adding preferred terms for paleo collection parts?

[AWildAshAppeared]

I'm not sure how to ask for these parts to be added to the code tables (or even which code tables to use):

• posterior trunk vertebra
• mid-trunk vertebra
• atlantal centrum
• presacral centrum

Trunk vertebrae is a preferred term for snake vertebrae; would "vertebra, posterior trunk" be a possibility? Or should it be "vertebra, trunk" and then use the anatomical direction "posterior"? Or would that create ambiguity (i.e. the posterior half of a trunk vertebra vs. the trunk vertebra's position in the axial skeleton)?

Frogs have an atlas and then a series of presacral vertebrae. The two centra I listed above are actually fused together. What would be the best way to add these parts? I was thinking about asking to add "centrum, atlas" to the part CT for the first, but I'm a little stumped on the second. Is it better to add "centrum, presacral" as a part name, or to use "centrum" with the anatomical direction "presacral" (which would need to be added to that CT)?

Thoughts? @Jegelewicz and @Nicole-Ridgwell-NMMNHS I would especially appreciate any feedback from a paleo collections standpoint.

[Jegelewicz]

I'm not sure how to ask for these parts to be added to the code tables

To request a new part name, submit a code table request, this issue template asks all of the appropriate questions

(or even which code tables to use):

From the Arctos main menu, select Search, Code Tables and you will get a list of all of the code tables:

A request for new part names would be a request to add to the Part Name Table.

Thoughts?

I am not a paleo expert, but I have not seen any of these terms so far in the paleo collections I have worked with. We are currently in the process of making our part names less messy and the terms you suggest would not contribute to that effort. Note we intend to replace all of the "centrum, whatever" terms with centrum and an appropriate part attribute.

Given that, here is what I suggest.

posterior trunk vertebra

part_name	part_remark	part_attribute_type_1	part_attribute_value_1
vertebra	trunk	anatomical direction reference	posterior

mid-trunk vertebra part_name	part_remark	part_attribute_type_1	part_attribute_value_1
vertebra	trunk	anatomical direction reference	medial

atlantal centrum

part_name	part_condition	part_remark
atlas	partial	atlantal centrum only

presacral centrum

part_name	part_remark
centrum	presacral

We should discuss whether the terms "trunk", "atlantal" and "presacral" should be added to anatomical direction reference

[Nicole-Ridgwell-NMMNHS]

I've not used posterior trunk and mid-trunk before, but I can definitely see how they would be necessary for snakes. I can also see how just using posterior as the direction reference wouldn't be clear. Medial for mid-trunk would not be correct. I would suggest adding "posterior trunk", "mid-trunk", and "presacral" to the anatomical direction reference table.

[Jegelewicz]

I would suggest adding "posterior trunk", "mid-trunk", and "presacral" to the anatomical direction reference table.

Would it be better to make use of precaudal and caudal? I don't understand the difference between "posterior trunk" and "mid-trunk". If you don't have the whole snake, how do you know the difference?

See https://en.wikipedia.org/wiki/Snake_skeleton#Vertebrae_and_ribs

I might be convinced that we need presacral, but I can't find a good definition which makes me think we shouldn't use it? Anyone have a definition that isn't "what the curator said"?

[Nicole-Ridgwell-NMMNHS]

Would it be better to make use of precaudal and caudal? I don't understand the difference between "posterior trunk" and "mid-trunk".

It is my understanding that anterior trunk, mid-trunk, and posterior trunk are divisions of precaudal vertebrae in snakes since the traditional vertebral divisions (cervical, thoracic, sacral) are difficult to apply (where does the neck begin if you have no forelimbs?) or not fine enough (if you have 50+ precaudals, you need something to differentiate them).

If you don't have the whole snake, how do you know the difference?

Fine anatomical features.

[AWildAshAppeared]

Would it be better to make use of precaudal and caudal? I don't understand the difference between "posterior trunk" and "mid-trunk". If you don't have the whole snake, how do you know the difference?

Precaudal and caudal are general terms. Anterior trunk, mid-trunk, posterior trunk, etc. are more specific descriptors. They are all structurally different. Sometimes it isn't possible to tell what specific part of the trunk a vertebra comes from, so then precaudal and caudal would be more appropriate to use. This paper has a nice breakdown of the trunk regions and the differences between them: https://www.researchgate.net/publication/236153064_The_Fossil_Snakes_of_Pit_91_Rancho_La_Brea_California

This is the best description I've been able to find about presacral vertebrae in frogs: "A hallmark feature of frogs and toads compared with other vertebrates is their reduced axial skeleton. Among adult anurans, the vertebral column consists of no more than nine presacral vertebrae, a single sacral vertebra and, postsacrally, the urostyle (Trueb, 1973; Púgener, 2002)." Taken from here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375812/#:~:text=A%20hallmark%20feature%20of%20frogs,1973%3B%20P%C3%BAgener%2C%202002)

[Jegelewicz]

OK, we can get definitions from the article (thanks!), but here is the way I think it should work for the snake/frog vertebra.

part name = vertebra with the appropriate "vertebra type" attribute:

We need a new code table for vertebra type (like we have for tooth type) with the following values

Term	Definition
atlas	The most superior (first) cervical vertebra of the spine and is located in the neck. Wikipedia
axis	The second cervical vertebra (C2) of the spine, immediately posterior to the atlas, upon which the head rests. Also epistropheus. Wikipedia
caudal	The bones that make up the tails of vertebrates. Wikipedia Vertebrae that bear a haemal spine ventral to the vertebral centrum. Fishbase
cervical	The vertebrae of the neck, immediately below the skull. Wikipedia
cloacal	Publication
dorsal	The dorsal vertebrae range from the bottom of the neck to the top of the pelvis. Dorsal vertebrae attached to the ribs are called thoracic vertebrae, while those without ribs are called lumbar vertebrae. Wikipedia
lumbar	In human anatomy, the five vertebrae between the rib cage and the pelvis. Wikipedia
postcloacal	Publication
precaudal	Centra other than those of the caudal fin. All anterior vertebrae to the one immediately anterior to the first centrum bearing a haemal spine. Fishbase
precloacal	Publication
presacral	Any of the vertebrae anterior to the sacrum or sacral vertebrae.
thoracic	Compose the middle segment of the vertebral column, between the cervical vertebrae and the lumbar vertebrae. Wikipedia
trunk	Generalized vertebra that lack the processes that distinguish them from atlas, axis, precloacal, cloacal and post-cloacal vertebrae. Publication
trunk, anterior	Publication
trunk, mid	Publication
trunk, posterior	Publication
sacral	The sacral vertebrae are those in the pelvic region, and range from one in amphibians, to two in most birds and modern reptiles, or up to three to five in mammals. Wikipedia

I didn't bother trying to type in the lengthy definitions for the various trunk vertebra - we can do that if we decided this makes sense.

These terms all appear to be the same thing - precloacal, presacral, trunk so I want to make sure we really need them all.

Does any of this bother anyone? I do feel like we are not being super normal here, but I also think that this is down in the weeds and that snake people will look for "trunk" stuff while amphibian people will look for "sacral" stuff. Thoughts?

Also, I was torn with regard to using the trunk, whatever format or just using whatever trunk. Preferences?

[dustymc]

new code table for vertebra type

I believe we already have too many; what could a new table do that https://arctos.database.museum/info/ctDocumentation.cfm?table=ctanatomical_direction cannot?

We should also consider merging https://arctos.database.museum/info/ctDocumentation.cfm?table=cttooth_type into ctanatomical_direction.

not being super normal here

If you mean in the sense of "one way to say things" then I agree - given the choice between using "sacral" from this part modifier table or the same term from that part modifier table, users will do a bit of both and we'll end up with yet another giant arbitrary mess in which nobody will be able to find anything. One "direction" table provides one clean path to 'find sacral stuff' while overpigeonholing serves no function.

[Nicole-Ridgwell-NMMNHS]

We should also consider merging

But tooth type (and from the above table atlas and axis) isn't anatomical direction reference (cue the we need an ontology discussion).

users will do a bit of both and we'll end up with yet another giant arbitrary mess in which nobody will be able to find anything

Agreed, I think it would be best to just throw all of this except for atlas and axis into anatomical direction.

[Jegelewicz]

I think it would be best to just throw all of this except for atlas and axis into anatomical direction.

I'm OK with that. So for now, we will just leave vertebra, atlas and vertebra, axis in the code table? Perhaps instead of tooth types, we should have "part name modifier" - or would that encompass all of the "direction" and "type" information?

[dustymc]

But tooth type (and from the above table atlas and axis) isn't anatomical direction reference

So we've named the table imperfectly - it seems that's almost inevitable (and mostly irrelevant, usually). It's the same sort of THING - this {sorta-vague doohickey} has attribute {placement-type-term}.

I'm not arguing that's any sort of correct, but it is functional and it is easy to use. The kiddos don't have to guess which of the 54 tables they might find 'molar' in or if 'caudal' is a type (eg vertebra) or direction. "Modifiers" don't apply to classes of parts, so 'molar vertebra' is possible whether we think 'molar' is something special or just a 'direction.' If there are no functional implications - and I'm not seeing them here - then I'll generally vote for simplicity.

"part name modifier"

I'm not sure that's quite right (not sure it isn't either), but I do support an 'encompass all of the "direction" and "type" information' approach.

ontology

Yup, that would (I'd hope) disallow that "molar tail." So who's gonna write the grant?

[Jegelewicz]

I've placed this at the top of items to discuss in the code table admins meeting this month.

[AWildAshAppeared]

Thank you @Jegelewicz ! Just so I can check back in on this, when is the next code table admins meeting?

[Nicole-Ridgwell-NMMNHS]

when is the next code table admins meeting?

Next Thursday

[Jegelewicz]

@ArctosDB/arctos-code-table-administrators suggest we change anatomical direction reference code table to "part_modifier" and put all of these attributes in a single code table as suggested in https://github.com/ArctosDB/arctos/issues/3710#issuecomment-875790265 and https://github.com/ArctosDB/arctos/issues/3710#issuecomment-875823847

[dustymc]

change anatomical direction reference code table to "part_modifier"

Works for me, but there's also no functionality embedded in the change - there's no reason not to add not-quite-right terms to https://arctos.database.museum/info/ctDocumentation.cfm?table=cttooth_type or https://arctos.database.museum/info/ctDocumentation.cfm?table=ctanatomical_direction pending a new unified CT.

@Jegelewicz it might be worth reviewing the definitions for both of those; they'll get transferred at some point and should be made to work in a more generic CT (if they don't already).

[Jegelewicz]

@AWildAshAppeared the attributes have been added to the anatomical direction reference code table. You can add these:

posterior trunk vertebra
mid-trunk vertebra
atlantal centrum
presacral centrum

in this way

posterior trunk vertebra

part_name	part_attribute_type_1	part_attribute_value_1	part_attribute_type_2	part_attribute_value_2
vertebra	anatomical direction reference	posterior	anatomical direction reference	trunk

mid-trunk vertebra part_name	part_attribute_type_1	part_attribute_value_1	part_attribute_type_2	part_attribute_value_2
vertebra	anatomical direction reference	mid	anatomical direction reference	trunk

atlantal centrum

part_name	part_condition	part_remark
vertebra, atlas	partial	atlantal centrum only

presacral centrum

part_name	part_attribute_type_1	part_attribute_value_1
centrum	anatomical direction reference	presacral

Will that be functional for you?

[AWildAshAppeared]

Will that be functional for you?

Yes, I think so. Thanks very much!