Arctos: osteoderms

[Jegelewicz]

There has been some effort recently to tighten up the terminology used for dermal bones. Right now we use both osteoderm and scute in the database. Scute is particularly problematic because it has been used as a catch-all term for both bony and keratinous structures in the skin as well as turtle shell which science has not decided is dermal bone or not.

My recommendation is to have part osteoderm (definition: dermally derived bone emplaced in the dermis) with the part attribute: osteoderm morphology (definition: terms differentiating osteoderms by shape and size) including ossicle, "scute, bony", spine, spike, and plate.

_Originally posted by @Nicole-Ridgwell-NMMNHS in https://github.com/ArctosDB/data-migration/issues/138#issuecomment-548523119_

[Jegelewicz]

Before I set this up - I'd like to see if anyone else has thoughts on this.

[dustymc]

I can't say anything useful about the specifics, but I think the trend of a general part name optionally clarified by specific attributes is a huge step in the right direction regarding discoverability. People who just want bumpy-things can find them without tracking down the maybe dozen of variants, people who want THAT bumpy thing can find it and it alone, yay everybody.

[Jegelewicz]

@mbprondzinski @dperriguey @jtgiermakowski @mvzhuang @atrox10 thoughts or comments before I proceed to set this up?

[mbprondzinski]

https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/scute

Just to add fuel to the fire... Sometimes I think Arctos way overthinks the searchability factor.

[Nicole-Ridgwell-NMMNHS]

Just to add fuel to the fire... Sometimes I think Arctos way overthinks the searchability factor.

It doesn't make sense to me to have to search under several different part names to find bony bits of armor.

[dustymc]

search under several different part names to find bony bits of armor.

That's the point of my suggestion (mostly stolen from @Jegelewicz - yay "the community"!) regarding part attributes (which could almost certainly use some UI refinement). Users who want some sort of bony-bit can find it by searching the one (eventually) part which encompasses all bony-bits. Users who want THAT bony-bit (and trust us and buy into our definitions and etc.) can add a "sub-part" parameter to get what they want and nothing else.

The same pattern could apply to a LOT of parts, and perhaps even be much more general than current values without losing any resolution. I'd love to see the 'first step' part vocabulary be perhaps a couple dozen terms with all the refinements a step further in; I suspect most users want skulls, skins, tissues, appendicular bones, etc., and with more extensive use of part attributes we might be able to get there while still allowing the occasional focused user to find the third left distal tarsal.

tl;dr: Agree, but that doesn't mean we have to lose information.

[Nicole-Ridgwell-NMMNHS]

I totally agree, was just trying to understand @mbprondzinski 's comment.

[Jegelewicz]

@Jegelewicz create code table for osteoderm type

Turn all parts with those names into osteoderm and add appropriate type.

[Jegelewicz]

Code Table Committee discussed this today and agreed that it would be good to create a new part attribute:

osteoderm morphology = terms differentiating osteoderms by shape and size.

with a code table to control the types

ctosteoderm

with the following values:

term | definition
-- | --
ossicle | a very small osteoderm element, generally smaller than 1 cm
scute, bony | non-specific osteoderm, usually used to describe osteoderms that are not ossicles, spines, spikes, or plates. Do not use for keratinous scutes.
spine | an osteoderm with a narrow, spine-like projection
spike | an osteoderm with a tall, conical projection
plate | https://en.wikipedia.org/wiki/Plate_(anatomy)#Flat_bones_(examples:_bony_plates,_dermal_plates)_of_vertebrates

@Nicole-Ridgwell-NMMNHS can you fill in missing definitions?

After this is set up, the following parts could be converted to "osteoderm" with the associated part attribute: scute, spine, however this is going to need manual review as both may refer to non-bony structures (porcupine quills, keratinous covering of turtle osteoderms).

[Nicole-Ridgwell-NMMNHS]

ossicle: a very small osteoderm element, generally smaller than 1 cm

[Nicole-Ridgwell-NMMNHS]

scute, bony: non-specific osteoderm, usually used to describe osteoderms that are not ossicles, spines, spikes, or plates. Do not use for keratinous scutes.

[Nicole-Ridgwell-NMMNHS]

spine: an osteoderm with a narrow, spine-like projection
spike: an osteoderm with a tall, conical projection

[Jegelewicz]

@dustymc Code Table Committee discussed this today and agreed that it would be good to create a new part attribute:

osteoderm morphology = terms differentiating osteoderms by shape and size.

with a code table to control the types

ctosteoderm

with the following values:

term | definition
-- | --
ossicle | a very small osteoderm element, generally smaller than 1 cm
scute, bony | non-specific osteoderm, usually used to describe osteoderms that are not ossicles, spines, spikes, or plates. Do not use for keratinous scutes.
spine | an osteoderm with a narrow, spine-like projection
spike | an osteoderm with a tall, conical projection
plate | https://en.wikipedia.org/wiki/Plate_(anatomy)#Flat_bones_(examples:_bony_plates,_dermal_plates)_of_vertebrates

After this is set up, the following parts could be converted to "osteoderm" with the associated part attribute: scute, spine, however this is going to need manual review as both may refer to non-bony structures (porcupine quills, keratinous covering of turtle osteoderms). Definitions for those parts will also need review.

[Jegelewicz]

See #2722 add types to sub-part table https://arctos.database.museum/info/ctDocumentation.cfm?table=ctpart_attribute_part

[dustymc]

https://arctos.database.museum/info/ctDocumentation.cfm?table=ctpart_attribute_part

Yes agreed a bajillion sub-THAT-part tables would be no fun at all.