part cleanup: carcass #4368
Comments
dustymc
added
Help wanted
No that isn't what I meant for those parts at all. I was looking for something that could represent a skinned body that was then preserved in alcohol. So not a whole organism and not a body, because it is definitely missing pieces. More like most the trunk, but including most of the neck vertebrae and some of the joints. We still do not have anything that matches that type of part in the code table for birds. I'll look around and see if I can find another part that might work for the UWYMV speciemns. |
|
I cleaned up UCM values |
|
UMZM only has a couple affected specimens, but we're in a similar boat as Beth with "carcass" meaning skinned but otherwise whole thorax + abdomen. The best word I can think of to describe this is "trunk," which isn't an option currently. |
|
@adhornsby @ewommack I suggest using body with the modifier postcranial We may want to consider the addition of a new modifier "skinless"? |
That is also one of the ways we use 'carcass'. We have used it for anything that is not a 'whole organism', but has enough connected parts to make using more specific part names (e.g. wing) not appropriate either. This applies to some roadkill, but we used it a lot for animals from the airport (e.g. the back half of a fox, or the 70% of a bird that went through an engine). |
|
This seems to be stuck - help?? |
|
@acdoll @adhornsby - what about partial organism And then we could use attributes for ETOH or formalin fixed, dried, stored in envelopes etc? |
|
Looks like 'carcass' is used for a couple of different things in UMNH:Mamm. Some are like what @ewommack mentioned where the skin is a party (probably a study skin) and then the rest of the specimen is just in alcohol. It looks like some of the specimens with 'carcass' are just whole organism skull-less and just need to be changed to that, but some seem to be skinless and skull-less, where the study skin & skull are in the dry collection and the rest of the animal just got dunked in ethanol. I agree with @ewommack that partial organism would be good, because even 'whole organism' with condition 'skull-less' is kind of misleading since a search for whole organisms would return the ones that have had skulls removed. Here's a question for everyone: if a skull is removed from a whole organism later, does the skull count as a subsample? I removed a bunch of skulls from whole organisms in fluid for a loan and marked the skulls as subsamples. A skull is its own part, but I sampled it from the whole organism after fixation. Example: UMNH:Mamm:35361 |
My answer is YES and you can have a subsample that is a different part than the part it was sampled from. So you would have part = whole organism, subsample = skull BUT, then you should also have subsample = "partial organism" or whatever we come up with and an appropriate disposition for the whole organism. Caveat - you could just create the part skull, but you should also create the part "partial organism" or whatever and apply an appropriate disposition to the whole organism part to indicate that it is no longer available. Pretty much accomplishes the same thing - although the "subsample" relationship makes it more clear IMO. |
|
I think having it down as a subsample sounds right. It means that the part came after the object was prepared completely before, and then at a later date we came it and took a part out of it. |
|
Just to be contradictory, then shouldn't all parts be a subsample of whole organism? If we list the skull as a part and post-cranial skeleton as a part, should the both be subsamples of a skeleton part? While Arctos has provided the capability to handle these material hierarchies, it should be up to each institution on how they choose to use it. |
Absolutely - that's another link in the chain of evidence, definitely a best practice. (And one which reality stomps all over, but given infinite resources....)
Not terribly surprising, probably a relic of when were we trying to treat things with parents as disposable (which obviously isn't the whole picture) - let me know if you have an example and I'll fix it.
Use organism plus - uhhh, something... (Condition?) (And "whole" should be in the same place, wherever that is, #4833)
Given a useful and non-overlapping/non-arbitrary definition, I don't object to keeping it, I just don't like what we have now (which implies neglect and I don't think is accurate). But, I think the proposed definition entirely overlaps '[whole] organism' - and '[whole] organism' seems like a decent guess/default/starting point for unchecked things in mysterious bags in freezers. |
Yes - but tradition. Anyway, the timing of what @kderieg322079 described lends itself to "subsampling"
and it totally is - someone asked for advice and we are giving it.
but I think they do? We pass parts in a big blob: so it's hard to say I'll be even more contradictory - we NEVER have a whole organism. An organism exists over time and gains and loses stuff as it goes - probably all of our "whole organism" parts should be carcasses or bodies. |
Sigh...true. I just used whole organism -> condition mount, for a mounted rattlesnake. It made sense to me, but really it should just be the skin and rattle -> mounted. It looks whole, but all of its insides are missing. |
I've see it both ways, I definitely looked at examples where they don't (https://arctos.database.museum/guid/DMNS:Mamm:21237). Did we set that to be conditional based on the part disposition? It would make sense to push out subsample parts with disposition of 'in collection', 'being processed', or 'on exhibit'; but maybe not for the others like 'used up' or 'discarded'. |
|
Thanks, that's coming from a function which returns distinct. (I believe the intent was a high-level simple view of what might be available, but there's such a convoluted history there that I'm not sure of anything.) Back to the high-level view, I think this is just a place where WHATEVER we do, as long as it involves cramming a bunch of complex data into a text field, will be (rightly!) hated by someone. https://github.com/ArctosDB/internal/issues/168 would change that - we'd just provide the data, if GBIF wants to pretend it's a string and your license allows such things then they can. Here's what we're currently sending: The alternative is... I can switch things around (again, probably) but as above I'd expect someone to hate it, whatever I do. See also #4688 - your disposition doesn't tell me anything (I can already see it's subsampled, it has a parent!) and the cleanup seems to be stuck. Any help in unsticking would be greatly appreciated.... |
|
I think we should leave things as they are. I am hoping that in the very near future we can upgrade our data at GBIF using their new model. |
It tells you (kind of) if it is available for use. I agree to leave this (what gets pushed) as it is for now. |
|
I suppose there's some argument that the only people who need to understand disposition is the people who can go dig the thing out of the collection, at least if they're willing to deal with requests for things that can't be loaned and etc. A fair number of Arctos users would assume "... and given away for consumptive use" because that's how subsampling was used at some point. I'm not sure why a naive user wouldn't assume you then launched it into the sun; that looks like a (not great description of a) process, not a disposition, from here..... |
dustymc
added
Priority - Wildfire Potential
|
@ccicero @dustymc how is this for collecting information? https://docs.google.com/forms/d/e/1FAIpQLSfhJdLaJ2IH9J65B2nST3fYfdxPhLGUxQB7uJhgo-nkN20wmQ/viewform?usp=sf_link |
|
I was going to create separate forms for each since there might be different sets of users...does that make sense or should they all be in one survey? |
|
I think one - I suspect people use those interchangeably (or various people use various terms to means the same thing, or...) - being forced into the context of each other seems critical. |
|
+1 |
|
Well - since EVERYBODY uses whole organism - does this go out to the AWG? |
|
|
Well - a lot of those "surely not's" also have no records in Arctos.... |
|
Anyhoo - I propose that we only send the survey to users of "body" and "carcass" since they will have good reason to look at why they choose one of those over "whole organism" which is I think where we want to start? |
|
I updated parts for MSB:Herp to 'whole organism', all instances referred to an entire organism or a mummified carcass (still a whole organism). |
|
In MVZ mammals, we use body to mean whole organism with skull removed. And carcass is what is left after removing the skin and skull. |
|
Sent to collections using carcass and body
Teresa J. Mayfield-Meyer |
|
Closing based on 2023-09-21 AWG Code Table Committee discussion |
|
Is carcass staying or going away? |
|
no action |
|
thanks |
|
https://handbook.arctosdb.org/how_to/How-To-Manage-Code-Table-Requests.html#specific-values-considerations see "Part Names (ctspecimen_part_name)" (and please fix whatever I got wrong!) |
|
I think that's fair. |
Is the documentation for carcass correct? If so, can we update to what's suggested? If not, what is a 'carcass'?
@ebraker
@leet1984
@mkoo
@ewommack
@campmlc
@ccicero
@kderieg322079
@catherpes,@catherpes
@amgunderson
@atrox10
@cjconroy
@jtgiermakowski
@acdoll
@jldunnum
@jrdemboski
The text was updated successfully, but these errors were encountered: