ID formula A sp.

[DerekSikes]

Can we somehow make our data consistent for genus-only level identifications? Currently, I train my people to use ID formula ' A sp. ' but often they forget. This means that the data are inconsistent - some genus-only determinations are formula A and others are formula A sp.

I suppose we would have to all agree to allow Arctos to use only ' A sp.' whenever and ID was genus-only (and Arctos would have to 'know' when this situation exists, which I think shouldn't be too hard). OR we could set a preference in our admin settings for each collection?

[ekrimmel]

I am in favor of enforcing consistency to A sp.

[sharpphyl]

We train our volunteers to use A sp.

[Jegelewicz]

I am also in favor of enforcing A sp.

[jtgiermakowski]

I am also in favor of "A sp."

[dustymc]

From another message:

we have a lot of the bat Lasionycteris noctivagans but also 28 that read Lasionycteris noctivagans ssp. As far as I know, there are no subspecies for this species. As far as I can tell, they are all classified as just Lasionycteris noctivagans. Why do some have ssp.?

They were entered that way.

http://handbook.arctosdb.org/documentation/bulkloader.html#taxonomy

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

If there's a single term ranked genus in the preferred classification, I could theoretically do something with it+incoming ID formula. I could also maybe check that A ssp. determinations involve something that looks like a species and that subspecies exist.

That would all add a LOT of work/processing/complexity. It's a bunch of code to maintain, it's a bunch of pointless Operator rules (it might force you to create subspecies you'll never use before you can use the "A ssp." formula, for example), and it forces users to figure out why we have two ways of saying exactly the same thing (if they're lucky enough to find both variants).

True consistency would also demand some rule regarding existing IDs when a subspecies of Lasionycteris noctivagans is named, which doesn't seem very realistic.

Can we take the obvious path and drop the A s[s]p. formulae instead? Anyone who REALLY wants the format could use the A {string} formula to create a functionally-equivalent ID.

[DerekSikes]

I would be happy to drop the A ssp. formula since it makes no sense to me. If a species has a subspecies it is added as a third name and it's obviously the subspecific name so there's no need to add a "ssp." I don't know any situation in which that would be helpful. However, I don't want to drop the A sp. formula because this is a long standing tradition (at least in entomology) to designate a genus-level identification. Granted these two formulae are equivalent if seen on a label or an Arctos record: Nicrophorus Nicrophorus sp. because both mean "this organism is one of the species in the genus Nicrophorus" but the first formulation just looks lazy and wrong. Surely Arctos knows when a taxon name is a genus, that's clearly specified in our classifications. What's so hard with "If the sciname = the genus name, then add "sp." to the ID automatically?

…

-Derek

On Wed, Jan 31, 2018 at 7:16 AM, dustymc ***@***.***> wrote: From another message: we have a lot of the bat Lasionycteris noctivagans but also 28 that read Lasionycteris noctivagans ssp. As far as I know, there are no subspecies for this species. As far as I can tell, they are all classified as just Lasionycteris noctivagans. Why do some have ssp.? They were entered that way. http://handbook.arctosdb.org/documentation/bulkloader.html#taxonomy http://arctos.database.museum/info/ctDocumentation.cfm? table=cttaxa_formula If there's a single term ranked genus in the preferred classification, I could theoretically do something with it+incoming ID formula. I could also maybe check that A ssp. determinations involve something that looks like a species and that subspecies exist. That would all add a LOT of work/processing/complexity. It's a bunch of code to maintain, it's a bunch of pointless Operator rules (it might force you to create subspecies you'll never use before you can use the "A ssp." formula, for example), and it forces users to figure out why we have two ways of saying exactly the same thing (if they're lucky enough to find both variants). True consistency would also demand some rule regarding existing IDs when a subspecies of Lasionycteris noctivagans is named, which doesn't seem very realistic. Can we take the obvious path and drop the A s[s]p. formulae instead? Anyone who REALLY wants the format could use the A {string} formula to create a functionally-equivalent ID. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1304 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIraM_bhofRarlVUmHHGCuNwS9xl4zM0ks5tQJHFgaJpZM4P_x9M> .

-- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Associate Professor of Entomology University of Alaska Museum 1962 Yukon Drive Fairbanks, AK 99775-6960 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 <http://www.akentsoc.org/contact.php>

[DerekSikes]

I should add that in some cases the A sp. does help disambiguate things... in rare cases a genus name might be mistaken for a higher taxon (I can only think off the top of my head of cross-kingdom homonyms like Diplura is an order in Animalia and I think a genus in plants.) Thus and ID of Diplura = "this is in the order Diplura", while and ID of "Diplura sp." = this is a species in the genus Diplura.

…

-Derek

On Wed, Jan 31, 2018 at 7:28 AM, Derek Sikes ***@***.***> wrote: I would be happy to drop the A ssp. formula since it makes no sense to me. If a species has a subspecies it is added as a third name and it's obviously the subspecific name so there's no need to add a "ssp." I don't know any situation in which that would be helpful. However, I don't want to drop the A sp. formula because this is a long standing tradition (at least in entomology) to designate a genus-level identification. Granted these two formulae are equivalent if seen on a label or an Arctos record: Nicrophorus Nicrophorus sp. because both mean "this organism is one of the species in the genus Nicrophorus" but the first formulation just looks lazy and wrong. Surely Arctos knows when a taxon name is a genus, that's clearly specified in our classifications. What's so hard with "If the sciname = the genus name, then add "sp." to the ID automatically? -Derek On Wed, Jan 31, 2018 at 7:16 AM, dustymc ***@***.***> wrote: > From another message: > > we have a lot of the bat Lasionycteris noctivagans but also 28 that read > Lasionycteris noctivagans ssp. As far as I know, there are no subspecies > for this species. As far as I can tell, they are all classified as just > Lasionycteris noctivagans. Why do some have ssp.? > > They were entered that way. > > http://handbook.arctosdb.org/documentation/bulkloader.html#taxonomy > > http://arctos.database.museum/info/ctDocumentation.cfm?table > =cttaxa_formula > > If there's a single term ranked genus in the preferred classification, I > could theoretically do something with it+incoming ID formula. I could also > maybe check that A ssp. determinations involve something that looks like a > species and that subspecies exist. > > That would all add a LOT of work/processing/complexity. It's a bunch of > code to maintain, it's a bunch of pointless Operator rules (it might force > you to create subspecies you'll never use before you can use the "A ssp." > formula, for example), and it forces users to figure out why we have two > ways of saying exactly the same thing (if they're lucky enough to find both > variants). > > True consistency would also demand some rule regarding existing IDs when > a subspecies of Lasionycteris noctivagans is named, which doesn't seem very > realistic. > > Can we take the obvious path and drop the A s[s]p. formulae instead? > Anyone who REALLY wants the format could use the A {string} formula to > create a functionally-equivalent ID. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#1304 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AIraM_bhofRarlVUmHHGCuNwS9xl4zM0ks5tQJHFgaJpZM4P_x9M> > . > -- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Associate Professor of Entomology University of Alaska Museum 1962 Yukon Drive Fairbanks, AK 99775-6960 ***@***.*** phone: 907-474-6278 <(907)%20474-6278> FAX: 907-474-5469 <(907)%20474-5469> 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 <http://www.akentsoc.org/contact.php>

-- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Associate Professor of Entomology University of Alaska Museum 1962 Yukon Drive Fairbanks, AK 99775-6960 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 <http://www.akentsoc.org/contact.php>

[dustymc]

long standing tradition (at least in [some limited scope])

That is also the origins of A ssp. (and a bunch of similar things in various niches).

IF a bunch of things in our classification data are true/consistent, tacking on .sp would not be particularly hard to implement (certainly easier than .ssp, which has a couple more "ifs" involved, likely less stability, and perhaps a narrower tradition). Maintenance - what happens when someone changes the lowest ranked term in a classification to/from genus? - is probably much less trivial. If the answer potentially involves changing thousands of IDs, things like processing power may become an issue as well.

I'm not particularly objecting to any part of this idea; weird but consistent data are certainly more accessible than sometimes-weird and inconsistent data. I'm just trying to figure out what might be involved, make sure we all understand what this might mean, point out where a clean-slate data modeling exercise might end up, etc.

https://arctos.database.museum/name/Diplura claims to be/have been used for

• Order of hexapod
• Genus of arachnid
• Genus of cnidarian
• Genus of lepidopteran
• Genus of seaweed
• Genus of bird
• I think multiple instances of some of those things
• Probably some other stuff

so I question the utility of the .sp as a disambiguator at the scale of Arctos.

[DerekSikes]

After more thought I'm willing to back down on wanting Arctos to retain the 'A sp.' formula. Not sure if anyone else feels strongly about it but keeping it adds complexity, leads to data inconsistency when it's sometimes forgotten to be used, and doesn't add much benefit.

…

-Derek

On Thu, Feb 1, 2018 at 8:46 AM, dustymc ***@***.***> wrote: long standing tradition (at least in [some limited scope]) That is also the origins of A ssp. (and a bunch of similar things in various niches). IF a bunch of things in our classification data are true/consistent, tacking on .sp would not be particularly hard to implement (certainly easier than .ssp, which has a couple more "ifs" involved, likely less stability, and perhaps a narrower tradition). Maintenance - what happens when someone changes the lowest ranked term in a classification to/from genus? - is probably much less trivial. If the answer potentially involves changing thousands of IDs, things like processing power may become an issue as well. I'm not particularly objecting to any part of this idea; weird but consistent data are certainly more accessible than sometimes-weird and inconsistent data. I'm just trying to figure out what might be involved, make sure we all understand what this might mean, point out where a clean-slate data modeling exercise might end up, etc. https://arctos.database.museum/name/Diplura claims to be/have been used for - Order of hexapod - Genus of arachnid - Genus of cnidarian - Genus of lepidopteran - Genus of seaweed - Genus of bird - I think multiple instances of some of those things - Probably some other stuff so I question the utility of the .sp as a disambiguator at the scale of Arctos. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1304 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIraM8sXt5FwKohK4nyUwoajSBxRCpe4ks5tQfiIgaJpZM4P_x9M> .

-- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Associate Professor of Entomology University of Alaska Museum 1962 Yukon Drive Fairbanks, AK 99775-6960 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 <http://www.akentsoc.org/contact.php>

[atrox10]

Hi all We do use it quite often in Herps at MVZ, when we only know things to Genus and not further. These are often things collected in Indonesia or Africa or places where lots of new species are being collected and described, or no one was able to figure out which species out of many it could be. Why are we talking about getting rid of this? In Herps, we typically do not describe things down to subspecies, only to species.

…

On Mon, Feb 5, 2018 at 3:08 PM, DerekSikes ***@***.***> wrote: After more thought I'm willing to back down on wanting Arctos to retain the 'A sp.' formula. Not sure if anyone else feels strongly about it but keeping it adds complexity, leads to data inconsistency when it's sometimes forgotten to be used, and doesn't add much benefit. -Derek On Thu, Feb 1, 2018 at 8:46 AM, dustymc ***@***.***> wrote: > long standing tradition (at least in [some limited scope]) > > That is also the origins of A ssp. (and a bunch of similar things in > various niches). > > IF a bunch of things in our classification data are true/consistent, > tacking on .sp would not be particularly hard to implement (certainly > easier than .ssp, which has a couple more "ifs" involved, likely less > stability, and perhaps a narrower tradition). Maintenance - what happens > when someone changes the lowest ranked term in a classification to/from > genus? - is probably much less trivial. If the answer potentially involves > changing thousands of IDs, things like processing power may become an issue > as well. > > I'm not particularly objecting to any part of this idea; weird but > consistent data are certainly more accessible than sometimes-weird and > inconsistent data. I'm just trying to figure out what might be involved, > make sure we all understand what this might mean, point out where a > clean-slate data modeling exercise might end up, etc. > > https://arctos.database.museum/name/Diplura claims to be/have been used > for > > - Order of hexapod > - Genus of arachnid > - Genus of cnidarian > - Genus of lepidopteran > - Genus of seaweed > - Genus of bird > - I think multiple instances of some of those things > - Probably some other stuff > > so I question the utility of the .sp as a disambiguator at the scale of > Arctos. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#1304 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ AIraM8sXt5FwKohK4nyUwoajSBxRCpe4ks5tQfiIgaJpZM4P_x9M> > . > -- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Associate Professor of Entomology University of Alaska Museum 1962 Yukon Drive <https://maps.google.com/?q=1962+Yukon+Drive+%0D+Fairbanks,+AK+99775&entry=gmail&source=g> Fairbanks, AK 99775-6960 ***@***.*** phone: 907-474-6278 <(907)%20474-6278> FAX: 907-474-5469 <(907)%20474-5469> 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 <http://www.akentsoc.org/contact.php> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1304 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AESS8QcD9MNrqx3OQKd9jGMunAkBwITfks5tR4oAgaJpZM4P_x9M> .

-- Carol L. Spencer, Ph.D. Staff Curator of Herpetology & Researcher Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California, Berkeley, CA, USA 94720-3160 atrox10@gmail.com or atrox@berkeley.edu 510-643-5778 http://mvz.berkeley.edu/

[sharpphyl]

We use A sp. fairly frequently and have not had a problem with volunteers not entering some type of binomial ID. We never use A spp. We would opt to keep the A sp. formula.

[DerekSikes]

If we got rid of the A sp. formula everyone would still be able to ID records/specimens only to genus. The IDs would looks like: Genusnameus instead of Genusnameus sp. In our collection we have lots of records of both kinds so the inconsistency bugs me and it's hard to enforce since my lab techs sometimes forget to add it. We considered making it automatic, but why have the 'sp.' at all? Just ID the record to genus and leave it like that.

…

-Derek

On Mon, Feb 5, 2018 at 2:23 PM, Carol ***@***.***> wrote: Hi all We do use it quite often in Herps at MVZ, when we only know things to Genus and not further. These are often things collected in Indonesia or Africa or places where lots of new species are being collected and described, or no one was able to figure out which species out of many it could be. Why are we talking about getting rid of this? In Herps, we typically do not describe things down to subspecies, only to species. On Mon, Feb 5, 2018 at 3:08 PM, DerekSikes ***@***.***> wrote: > After more thought I'm willing to back down on wanting Arctos to retain the > 'A sp.' formula. > > Not sure if anyone else feels strongly about it but keeping it adds > complexity, leads to data inconsistency when it's sometimes forgotten to be > used, and doesn't add much benefit. > > -Derek > > On Thu, Feb 1, 2018 at 8:46 AM, dustymc ***@***.***> wrote: > > > long standing tradition (at least in [some limited scope]) > > > > That is also the origins of A ssp. (and a bunch of similar things in > > various niches). > > > > IF a bunch of things in our classification data are true/consistent, > > tacking on .sp would not be particularly hard to implement (certainly > > easier than .ssp, which has a couple more "ifs" involved, likely less > > stability, and perhaps a narrower tradition). Maintenance - what happens > > when someone changes the lowest ranked term in a classification to/from > > genus? - is probably much less trivial. If the answer potentially > involves > > changing thousands of IDs, things like processing power may become an > issue > > as well. > > > > I'm not particularly objecting to any part of this idea; weird but > > consistent data are certainly more accessible than sometimes-weird and > > inconsistent data. I'm just trying to figure out what might be involved, > > make sure we all understand what this might mean, point out where a > > clean-slate data modeling exercise might end up, etc. > > > > https://arctos.database.museum/name/Diplura claims to be/have been used > > for > > > > - Order of hexapod > > - Genus of arachnid > > - Genus of cnidarian > > - Genus of lepidopteran > > - Genus of seaweed > > - Genus of bird > > - I think multiple instances of some of those things > > - Probably some other stuff > > > > so I question the utility of the .sp as a disambiguator at the scale of > > Arctos. > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > <#1304 (comment) >, > > or mute the thread > > <https://github.com/notifications/unsubscribe-auth/ > AIraM8sXt5FwKohK4nyUwoajSBxRCpe4ks5tQfiIgaJpZM4P_x9M> > > . > > > > > > -- > > +++++++++++++++++++++++++++++++++++ > Derek S. Sikes, Curator of Insects > Associate Professor of Entomology > University of Alaska Museum > 1962 Yukon Drive <https://maps.google.com/?q=1962+Yukon+Drive&entry=gmail&source=g> > <https://maps.google.com/?q=1962+Yukon+Drive+%0D+ Fairbanks,+AK+99775&entry=gmail&source=g> > Fairbanks, AK 99775-6960 > > ***@***.*** > > phone: 907-474-6278 <(907)%20474-6278> <(907)%20474-6278> > FAX: 907-474-5469 <(907)%20474-5469> <(907)%20474-5469> > > 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 <http://www.akentsoc.org/contact.php> > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#1304 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ AESS8QcD9MNrqx3OQKd9jGMunAkBwITfks5tR4oAgaJpZM4P_x9M> > . > -- Carol L. Spencer, Ph.D. Staff Curator of Herpetology & Researcher Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California, Berkeley, CA, USA 94720-3160 ***@***.*** or ***@***.*** 510-643-5778 <(510)%20643-5778> http://mvz.berkeley.edu/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1304 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIraMyLoAtkvQXR8w7EIxqYXNy12RqIGks5tR416gaJpZM4P_x9M> .

-- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Associate Professor of Entomology University of Alaska Museum 1962 Yukon Drive Fairbanks, AK 99775-6960 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 <http://www.akentsoc.org/contact.php>

[sharpphyl]

We can certainly type in Genus sp. if there is no formula to build it, but we would never identify a specimens (mollusca and other marine invertebrates) with just the genus name.

[atrox10]

I agree with Phyllis, why can’t we keep the A.sp designation?

On Mon, Feb 5, 2018 at 3:34 PM Phyllis Sharp ***@***.***> wrote: We can certainly type in Genus sp. if there is no formula to build it, but we would never identify a specimens (mollusca and other marine invertebrates) with just the genus name. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1304 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AESS8RUOt24JFIfwdC-654pkLjXqkV6jks5tR4__gaJpZM4P_x9M> .

-- Sent from Gmail Mobile

[dustymc]

inconsistency bugs me

Me too!

The inconsistency just stops users (including curatorial users) from finding what they're looking for - we have denormalized data, 2 ways of saying the same thing.

never

http://arctos.database.museum/guid/DMNS:Inv:18559
http://arctos.database.museum/guid/DMNS:Inv:9836

Despite good intentions and careful users, if something like this CAN happen it inevitably WILL.

Attached are IDs by collection where both A sp. (CNT_ASP) and A (CNT_NOSP) taxa formulae have been used for a taxon. This isn't the whole picture, but I think it's pretty strong evidence that the inconsistency is widespread.

temp_asp.csv.zip

[sharpphyl]

Yep. The specimen without sp. came in during our initial upload when we knew nothing about how Arctos worked. Will correct it and any others I can find. Hints are welcome.

…

On Mon, Feb 5, 2018 at 6:54 PM, dustymc ***@***.***> wrote: inconsistency bugs me Me too! The inconsistency just stops users (including curatorial users) from finding what they're looking for - we have denormalized data, 2 ways of saying the same thing. never http://arctos.database.museum/guid/DMNS:Inv:18559 http://arctos.database.museum/guid/DMNS:Inv:9836 Despite good intentions and careful users, if something like this CAN happen it inevitably WILL. Attached are IDs by collection where both A sp. (CNT_ASP) and A (CNT_NOSP) taxa formulae have been used for a taxon. This isn't the whole picture, but I think it's pretty strong evidence that the inconsistency is widespread. temp_asp.csv.zip <https://github.com/ArctosDB/arctos/files/1697434/temp_asp.csv.zip> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1304 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AOqArb_BrxXYe5Cx6iBYijTP9Ixizn3uks5tR7DDgaJpZM4P_x9M> .

[sharpphyl]

OK, I found the attached file. I'm fine with Arctos automatically adding sp. to any stand-alone genus. But I don't get why you're suggesting that we eliminate the A sp. formula? What am I missing?

…

On Mon, Feb 5, 2018 at 7:10 PM, Phyllis Sharp ***@***.***> wrote: Yep. The specimen without sp. came in during our initial upload when we knew nothing about how Arctos worked. Will correct it and any others I can find. Hints are welcome. On Mon, Feb 5, 2018 at 6:54 PM, dustymc ***@***.***> wrote: > inconsistency bugs me > > Me too! > > The inconsistency just stops users (including curatorial users) from > finding what they're looking for - we have denormalized data, 2 ways of > saying the same thing. > > never > > http://arctos.database.museum/guid/DMNS:Inv:18559 > http://arctos.database.museum/guid/DMNS:Inv:9836 > > Despite good intentions and careful users, if something like this CAN > happen it inevitably WILL. > > Attached are IDs by collection where both A sp. (CNT_ASP) and A > (CNT_NOSP) taxa formulae have been used for a taxon. This isn't the whole > picture, but I think it's pretty strong evidence that the inconsistency is > widespread. > > temp_asp.csv.zip > <https://github.com/ArctosDB/arctos/files/1697434/temp_asp.csv.zip> > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#1304 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AOqArb_BrxXYe5Cx6iBYijTP9Ixizn3uks5tR7DDgaJpZM4P_x9M> > . >

[campmlc]

My understanding is that the problem lies in taxonomy - Arctos cannot readily distinguish between a stand-alone genus and the same taxon term used for other organisms in a different hierarchy, as in the example below, so it would be difficult to add the sp. automatically. Is this correct, Dusty? Couldn't there be a trigger to add it only to generic level temrs if a name lacks the binomial at the species level? I can see that it is useful in the sense that it indicates the specimen has been examined and that is all the identifying agent currently knows, rather than oops, it did not get entered properly. https://arctos.database.museum/name/Diplura claims to be/have been used for - Order of hexapod - Genus of arachnid - Genus of cnidarian - Genus of lepidopteran - Genus of seaweed - Genus of bird On Mon, Feb 5, 2018 at 7:19 PM, Phyllis Sharp <notifications@github.com> wrote:

…

OK, I found the attached file. I'm fine with Arctos automatically adding sp. to any stand-alone genus. But I don't get why you're suggesting that we eliminate the A sp. formula? What am I missing? On Mon, Feb 5, 2018 at 7:10 PM, Phyllis Sharp ***@***.***> wrote: > Yep. The specimen without sp. came in during our initial upload when we > knew nothing about how Arctos worked. Will correct it and any others I can > find. Hints are welcome. > > On Mon, Feb 5, 2018 at 6:54 PM, dustymc ***@***.***> wrote: > >> inconsistency bugs me >> >> Me too! >> >> The inconsistency just stops users (including curatorial users) from >> finding what they're looking for - we have denormalized data, 2 ways of >> saying the same thing. >> >> never >> >> http://arctos.database.museum/guid/DMNS:Inv:18559 >> http://arctos.database.museum/guid/DMNS:Inv:9836 >> >> Despite good intentions and careful users, if something like this CAN >> happen it inevitably WILL. >> >> Attached are IDs by collection where both A sp. (CNT_ASP) and A >> (CNT_NOSP) taxa formulae have been used for a taxon. This isn't the whole >> picture, but I think it's pretty strong evidence that the inconsistency is >> widespread. >> >> temp_asp.csv.zip >> <https://github.com/ArctosDB/arctos/files/1697434/temp_asp.csv.zip> >> >> — >> You are receiving this because you commented. >> Reply to this email directly, view it on GitHub >> <#1304 (comment) >, >> or mute the thread >> <https://github.com/notifications/unsubscribe-auth/AOqArb_ BrxXYe5Cx6iBYijTP9Ixizn3uks5tR7DDgaJpZM4P_x9M> >> . >> > > — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1304 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AOH0hFOi5u3ieUznq3T_ka7Gn_-7e7rKks5tR7avgaJpZM4P_x9M> .

[dustymc]

Arctos cannot readily distinguish between a stand-alone genus and the same taxon term used for other organisms in a different hierarchy

#1304 (comment)

That's not the problem. I'm concerned about what happens when someone finds a clever way to add/remove genus for a monomial used in (perhaps thousands of) identifications. Do we really want scripts changing identifications, or to lock classifications because of identifications, or WHATEVER it is that we'd need to do to enforce this?

indicates the specimen has been examined

"Genus sp." and "Genus" provide the same information. One adds some unnecessary complexity, and perhaps makes it slightly more difficult to find those specimens which have multinomial determinations (vs. those that look like multinomials because we've tacked on a "traditional" string). Together they provide two ways of doing about the same thing, we act inconsistently because we can, and that makes it a bit harder to find what you're looking for and messes with "number of species..." data and etc.

There are three possibilities:

1. Do nothing, keep the "A sp." formula, use it arbitrarily.
2. Add a bunch of complexity for reasons that make no sense to me, but which does make things more consistent.
3. Drop some complexity in procedures, forms, and data, and make everything more accessible by doing so.

[Jegelewicz]

AWG says enforce A sp. for species name.

[campmlc]

OK to go with mandatory sp. per AWG 4-12-18

[dustymc]

AWG 20180421:

• force .sp
• .ssp is a different discussion

[dustymc]

generate report

• flip genus-only IDs to .sp
• OR flip "A" formula genus-only IDs to A {string} and keep the namestring

[dustymc]

I'm just ignoring .ssp because nobody's asked for any impossible things with it yet!

I don't think most users will infer effort (or whatever's being attempted) from the format of the identification string.

Being forced into complicated situations - having to search for multiple things or use substring searches to find all of what you're looking for - does not seem like something a user would ever want to encounter.

[mbprondzinski]

Why can't Arctos ask, "Is this a genus" for a single entry and if you check affirmative, then it can add the "sp".

[DerekSikes]

Mary Beth, I know it's a long thread... so here's your answer but there are others in the thread: There are problems with enforcing this idea of ensuring all genus-only IDs have 'sp.' added. 1) some taxon names lack rank & thus Arctos won't know it's a genus 2) how would this work? would one choose ID formula A and then during the 'create new id' save process Arctos would check if the name is a genus & automatically add a 'sp.' to the end? What about bulkloading names? 3) we'd still need to clean up all the already existing genus-only identifications by adding 'sp.' to those without 4) GBIF and other aggregators strip the 'sp.' off at their end anyhow. For those who like having 'sp.' after genus-only identifications they could still apply this using the A {string} although this would take a little more typing & greater chance for errors being saved (eg 'sp' or 'spp' or 'ssp' instead of the intended 'sp.') and finally... remember that these two identifications have the same meaning; Genusname sp. Genusname Adding the 'sp.' adds no extra information, adds complexity, can't be enforced, creates inconsistency, etc.

…

-Derek

On Wed, Nov 6, 2019 at 5:43 AM Mary Beth ***@***.***> wrote: Why can't Arctos ask, "Is this a genus" and if you check affirmative, then it can add the "sp". — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1304?email_source=notifications&email_token=ACFNUMYNV3P2AYUNVX6MGITQSLJXPA5CNFSM4D77D5GKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDGYOBY#issuecomment-550340359>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFNUM5YIS47M2GKU5SXTBTQSLJXPANCNFSM4D77D5GA> .

-- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Professor of Entomology University of Alaska Museum 1962 Yukon Drive Fairbanks, AK 99775-6960 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

[mbprondzinski]

Hi Derek, Actually, I have no preferences one way or the other…I have my own issues with Arctos! But, I don’t see why Arctos can’t ask if the single taxon entry is a “Genus” to determine the taxonomy, when it can certainly red-line everything that is “wrong” …by ITS definition… on entry. I’m finding that out on every record that I try to enter individually. I am getting quite good at discerning the “Arctos language” the longer I spend trying to enter one friggin’ record over and over and over again ☺ You’re right: spending the time reading these issues is another job in itself. I got tired towards the end and just chimed in my two-cents worth. Thanks for the response! Mary Beth From: DerekSikes <notifications@github.com> Sent: Wednesday, November 6, 2019 11:07 AM To: ArctosDB/arctos <arctos@noreply.github.com> Cc: Prondzinski, Mary Beth <mbprondzinski@ua.edu>; Comment <comment@noreply.github.com> Subject: Re: [ArctosDB/arctos] ID formula A sp. (#1304) Mary Beth, I know it's a long thread... so here's your answer but there are others in the thread: There are problems with enforcing this idea of ensuring all genus-only IDs have 'sp.' added. 1) some taxon names lack rank & thus Arctos won't know it's a genus 2) how would this work? would one choose ID formula A and then during the 'create new id' save process Arctos would check if the name is a genus & automatically add a 'sp.' to the end? What about bulkloading names? 3) we'd still need to clean up all the already existing genus-only identifications by adding 'sp.' to those without 4) GBIF and other aggregators strip the 'sp.' off at their end anyhow. For those who like having 'sp.' after genus-only identifications they could still apply this using the A {string} although this would take a little more typing & greater chance for errors being saved (eg 'sp' or 'spp' or 'ssp' instead of the intended 'sp.') and finally... remember that these two identifications have the same meaning; Genusname sp. Genusname Adding the 'sp.' adds no extra information, adds complexity, can't be enforced, creates inconsistency, etc.

…

-Derek

On Wed, Nov 6, 2019 at 5:43 AM Mary Beth ***@***.******@***.***>> wrote: Why can't Arctos ask, "Is this a genus" and if you check affirmative, then it can add the "sp". — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1304?email_source=notifications&email_token=ACFNUMYNV3P2AYUNVX6MGITQSLJXPA5CNFSM4D77D5GKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDGYOBY#issuecomment-550340359>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFNUM5YIS47M2GKU5SXTBTQSLJXPANCNFSM4D77D5GA> .

-- +++++++++++++++++++++++++++++++++++ Derek S. Sikes, Curator of Insects Professor of Entomology University of Alaska Museum 1962 Yukon Drive Fairbanks, AK 99775-6960 dssikes@alaska.edu<mailto: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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#1304?email_source=notifications&email_token=AKJWLEEWTDIH3ITWBWJIHRLQSL2RTA5CNFSM4D77D5GKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDHIRZA#issuecomment-550406372>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKJWLEEXXZS2KFYBKE5YBGDQSL2RTANCNFSM4D77D5GA>.

[Jegelewicz]

Issue Summary:

It is proposed that we remove the taxon formula "A sp." from the Taxa Formula Code Table. At the same time, any identification using this formula will have the " sp." removed. Any collection wishing to retain " sp." will need to notify Dusty prior to the change. Their identifications will be converted to the "A string" formula and will be formatted as Genus {Genus sp.}.

If approved, an announcement will be made to the Community and collections will be given a date by which to decide.

Derek has written a fairly nice summary of the long discussion above that led to this conclusion:

There are problems with enforcing this idea of ensuring all genus-only IDs have 'sp.' added.

1. some taxon names lack rank & thus Arctos won't know it's a genus
2. how would this work? would one choose ID formula A and then during the 'create new id' save process Arctos would check if the name is a genus & automatically add a 'sp.' to the end? What about bulkloading names?
3. we'd still need to clean up all the already existing genus-only identifications by adding 'sp.' to those without
4. GBIF and other aggregators strip the 'sp.' off at their end anyhow.

For those who like having 'sp.' after genus-only identifications they could still apply this using the A {string} although this would take a little more typing & greater chance for errors being saved (eg 'sp' or 'spp' or 'ssp' instead of the intended 'sp.')

and finally... remember that these two identifications have the same meaning;

Genusname sp.

Genusname

Adding the 'sp.' adds no extra information, adds complexity, can't be enforced, creates inconsistency, etc.

[ccicero]

So where are we on the 'ssp' part of the discussion. We use that all the time for taxa that we're unable to ID to subspecies, which is important for birds. I don't think using the string for that is a good idea. Are we keeping ssp in the formula?

[Jegelewicz]

@ccicero let's save that for another day and focus on this one thing for now.

[ccicero]

Fine with me. I just wanted to make sure that you also weren't getting rid of the ssp option. Thanks!

[campmlc]

AWG Recommend that we announce the decision to remove sp. via email to all Arctos.

[campmlc]

@ewommack

[ewommack]

Added an issue in the Newsletter repository for the article.

[ewommack]

I've put this down for a newsletter article, but the thread says a general email. I think an article sounds more appropriate, but I wanted to double check.

[campmlc]

Newsletter sounds good!

…

On Mon, Aug 24, 2020 at 11:49 AM Elizabeth Wommack ***@***.***> wrote: * [EXTERNAL]* I've put this down for a newsletter article, but the thread says a general email. I think an article sounds more appropriate, but I wanted to double check. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1304 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADQ7JBDIS4IDBA3XNY4XLLDSCKRZNANCNFSM4D77D5GA> .

[Jegelewicz]

This was published in the last newsletter - can we implement?

[dustymc]

I'm ready when you are - is that an official "go"?

Unless I hear otherwise before the official"go" I will

• change formula from A sp. to A
• remove trailing .sp from relevant identification.scientific_name

[ewommack]

In the newsletter we gave people until the 30 Nov to get issues to @dustymc through GitHub Issues...so maybe implement on 1 Dec?

[Jegelewicz]

Schedule for December 1 unless someone decides to comment. Thanks @ewommack for keeping me in line!

[acdoll]

This doesn't appear to have been implemented yet. @dustymc? I don't believe we heard any objections after the newsletter went out. @ewommack - did you receive any feedback?

[dustymc]

Thanks @acdoll

Done, backup at temp_cache.identification20201231

[ewommack]

Nope nothing came through the communication channels, and the article directed people submit to the issue. I think we're good.