Define collecting source

Jegelewicz commented 4 years ago

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.

ewommack commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

I'm in favor of replacing 'wild caught' with 'not captive'

On Tue, Feb 11, 2020 at 7:57 AM dustymc notifications@github.com wrote:

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.

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ewommack commented 4 years ago

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

Jegelewicz commented 4 years ago

captive will not change.

wild caught will change to not captive

ewommack commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

How about: From Field From Captivity

On Tue, Feb 11, 2020 at 11:43 AM Teresa Mayfield-Meyer < notifications@github.com> wrote:

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.

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Jegelewicz commented 4 years ago

Field! so simple - I like that!!!

dustymc commented 4 years ago

@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 commented 4 years ago

I also like field MUCH better than "not captive".

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Field! so simple - I like that!!!

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DerekSikes commented 4 years ago

So.... I have a problem with 'field'

We sometimes capture arthropods indoors that are "wild" in that they are not pets, not captive and usually not wanted indoors. I would use 'wild caught' for this and thought that fit ok, but 'not captive' is even better.

'field' seems a step backwards since indoors is hardly the 'field' and totally fails to explain the importance that we're trying to convey - the organism was not captive.

Also, 'field' implies a geographic (eg not in this sort of place, but in that sort of place) or even habitat component (someone somewhere might think it was caught in a "meadow") which isn't what these data are meant to convey - the data are meant to convey whether the organism was captive or not. So I vote for 'not captive'

-Derek

On Tue, Feb 11, 2020 at 7:46 PM Carol Spencer notifications@github.com wrote:

I also like field MUCH better than "not captive".

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Field! so simple - I like that!!!

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dssikes@alaska.edu

phone: 907-474-6278 FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records http://arctos.database.museum/uam_ento_all http://www.uaf.edu/museum/collections/ento/ +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

Jegelewicz commented 4 years ago

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 commented 4 years ago

I like "field" or better, "field collected". I disagree that "field" or "field collected" is inappropriate for e.g. a spider in a house. If a house is the habitat where a spider occurs, then the 'field" is the human-modified environment. "Field collected" works for minerals as well as for organisms. It distinguishes from captive, it implies that a researcher actively sought out the organism or object in question and removed it from its environment.

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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.

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dustymc commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

Jegelewicz commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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.)

DerekSikes commented 4 years ago

I like Teresa's idea:

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

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.

On Wed, Feb 12, 2020 at 1:48 PM dustymc notifications@github.com wrote:

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}.

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phone: 907-474-6278 FAX: 907-474-5469

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DerekSikes commented 4 years ago

I vote yes to this

On Wed, Feb 12, 2020 at 2:08 PM Teresa Mayfield-Meyer < notifications@github.com> wrote:

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

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.)

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dssikes@alaska.edu

phone: 907-474-6278 FAX: 907-474-5469

University of Alaska Museum - search 400,276 digitized arthropod records http://arctos.database.museum/uam_ento_all http://www.uaf.edu/museum/collections/ento/ +++++++++++++++++++++++++++++++++++

Interested in Alaskan Entomology? Join the Alaska Entomological Society and / or sign up for the email listserv "Alaska Entomological Network" at http://www.akentsoc.org/contact_us

campmlc commented 4 years ago

As I've mentioned elsewhere, there is more info contained in "wild-caught" and "field" than "suitable for range mapping". These terms as refer to suitability for dietary, ecological, and isotopic studies, eg fitness for use of the specimens for research. I argue strongly that if we eliminate "wild-caught", which is reasonable, we need to replace with something that continues to capture the same concept, e.g. "field". This will not necessarily apply to all collections. I argue that that is acceptable. Sometimes trying to make a one size fits all category that can be broadly applied makes data too vague. obscure, and un-searchable for everyone, which defeats the purpose of the standardization.

dustymc commented 4 years ago

purpose of the standardization

A main purpose is discoverability.

If "A" and "B" are functionally identical, then keeping them separate prevents users from finding what they want. There is a workaround; two searches, or an "A or B" search, produces the desired results, but it should be assumed that very few users will find that path.

If "A" and "B" are functionally different, then lumping them into "C" prevents users from finding what they want. There is no workaround for this; if we must choose an evil, let's not choose this one.

As I mentioned somewhere in this mess, I think we first need to decide WHAT we're trying to say, THEN decide how to say it. That is, how many THINGS are we trying to convey with these data? Is it binary ("normal" vs. "somehow weird"), is there a "salamander in the parking lot" middle ground, are "normal" for a parasite or algae and "normal" for a mammal somehow different, etc.

more info contained in "wild-caught" and "field" than "suitable for range mapping".

There definitely should be. On that note and vaguely related, I think perhaps we need a 'capture' specimen event type. Both collect and capture are 'valid for range maps,' but materials gathered from "collect" events (which presumably very quickly result in a dead animal) and "capture" events (which often involve samples taken from a stressed animal) may be useful for different purposes. (Or maybe that's better done as something like https://github.com/ArctosDB/arctos/issues/1942#issuecomment-473356057)

ewommack commented 4 years ago

Since collection source isn't a required field for data entry, do we know how many collections actually use it consistently? Perhaps understanding where it has been used most in Arctos will help in redefining it, or a decision to create a new specimen event type.

dustymc commented 4 years ago


UAM@ARCTOS> select collecting_source, guid_prefix,count(*) c from collection,cataloged_item,specimen_event where collection.collection_id=cataloged_item.collection_id and cataloged_item.collection_object_id=specimen_event.collection_object_id group by collecting_source,guid_prefix order by collecting_source,guid_prefix;

COLLECTING_SOURCE          GUID_PREFIX        C
------------------------------ --------------- --------
captive                ALMNH:ES           1
captive                ASNHC:Bird        32
captive                ASNHC:Mamm       319
captive                CHAS:Bird          5
captive                CHAS:Ento         11
captive                CHAS:Herb         33
captive                CHAS:Herp          1
captive                CHAS:Mamm          4
captive                CHAS:Teach       101
captive                DGR:Bird           1
captive                DGR:Mamm          79
captive                DMNS:Bird        240
captive                DMNS:Herp         62
captive                DMNS:Mamm        444
captive                KNWR:Ento         11
captive                MLZ:Bird         194
captive                MLZ:Fish           2
captive                MSB:Bird         345
captive                MSB:Fish          84
captive                MSB:Host        2537
captive                MSB:Mamm        7163
captive                MSB:Para         514
captive                MSBObs:Mamm        3
captive                MVZ:Bird         436
captive                MVZ:Egg            9
captive                MVZ:Herp         288
captive                MVZ:Hild          28
captive                MVZ:Mamm        3483
captive                MVZObs:Herp        1
captive                NMMNH:Bird         4
captive                NMMNH:Herb        39
captive                NMU:Mamm           1
captive                OWU:Mamm           6
captive                OWU:Rept          10
captive                UAM:Ento           5
captive                UAM:Fish           4
captive                UAM:Herb          27
captive                UAM:Mamm         361
captive                UCM:Bird          27
captive                UCM:Egg            1
captive                UCM:Fish          38
captive                UCM:Herp         167
captive                UCM:Mamm          34
captive                UMNH:Mamm        400
captive                UMZM:Bird         17
captive                UMZM:Mamm         17
captive                UNR:Fish           2
captive                UNR:Herp          13
captive                UNR:Mamm           6
captive                USNPC:Para        40
captive                UTEP:Bird        282
captive                UTEP:Herb        579
captive                UTEP:Herp        142
captive                UTEP:HerpOS       21
captive                UTEP:Inv           1
captive                UTEP:Mamm         46
captive                UTEP:Teach         8
captive                UWBM:Herp         66
captive                UWBM:Mamm         31
captive                UWYMV:Bird        28
captive                UWYMV:Herp         5
captive                UWYMV:Mamm        34
field photo            DMNS:Para          1
field photo            KNWR:Herb          1
field photo            MVZObs:Herp        1
field photo            NMU:Mamm           1
field photo            UAM:Ento           1
field photo            UAMObs:Ento       98
field photo            UAMObs:Fish        8
field photo            UAMObs:Mamm       27
field photo            UCM:Obs           39
field photo            UTEPObs:Herp       1
museum photo               UAMObs:Ento        1
unknown                CHAS:Mamm          2
unknown                CHAS:Teach         9
unknown                DMNS:Bird         19
unknown                DMNS:Egg           5
unknown                DMNS:Inv        8759
unknown                DMNS:Mamm        427
unknown                MLZ:Bird           1
unknown                MSB:Bird          69
unknown                MSB:Host          23
unknown                MSB:Mamm         113
unknown                MSB:Para         172
unknown                MVZ:Bird        1182
unknown                MVZ:Egg           36
unknown                MVZ:Herp        1887
unknown                MVZ:Hild         310
unknown                MVZ:Mamm         327
unknown                NMMNH:Bird         2
unknown                NMU:Mamm           3
unknown                UAM:ES          1530
unknown                UAM:Ento          69
unknown                UAM:Herb           2
unknown                UAM:Inv            7
unknown                UAM:Mamm           9
unknown                UAMObs:Ento       39
unknown                UAMObs:Mamm        4
unknown                UCM:Fish           8
unknown                UCM:Herp           4
unknown                UCM:Mamm           4
unknown                UMZM:Bird       5744
unknown                UMZM:Mamm      13153
unknown                UNM:ES             1
unknown                UNR:Fish          18
unknown                UTEP:Herb          1
unknown                UTEP:Inv           1
unknown                UTEP:Teach         3
unknown                UWBM:Herp         17
unknown                UWBM:Mamm         37
unknown                UWYMV:Bird        11
unknown                UWYMV:Herp       361
wild caught            ALMNH:ES        9614
wild caught            ALMNH:Inv          1
wild caught            APSU:Herp         75
wild caught            ASNHC:Bird      2020
wild caught            ASNHC:Mamm     18440
wild caught            BYU:Herp       14395
wild caught            CHAS:Bird        378
wild caught            CHAS:Egg           1
wild caught            CHAS:Ento         48
wild caught            CHAS:Fish         24
wild caught            CHAS:Herb          2
wild caught            CHAS:Herp       7400
wild caught            CHAS:Inv        7071
wild caught            CHAS:Mamm       3216
wild caught            CHAS:Teach       117
wild caught            COA:Bird         878
wild caught            COA:Egg          119
wild caught            COA:Ento          37
wild caught            COA:Herp          61
wild caught            COA:Mamm         187
wild caught            DGR:Bird        2634
wild caught            DGR:Ento          35
wild caught            DGR:Mamm         667
wild caught            DMNS:Bird      55173
wild caught            DMNS:Egg        7141
wild caught            DMNS:Herp         85
wild caught            DMNS:Inv       20923
wild caught            DMNS:Mamm      19031
wild caught            DMNS:Para        884
wild caught            HWML:Para      26958
wild caught            KNWR:Ento       8758
wild caught            KNWR:Herb       1706
wild caught            KNWR:Inv          44
wild caught            KNWRObs:Bird     515
wild caught            KNWRObs:Fish      11
wild caught            KNWRObs:Herb      37
wild caught            KNWRObs:Mamm       3
wild caught            KWP:Ento       27848
wild caught            MLZ:Bird       62581
wild caught            MLZ:Egg           38
wild caught            MLZ:Fish         149
wild caught            MLZ:Herb          15
wild caught            MLZ:Mamm        2174
wild caught            MSB:Bird       49538
wild caught            MSB:Fish      102520
wild caught            MSB:Herp         429
wild caught            MSB:Host       20445
wild caught            MSB:Mamm      329921
wild caught            MSB:Para       21863
wild caught            MVZ:Bird      208186
wild caught            MVZ:Egg        15316
wild caught            MVZ:Fish         153
wild caught            MVZ:Herp      276105
wild caught            MVZ:Hild         323
wild caught            MVZ:Mamm      254811
wild caught            MVZObs:Bird     4857
wild caught            MVZObs:Herp       29
wild caught            MVZObs:Mamm      101
wild caught            NBSB:Bird        321
wild caught            NMU:Bird          13
wild caught            NMU:Mamm         448
wild caught            OWU:Bird           1
wild caught            OWU:ES           284
wild caught            OWU:Fish          21
wild caught            OWU:Mamm         153
wild caught            OWU:Para           5
wild caught            OWU:Rept         213
wild caught            UAM:Bird       37902
wild caught            UAM:EH             1
wild caught            UAM:ES         40292
wild caught            UAM:Ento      341395
wild caught            UAM:Env          334
wild caught            UAM:Fish        9850
wild caught            UAM:Herb      199669
wild caught            UAM:Herp         697
wild caught            UAM:Inv        16595
wild caught            UAM:Mamm      209080
wild caught            UAMObs:Bird      163
wild caught            UAMObs:Ento    33076
wild caught            UAMObs:Fish        5
wild caught            UAMObs:Mamm      185
wild caught            UAMb:Herb      74548
wild caught            UCM:Bird       11980
wild caught            UCM:Egg            1
wild caught            UCM:Fish        3582
wild caught            UCM:Herp       67176
wild caught            UCM:Mamm       18015
wild caught            UMNH:Bird         92
wild caught            UMNH:Herp          9
wild caught            UMNH:Mamm       2973
wild caught            UMZM:Bird        400
wild caught            UMZM:Mamm       2660
wild caught            UNR:Bird         196
wild caught            UNR:Fish         815
wild caught            UNR:Herp        4500
wild caught            UNR:Mamm        1329
wild caught            USNPC:Para       771
wild caught            UTEP:Bird        555
wild caught            UTEP:ES            2
wild caught            UTEP:Ento       8548
wild caught            UTEP:Fish          7
wild caught            UTEP:Herb      83282
wild caught            UTEP:Herp      28275
wild caught            UTEP:HerpOS     2145
wild caught            UTEP:Inv       13364
wild caught            UTEP:Mamm       8400
wild caught            UTEP:Teach         5
wild caught            UTEP:Zoo          28
wild caught            UTEPObs:Ento       2
wild caught            UTEPObs:Herp     170
wild caught            UWBM:Herp       7863
wild caught            UWBM:Mamm        115
wild caught            UWYMV:Bird      2311
wild caught            UWYMV:Egg          2
wild caught            UWYMV:Herp        14
wild caught            UWYMV:Mamm      6312
wild caught            WNMU:Bird       1339
wild caught            WNMU:Fish        379
wild caught            WNMU:Mamm       6888
                   ALMNH:ES         963
                   APSU:Herp       7011
                   ASNHC:Mamm         4
                   BYU:Herp         183
                   CHAS:Bird      26495
                   CHAS:EH         1020
                   CHAS:Egg        4167
                   CHAS:Ento      26119
                   CHAS:Fish         29
                   CHAS:Herb        117
                   CHAS:Herp          1
                   CHAS:Inv       16019
                   CHAS:Mamm       5320
                   CHAS:Teach      1810
                   DMNS:Bird        170
                   DMNS:Egg           2
                   DMNS:Herp         74
                   DMNS:Inv         514
                   DMNS:Mamm        316
                   DMNS:Para         51
                   JSNM:Paleo         3
                   KNWR:Ento         47
                   KNWR:Herb        805
                   KNWRObs:Herb     830
                   KWP:Ento       37774
                   MSB:Bird         884
                   MSB:Herp       56278
                   MSB:Host         713
                   MSB:Mamm        2072
                   MSB:Para        7670
                   MVZ:Bird         205
                   MVZ:Egg          377
                   MVZ:Herp       19323
                   MVZ:Mamm         285
                   NMMNH:Bird       520
                   NMMNH:Ento      7320
                   NMMNH:Herb      3599
                   NMMNH:Herp        29
                   NMMNH:Mamm      5788
                   NMMNH:Paleo    12099
                   NMU:Bird         307
                   NMU:Mamm        2270
                   NMU:Para          22
                   OWU:Bird          27
                   OWU:ES            80
                   OWU:Fish           2
                   OWU:Mamm          11
                   OWU:Rept           2
                   UAM:Alg         4639
                   UAM:Arc       651818
                   UAM:Art         5198
                   UAM:Bird         234
                   UAM:EH         37605
                   UAM:ES          9080
                   UAM:Ento        9003
                   UAM:Fish         326
                   UAM:Herb         692
                   UAM:Herp           2
                   UAM:Inv         3707
                   UAM:Mamm        1200
                   UAMObs:Bird        1
                   UAMObs:Ento     6620
                   UAMObs:Mamm       39
                   UAMb:Herb          7
                   UCM:Bird         248
                   UCM:Egg         2610
                   UCM:Fish          16
                   UCM:Herp         183
                   UCM:Mamm         409
                   UCM:Obs          213
                   UCSC:Bird       1573
                   UCSC:Herp         79
                   UCSC:Mamm        197
                   UMNH:Bird      20741
                   UMNH:Herp      22431
                   UMNH:Mamm      40222
                   UMNH:Teach       406
                   UNM:ES          1561
                   UNR:Bird           2
                   UNR:Fish        2980
                   UNR:Herp          34
                   UNR:Mamm         723
                   UTEP:Arc         451
                   UTEP:Bird       2240
                   UTEP:ES        23876
                   UTEP:Ento          2
                   UTEP:Fish        235
                   UTEP:Herb        128
                   UTEP:Herp        442
                   UTEP:HerpOS       64
                   UTEP:Inv         305
                   UTEP:Mamm          2
                   UTEP:Teach       228
                   UTEP:Zoo         123
                   UTEPObs:Herp      19
                   UWBM:Herp        893
                   UWBM:Mamm      55666
                   UWYMV:Bird        78
                   UWYMV:Fish       738
                   UWYMV:Herp         5
                   UWYMV:Mamm         5

Jegelewicz commented 4 years ago

@campmlc just had an email exchange with someone who was running into problems with this.

Thank you Mariel,

Since I am mostly looking at NM records, my problems are mostly stemming from the UTEP collection. I tried searching for all collections except the UTEP Arch collection but that does not seem to cull out many arch records for modern mammals. I will try using the “wild caught” option, but this would also exclude modern animals found dead. It would be nice if there were a way to easily click radiobutton for Modern Records (e.g., since 1482 or something like that). Another problem I have noticed is that many users of ARCTOS are not realizing they are getting archaeological records. This is causing some wild distributions to be reported. I have not seen any published yet but have caught some in draft form.

Actually, wild caught is being used to distinguish from captive, and has been broadly applied, so this will include DOAs and things not technically "caught" but "found". Again, this is a lively topic of current discussion on how to clarify and standardize the vocabulary (so that it fits across many collection types, including ethnography, herbaria, art, and paleo), and your perspective and suggestions are very helpful!

Jegelewicz commented 4 years ago

Also this.

Ambiguities in the definitions and understanding of terms such as “biodiversity” and “invasive species” have contributed to confusion among scientists, policy-makers, and the public. They may also contribute to opposing positions around NNS. Indeed, the term “biodiversity” can have both scientific and cultural meanings.

dustymc commented 4 years ago

https://github.com/ArctosDB/arctos/issues/1942#issuecomment-473356057 is capable of "it apparently got there by natural means" and "but we found it dead on the road." It also allows asserting things like "invasive" and "introduced" as method-backed opinions (any number of them on any record) attributed to specific agents.

campmlc commented 4 years ago

Following back up on this. I need to decide whether to use "captive" or "wild caught" for malarial parasites derived from the following source: "Parasite Strain From Takydromus Smaragdinus, Amami I., Ryukyus, Japan " Captive is not the correct term here. Neither is wild caught. I am using "experimental" as an attribute, as we discussed. But I would much prefer to have "experimental" in collecting source. Why not allow it here and flag it as "not in-situ", as we do with "captive"?

dustymc commented 4 years ago

Neither is wild caught.

Why not? What are you trying to to?

"experimental"

That definitely needs sorted out - those data are in several forms/places, I don't think they can be useful.

"experimental" in collecting source

Seems reasonable-ish to me, "introduced" would get more use and be understood by a larger audience.

and flag it as "not in-situ", as we do with "captive"?

We do what?!

campmlc commented 4 years ago

While they may have originally been wild caught, parasites and pathogens that are passed through iterations of captive hosts in experimental settings undergo physiological and genetic changes; putting "wild-caught" for an experimental parasite that has gone through successions of experimental hosts is misleading. Experimental and introduced are not the same, so having two separate values would be helpful. At one point in this very long discussion, we had proposed that the purpose of collection source was to identify whether or not a particular occurrence record would be mappable or not. Not the case anymore?

On Mon, Aug 31, 2020 at 9:55 AM dustymc notifications@github.com wrote:

[EXTERNAL]*

Neither is wild caught.

Why not? What are you trying to to?

"experimental"

That definitely needs sorted out - those data are in several forms/places, I don't think they can be useful.

"experimental" in collecting source

Seems reasonable-ish to me, "introduced" would get more use and be understood by a larger audience.

and flag it as "not in-situ", as we do with "captive"?

We do what?!

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dustymc commented 4 years ago

Experimental and introduced are not the same

Did you put it there? Yes==>introduced; no==>wild-caught, no?

I suggested in some other thread that we could have a "sub-collecting-event" field to clarify - cultivated, invasive, "experimental" (which might be difficult to functionally separate from "cultivated"), but I don't think that went anywhere.

Jegelewicz commented 4 years ago

I think we first need to decide WHAT we're trying to say, THEN decide how to say it. That is, how many THINGS are we trying to convey with these data? Is it binary ("normal" vs. "somehow weird"), is there a "salamander in the parking lot" middle ground, are "normal" for a parasite or algae and "normal" for a mammal somehow different, etc.

I think this needs sorting out first because I think we are attempting to use a single field for more than one kind of data.

What IS the definition for the FIELD collecting source? In other words, what is the information in this field meant to convey?

I suggested:

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.)

which is a slight variation from https://github.com/ArctosDB/arctos/issues/1942#issuecomment-473356057 which describes the "sub-field" establishment means that @dustymc is referring to above.

DerekSikes commented 4 years ago

My two cents:

If we make 'field photo' go away then we need to change 'wild caught' to 'wild' because what else would we use for an observation record of a specimen that is not caught?

-Derek

On Mon, Aug 31, 2020 at 9:20 AM Teresa Mayfield-Meyer < notifications@github.com> wrote:

I think we first need to decide WHAT we're trying to say, THEN decide how to say it. That is, how many THINGS are we trying to convey with these data? Is it binary ("normal" vs. "somehow weird"), is there a "salamander in the parking lot" middle ground, are "normal" for a parasite or algae and "normal" for a mammal somehow different, etc.

I think this needs sorting out first because I think we are attempting to use a single field for more than one kind of data.

What IS the definition for the FIELD collecting source? In other words, what is the information in this field meant to convey?

I suggested:

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

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.)

which is a slight variation from #1942 (comment) https://github.com/ArctosDB/arctos/issues/1942#issuecomment-473356057 which describes the "sub-field" establishment means that @dustymc https://github.com/dustymc is referring to above.

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dustymc commented 4 years ago

naturally occurring population

I don't think we can usefully define that; what precisely is "naturally occurring"? A Nile crocodile in the Yukon River is easy, a polar bear in Barrow is easy, but what about the "well kinda but not really" things like dingos, etc., etc., etc.?

change 'wild caught' to 'wild'

Seems like a workable improvement. It's vague enough to defend, and we can always clarify ("wild, plus native/introduced/invasive/experimental/whatever") with a new attribute as discussed in 1942.

jldunnum commented 4 years ago

I agree, don't think there is any meaningful reason to discriminate between a specimen from a "naturally occurring population" or a specimen from a population that is the result of some introduction event in the past. Very valid reasons to want to map both those things. A zoo or lab animal is one thing and should be excluded from mapping but something like Rattus rattus in NY city is another. The distributional ranges of species which are invasives or introduced are still part of their distributions.

Jonathan L. Dunnum Ph.D. Senior Collection Manager Division of Mammals, Museum of Southwestern Biology University of New Mexico Albuquerque, NM 87131 (505) 277-9262 Fax (505) 277-1351

MSB Mammals website: http://www.msb.unm.edu/mammals/index.html Facebook: http://www.facebook.com/MSBDivisionofMammals

Shipping Address: Museum of Southwestern Biology Division of Mammals University of New Mexico CERIA Bldg 83, Room 204 Albuquerque, NM 87131

From: dustymc notifications@github.com Sent: Monday, August 31, 2020 1:14 PM To: ArctosDB/arctos arctos@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [ArctosDB/arctos] Define collecting source (#2494)

[EXTERNAL]

naturally occurring population

I don't think we can usefully define that; what precisely is "naturally occurring"? A Nile crocodile in the Yukon River is easy, a polar bear in Barrow is easy, but what about the "well kinda but not really" things like dingos, etc., etc., etc.?

change 'wild caught' to 'wild'

Seems like a workable improvement. It's vague enough to defend, and we can always clarify ("wild, plus native/introduced/invasive/experimental/whatever") with a new attribute as discussed in 1942.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ArctosDB/arctos/issues/2494#issuecomment-683976901, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AED2PA6ZYAXITYGO6LFJSVLSDPZCBANCNFSM4KTD73AA.

Jegelewicz commented 4 years ago

campmlc commented 4 years ago

I also think that in some cases, experimental records should be mappable. For example, a strain of malaria from Japan, Honshu that is being reared for study in a lab. It IS a strain from Honshu, but it needs to be flagged as experimental. I agree with Teresa that if mappability is a concern, it should be its own field. Really, should we as curators actually be the ones deciding whether something is mappable or not? Shouldn't this be a decision made by researchers, according to their own criteria for their particular study? If we remove mappability from this discussion, then we could just use establishment means, with the experimental ones being "captive" with attribute "experimental".

On Tue, Sep 1, 2020 at 8:17 AM Teresa Mayfield-Meyer < notifications@github.com> wrote:

[EXTERNAL]*

See also tdwg/dwc#235 https://github.com/tdwg/dwc/issues/235

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tucotuco commented 4 years ago

I agree that mappability is a completely separate issue that has nothing to do with establishment, though could be used in combination with it. I also think it is a really bad idea to a priori circumscribe the uses to which data might be put. If you do, what just happened to ground-breaking research? I don't think you need attributes for mappability, though you might want to make a simple flag that summarizes the otherwise more complex notion of an unambiguously georeference (not points, not missing datums, etc.). To me, that's what mappable means.

There has been a lot of deep discussion about establishment in this and related issues. I really hope Arctos participates in the Darwin Core review and offers up solutions for any gaps that might remain in the proposals that you all have considered. If not, don't come complaining about how Darwin Core is "broken" (at least with respect to these terms). ;-)

Jegelewicz commented 4 years ago

I also think it is a really bad idea to a priori circumscribe the uses to which data might be put.

ArctosDB / arctos

Define collecting source #2494