Remove part preservation = fossil and change to cataloged item type FossilSpecimen

Nicole-Ridgwell-NMMNHS commented 2 months ago

We currently have two ways of saying something is a fossil. The first is a part attribute, preservation = fossil. The second is cataloged item type FossilSpecimen. The second is necessary for our data to be correctly categorized by GBIF as a fossil. I'm beginning to think the part attribute is redundant (and is also cumbersome to use for specimens with either a lot of parts or a lot of part attributes). I can't think of an instance where it is actually necessary to indicate on a part-by-part basis that something is a fossil. Even if you have the original fossil and a reproduction of that fossil cataloged together, you can still enter preservation = reproduction for the cast/print part.

Thoughts?

@Jegelewicz @KatherineLAnderson @WaigePilson @ronaldeng @aklompma

Making this a code table request:

Initial Request

Goal

Remove redundancy. See explanation above.

Table

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

Proposed Value

Convert part preservation = fossil to cataloged item type = FossilSpecimen

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Jegelewicz commented 2 months ago

@dustymc can we get data on who is using part preservation = fossil?

dustymc commented 2 months ago

cataloged item type FossilSpecimen

I don't think those are quite the same thing, but that's probably just pedantic.

I can't think of an instance where it is actually necessary to indicate on a part-by-part basis that something is a fossil.

Hu. Someone always shows up and moves the goalpost around when there's a serious question about what is and is not a fossil, "it's not a useful thing to say" explains that nicely. Part attributes like "permineralized" or "before some date" (could) exist if anyone wants to say the things that 'fossil' is usually suggested to encompass. I like!

two ways

If only!

https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecimen_part_name#fossil https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecimen_part_name#trace_fossil https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecimen_part_name#amber https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecimen_part_name#cast https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecimen_part_name#coprolite

Preservation-Data:

temp_fossil.csv.zip

Summary:

 guid_prefix | count 
-------------+-------
 OWU:ES      |    68
 UNM:Paleo   |  1487
 KSB:Teach   |     1
 UAM:ES      |    50
 NMMNH:Paleo |  4872
 ALMNH:Paleo |   213
 CRCM:Mamm   |     4
 JSNM:Paleo  |   178
 CRCM:Paleo  |   116
 DMNS:Inv    |    82
 UTEP:ES     |    11
 UTEP:Inv    |   746
 CHAS:Inv    |     1

Ping:

@mvzhuang @acdoll @sharpphyl @aklompma @droberts49 @Jegelewicz @wellerjes @jrpletch @Nicole-Ridgwell-NMMNHS @cefilipek @genevieve-anderegg @jessicatir

Part-Type Data:

temp_part_fossil.csv.zip

Summary:


 guid_prefix | count 
-------------+-------
 UTEP:Ento   |     1
 MSB:Fish    |    72
 CHAS:Teach  |   104
 UTEP:HerpOS |     1
 MVZ:Mamm    |    66
 UCM:Herp    |    20
 UNM:Paleo   |    66
 TCDGM:Paleo |   328
 ALMNH:Paleo |  2226
 UCM:Fish    |     3
 JSNM:Paleo  |  1244
 UTEP:ES     |     2
 UCM:Mamm    |    16
 UTEP:Mamm   |     1
 MVZ:Herp    |     1
 MVZ:Bird    |     3
 OWU:ES      |    10
 NMMNH:Paleo |  6624
 UAM:ES      |  1496
 DMNS:Mamm   |     1
 PSM:Paleo   |  3911
 UMZM:Mamm   |     1

Ping

@jrdemboski @campmlc @adhornsby @ccicero @mkoo @cjconroy @atrox10 @mvzhuang @acdoll @aklompma @ebraker @droberts49 @Jegelewicz @wellerjes @jrpletch @Nicole-Ridgwell-NMMNHS @cefilipek @ufarrell

KatherineLAnderson commented 2 months ago

Thanks for starting this thread, @Nicole-Ridgwell-NMMNHS !

I feel as though this is redundant (although I'd be curious to know Dusty's pedantic distinction!)... if someone wants to add more information about how the object is fossilized (e.g., natural cast), they could use the preservation part attribute. But generally speaking, unless otherwise stated via part attributes or the catalogued item type, I'd assume an object in a paleo collection is a "fossil" (however you want to define that). This is why I first wondered if including that part attribute was necessary at all, or just stating the obvious--but if searching multiple collections or one collection with both recent and fossil specimens, it felt useful to be explicit. But then, as Nicole pointed out, that's recorded elsewhere in the catalogued item type.

I reached out to Nicole asking about this as I'm getting ready to bulkload parts, and I have added preservation=fossil to my working spreadsheets, but it'd be great to get some resolution on this before I pull the trigger.

dustymc commented 2 months ago

pedantic distinction

Parts are probably-ephemeral THINGS: you can touch them, but you can also lose them, saw them in half to make two new parts while destroying the old, give them away, use them up, yada yada.

Cataloged items are forever (we hope/wish) CONCEPTS. The 'type' is a sort of summary (I think - it's also just something that GBIF forces us to use...) which probably comes from parts, but not in such a way that it can be calculated from the part data. It'll probably also persist after the part is gone - "this record represents a fossil, but you can't directly check that because we used up the material."

preservation part attribute

It's bison meat, it's preserved by freezing. (And its 36KY old, which some people think makes it a fossil - so not just preservation, but yea/mostly.)

added preservation=fossil

I can't imagine the term surviving this issue, but I fail at imaginging lots of things and can help clean up when/if we get there....

KatherineLAnderson commented 2 months ago

I can't imagine the term surviving this issue

Should I continue with including it in my parts bulkloads for now?

Jegelewicz commented 2 months ago

Should I continue with including it in my parts bulkloads for now?

I'd say yes. When this is resolved, we will migrate data (or remove) as needed).

adhornsby commented 1 month ago

The UMZM record is a cast of a skull -- I updated the part so it wouldn't get mixed up with any fossil updates.

Nicole-Ridgwell-NMMNHS commented 1 month ago

Someone always shows up and moves the goalpost around when there's a serious question about what is and is not a fossil, "it's not a useful thing to say" explains that nicely

It is, but I think mostly in the sense of "hey, this shouldn't be a part of modern organism ranges" and "hey, pay attention to the geology/time component". Which makes

The 'type' is a sort of summary

more useful than part-level distinctions.

Nicole-Ridgwell-NMMNHS commented 3 weeks ago

I've updated this to a code table request, see https://github.com/ArctosDB/arctos/issues/7736#issue-2269426015

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