Geology - Add Biostratigraphy

[Nicole-Ridgwell-NMMNHS]

Table [Geology Attributes] (http://arctos.database.museum/info/ctDocumentation.cfm?table=CTGEOLOGY_ATTRIBUTE)

Value Biostratigraphy

Definition A body of rock strata that is defined or characterized on the basis of its contained fossils - Salvador, A. (ed.) 1994. International stratigraphic guide. Boulder, CO: Geological Society of America.

Context Another category needs to be created in geology for biostratigraphic and biochronologic units. The difference between these two is equivalent to the difference between chronostratigraphy and geochronology. A biozone (biostratigraphy) is rocks containing certain index taxa and a biochron (biochronology) is the time represented by that taxon range. The units used for some taxa may be biozones (ex. Ammonites); the units for other taxa may be biochrons (ex. North American Land Mammal Ages), but biochrons are theoretically always based on biozones. Some biozones and biochrons may have subintervals. A question to consider is can we group these by the kind of index taxon used (ex. North American Land Mammals vs. Western Interior Seaway Ammonites)?

A useful reference for background information: Late Cretaceous and Cenozoic Mammals of North America: Biostratigraphy and Geochronology especially the definitions starting on page xi.

[dustymc]

I added some stuff to the code table.

Similar to the other issue, it would be REALLY useful if you could elaborate on what's assertions - what's derived directly from and associated with specimens - and what's something else.

[Nicole-Ridgwell-NMMNHS]

Thanks for adding the biostratigraphy section to the code table!

I don't think I explained the structure well enough, probably because I'm not sure of the best way to structure it. This is how it is currently:

Biostratigraphy ( )

• Ammonites (biozone)
• North American Land Mammal Ages (biochron)

That isn't exactly correct, but I can think of two possible ways to do it. Here is the first with some example units added:

Biostratigraphy ( )

• Ammonites ()
  • Baculites grandis (biozone)
• North American Land Mammal Ages ()
  • Puercan (biochron)

OR it might be more intuitive in searches to organize it like this:

Biostratigraphy ( )

• Baculites grandis (ammonite biozone)
• Puercan (North American Land Mammal Age)

I'm leaning toward the second option.

Similar to the other issue, it would be REALLY useful if you could elaborate on what's assertions

Biostratigraphy is more like lithostratigraphy in that it is almost always derived from first-hand observations or data. So yes, biostratigraphy is an actual assertion.

[dustymc]

I'd lean heavily towards the first option - the stuff in parentheses is mean to to be a finite number of categories, and ends up here...

Is eg Puercan 100% absolutely (eg, by definition) embedded in North American Land Mammal Age, or is it more like rocks with fuzzy edges and loose associations with other stuff? If it's the former, this seems entirely correct. If the latter, maybe we should drop North American Land Mammal Age from this list and get that from some external "non-authority" source (even if it's a google doc that we maintain) or something?

[Nicole-Ridgwell-NMMNHS]

I'd lean heavily towards the first option - the stuff in parentheses is mean to to be a finite number of categories, and ends up here...

That's actually why I suggested ArctosDB/arctos#2, so that it would show up on that list. Not everyone working with this data will be familiar with the subtle distinction between biozones and biochrons (I had to look it up), but they will know if they are searching for a NALMA, ammonite zone, etc. Each of these is a system with many units. For example there are probably hundreds of ammonite zones worldwide. There are 20+ NALMA units and these are commonly used instead of stages/ages as a way to talk about the Cenozoic timescale. Now that I think about it, we should simplify this to just Land Mammal Ages to include the mammal systems in use on other continents.

While not technically finite, there are a limited # of major clades useful for biostratigraphy, but I also understand not wanting that drop-down list to get out of hand. In our collection we use only 3 taxon systems for biostratigraphy (NALMAs, Ammonites, and Land-Vertebrate Faunachrons), however that last one is not widely used outside of our institution. If I had to guess there are probably at least 15 different systems used in all of paleo.

Is eg Puercan 100% absolutely (eg, by definition) embedded in North American Land Mammal Age

Yes, by definition Puercan is a North American Land Mammal Age.

To try to clarify: each taxon group (ammonites, mammals, etc.) is a discrete biostratigraphic system used to help date rocks. The units within each system belong by definition to that system. These systems can overlap in time and geography

[dustymc]

That sounds manageable enough either way.

Baculites grandis (ammonite biozone)
Puercan (North American Land Mammal Age)

Does seem more searchable if I'm understanding - it'll support "stuff from any division of 'ammonite biozone'."

[Nicole-Ridgwell-NMMNHS]

I'm going to discuss with our curators the best way to put this in.

[Nicole-Ridgwell-NMMNHS]

Ok, so I have gone through all of the biostratigraphy in our database and talked to our curators and I think that the organization in the attached zip file most accurately represents the geology and will make it easiest for people to find what they want in a search. I did ultimately separate biochronology and biostratigraphy.

Biochrons_Biozones.zip

The file includes all the biochrons and biozones in our database.

[Jegelewicz]

@dustymc I am now at NMMNHS and I can get this stuff in (see above) if you create the following root attributes for me:

Biochronology: https://en.wikipedia.org/wiki/Biochronology Land Mammal Ages: https://en.wikipedia.org/wiki/Biochronology#Land_mammal_ages Land Vertebrate Faunachrons: Published, but not on line Ammonite Zones: "Ammonites are excellent index fossils, and it is often possible to link the rock layer in which a particular species or genus is found to specific geologic time periods". https://en.wikipedia.org/wiki/Ammonoidea Conchostracan Zones: "extinct species of these crustaceans are often studied by geologists. They help identify the age of the corresponding strata. " https://en.wikipedia.org/wiki/Clam_shrimp Trilobite Zones: https://en.wikipedia.org/wiki/Trilobite_zone Mammal Zones: zones related to specific mammal species

and the following attributes for use in Biochronology:

Land Mammal Age Land Mammal Age Subinterval Faunachron biozone

All of which makes me wonder. Why don't we have a code table for the "attribute" in geology (Stage/Age, formation, etc.) that we can maintain? and Why can't I create geology terms with no "attribute" to help me organize the geology table? Just thinking that would relieve you of this function....

[Jegelewicz]

Nevermind on question 2 and the "attributes" - I see I can add those myself!

[dustymc]

@Jegelewicz you can do that - it's just data....

Why don't we have a code table for the "attribute" in geology (Stage/Age, formation, etc.) that we can maintain?

Because we treat the whole thing as the authority - the 'code table' generates itself from the data.

Why can't I create geology terms with no "attribute" to help me organize the geology table?

Because we're doing weird things that the model wasn't built to accommodate. You can cheat, though...

That's a single space in Attribute, which isn't ideal but is functional.

You can create "root" terms like that, then use the 'create hierarchies' section to put them together however you want.

"attribute"

We'll review all of this when we go there - I think that will push us to having some more code tables.

[Jegelewicz]

OK, got it - as with everything - needs some documentation. I'll work on that too.

[Jegelewicz]

Calling this one done - https://handbook.arctosdb.org/documentation/geology.html#biostratigraphy