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Arctos Documentation and How-To Guides
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updating taxonomy: _Sorex monticolus_ should be _Sorex monticola_ #179

Open KyndallH opened 4 years ago

KyndallH commented 4 years ago

I looked at the handbook but couldn't find the right way to propose a taxonomic change in Arctos. I don't want to go and change it for everyone but it looks like it does need to be updated and I'm not sure the proper procedure.

_Sorex monticolus should be Sorex monticola.

Screen Shot 2020-08-17 at 4 02 40 PM

Woodman, N. 2018. A Taxonomic Checklist of American Recent Eulipotyphla: Nesophontids, Solenodons, Moles, and Shrews in the New World. Smithsonian Contributions to Zoology 650:i–vi, 1–109, 27 figures (published online 16 November 2018). https://smithsonian.figshare.com/articles/American_Recent_Eulipotyphla_Nesophontids_Solenodons_Moles_and_Shrews_in_the_New_World/9761753

KyndallH commented 4 years ago
Screen Shot 2020-08-17 at 4 20 24 PM

Merriam, C. H. (1895). Synopsis of the American shrews of the genus Sorex. North American Fauna, 57-125.

dustymc commented 4 years ago

I think that's probably just a new ID using https://arctos.database.museum/info/ctDocumentation.cfm?table=ctnature_of_id&field=revised%20taxonomy and we can expect it to flipflop back and forth every couple decades because taxonomy, but if everyone using us gets on board I could help switch IDs and us could be quarantined (from where it can support search but cannot be used in identifications).

FYI most of https://arctos.database.museum/info/ctDocumentation.cfm?table=cttaxon_relation&field=potential%20alternate%20spelling are similar.


arctosprod@arctos>> select count(*) from taxon_relations where taxon_relationship ='potential alternate spelling';
 count 
-------
 87100
select 
  identification.scientific_name,
  guid_prefix,
  count(*)
from
  identification inner join identification_taxonomy on identification.identification_id=identification_taxonomy.identification_id
  inner join taxon_name on identification_taxonomy.taxon_name_id=taxon_name.taxon_name_id
  inner join cataloged_item on identification.collection_object_id=cataloged_item.collection_object_id
  inner join collection on cataloged_item.collection_id=collection.collection_id
where
  taxon_name.scientific_name like 'Sorex montic%'
group by
   identification.scientific_name,
  guid_prefix
order by
  guid_prefix,
  identification.scientific_name
;

        scientific_name         | guid_prefix | count 
--------------------------------+-------------+-------
 Sorex monticolus               | ASNHC:Mamm  |     2
 Sorex monticolus               | BYU:Mamm    |   125
 Sorex monticolus               | DGR:Mamm    |     5
 Sorex monticolus               | DMNS:Mamm   |   295
 Sorex monticolus obscurus      | DMNS:Mamm   |   194
 Sorex monticolus               | MSB:Host    |     1
 Sorex monticolus               | MSB:Mamm    |  3370
 Sorex monticolus alascensis    | MSB:Mamm    |    12
 Sorex monticolus bairdi        | MSB:Mamm    |     1
 Sorex monticolus cf.           | MSB:Mamm    |    81
 Sorex monticolus elassodon     | MSB:Mamm    |     8
 Sorex monticolus monticolus    | MSB:Mamm    |   140
 Sorex monticolus neomexicanus  | MSB:Mamm    |    48
 Sorex monticolus obscuroides   | MSB:Mamm    |     3
 Sorex monticolus obscurus      | MSB:Mamm    |   406
 Sorex monticolus shumaginensis | MSB:Mamm    |    18
 Sorex monticolus               | MVZ:Mamm    |    19
 Sorex monticolus alascensis    | MVZ:Mamm    |   150
 Sorex monticolus elassodon     | MVZ:Mamm    |    76
 Sorex monticolus isolatus      | MVZ:Mamm    |    31
 Sorex monticolus longicauda    | MVZ:Mamm    |    73
 Sorex monticolus longicaudus   | MVZ:Mamm    |    20
 Sorex monticolus malitiosus    | MVZ:Mamm    |    21
 Sorex monticolus mixtus        | MVZ:Mamm    |     5
 Sorex monticolus monticolus    | MVZ:Mamm    |    35
 Sorex monticolus obscurus      | MVZ:Mamm    |   889
 Sorex monticolus setosus       | MVZ:Mamm    |   132
 Sorex monticolus shumaginensis | MVZ:Mamm    |     4
 Sorex vagrans vagrans          | MVZ:Mamm    |     5
 Sorex monticolus               | NMMNH:Mamm  |    41
 Sorex monticolus               | NMU:Mamm    |    11
 Sorex monticolus               | UAM:Mamm    |  5338
 Sorex monticolus ?             | UAM:Mamm    |     9
 Sorex monticolus               | UCM:Mamm    |   175
 Sorex monticolus alascensis    | UCM:Mamm    |     3
 Sorex monticolus longicauda    | UCM:Mamm    |     2
 Sorex monticolus monticolus    | UCM:Mamm    |     4
 Sorex monticolus obscurus      | UCM:Mamm    |   129
 Sorex monticolus shumaginensis | UCM:Mamm    |    15
 Sorex monticolus alascensis    | UMNH:Mamm   |     9
 Sorex monticolus obscurus      | UMNH:Mamm   |   792
 Sorex monticolus shumaginensis | UMNH:Mamm   |     5
 Sorex monticolus               | UMZM:Mamm   |   219
 Sorex monticolus               | UTEP:ES     |     1
 Sorex monticolus cf.           | UTEP:ES     |     2
 Sorex monticolus               | UTEP:Mamm   |    48
 Sorex monticolus               | UWBM:Mamm   |  2091
 Sorex monticolus               | UWYMV:Mamm  |     1
 Sorex monticolus longicaudus   | UWYMV:Mamm  |     1
 Sorex monticolus obscurus      | UWYMV:Mamm  |     3
 Sorex monticolus               | WNMU:Mamm   |    22
Jegelewicz commented 4 years ago

That's a lot of folks to get on board....probably only one or two will even see this issue. I think it will require direct notification to managers of the above collections.

cjconroy commented 4 years ago

I think the most pragmatic thing for you to do is to add Sorex monticola and move your own collections there if you like, and send an email to all other mammal collection managers. I appreciate you bringing up this issue, but the MVZ may not want to go that way, or we may want to just see what happens over a few years of debate. But, it is now on my list of taxonomic issues to review. MVZ also apparently has Sorex monticolus longicauda and Sorex monticolus longicaudus for us to review.

DerekSikes commented 4 years ago

I agree - make a taxonomy record with the correct spelling (if one doesn't already exist) & then make a relationship under 'edit name & related data' with the incorrect spelling using the 'potential alternative spelling'

This way anytime someone searches on Sorex monticolus to add that name as the ID for their record, Sorex monticola will also appear (and vice versa). If you change S. monticolus to status = invalid that could help encourage & inform users.

Not sure everyone does this but it seems to me the best practice is to create an ID that matches whatever is on the physical label, misspellings and all, and then create a new ID that 'corrects' the original, if needed.

-Derek

On Tue, Aug 18, 2020 at 1:43 PM cjconroy notifications@github.com wrote:

I think the most pragmatic thing for you to do is to add Sorex monticola and move your own collections there if you like, and send an email to all other mammal collection managers. I appreciate you bringing up this issue, but the MVZ may not want to go that way, or we may want to just see what happens over a few years of debate. But, it is now on my list of taxonomic issues to review. MVZ also apparently has Sorex monticolus longicauda and Sorex monticolus longicaudus for us to review.

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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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Jegelewicz commented 4 years ago

If you change S. monticolus to status = invalid that could help encourage & inform users.

Yes to this, also add preferred name = Sorex monticola

Jegelewicz commented 4 years ago

Not sure everyone does this but it seems to me the best practice is to create an ID that matches whatever is on the physical label, misspellings and all, and then create a new ID that 'corrects' the original, if needed.

Agree, but instead of creating a name for the incorrect spelling, it would be preferable to use the A {string}. So in this case, the identification for the misspelling would be Sorex {Sorex monticolus}.

jldunnum commented 3 years ago

Hey Kyndall, I think I added it a while back and we are now using it, but left the other spelling because not everyone may be in agreement.

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: Kyndall Hildebrandt notifications@github.com Sent: Monday, January 25, 2021 7:36 AM To: ArctosDB/documentation-wiki documentation-wiki@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [ArctosDB/documentation-wiki] updating taxonomy: Sorex monticolus should be Sorex monticola (#179)

[EXTERNAL]

I looked at the handbook but couldn't find the right way to propose a taxonomic change in Arctos. I don't want to go and change it for everyone but it looks like it does need to be updated and I'm not sure the proper procedure.

_Sorex monticolus should be Sorex monticola.

[Screen Shot 2020-08-17 at 4 02 40 PM]https://user-images.githubusercontent.com/16887896/90456097-73c88180-e0a4-11ea-9940-93d5db9bfd71.png

Woodman, N. 2018. A Taxonomic Checklist of American Recent Eulipotyphla: Nesophontids, Solenodons, Moles, and Shrews in the New World. Smithsonian Contributions to Zoology 650:i–vi, 1–109, 27 figures (published online 16 November 2018). https://smithsonian.figshare.com/articles/American_Recent_Eulipotyphla_Nesophontids_Solenodons_Moles_and_Shrews_in_the_New_World/9761753

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ArctosDB/documentation-wiki/issues/179, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AED2PA5H7WOQK34JB4OL5TLS3V6YFANCNFSM4WR264GA.

campmlc commented 3 years ago

If you are certain a name shouldn't be used, you can go through the process of quarantining it, but you need to get all collections to correct their specimens before that can happen, if I understand correctly.

On Mon, Jan 25, 2021, 7:56 AM jldunnum notifications@github.com wrote:

  • [EXTERNAL]*

Hey Kyndall, I think I added it a while back and we are now using it, but left the other spelling because not everyone may be in agreement.

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: Kyndall Hildebrandt notifications@github.com Sent: Monday, January 25, 2021 7:36 AM To: ArctosDB/documentation-wiki documentation-wiki@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [ArctosDB/documentation-wiki] updating taxonomy: Sorex monticolus should be Sorex monticola (#179)

[EXTERNAL]

I looked at the handbook but couldn't find the right way to propose a taxonomic change in Arctos. I don't want to go and change it for everyone but it looks like it does need to be updated and I'm not sure the proper procedure.

_Sorex monticolus should be Sorex monticola.

[Screen Shot 2020-08-17 at 4 02 40 PM]< https://user-images.githubusercontent.com/16887896/90456097-73c88180-e0a4-11ea-9940-93d5db9bfd71.png

Woodman, N. 2018. A Taxonomic Checklist of American Recent Eulipotyphla: Nesophontids, Solenodons, Moles, and Shrews in the New World. Smithsonian Contributions to Zoology 650:i–vi, 1–109, 27 figures (published online 16 November 2018).

https://smithsonian.figshare.com/articles/American_Recent_Eulipotyphla_Nesophontids_Solenodons_Moles_and_Shrews_in_the_New_World/9761753

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub< https://github.com/ArctosDB/documentation-wiki/issues/179>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AED2PA5H7WOQK34JB4OL5TLS3V6YFANCNFSM4WR264GA

.

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dustymc commented 3 years ago

This need documentation, including