Arctos: Problem Formations need clean-up

[Jegelewicz]

I am going to use this issue to list problematic formations as I work to clean up the lithostratigraphic_formation code table.

[Jegelewicz]

Bafunzawa Formation

The only mention of this I can find anywhere is in here. Where it is referred to as "Bafunzawa coal-bearing member". Suggest this be moved to the lithostratigraphic_member code table

[Jegelewicz]

Basalt and Red Beds

I cannot find any documentation for this term and it is not being used. Suggest delete.

[Jegelewicz]

Blue Gray Clay Formation

I cannot find any documentation for this term. @mbprondzinski it is in use by ALMNH - do you have any documentation for it?

See:
https://github.com/ArctosDB/arctos/issues/2975#issuecomment-666594913
https://github.com/ArctosDB/arctos/issues/2975#issuecomment-667142636
https://github.com/ArctosDB/arctos/issues/2975#issuecomment-667187463
https://github.com/ArctosDB/arctos/issues/2975#issuecomment-667187899
https://github.com/ArctosDB/arctos/issues/2975#issuecomment-667210816
https://github.com/ArctosDB/arctos/issues/2975#issuecomment-667217976
https://github.com/ArctosDB/arctos/issues/2975#issuecomment-667222159
https://github.com/ArctosDB/arctos/issues/2975#issuecomment-667572385

[mbprondzinski]

Hmm, let me look.

From: Teresa Mayfield-Meyer [e-mail]
Sent: Wednesday, July 29, 2020 3:31 PM
To: ArctosDB/arctos [e-mail]
Cc: Prondzinski, Mary Beth [e-mail]; Mention [e-mail]
Subject: Re: [ArctosDB/arctos] Problem Formations need clean-up (#2975)

Blue Gray Clay Formation

I cannot find any documentation for this term. @mbprondzinskihttps://github.com/mbprondzinski it is in use by ALMNH - do you have any documentation for it?

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[Jegelewicz]

Corrected
Blue Mountain Series Formation

The actual name, according to Macrostrat is Blue Mountain Formation. It is in use by one locality. I tried removing it from the locality so that I could update the name in the code table, but I ended up with this error:

Message: ERROR: function iscodetabletermused(unknown, character varying) does not exist Hint: No function matches the given name and argument types. You might need to add explicit type casts. Where: PL/pgSQL function trigger_fct_trg_ctlithostratigraphic_formation_ud() line 11 at PERFORM
Detail:
Check the Arctos Handbook for more information on errors.

This message has been logged as C2D4D8BB-E9DF-4D2C-B965A9541EEB991E Please contact us with any information that might help us to resolve this problem. For best results, include the error and a detail description of how it came to occur in the Issue.

@dustymc can you help me out?

[dustymc]

function rebuild, confirmed by editing locality 10907390

[mbprondzinski]

Can you give me a catalogue record where blue gray clay formation is used?

[Jegelewicz]

@mbprondzinski here is one https://arctos.database.museum/guid/ALMNH:ES:90

But there are a whole bunch of them - a lot in the Bogue chitto creek localities.

[Jegelewicz]

Complete
Briones Formation

Should be Briones Sandstone Formation according to Macrostrat. Removed from two localities, updated and added back.

[Jegelewicz]

Complete
Byoritsu Formation

I can find a few references:
https://pubs.usgs.gov/pp/0339/report.pdf
https://www.jstage.jst.go.jp/article/pjab1912/6/8/6_8_313/_pdf

However, there is nothing here, which seems like a really good resource for strata in Japan.

Unsure what to do with this.

See https://github.com/ArctosDB/arctos/issues/2975#issuecomment-666525587

Added Byoritsu Beds, updated locality to use this attribute and deleted Byoritsu Formation.

There is only one locality using this term - and oddly it is in South America, so not sure it makes a lot of sense?

includes

According to Macneil, this is from Goko, Formosa. From the Tusyo ss which is the uppermost Byoritsu Fm. According to the Lexicon Stratigraphique, the Byoritsu Fm is a local name for the Miaoli Fm. The Lexicon also says that the Tusyo ss is a separate unit unconnected with the Miaoli, or rather, it implies this is the face that no mention is made of the Tusyo ss as a member of any other formation.

Annotated the record - I think Higher Geography is incorrect.

[Jegelewicz]

Complete
Caballerro Formation
A misspelling of Caballero Formation. Changed localities where it was used to Caballero Formation and deleted.

[Jegelewicz]

Complete
Carlile Formation

Per Macrostrat, it appears that the most prevalent term for this formation is Carlile Shale Formation. Should we change our term?

@Nicole-Ridgwell-NMMNHS NMMNH:Paleo is using this a lot. What are your thoughts?

See https://github.com/ArctosDB/arctos/issues/2975#issuecomment-666510174
https://github.com/ArctosDB/arctos/issues/2975#issuecomment-666527302

Added Carlile Shale Formation, changed all Carlile Formation to Carlile Shale Formation and deleted Carlile Formation

[Jegelewicz]

Complete
Chekhov Formation

I cannot find any documentation for this term. It is in use by UAM:ES.

See https://github.com/ArctosDB/arctos/issues/2975#issuecomment-666513106

[Nicole-Ridgwell-NMMNHS]

Carlile Formation

Yes, we should update to Carlile Shale Formation

edit: Geolex agrees https://ngmdb.usgs.gov/Geolex/Units/Carlile_6965.html

[Jegelewicz]

Carlile Formation

Yes, we should update to Carlile Shale Formation

edit: Geolex agrees https://ngmdb.usgs.gov/Geolex/Units/Carlile_6965.html

@dustymc can you do this for me? I cannot change because the term is in use.

Carlile Formation change to Carlile Shale Formation.

[dustymc]

Not safely. Add the new, I can update the data, then you can delete the old.

[Nicole-Ridgwell-NMMNHS]

Chekhov Formation

Here is the most recent article I could find that is both accessible and in English (p. 273).
https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1440-1738.1998.00174.x

The most recent reference I found was a 2018 Russian paper.

[Nicole-Ridgwell-NMMNHS]

Byoritsu Formation

Everything I'm finding calls it a bed and places it in Taiwan, which would explain why it doesn't show up in the database for Japan.

Also, from Geological Formation Names of China (1866—2000)

I would change it to bed and use https://www.jstage.jst.go.jp/article/pjab1912/6/8/6_8_313/_pdf as the reference.

[Jegelewicz]

@dustymc Carlile Shale Formation added.

[dustymc]

update locality_attributes set attribute_value='Carlile Shale Formation' where attribute_value='Carlile Formation';

UPDATE 72
Time: 1400.851 ms (00:01.401)

[mbprondzinski]

I'm still working on Blue Gray clay formation. It appears to be in Dallas County, but the site F-23 may have more information in Curran's field notes. I will be in the office tomorrow and I will see if I can find something in his thesis. I've got a couple of Geologists working on this as well.

[mbprondzinski]

Blue Gray Clay Formation

I cannot find any documentation for this term. @mbprondzinski it is in use by ALMNH - do you have any documentation for it?

Okay, here are two options: "site identifier = Quaternary alluvium" and "informal chronostratigraphy = blue gray clay (formation)" No one could come up with a formal formation and Curren's thesis offered little help. What would you suggest?

[Jegelewicz]

The term isn't chronostratigraphy, so I don't think we should add it to the informal chronostratigraphy table. I honestly think that "Blue Gray Clay is just descriptive of the layer which also doesn't seem like a site identifier, but something that should go in the remark of whatever chronostratigraphy is given. @Nicole-Ridgwell-NMMNHS what are your thoughts on this?

[Nicole-Ridgwell-NMMNHS]

"site identifier = Quaternary alluvium" and "informal chronostratigraphy = blue gray clay (formation)"

site identifier is for any locality identifiers (another name, a field number, etc) other than locality_name, assigned to the site. Informal chronostratigraphy is for chronostrat used in the literature that is not in https://stratigraphy.org/icschart/ChronostratChart2020-01.pdf. Formations are lithostratigraphy.

I suggest System/Period; Quaternary with the rest (alluvium, "Blue Gray Clay Formation") in verbatim locality.

We need to work on documentation for the new locality attributes

edit: I think putting in System/Period remark would also be fine.

[mbprondzinski]

Maybe it’s not to you and me, but obviously it’s been used as a formation description here in Alabama.

From: Teresa Mayfield-Meyer [e-mail]
Sent: Friday, July 31, 2020 10:40 AM
To: ArctosDB/arctos [e-mail]
Cc: Prondzinski, Mary Beth [e-mail]; Mention [e-mail]
Subject: Re: [ArctosDB/arctos] Problem Formations need clean-up (#2975)

The term isn't chronostratigraphy, so I don't think we should add it to the informal chronostratigraphy table. I honestly think that "Blue Gray Clay is just descriptive of the layer which also doesn't seem like a site identifier, but something that should go in the remark of whatever chronostratigraphy is given. @Nicole-Ridgwell-NMMNHShttps://github.com/Nicole-Ridgwell-NMMNHS what are your thoughts on this?

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[mbprondzinski]

Then create a term “informal lithostratigraphy.”

From: Nicole-Ridgwell-NMMNHS [e-mail]
Sent: Friday, July 31, 2020 10:41 AM
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Subject: Re: [ArctosDB/arctos] Problem Formations need clean-up (#2975)

"site identifier = Quaternary alluvium" and "informal chronostratigraphy = blue gray clay (formation)"

site identifier is for any locality identifiers (another name, a field number, etc) other than locality_name, assigned to the site. Informal chronostratigraphy is for chronostrat used in the literature that is not in https://stratigraphy.org/icschart/ChronostratChart2020-01.pdf. Formations are lithostratigraphy.

I suggest System/Period; Quaternary with the rest (alluvium, "Blue Gray Shale Formation") in verbatim locality.

We need to work on documentation for the new locality attributes

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[Nicole-Ridgwell-NMMNHS]

Then create a term “informal lithostratigraphy.”

The only reason we have informal chronostratigraphy is that our chronostratigraphy tables are limited to what is in the international chronostratigraphic chart. Even units that we put in the informal lithostratigraphy table have to have documentation.

Do you have documentation for Blue Gray Clay Formation? A quick search in google scholar pulls up nothing for me.

[mbprondzinski]

Okay, so I asked if there was a reference to the "blue-gray clay formation" in Jim Lacefield's book, "Lost Worlds in Alabama Rocks" and again no formal referred name. So do what you want with it. There are close to 400 records with that formation listed in our database. Also, the Chilatchee Creek, Site F-23, appears to be in Dallas County, but it is listed as being in Wilcox County in Curran's thesis. There is no county entered in the records, but the USGS website says it is in Dallas County (very close to the Wilcox county border). Should we add the county and which one???

[Jegelewicz]

@mbprondzinski I can't get to this until late on Monday, but I will work up a possible solution and get back to you!

/remind me to work on this tomorrow at 3PM

[reminders[bot]]

@Jegelewicz set a reminder for Aug 3rd 2020

[Jegelewicz]

Okay, so I asked if there was a reference to the "blue-gray clay formation" in Jim Lacefield's book, "Lost Worlds in Alabama Rocks" and again no formal referred name. So do what you want with it. There are close to 400 records with that formation listed in our database.

I think that perhaps we need a new locality attribute, which I will suggest in a new issue.

the Chilatchee Creek, Site F-23, appears to be in Dallas County, but it is listed as being in Wilcox County in Curran's thesis. There is no county entered in the records, but the USGS website says it is in Dallas County (very close to the Wilcox county border). Should we add the county and which one???

I think there are two possible solutions to this.

1. We could add this information to the current locality in the remarks.
2. We could add Dallas County to the current locality AND create a second event with the locality placed in Wilcox County.

I prefer the second because it narrows the locality down to two counties instead of the entire state of Alabama and it means that the specimens will show up in both a search for Dallas County and a search for Wilcox County. This also allows us to say "Curran said Wilcox County" and "USGS says Dallas County".

@mbprondzinski I have set up the records in locality F-23 with the second option - let me know if that works for you!

[reminders[bot]]

:wave: @Jegelewicz, work on this

[mbprondzinski]

Yes, I would agree that the second option makes it less ambiguous and easier to find. Thanks, I would never have thought of that!

---

From: reminders[bot] [e-mail]
Sent: Monday, August 3, 2020 10:32 AM
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Subject: Re: [ArctosDB/arctos] Problem Formations need clean-up (#2975)

👋 @Jegelewiczhttps://github.com/Jegelewicz, work on this

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[Jegelewicz]

Complete
Elk River Beds Formation

The Elk River Formation exists, but there are no Elk River Beds. Only one locality is using the attribute - removed it, changed the name to Elk River Formation and re-added with Elk River Beds Formation in attribute remark.

[Jegelewicz]

Fairbanks Basalt

Seems like just a descriptive term, I can find no mention of it as an actual formation but as a type of rock in some formations: https://mrdata.usgs.gov/sim3340/show-sim3340.php?seq=C004&src=LG002_230

[Nicole-Ridgwell-NMMNHS]

This is the only reference I found, and it also does not treat them as a formal unit. PALEOMAGNETISM OF THE FAIRBANKS BASALTS, INTERIOR ALASKA

[Jegelewicz]

Jack Limestone

I can't find anything on this - in use by one UAM locality.

[Nicole-Ridgwell-NMMNHS]

I assume the locality is in Alaska?

[Jegelewicz]

yup

[Nicole-Ridgwell-NMMNHS]

referenced on page 73 here: https://scholarworks.alaska.edu/bitstream/handle/11122/9243/Packer_D_1972.pdf?sequence=1

which led me to this map where the Jack Limestone is mapped: https://ngmdb.usgs.gov/Prodesc/proddesc_53044.htm

Base on the map, I would leave it in there.

[Jegelewicz]

Complete
Kultheith Formation

Might be a thing? Mentioned in some papers, but can't find one that creates it.

See https://github.com/ArctosDB/arctos/issues/2975#issuecomment-703032281 Added link to code table.

[Jegelewicz]

Complete
Lehman Limestone Formation

Only one locality (NMMNH 7426) uses this. I can find evidence for a Lehman Limestone in Nevada and Utah, but not in NY. @Nicole-Ridgwell-NMMNHS suggestions? See https://github.com/ArctosDB/arctos/issues/2975#issuecomment-700777239

[Jegelewicz]

Complete
Lisburne Limestone

I can find Lisburne Group, but not Lisburne Limestone Formation. Term not in use, deleted

[Jegelewicz]

Complete
Lower Chalk Formation

No support found. Term not in use, deleted.

[mbprondzinski]

Are any of these in record remarks? Just curious...

[Jegelewicz]

Complete
Lower Poul Creek

Poul Creek Formation exists in code table. Term not in use, deleted.

[Jegelewicz]

Are any of these in record remarks? Just curious...

If they are in remarks, then they are still there! I am only searching the lithostratigraphic formation terms from the code table, which I am attempting to get cleaned up.

[Jegelewicz]

Complete
Lower Yakataga Formation

Yakataga Formation exists in code table. Term not in use, deleted.

[Jegelewicz]

Complete
Lower Portland Formation

"Lower" belongs in remarks. One NMMNH locality changed to "Portland Formation" with "lower" in remark and term deleted.

[Jegelewicz]

Complete
Lutetian Limestone

Lutetian is a Stage/Age. Only one locality using the attribute. @sharpphyl I added the Stage/Age Lutetian to that locality and removed this formation. The deleted if from the code table.

[mbprondzinski]

What if someone tries to add them after-the-fact? Will there be a record of them having been removed? And shouldn't people who have these listed in remarks know that they are being removed from the code table?

[Jegelewicz]

What if someone tries to add them after-the-fact?

Most of these were added a long time ago - before there was a code table, then they were used to create the code table with very little questioning of whether they were real formations or not. I think terms will be much better vetted in the future and the @ArctosDB/arctos-code-table-administrators will help to keep undefined terms out of the code table.

Will there be a record of them having been removed?

It's in this thread - that's the best I can do.

And shouldn't people who have these listed in remarks know that they are being removed from the code table?

I don't understand the question. If they have these terms in remarks - that is where they should be because they don't belong in the code table (at least I can't find some support that the terms exist).

[mbprondzinski]

I don't understand the question. If they have these terms in remarks - that is where they should be because they don't belong in the code table (at least I can't find some support that the terms exist).

The reason I'm asking is because if I were to upload new records with a verbatim formation that wasn't listed in the code table, it would have to be put into remarks and then later added. I'm just thinking of the "blue gray formation" that we have in hundreds of records, which I know has already been addressed, but what if there are others? Lisburne sounds a lot like Lisbon, which could be a typo or other data entry mistake.

[dustymc]

https://arctos.database.museum/info/ctDocumentation.cfm?table=ctlocality_attribute_type "geology remarks" is a good place for "something about geology, but we can't formalize it right now" kinds of information.

At the catalog record level, https://arctos.database.museum/info/ctDocumentation.cfm?table=ctflags could be used to add a "geology needs help" flag.

There is a change log for ctlithostratigraphic_formation.

[Jegelewicz]

The reason I'm asking is because if I were to upload new records with a verbatim formation that wasn't listed in the code table, it would have to be put into remarks and then later added.

Dusty said it!

https://arctos.database.museum/info/ctDocumentation.cfm?table=ctlocality_attribute_type "geology remarks" is a good place for "something about geology, but we can't formalize it right now" kinds of information.

[Jegelewicz]

Madera Formation

Should be Madera Limestone Formation - https://macrostrat.org/sift/#/strat_name/3693

105 localities are using this attribute. This is going to take me a white to fix.

[Jegelewicz]

Complete
Madison

Term not in use, deleted.

[Jegelewicz]

Mankomen Formation

Macrostrat says Mankomen is a group https://macrostrat.org/sift/#/strat_name/2539. So does Geolex https://ngmdb.usgs.gov/Geolex/UnitRefs/MankomenRefs_5978.html.

In use by Alaska.

See https://github.com/ArctosDB/arctos/issues/2975#issuecomment-700930938

Added the group to the code table and to all localities using this formation. Do we need approval from UAM to remove the formation from the localities and so from the code table? @KatherineLAnderson @DerekSikes

[Jegelewicz]

Complete
Maruyamian Formation

Can't find any support for this. In use by Alaska. See https://github.com/ArctosDB/arctos/issues/2975#issuecomment-700926757

Changed to Maruyama Formation with Maruyamian Formation in remark and deleted Maruyamian Formation

[Nicole-Ridgwell-NMMNHS]

Lehman Limestone Formation

Only one locality (NMMNH 7426) uses this. I can find evidence for a Lehman Limestone in Nevada and Utah, but not in NY.

This is one that will only be solved by digging around in our records, but here is what I suspect:

• The locality is a legacy Rousseau Flower locality that was created from his archival records
• The database doesn't list any specimens in this locality, but a lot of the specimens we have from him are not linked to localities. Maybe we'll eventually find the specimen(s) which will give us more data.
• While Flower did do a lot of collecting in New York, I found a publication where he mentions collecting several specimens from the Lehman Formation in Utah.

So: Lets keep Lehman in the code table as a formation in Utah and Nevada, keep this locality linked to it, make a note in remarks that there is a mismatch between formation and higher geography that needs to be resolved.

[Nicole-Ridgwell-NMMNHS]

Maruyamian Formation

Maybe this is supposed to be the Maruyama Formation (Sakhalin Island, ~Miocene age)? https://www.jstage.jst.go.jp/article/jgeography1889/109/2/109_2_203/_pdf

Edit: Quick search verified the Alaska locality is in Sakhalin

[Nicole-Ridgwell-NMMNHS]

Mankomen Formation

Macrostrat says Mankomen is a group https://macrostrat.org/sift/#/strat_name/2539. So does Geolex https://ngmdb.usgs.gov/Geolex/UnitRefs/MankomenRefs_5978.html.

In use by Alaska.

I support changing to group, does Alaska paleo/geo have anyone we can run this by first?

[Jegelewicz]

Complete
McCarthy Shales

Probably meant to be McCarthy Formation https://macrostrat.org/sift/#/strat_name/1251 which has been added to the code table.

Not in use - deleted

[Jegelewicz]

Middle Etolon Suite

Not even a formation and not in use. Deleted

[KatherineLAnderson]

Just popping in to say I'm no longer the collection manager of Earth
Sciences at the University of Alaska Museum. Please contact Pat
Druckenmiller via email, or tag Dustin Stewart (who I think is a member of
this github).

On Tue, Sep 29, 2020 at 1:31 PM Teresa Mayfield-Meyer <
[email protected]> wrote:

Middle Etolon Suite

Not even a formation and not in use. Deleted

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[Jegelewicz]

Complete
Mt. Laurel Formation

Macrostrat and Wikipedia both spell this Mount Laurel. Added this spelling, changed localities to use it with Mt. Laurel in remark and deleted.

[Jegelewicz]

Complete
Onandaga Formation

Misspelling of Onondaga Formation. Change NMMNH localities using Onandaga to Onondaga with "Onandaga" in remark. Delete Onandaga.

[Jegelewicz]

Complete
Ortiz Gravel Formation

Duplication of Ortiz Formation? I don't find Ortiz Gravel Formation anywhere. In use by one NMMNH locality. Suggest changing to Ortiz Fomation with Ortiz Gravel in remark and delete from code table.

See https://github.com/ArctosDB/arctos/issues/2975#issuecomment-702430145 Moved to geology remarks and deleted from code table.

[Nicole-Ridgwell-NMMNHS]

Duplication of Ortiz Formation?

Nope, Ortiz Formation is in Puerto Rico. Ortiz gravels are Plio/Pleistocene deposits by Albuquerque and Santa Fe. Not a formal unit, move to Geology Remarks.

[Nicole-Ridgwell-NMMNHS]

Kultheith Formation

Might be a thing? Mentioned in some papers, but can't find one that creates it.

This one was challenging to track down, but here it is: https://pubs.usgs.gov/mf/1985/1645b/report.pdf