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
All 47 comments
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?
ewommack
on 11 Feb 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.
dustymc
on 11 Feb 2020
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"
Jegelewicz
on 11 Feb 2020
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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DerekSikes
on 11 Feb 2020
So a replacement of wild caught and captive with:
found - not captive
found - captive
?
ewommack
on 11 Feb 2020
captive will not change.
wild caught will change to not captive
Jegelewicz
on 11 Feb 2020
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.
ewommack
on 11 Feb 2020
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.
Jegelewicz
on 11 Feb 2020
How about:
From Field
From Captivity
On Tue, Feb 11, 2020 at 11:43 AM Teresa Mayfield-Meyer <
[email protected]> 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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mkoo
on 11 Feb 2020
Field! so simple - I like that!!!
Jegelewicz
on 11 Feb 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?
dustymc
on 11 Feb 2020
I also like field MUCH better than "not captive".
On Tue, Feb 11, 2020 at 12:51 PM Teresa Mayfield-Meyer <
[email protected]> wrote:
Field! so simple - I like that!!!
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atrox10
on 12 Feb 2020
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".
On Tue, Feb 11, 2020 at 12:51 PM Teresa Mayfield-Meyer <
[email protected]> wrote:Field! so simple - I like that!!!
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University of Alaska Museum
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FAX: 907-474-5469
University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
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DerekSikes
on 12 Feb 2020
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.
Jegelewicz
on 12 Feb 2020
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.
On Wed, Feb 12, 2020 at 12:45 PM Teresa Mayfield-Meyer <
[email protected]> wrote:
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content is safe. (2.3)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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campmlc
on 12 Feb 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.
dustymc
on 12 Feb 2020
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.
Jegelewicz
on 12 Feb 2020
dustymc
on 12 Feb 2020
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.)
Jegelewicz
on 12 Feb 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}.
dustymc
on 12 Feb 2020
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
on 13 Feb 2020
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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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960
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/
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DerekSikes
on 13 Feb 2020
I vote yes to this
On Wed, Feb 12, 2020 at 2:08 PM Teresa Mayfield-Meyer <
[email protected]> 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-sourcewhich 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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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960
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
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DerekSikes
on 13 Feb 2020
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.
campmlc
on 19 Feb 2020
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)
dustymc
on 19 Feb 2020
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.
ewommack
on 20 Feb 2020
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
@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
on 21 Feb 2020
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.
Jegelewicz
on 21 Feb 2020
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.
dustymc
on 21 Feb 2020
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"?
campmlc
on 31 Aug 2020
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?!
dustymc
on 31 Aug 2020
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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campmlc
on 31 Aug 2020
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.
dustymc
on 31 Aug 2020
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.
Jegelewicz
on 31 Aug 2020
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 <
[email protected]> 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-sourcewhich 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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Derek S. Sikes, Curator of Insects
Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960
phone: 907-474-6278
FAX: 907-474-5469
he/him/his
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DerekSikes
on 31 Aug 2020
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.
dustymc
on 31 Aug 2020
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.
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jldunnum
on 31 Aug 2020
Jegelewicz
on 1 Sep 2020
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 <
[email protected]> wrote:
- [EXTERNAL]*
See also tdwg/dwc#235 https://github.com/tdwg/dwc/issues/235
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campmlc
on 1 Sep 2020
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). ;-)
tucotuco
on 1 Sep 2020
I also think it is a really bad idea to a priori circumscribe the uses to which data might be put.
See also #3067
Jegelewicz
on 1 Sep 2020
There is no "mappability" and I don't think we could do that if we wanted to, which we hopefully don't. There is a desire to flag things that eg don't make great rangemaps, to prevent Curators from deleting data along with making things easy for folks building maps or analyzing spatial data.
It appears to me that we need two levels of flag, one very general and a bit subjective ("wild"/"captive"), the other more refined and (potentially) backed by some evidence ("invasive, according to {determiner} using {method} on {date}").
dustymc
on 1 Sep 2020
the other more refined and (potentially) backed by some evidence
("invasive, according to {determiner} using {method} on {date}").
I've long wanted some way to flag species (not specimens) but we have no
structure to do so. This idea of flagging specimens as 'invasive' is not
good - too easy for some specimens of that invasive species to get flagged
as invasive while others don't in the same region (where all of them should
be flagged as invasive).
What we need is something in between species and specimens that allows
curators to mark up species based on their data sets own peculiar needs.
I'm writing a paper on the non-native species of nonmarine invertebrates in
Alaska. As a work around I've added the term 'nonnative' to the specimen
remarks of 1 specimen per species. I search on that list, then I get all
the species names & search using all those names - to find ALL the specimen
records of species that are nonnative to Alaska. I'm sure there's a better
way to do this but we don't have the structure.
-Derek
On Tue, Sep 1, 2020 at 7:25 AM dustymc notifications@github.com wrote:
There is no "mappability" and I don't think we could do that if we wanted
to, which we hopefully don't. There is a desire to flag things that eg
don't make great rangemaps, to prevent Curators from deleting data along
with making things easy for folks building maps or analyzing spatial data.It appears to me that we need two levels of flag, one very general and a
bit subjective ("wild"/"captive"), the other more refined and (potentially)
backed by some evidence ("invasive, according to {determiner} using
{method} on {date}").—
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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960
phone: 907-474-6278
FAX: 907-474-5469
he/him/his
University of Alaska Museum - search 400,276 digitized arthropod records
http://arctos.database.museum/uam_ento_all
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++
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DerekSikes
on 1 Sep 2020
something in between species and specimens
That would necessarily involve spatial and temporal data, correct? If it's on that side of the line then it's native, this side invasive. From that there would necessarily be a precision component - you can't say anything about those records that are known only to be "somewhere near the line." A species might progress from "incidental" to "invasive" to "they've always been here" by themselves over time. The data object at which all of those things - plus things like taxon concepts (are we really talking about the same entity?) and identifications (are we sure it's that species?) - converge is the catalog record.
If you had a checklist of say "native bugs of alaska" (project taxonomy was envisioned for that sort of thing) then you could (perhaps with some development) find bugs + alaska + not in the list (and perhaps add a time component, and define "alaska" however you want, and ....).
Collecting source would support bugs + alaska + not in the list + not in the zoo or pet store.
You might do some analysis on the results, and decide that THESE bugs are invasive while THOSE are incidental. The "sub-collecting-event" attribute would allow you to record that in a way which might be useful for future queries.
dustymc
on 1 Sep 2020
a checklist of say "native bugs of alaska" (project taxonomy was envisioned
for that sort of thing)
This sounds great. Is this in development 'project taxonomy'?
-Derek
On Tue, Sep 1, 2020 at 9:20 AM dustymc notifications@github.com wrote:
something in between species and specimens
That would necessarily involve spatial and temporal data, correct? If it's
on that side of the line then it's native, this side invasive. From that
there would necessarily be a precision component - you can't say anything
about those records that are known only to be "somewhere near the line." A
species might progress from "incidental" to "invasive" to "they've always
been here" by themselves over time. The data object at which all of those
things - plus things like taxon concepts (are we really talking about the
same entity?) and identifications (are we sure it's that species?) -
converge is the catalog record.If you had a checklist of say "native bugs of alaska" (project taxonomy
was envisioned for that sort of thing) then you could (perhaps with some
development) find bugs + alaska + not in the list (and perhaps add a time
component, and define "alaska" however you want, and ....).Collecting source would support bugs + alaska + not in the list + not in
the zoo or pet store.You might do some analysis on the results, and decide that THESE bugs are
invasive while THOSE are incidental. The "sub-collecting-event" attribute
would allow you to record that in a way which might be useful for future
queries.—
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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960
phone: 907-474-6278
FAX: 907-474-5469
he/him/his
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
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DerekSikes
on 1 Sep 2020
It's been there for a very long time - bottom of the edit project page - but could probably use some polish if there was a use case.
dustymc
on 1 Sep 2020
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