part name cleanup

[dustymc]

!!! IMPORTANT !!!

This issue is ongoing; most of what's here has been done. Scroll to the bottom for the latest.

!!! IMPORTANT !!!

can we change "fetus" to "whole organism" and add an age class?

can we change "embryo" to "whole organism" and add an age class?

can we change "other" to "unknown" (or vise-versa)?

can we change...

• video
• video recording
• photo observation
• photo whole organism
• photograph
• image

... to "media" (and add a remark???)

Can we change phalanges to phalange?

Can we move "partial ..." to condition and remove it from part name?

UAM@ARCTOS> select distinct part_name from ctspecimen_part_name where part_name like '%partial%';

PART_NAME
------------------------------------------------------------------------------------------------------------------------
partial organism (70% ethanol)
partial skeleton
partial organism (80% ethanol)
partial skeleton (dry)
partial strobila (slide)
partial organism (95% ethanol)

6 rows selected.

[ekrimmel]

this is looking good!

[DerekSikes]

pinned nest is real - this is for small yellowjacket nests that fit inside a normal insect drawer.

pinned tissue is weird for sure but checking it out:

http://arctos.database.museum/guid/KNWR:Ento:10411

shows that this general term applies. We could remove the general term and replace it with pinned exuvium

for that record.

The other 2 records could have this term replaced with pinned genitalia

http://arctos.database.museum/guid/UAM:Ento:357632 http://arctos.database.museum/guid/UAM:Ento:357631

to be more precise?

-Derek

On Wed, Aug 2, 2017 at 9:18 AM, dustymc notifications@github.com wrote:

Still to-do: https://docs.google.com/spreadsheets/d/1J5tL20-_ TTZgoFogq1ejZ6B3M1u1ZLOob9N6eNTo5A4/edit#gid=555921353

Moving on....

These still seem unlikely:

pinned nest pinned tissues

There are a few "visual outliers" that I keep noticing, but not sure what do to with them. (Maybe they don't need anything.)

"contents" do not sort nicely, and contains..

bill content (dry) cheek content (dry) crop content (70% ethanol) egg contents (frozen) hindgut content (70% ethanol) stomach content

There are some random "...bone" things that probably aren't very discoverable

bone bone (frozen) bone marrow (frozen) ear bone leg bone leg bone (frozen) long bone

Ditto "swab"

buccal and cloacal swab (RNAlater) cloacal swab (RNAlater) dorsum swab nasal swab (frozen) oral swab oral swab (formalin) oral swab (frozen)

various plant-bits floating around ungrouped:

cone seed fruit probably other stuff

coal ball

¯*(ツ)*/¯

MAYBE it would somehow be useful to group part-parasites (cestode, nemadode, etc.) - "parasite, cestode, bla (stuff)" is the best I can come up with...

Thoughts?

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[dustymc]

Thanks @DerekSikes !

"Is not horrible mistake" is about where I am now, so I'm fine with keeping "pinned tissues" or updating it or whatever - let me know what you prefer.

I'll add a definition to pinned nest, and try to keep in mind that not all nests are piles of sticks....

[dustymc]

@ekrimmel I agree, this feels like real progress!

[dustymc]

Still to-do:

1. https://docs.google.com/spreadsheets/d/1J5tL20-_TTZgoFogq1ejZ6B3M1u1ZLOob9N6eNTo5A4/edit#gid=555921353

2. "visual outliers"

Moving on again....

In an attempt to NOT say the exact same thing two ways, I added to http://handbook.arctosdb.org/how_to/Code-Tables.html

Do not include both “thing (modifier)” and “thing” in the code table. Avoid creating new “bare” terms (“thing”) in order to avoid this problem in the future. Parts of unknown preservation/preparation should be explicit: “thing (unknown).”

And there is another spreadsheet at https://docs.google.com/spreadsheets/d/1GSY8DM6WzUvUADxWgpad44CLw7yor3Gisr8k-EittA0/edit?usp=sharing

The spreadsheet contains "unmodified" parts (those without comma or parens) and their potential modified equivalents.

It will contain a row with the "unmodified" part in both old and new; if the unmodified part is to be retained, these should be defined and and all other "suggestions" should be deleted. Also do this if there's not enough information in the spreadsheet to tell what the "old" part might be - I'm not asking anyone to dig up specimens etc., I'm just trying to get rid of "obviously the same as" duplicates.

I could be convinced that we should eliminate all bare terms NOW - "skeleton" should become "skeleton (unknown)" or something of the sort - but that would probably break everyone's reports and it's just sort of goofy.

Alternatively, perhaps it's useful to just define all "bare" parts as "...unknown preservation/preparation" and eliminate all "part (unknown)" type values. I can build more spreadsheets if I've got this backwards.

The spreadsheet will contain mostly very bad suggestions.

ectoparasite | ectoparasite (K2Cr2O7)

K2Cr2O7 is not the default state for ectos, so these can be simply DELETED. (I'm working on that - the easy stuff - now.)

The end result should be unique values in OLD (and I won't load this until that's true), something in all remaining DEF_OF_NEW columns (many should already be defined - yay us!), and in NEW either...

1. a repeat of OLD (eg, "update nothing for this"), or
2. a value which will replace OLD (because it's the same thing, just more explicit/clear)

[KatherineLAnderson]

We use "bone" for unidentifiable bone fragments, and "long bone" for limb bones that are not more specifically identifiable. I don't think these terms need to be changed. Same for cone, seed, and coal ball.

"Bone (frozen)" and "bone marrow (frozen)" are only used in our collection for subsamples from one specimen (Blue Babe); the skeletal element the samples are taken from (if known) are included in the remarks. These terms are probably used more extensively in other collections (?) so open to suggestions.

[campmlc]

Yes, this is getting so much better!

"contents" probably are best left as is because it makes more sense to start to enter "stomach" and tab and then see "stomach contents as an option", rather than entering "contents" etc.

For pinned or any other type of mounting, preservation type etc., shouldn't we standardize and put this after the part name, e.g. "nest, pinned" or "exuvium, pinned"?

For parasites, we could do "endoparasite, cestode (70% ethanol)", "ectoparasite (70% ethanol)". The current and worsening complexity of this is one of the primary reasons we need to separate out preservation/fixation/storage container into new part attributes.

Because there are many of us advocating for splitting out preservation etc as a hopefully soon-to-be administered solution, perhaps we should standardize all parts as "part (preservation)", including "(unknown)", because this could help make the eventual split?

On Wed, Aug 2, 2017 at 4:14 PM, Katherine L. Anderson < notifications@github.com> wrote:

We use "bone" for unidentifiable bone fragments, and "long bone" for limb bones that are not more specifically identifiable. I don't think these terms need to be changed. Same for cone, seed, and coal ball.

"Bone (frozen)" and "bone marrow (frozen)" are only used in our collection for subsamples from one specimen (Blue Babe); the skeletal element the samples are taken from (if known) are included in the remarks. These terms are probably used more extensively in other collections (?) so open to suggestions.

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[dustymc]

Thanks @KatherineLAnderson - it's always useful to know a bit more about how these things are used.

I have 2 (minor, I think) objections to "bone":

1. I don't know what makes it different than "skeletal element."
2. I don't know how it's preserved/prepared.

(1) will hopefully sort itself out as we add definitions, (2) really only bothers me in the case of having eg, "brain" and "brain (unknown)." I don't think we need two ways of saying "we don't know."

I dislike "long bone" just because it doesn't sort well - users see "bone...500 unrelated things....long bone...500 more things....skeletal element...." - nobody's going to find what they want in that.

I suppose that's also an argument for "bone, rib" instead of just "rib."

Ditto seed and cone - if they're together (eg, because the part name is "plant-bit, ...."), I might realize that some cones have seeds or something; if they're not, I'll probably find one or the other and not (all of) what I'm looking for.

You might consider making those de facto subsamples into actual subsamples. Doing so creates a strong path back to the "donor" part, and also protects the donor (eg, from deletion). Remarks are just ignored....

@campmlc "stom" should find everything containing the substring (if not let me know and I'll fix it). As above, my concern is only discovery (a botanist looking for seeds might want all the "... content" together) and I think that's very minor at this point.

Yes, it should be "thing, pinned" not "pinned thing." Might take me a while to get used to that...

I think "requiring" preservation/preparation makes some sense, but I'd also expect a revolt the next time someone ends up with "skull (unknown)" on their labels.

You can split preservation out now, but I think we need some consensus on https://github.com/ArctosDB/arctos/issues/1119#issuecomment-317047694 before further developing tools.

[KatherineLAnderson]

With regard to "bone":

1. We prefer "bone" because it is more specific than "skeletal element" (which could include bones+teeth depending on how it is defined). So yes, it will sort out with definitions.
2. "Bone" doesn't necessarily need a qualifier. It is used in the same sense as "humerus" (or any other specific element) which doesn't have a qualifier and is preserved/prepared in the same way (at least in the UAMES collection).

Can we change "long bone" to "bone, long bone"? (Definition: "limb bone missing epiphyses") Or something similar. I see your point but would like to retain the term if possible.

What do you suggest for the plant bits? Our paleobotany collection is largely undigitized, so I'm on board for changes now so we are consistent/efficient in part name usage later.

[dustymc]

Thanks again @KatherineLAnderson.

I know (roughly, I think!) what a "bone" is and so also prefer it to "skeletal element" - I still have pretty much no idea what that might be. (Bones, teeth - and other crunchy bits????)

I think, as unrealistic as it may turn out to be "in the wild," that I'd like to see qualifiers on everything; not having them is a significant part of what lead us here. E.g., "frozen bone" may turn out to be a good source of DNA, "petrified bone" maybe not so much, and I can't tell them apart if they're both recorded as "bone." (Would UAM:ES do something different for eg, a normal rocky hadrosaur "bone" vs. blue babe?)

at least in the UAMES collection

That is something we need to avoid. Users should not have to guess at our administrative decisions in order to find material. (Think Blue Babe - UAM:ES and UAM:Mamm have cataloged the same thing. One search should find either both or neither. Where something is cataloged has nothing to do with what that something IS.) This ties in to the point about qualifiers - "prepared/preserved in the normal fashion" IS (somewhat, sometimes...) a discipline-specific thing, so I think we should just avoid that by always being specific.

bone, long bone

That sorts nicely, but it's a mouthful! AWG, can we discuss? Is "bone, rib" (and similar) acceptable as well?

plant bits

I have no suggestions, and I think we can safely ignore that for now. Maybe something will emerge as we deal with the more familiar stuff.

---

"easy stuff" lingering from above:

• Can we replace "carcass" with "whole organism, skinned" or develop a definition which does not overlap with "whole organism"?

• What is a "body"? @ccicero ??

[dustymc]

Closing....