Teach collections need parts #1203
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Yes, that's what collection type does. http://handbook.arctosdb.org/documentation/catalog.html#collection-code I need a list of parts that you want associated with Teach and, if they're not defined, definitions. (Code tables can no longer be updated without definitions.) http://arctos.database.museum/info/ctDocumentation.cfm?table=CTSPECIMEN_PART_NAME This situation will exist across all type-specific code tables. |
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I guess I figured it would be likely that many of the part names will be needed, so why not add all of them. If it is preferable to add as we need them, then here is what I need for now: antler |
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Definitions please. I'm happy to help, but I seriously have no earthly idea what "skeletal element(s)" is or how it might differ from the half-dozen or so other things that look to me like "we hacked something random off some critter" parts. I suspect the people who use it and search for it don't either, so now it's not possible to do much with undefined parts. Definitions do need to work across all collection types - here's how these are currently used: antler It seems unlikely that a Teach collection will contain ~500 types of tissues, and I'd rather not have un-used parts looking like they're "claimed" - that complicates eg #1131. |
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SUGGESTIONS: please edit this comment as necessary. antler is used for cervids and pronghorn - not sure if we need an inclusive definition or to move pronghorn to "horn sheath" (or ??) egg: I'd think this would require a preservation method?? egg shell (dry): Dried shell of an egg, usually stored at room temperature. feather: epidermal growth of birds mounted skeleton: Entire skeleton assembled for display postcranial skeleton skeleton not including skull skeletal element(s) skeleton: entire skeleton mounted skin: (vs. study?) skin (ethanol) study skin: (vs. mounted?) skull: cranium + mandible tail: Entire tail including caudal vertebrae, tissues, skin, feathers or scales, etc. whole organism: Entire organism or individual. whole organism (50% isopropanol): Entire organism or individual, .... whole organism (70% ethanol): Entire organism or individual, .... wing: |
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So I need to define all of these things that we are already using? I am not sure that this should be up to just me! Perhaps this needs to be labeled "Needs Discussion". |
No, sorry, I'm not trying to put this all off on you. I'm just trying to stop digging, having found ourselves in the bottom of a hole... I don't even really expect GOOD definitions at this point - we probably have too much background noise for that to happen - but if you can tell me something about why you want to use eg "wing" instead of the other wing-options it might lead to - well, I have no idea, but I hope somewhere better! (In that particular case I of suspect we have 9 ways of saying one thing, and if that's the case then getting rid of 8 of them is a pretty significant step.)
Done. |
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Here is what I feel comfortable defining from my list. antler - extensions of the skull grown by members of the deer family Finally, I propose we add: Comments, questions and additions are welcome, but I am trying to get my teaching collection up and running before the fall semester, so I hope we can get some of this resolved quickly. |
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Teresa, some of this is in conflict with other collections usage, such as
skeleton, which has been used with skull as separate part. Also, study
skins can be mammals or other taxa. Antlers can be proghorn. Just points to
why we need definitions, but this shouldn't have to hold you up. I am
traveling with limited internet, but can try to add comments and
definitions over next week.
Mariel
On Jul 14, 2017 5:22 PM, "Teresa Mayfield" <notifications@github.com> wrote:
Here is what I feel comfortable defining from my list.
antler - extensions of the skull grown by members of the deer family
egg (50% isopropanol) - whole ovum, stored in a solution of 50% isopropanol
egg (70% ethanol) - whole ovum, stored in a solution of 70% ethanol
egg shell (dry) - outer covering of an egg with contents removed
feather - any of the flat appendages growing from a bird's skin and forming
its plumage, consisting of a partly hollow horny shaft fringed with vanes
of barbs
mounted skeleton - articulated skeleton mounted for display
mounted skin - taxidermy mount for display
postcranial skeleton - skeleton excluding skull
skeletal element(s) - any parts of an incomplete skeleton
skeleton - complete skeleton, including skull
skin (50% isopropanol) - skin removed from body, stored in a solution of
50% isopropanol
skin (70% ethanol) - skin removed from body, stored in a solution of 70%
ethanol
skull - cranium and mandibles
study skin - dry skin from which almost all of the body has been removed
and replaced with cotton so that the final result resembles a bird lying on
its back with its wings folded
whole organism (dry) - entire organism, air dried
whole organism (50% isopropanol) - entire organism or individual, stored in
a solution of 50% isopropanol
whole organism (70% ethanol) - entire organism or individual, stored in a
solution of 70% ethanol
wing (dry) - entire wing, dried
Finally, I propose we add:
*herbarium sheet - material that has been dried, pressed and mounted on a
sheet*
to Teach as well as Herb collections. I would much prefer that my pressed
plant parts be herbarium sheets as opposed to "whole organism" as they are
generally NOT the entire plant.
Comments, questions and additions are welcome, but I am trying to get my
teaching collection up and running before the fall semester, so I hope we
can get some of this resolved quickly.
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I think I killed off "herbarium sheet" in the first place, so I suppose I need to object to its resurrection.... "whole organism" is often not the whole organism either - many of them have tissues removed etc. There's plenty of room to object to the word "organism" when talking about plants and squishy marine-things and etc. as well. As always I don't much care about the specific terminology, but I think "herbarium sheet" and "whole organism" and whatever might get introduced if we get a slime mold collection all mean about the same thing ("most of the normal thing, prepared in the normal way...") and I maintain that users should not have to guess at our administrative decisions (eg, collection or collection-type specific vocabulary) to find what they're looking for. All that said, this is about No.800 on my list of part-priorities at the moment, and if having "whole-ish plant" and "whole-ish not-plant" somehow provide significant usability benefits for ya'll I can make that happen. Mostly so I don't forget: Some loosely-coupled apps create "whole organism" in Herb collections; those would need tracked down and adjusted if this goes through. |
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My suggestions and a couple additions that we would need are below. I am fine with using "whole organism" for "herbarium sheet"...
@dustymc only No. 800?! You must be having a slow week :) |
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Done, except... I did not add "shell" to the Teach collections or change the definition - using the same term for turtles and clams would make finding specimens difficult (and the clam-people got here first!). Should I add "plastron" and "carapace" to Teach? Note that "whole organism (dry)" is NOT used by Herb collections - they use plain ol' "whole organism." Which brings us back to the longstanding question, what DO we mean by "thing" when we also have part "thing (prepared in the way you'd expect")? Other than making sure that most users don't find all of what they want.... Is "pinned" vs. "dry" really useful? Same thing but impaled, no? @DerekSikes |
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We could eliminate many of these issues if we separated part fixation and
storage vocab from part names. The number of parts could be reduced
significantly if "dry" or "70% ethanol" were separate fields. This could be
part of condition, so that a part collected in formalin but later
transferred to ethanol could show the history and prevent that part from
showing up on searches for DNA. The current number of parts+preservation
types is unmanageable for our collections.
…On Jul 17, 2017 11:27 AM, "dustymc" ***@***.***> wrote:
Done, except...
I did not add "shell" to the Teach collections or change the definition -
using the same term for turtles and clams would make finding specimens
difficult (and the clam-people got here first!). Should I add "plastron"
and "carapace" to Teach?
Note that "whole organism (dry)" is NOT used by Herb collections - they
use plain ol' "whole organism." Which brings us back to the longstanding
question, what DO we mean by "thing" when we also have part "thing
(prepared in the way you'd expect")? Other than making sure that most users
don't find all of what they want....
Is "pinned" vs. "dry" really useful? Same thing but impaled, no?
@DerekSikes <https://github.com/dereksikes>
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That's possible now: #1119 (comment). I'm happy to move existing not-part-type data into either of those structures and out of part name if that's where ya'll want to go.
Condition is uncontrolled so you can put whatever you want in there, but "preserved in formalin" and "is rotten" seem like very different types of data to me and so probably deserve to be structurally separate.
Agreed - SOMETHING needs to change! |
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Thanks Dusty!
Hear, and that makes sense. Yes, please on plastron and carapace.
I would be pleased to stop putting part fixation/storage vocab in the part name. Seems like that's where a lot of our discrepancies between what each collection needs come from.
IMO no, especially when our pinned specimens age, degrade, fall off their pins and get rehoused differently. I was just trying to follow part names that already exist in use in different types of collections, but am more than happy to stick to "whole organism (dry)" for pinned insects here. |
done
I'm trying to avoid saying the same thing multiple ways "because that's how we've always done it" etc. - not-quite-the-same-thing because there's useful information in the difference is worth keeping. |
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Just uploaded my first batch of teaching specimens and they are stuck in the bulkloader with the following error: |
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I don't see them in the bulkloader - email me your data, please. |
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May we please have a "whole organism (dry)" part added to TEACH? Or a "whole organism"? At this point I've lost track of where the parts discussion stands because it got sidetracked into genetic land priorities, so this is just a selfish request for a specimen stuck in our bulkloader. |
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Done (with parens).
And there's a preview of the next spreadsheet! |
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thank you! |
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CLosing - I think this is all done? |
Since the Teach collections could include any object from any kind of collection, it needs access to all of the part names. I tried to upload some teaching collection stuff today and nothing will load because there are no part names associated with Teach.
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