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Define collecting source #2494

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Jegelewicz opened this issue Feb 11, 2020 · 69 comments
Closed

Define collecting source #2494

Jegelewicz opened this issue Feb 11, 2020 · 69 comments
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@dustymc
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Collection Type - Cultural Collections Art, Ethnography, etc collection related Function-CodeTables Priority-Normal (Not urgent) Normal because this needs to get done but not immediately.
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@Jegelewicz
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Issue Documentation is http://handbook.arctosdb.org/how_to/How-to-Use-Issues-in-Arctos.html

Goal
See discussion in #2070

Context
I think we have determined that "wild caught" and "captive" are not appropriate collecting source terms for paleo collections. We have suggested "found" as an alternative, but

Where's the distinction between "found" and "wild caught"? http://arctos.database.museum/info/ctDocumentation.cfm?table=CTCOLLECTING_SOURCE (So by our definitions 'found'==not captive - OK, but....)

OK, but wild caught still seems super inappropriate for paleo (where we don't "catch" anything) and even more so for mineral specimens when we get to them. The definition of wild caught always seems to pertain to an animal

(of an animal) taken from the wild rather than bred from captive stock.

It just feels wrong every time I enter it for something that lived so far back in geologic time that I can barely comprehend the age.

From my perspective, it seems like all we have been trying to do with collecting source is determine if a biological specimen was captive/cultivated or not. If that is all we want this to do, then why not be explicit?

But also - how are art, ethnology, history collections supposed to use this field?

Table
http://arctos.database.museum/info/ctDocumentation.cfm?table=CTCOLLECTING_SOURCE

Value
not captive

Definition
specimen or object was not held in captivity or cultivated

Priority
Please assign a priority-label.
@Jegelewicz Jegelewicz added Priority-Normal (Not urgent) Normal because this needs to get done but not immediately. Function-CodeTables Collection Type - Cultural Collections Art, Ethnography, etc collection related labels Feb 11, 2020
@Jegelewicz Jegelewicz added this to the Needs Discussion milestone Feb 11, 2020
@ewommack
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I feel like found could mean anything though.
I found it in an attic.
I found it in the lab of the professor that retired.
How is found different for something you pick up in the wild and something that is raised in captivity?

@dustymc
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dustymc commented Feb 11, 2020

I think this is a two-step process: work out what we're trying to say, then how we say it.

I believe "wild caught" essentially means "it got there by itself," which I think is also the intent behind "found" (as suggested in the other thread). If we have two ways of saying the same thing, then eg, land managers would have to perform two queries to find the 'natural' things from their land.

Are those terms both attempting to represent the same concept?

If so, we need to find a term that's acceptable to everyone.

If not, we need to find definitions that clearly separate the terms.

how are art, ethnology, history collections supposed to use this field?

They don't have to; NULL=="we have nothing to say." If they do need this (and I can't imagine why they would, given that they have eg, 'manufacture' specimen_event_type) they'll very likely need to come up with relevant values.

@Jegelewicz
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I feel like found could mean anything though.
I found it in an attic.
I found it in the lab of the professor that retired.
How is found different for something you pick up in the wild and something that is raised in captivity?

That is why I proposed "not captive"

@DerekSikes
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DerekSikes commented Feb 11, 2020 via email

@ewommack
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So a replacement of wild caught and captive with:
found - not captive
found - captive
?

@Jegelewicz
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captive will not change.

wild caught will change to not captive

@ewommack
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I think I'm still getting caught up on not captive seeming too broad of a term for living organisms.

What about for individuals that you caught in the wild, and then brought into the lab or a botanical garden. I would designate them as wild caught, since they are from the wild population, but I wouldn't call them not captive since they spent time in captivity.

@Jegelewicz
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Jegelewicz commented Feb 11, 2020 •
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What about for individuals that you caught in the wild, and then brought into the lab or a botanical garden. I would designate them as wild caught, since they are from the wild population, but I wouldn't call them not captive since they spent time in captivity.

All previous discussions about this have been to record the collecting source as "wild caught" (not captive), then add the attribute "verbatim collection date" for the date it was "removed from captivity" as it were.

I have always thought this requires two events. One with "not captive" for removal from the wild and a second with "captive". The difference between the event dates would indicate how long the organism was held in captivity.

@mkoo
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mkoo commented Feb 11, 2020 via email

@Jegelewicz
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Field! so simple - I like that!!!

@dustymc
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dustymc commented Feb 11, 2020

@ewommack as @Jegelewicz said there are two ways to approach that

  1. "verbatim collection date" is what everybody does, although it's a little duct-tapey
  2. Multiple events, with the original (presuming no previous biopsies-or-whatever) 'not captive' and the rest whatever the opposite of that turns out to be.

Seems we are converging on the idea of captive/not. I think 'field' is my favorite not-captive suggestion so far, but I don't think eg botgarden folks will be happy with 'captive.' laboratory? experimental? cultivated? unnatural?

@atrox10
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atrox10 commented Feb 12, 2020 via email

@dustymc dustymc mentioned this issue Feb 12, 2020
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@DerekSikes
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DerekSikes commented Feb 12, 2020 via email

@Jegelewicz
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the data are meant to convey whether the organism was captive or not.

IS that what everyone believes?

What about for individuals that you caught in the wild, and then brought into the lab or a botanical garden. I would designate them as wild caught, since they are from the wild population, but I wouldn't call them not captive since they spent time in captivity.

It seems there is not a real agreement about what "collecting source" is supposed to convey.

@campmlc
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campmlc commented Feb 12, 2020 via email

@dustymc
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dustymc commented Feb 12, 2020

believes

There's no reason to take it on faith, we have documentation!

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

caught in the wild, and then brought into the lab

That's just not something a single event is capable of fully conveying. I think we've mostly gotten away with the simple approach because it's generally pretty easy to detect things like ringed seals popping up in the San Diego Zoo on a rangemap as outliers. Things like blood chemistry are probably not so obvious, and there is a mechanism to be more explicit.

@Jegelewicz
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There's no reason to take it on faith, we have documentation!

I disagree. We have definitions for the terms used in this field, but where is the definition for the field itself?

I am not convinced we really know what this field is expected to do for anyone.

@dustymc
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dustymc commented Feb 12, 2020

http://handbook.arctosdb.org/documentation/specimen-event.html#collecting-source

@Jegelewicz
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Collecting Source is a broad categorization of how the specimen came to be at the associated event.

Given this definition, "field" seems inappropriate (although "wild caught" does too). If I didn't know what the choices were, I would think that "flew" was an appropriate response. Why are we being so vague? Why not just come out and say

Collecting Source describes the suitability of the occurrence for range mapping.

And make the choices

  • suitable for range mapping - collected from a naturally occurring population

  • not suitable for range mapping - collected from a non-naturally occurring population (lab, experimental, cultivated, captive, etc.)

@dustymc
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dustymc commented Feb 12, 2020

suitability of the occurrence for range mapping

That's where it came from, and I suspect that's about what it's useful for now. Ideally it'd also extend to things like suitability of a tissue sample for {whatever's influenced by captivity}.

@Jegelewicz Jegelewicz changed the title Request a more neutral term than "wild caught" as collecting source Define collecting source Feb 12, 2020
@Jegelewicz
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Code Table Admins - for your consideration.

With regard to the COLLECTING_SOURCE field, I suggest that we replace

Collecting Source is a broad categorization of how the specimen came to be at the associated event.

which currently has the terms

COLLECTING_SOURCE Documentation
captive Specimen was taken from captivity.
field photo PLEASE MAKE THIS GO AWAY MVZ
museum photo PLEASE MAKE THIS GO AWAY MVZ
unknown Specimen somehow magically appeared in the collection.
wild caught Specimen was not taken from captivity.

with

Collecting Source describes the suitability of the occurrence for range mapping.

using the terms

COLLECTING_SOURCE Documentation
suitable for range mapping collected from a naturally occurring population
not suitable for range mapping collected from a non-naturally occurring population (lab, experimental, cultivated, captive, etc.)

@Jegelewicz
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Is the idea to remove this value? Why?

Were they in the wild when you took the photo? Then, wild caught. Essentially "field photo" is just another way of saying "wild". BTW, I think we should go with your suggestion - #2494 (comment)

@DerekSikes
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But if the specimen is not caught, only photographed, then 'wild caught' is not appropriate.

@campmlc
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campmlc commented Sep 14, 2021

Agree with "wild" vs "captive"

@Jegelewicz
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But if the specimen is not caught, only photographed, then 'wild caught' is not appropriate.

Agree - change to "wild" is recommended.

@Jegelewicz
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Change "wild caught" to "wild", then get everyone on board with changing all "field photo" to "wild"

@DerekSikes
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DerekSikes commented Sep 16, 2021 via email

@Jegelewicz Jegelewicz mentioned this issue Sep 20, 2021
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@Jegelewicz
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AWG says change wild caught to wild.

Change field photo to wild as well - @dustymc to provide csv as requested so that collections affected can find what was changed.

I will work with @gradyjt to get their parts and events corrected.

@gradyjt
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gradyjt commented Oct 7, 2021 via email

@Jegelewicz
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Sure! Do you have some time tomorrow?

@Jegelewicz Jegelewicz modified the milestones: Needs Discussion, Next Task Oct 7, 2021
@gradyjt
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gradyjt commented Oct 7, 2021 via email

@Jegelewicz
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Just sent a calendar invite - let me know if you need a different time!

@ebraker
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ebraker commented Oct 7, 2021

@dustymc can we get a final report before you merge 'field photo' and 'wild' with the following fields?:

GUID | specimen_event_type | part_name | nature_of_ID | has media (y/n)

This would help me in cross-checking across various fields before that goes away (and hopefully it is useful for others). At minimum, GUID is needed for the "exit reports" that we discussed today so that people can always return to an issue and track down the affected records if they did not have the opportunity to clean ahead of changing values. Thanks :)

@dustymc
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dustymc commented Oct 8, 2021

@ebraker et al. is this CSV suitable? I smooshed media_id and parts together, and it will be one row per identification (so guid may be repeated). This is only event-stacks with field photo (may also cause multiple rows), the record may have any number with different values.

Let me know if you want something else.

Some code uses 'wild caught' so I'll schedule this in with next release, probably early next week. (So check out #3436!)

I'll reuse the definition of 'wild caught' for 'wild' unless someone has something better to offer. (Or maybe that should be a quick CT request? Whatchathink @Jegelewicz ?)

Event did not occur in captivity.


create table temp_ffup as
select  
	guid_prefix || ':' || cat_num guid,
	specimen_event_type,
	string_agg(part_name,'|') as parts,
	nature_of_ID,
	accepted_id_fg,
	string_agg(media_id::text,'|')
from
	collection
	inner join cataloged_item on collection.collection_id=cataloged_item.collection_id 
	inner join specimen_event on cataloged_item.collection_object_id=specimen_event.collection_object_id
	inner join identification on cataloged_item.collection_object_id=identification.collection_object_id
	left outer join specimen_part on cataloged_item.collection_object_id=specimen_part.derived_from_cat_item
	left outer join media_relations on cataloged_item.collection_object_id=media_relations.cataloged_item_id
where
	collecting_source='field photo'
group by
	guid_prefix || ':' || cat_num,
	specimen_event_type,
	nature_of_ID,
	accepted_id_fg
;

temp_ffup.csv.zip

@Jegelewicz
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I'll reuse the definition of 'wild caught' for 'wild' unless someone has something better to offer. (Or maybe that should be a quick CT request? Whatchathink @Jegelewicz ?)

We agreed in AWG to go with the definition of 'wild caught' for 'wild', so reuse makes perfect sense.

@ebraker
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ebraker commented Oct 8, 2021

Thanks @dustymc! This is perfect.

@dustymc
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dustymc commented Oct 12, 2021

Fresh pull:
temp_ffup_latest.csv.zip

@dustymc dustymc closed this as completed Oct 12, 2021
@dustymc dustymc mentioned this issue Oct 19, 2021
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