouse]

Thanks, @michellelocke. That's what I figured for Entomology where each "child" Material Sample would have its own identity and linked back to the parent Material Sample to retrace that association/provenance. Both Material Samples may be affixed to one another (minuten with a gel capsule on same pin as the whole organism) but they'd be considered different Material Samples because whatever is in the gel capsule may have its own unique identifier.

[banchinic]

I don't see a use case for this for us either in the way I picture the DB. We do take spores from one specimen to make multiple new things (other pot culture, in vitro culture, slides, etc) but all the cultures would have their own identifier and be their own specimen with linkage to the parent.

However I'm not sure I understand David's comment: ''if necessary, such that downstream details like determinations are appropriately tracked.'' We do need to have determination and identification that follow when we create a new specimen from a parent culture. Also, we might have more than one species per pot that we split in two to try to isolate the species, but again they would all be their own specimen with linkage to the previous one.

[dshorthouse]

We do need to have determination and identification that follow when we create a new specimen from a parent culture. Also, we might have more than one species per pot that we split in two to try to isolate the species, but again they would all be their own specimen with linkage to the previous one.

What I was getting at here is the very common situation in Entomology & Botany too I assume where a bit of tissue is removed and sent off for barcoding and what comes back is a new determination that may, and frequently does, differ from the determination on the parent. And so, we have multiple sets of determinations that need to be maintained per chain of Material Samples.

That said, what I was getting at is whether or not the Material Sample type (as defined here) might be several and one of the a priori items acting as an anchor for which splits are then executed. In the case of the tissues (eg a leg in Entomology) these are ordinarily a posteriori designations. In other words, a leg is removed from a Material Sample and then it is the child. But, might there be situations where a Material Sample consists of more than one type & this is known (and tracked) ahead of time? So for example, a single Material Sample may consist of both casts and skeletons but when we go to split it for further analyses, we split on the bone and leave the cast type untouched. That's a lousy example, but I hope you see what I mean. Is it sufficient to say, "I split the Material Sample" into child items (and then to merely later designate what the child Material Sample type is) & not additionally specify which of the types in a composite Material Sample (if there is such a thing) was split?

[shannonasencio]

DAO and DAOM are in a similar situation. We may split apart parts of a collection, but each would receive its own unique identifier. We would need a way to associate the split out components, and to define that relationship (e.g. duplicate specimen, boxed fruits).

[dshorthouse]

The MIDS group has three terms in the development of its standard:

objectType: High-level terms for the classification of curated objects. A more generic classification of items in the collection than described in preparationType. preparationType: fossil, cast, photograph, DNA extract, skin, skull, skeleton, whole animal (ETOH), tissue (EDTA)

There is also a proposed DwC term:

materialSampleType: lot, whole specimen, specimen part, tissue sample, multiple fossils, serial thin sections, microfossil, water sample, soil sample, microbial sample, nest

There's arguably significant overlap among all these things. What, if any, is the difference for us especially now that we have deployed #34?

[dshorthouse]

Also, are there some logical rules that should come into play when a preparationType is chosen such that illogical choices are made (eg "whole organism" value in the child MaterialSample from a parent with value "leg")?