Arctos: 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 [e-mail] 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.

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

[email protected]

phone: [phone]
FAX: [phone]

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]

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 [e-mail] 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 [e-mail] 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.

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

[email protected]

phone: [phone] <(907)%20474-6278>
FAX: [phone] <(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
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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Associate Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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
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[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 [e-mail] 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.

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

[email protected]

phone: [phone]
FAX: [phone]

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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[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 [e-mail] 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 [e-mail] 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.

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+++++++++++++++++++++++++++++++++++
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

[email protected]

phone: [phone] <(907)%20474-6278>
FAX: [phone] <(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

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Staff Curator of Herpetology & Researcher
Museum of Vertebrate Zoology
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University of California, Berkeley, CA, USA 94720-3160
[email protected] or [email protected]
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 [e-mail] 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 [e-mail]
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 [e-mail]
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.

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--

+++++++++++++++++++++++++++++++++++
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
Fairbanks,+AK+99775&entry=gmail&source=g>
Fairbanks, AK 99775-6960

[email protected]

phone: [phone] <(907)%20474-6278> <(907)%20474-6278>
FAX: [phone] <(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
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--
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
[email protected] or [email protected]
510-643-5778 <(510)%20643-5778>
http://mvz.berkeley.edu/

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

[email protected]

phone: [phone]
FAX: [phone]

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
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[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 [e-mail]
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.

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[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 [e-mail] 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

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[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 [e-mail] 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 [e-mail] 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

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[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 [e-mail]
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 [e-mail] 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 [e-mail]
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

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[dustymc]

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

https://github.com/ArctosDB/arctos/issues/1304#issuecomment-362346522

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

[Jegelewicz]

@dustymc status?

[Jegelewicz]

Can we get it done, or is there areason we are putting it off?

[ccicero]

Please do not get rid of ssp - we use that all the time. We identify bird specimens to subspecies if we can. If a species is polytypic and we can't determine the ssp, then we will use the formula A ssp. Beth confirms that she does the same for UWYMV.

Let's discuss this issue again at the next AWG - I'm not totally clear on all of the issues in this long thread. Thanks.

[dustymc]

I'm still not clear on how this could be accomplished.

If the goal is truly consistent data, then this will disable most current ways to editing taxonomy - eg, if we require identifications to genus-level terms to use certain formula then we can't change the rank of those genus-level terms without changing IDs. Most of the current tools generally work by replacing classifications, which triggers would necessarily see as changes. If we are going to introduce that level of complexity we should do it for subpsecies as well, which I think effectively blocks creating a subspecific name for a species which has been used in identifications. (The sp. rule would block creating the first species for a genus that has none as well, but there are in theory no bare genera while there are lots of species with yet-undescribed subspecies so that somehow seems more tractable.)

I REALLY don't know how this would work under https://github.com/ArctosDB/arctos/issues/1852, where the ideas that "this term is a genus" and "this term is some other rank" and "this term isn't ranked" are all very different THINGS which could all be used for specific individuals in the same collection.

I suppose I could get around all of that by just changing effected identifications with taxonomy changes, but that seems incredibly dangerous and I doubt we have the processors to support it anyway.

If this is just something that runs at eg, record creation then it can't create truly consistent data.

Am I not understanding something fundamental in what ya'll are asking for?

[dustymc]

Two more reasons to hate this popped up today.

1) For @ccicero https://arctos.database.museum/guid/MVZ:Bird:191858 uses a complex ID with one of the taxa to genus. It's possible to get "Strix varia varia and Peromyscus sp." via the A {string} formula, but that leaves you having to (mis)spell all that and users trying to find it. Feeding the pick "Peromyscus sp." causes weirdness as well - "Peromyscus" always works, everywhere.

2) From the "unshare with iDigBio?" email with @DerekSikes and @tucotuco

the recommended way to publish a record such as the 'sp. nov. a' one is to not include the the 'sp. nov. a' in the scientific name, because it isn't one. The scientificName would be the genus, and the 'sp. nov. a' would be in identificationQualifier.

which I think means we should unroll other formulae it for DWC - that looks like more work, more processors, and mismatched data to me.

[DerekSikes]

just to add my 2 cents re: iDigBio - they're screwing around with
identifications in lots of ways. Basically it seems like any time they
don't get a perfect genus + species match they make shit up. I had
specimens identified only as Acari (=a higher taxon (order/class) of mites)
and they decided to add family and genus names to the record.

Whatever issues are caused by the A + string formula... getting rid of it
won't stop/mitigate/reduce iDigBio's insanity.

I think I recall them needing ranks to come with the names... which makes
sense. If they don't know if the name on a record is a genus or a class
they've got a lot more chances to get things wrong.

Are we sending ranks with our names?

-Derek

On Mon, May 13, 2019 at 7:40 PM dustymc [e-mail] wrote:

Two more reasons to hate this popped up today.

1.

For @ccicero https://github.com/ccicero
https://arctos.database.museum/guid/MVZ:Bird:191858 uses a complex ID
with one of the taxa to genus. It's possible to get "Strix varia varia and
Peromyscus sp." via the A {string} formula, but that leaves you having to
(mis)spell all that and users trying to find it. Feeding the pick
"Peromyscus sp." causes weirdness as well - "Peromyscus" always works,
everywhere.
2.

From the "unshare with iDigBio?" email with @DerekSikes
https://github.com/DerekSikes and @tucotuco
https://github.com/tucotuco

the recommended way to publish a record such as the 'sp. nov. a' one is to
not include the the 'sp. nov. a' in the scientific name, because it isn't
one. The scientificName would be the genus, and the 'sp. nov. a' would be
in identificationQualifier.

which I think means we should unroll other formulae it for DWC - that
looks like more work, more processors, and mismatched data to me.

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University of Alaska Museum
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[email protected]

phone: [phone]
FAX: [phone]

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[dustymc]

No, "clean" names likely won't fix iDigBio, but that does seem to be what the Standard calls for.

We do send taxonRank (in addition to ranked terms) when possible - https://github.com/ArctosDB/arctos/issues/1338.

[Jegelewicz]

The scientificName would be the genus, and the 'sp. nov. a' would be in identificationQualifier.

identificationQualifier - perhaps we need this field in Arctos? For biological names at least, the identification is limited to a name from the names table and anything else "sp.", "sp. nov.", etc. goes in the qualifier.

[dustymc]

Arctos is not that simple.

https://arctos.database.museum/guid/MVZ:Bird:191858 uses two names.

"Working names" are not particularly formulaic.

Etc.

For "simple" complex IDs, it should be easy enough to derive the "qualifier" from the formula (http://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXA_FORMULA). I'm not sure what we might do for "A {string}" IDs, but they are all (ish...) linked to at least one taxon, even if it's occasionally http://arctos.database.museum/name/unidentifiable. Perhaps the identification is the "qualifier" for those?? @tucotuco suggestions??

[Jegelewicz]

https://arctos.database.museum/guid/MVZ:Bird:191858 uses two names.

Yeah, but they are still two names that could be resolved appropriately, correct? Right now, it appears that only one of the two is showing up, probably because of what iDigBio does to "clean" the data. I think we should address this kind of issue separately with them. Never mind that the Peromyscus here should get a new catalog number and a relationship.....

For "simple" complex IDs, it should be easy enough to derive the "qualifier" from the formula (http://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXA_FORMULA).

Perfect! Can we make it so for the next publication to VertNet?

I'm not sure what we might do for "A {string}" IDs, but they are all (ish...) linked to at least one taxon, even if it's occasionally http://arctos.database.museum/name/unidentifiable. Perhaps the identification is the "qualifier" for those?

I think that makes sense. The linked taxon(taxa) is/are the identification and the "identification" is the qualifier. So for http://arctos.database.museum/guid/UAM:EH:UA67-133-0001

identification = Rangifer tarandus, Canis lupus, Gulo gulo (not sure how iDigBio would handle that one, but we can deal with that later....if their stuff is even published to iDigBio)

IdentificationQualifier = Parka, Fur

[tucotuco]

Sorry for the late reply. Been a little distracted since 5 June when the
ectoparasite turned endo. ;-)

The issue is Darwin Core's model that expects separate records for separate
taxa. The train of reasoning is:
1) The data sets consist of Occurrence records
2) Occurrences are "An existence of an Organism (sensu
http://rs.tdwg.org/dwc/terms/Organism) at a particular place at a
particular time."
3) Organisms are "A particular organism or defined group of organisms
considered to be taxonomically homogeneous."

3 is the kicker. But that is just for the bird mouse example. Hybrids are
a different story. Problem is, hybrids are identified by multiple
scientific names, and Darwin Core's taxon fields only accommodate one
taxon. The only thing we're left with, if we want to be true to the Darwin
Core definitions, is to put the hybrid formula in previousIdentifications
and/or identificationRemarks, given that it is the result of an
Identification process, the most specific taxon in common among those in
the hybrid formula could go in the taxon fields. The
identificationQualifier doesn't cover hybrid formulas, as those aren't
about doubt. This isn't very satisfying, but it preserves the semantics of
the Darwin Core fields.

On Tue, May 14, 2019 at 3:13 PM Teresa Mayfield-Meyer <
[email protected]> wrote:

https://arctos.database.museum/guid/MVZ:Bird:191858 uses two names.

Yeah, but they are still two names that could be resolved appropriately,
correct? Right now, it appears that only one of the two is showing up,
probably because of what iDigBio does to "clean" the data. I think we
should address this kind of issue separately with them. Never mind that the
Peromyscus here should get a new catalog number and a relationship.....

For "simple" complex IDs, it should be easy enough to derive the
"qualifier" from the formula (
http://arctos.database.museum/info/ctDocumentation.cfm?table=CTTAXA_FORMULA
).

Perfect! Can we make it so for the next publication to VertNet?

I'm not sure what we might do for "A {string}" IDs, but they are all
(ish...) linked to at least one taxon, even if it's occasionally
http://arctos.database.museum/name/unidentifiable. Perhaps the
identification is the "qualifier" for those?

I think that makes sense. The linked taxon(taxa) is/are the identification
and the "identification" is the qualifier. So for
http://arctos.database.museum/guid/UAM:EH:UA67-133-0001

identification = Rangifer tarandus, Canis lupus, Gulo gulo (not sure how
iDigBio would handle that one, but we can deal with that later....if their
stuff is even published to iDigBio)

IdentificationQualifier = Parka, Fur

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[dustymc]

The linked taxon(taxa) is/are the identification

No, the identification - what the collection called it - is "Parka, Fur." Once we get a little deeper into Getty-or-something that might even be a real taxon.

Even then, it will maintain a loose relationships to some other (Linnean in this case) taxa. Those have little to do with the identification, think of them as "search aids."

[Jegelewicz]

Revisiting - AWG had authorized enforcement of sp. for Genus only identifications - this seems like a bad idea. Perhaps it would be better to create a low quality data report that coll managers could run to find inconsistencies? With some sort of easy way to change all without sp. to include it or the other way around if that is what is desired? Possible?

[sharpphyl]

BTW, is anyone else having a problem with building a taxon with sp. such as "Conus sp."? We had no problem until a few months ago when we started to get the errors below and had to put in just the genus and then add the sp. (or other qualifier) in the bulkloader.

If I select "build" and then select A sp. I get this error message.

After I say OK, the sp. shows up in the taxon name field but if I select a genus to go with it I get this.

I can create taxon names with cf., aff. etc. but not sp.

[dustymc]

had to put in just the genus and then add the sp. (or other qualifier) in the bulkloader.

The search is for names - there are no "... sp." names.

"build" and then select A sp.

I added it.

The bulkloader (including this form) works with strings - the 'pick' is more of a 'suggestor' and you can just type anything.

[sharpphyl]

I added it.

Looks like that fixed it. Thanks.

[Jegelewicz]

Perhaps it would be better to create a low quality data report that coll managers could run to find inconsistencies? With some sort of easy way to change all without sp. to include it or the other way around if that is what is desired? Possible?

Discuss in October - need @DerekSikes in on it!

[Jegelewicz]

Can we disallow the use of A sp. for a collection? @DerekSikes prefers this solution.

[Jegelewicz]

Or we could add sp. to any name that has a rank of genus? (Anyone who wants to could still use A string to get the same result.)

[Jegelewicz]

Bring to AWG

[DerekSikes]

I vote for removal of A sp. as an option & letting collections that want to
keep using 'sp.' after a genus name to use the A {string} formula to do so.

I also want some way to clean up the inconsistencies in my data (some
genus-only IDs with 'sp.' and some without) without creating new
identifications.

-Derek

On Wed, Oct 16, 2019 at 12:52 PM Teresa Mayfield-Meyer <
[email protected]> wrote:

Bring to AWG

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University of Alaska Museum
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[email protected]

phone: [phone]
FAX: [phone]

University of Alaska Museum - search 400,276 digitized arthropod records
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[dustymc]

disallow the use of A sp. for a collection

Seems technically plausible, but doesn't fix purposeful inconsistencies and likely isn't trivial to implement. Can we just disallow the use of A sp.? A {string} is a functionally-equivalent replacement - they're both strings that are not (necessarily) exact copies of the referenced name.

add sp. to any name

That is not compatible with the data.

[Jegelewicz]

Can we just disallow the use of A sp.? A {string} is a functionally-equivalent replacement - they're both strings that are not (necessarily) exact copies of the referenced name.

We could be happy with this.

[ccicero]

I'm ok with this as long as the documentation is updated so users know that's how to enter IDs where only the genus is known and they want to specify 'sp'. Same could be done for 'A ssp.' What about 'A aff' or 'A cf' ? If we're going to make this change for A sp., then we should do the same for the others.

Can we add a 'hint' to the form, e.g., "Use the A {string} option to add 'sp' or 'ssp' or 'aff' or 'cf' or any other non-nomenclatural modifier to the identification."

[dustymc]

functionally-equivalent

I take that halfway back. Once the data are created, all not-quite-taxon-name IDs are functionally equivalent. For the purposes of creating IDs, they aren't. If we drop that formula we'll end up with Bla cf. bla and Bla bla cf. and cf. Bla bla. Those are all arguably different things so that may be more correct, but they're also not predictable-->not discoverable as strings. Give 100 people the opportunity to enter "Palaeospiroplectammina tchernyshinensis subsp. rectoseptata ssp." (if anyone was wondering what the longest name in Arctos is, there you go!) from their keyboard and you'll probably get about 90 variations. Etc. I'm not sure how to weight any of that, but possibly worth considering.

[DerekSikes]

This is a good reason to take this slowly - how about we back off to just
consideration of removal of the 'A sp.' formula and keep the others intact.

-Derek

On Wed, Oct 16, 2019 at 3:20 PM dustymc [e-mail] wrote:

functionally-equivalent

I take that halfway back. Once the data are created, all
not-quite-taxon-name IDs are functionally equivalent. For the purposes of
creating IDs, they aren't. If we drop that formula we'll end up with Bla
cf. bla and Bla bla cf. and cf. Bla bla. Those are all arguably different
things so that may be more correct, but they're also not predictable-->not
discoverable as strings. Give 100 people the opportunity to enter
"Palaeospiroplectammina tchernyshinensis subsp. rectoseptata ssp." (if
anyone was wondering what the longest name in Arctos is, there you go!)
from their keyboard and you'll probably get about 90 variations. Etc. I'm
not sure how to weight any of that, but possibly worth considering.

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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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[ccicero]

This is a long thread. What is the main reason to get rid of 'A sp.' ?

[DerekSikes]

Because techs can't be consistent and sometimes enter a genus only ID as
formula A and sometimes as formula A sp.

This leads to 2 separate identifications that have the same meaning and
screw up any summary of the data that hopes to list a minimal number of
unique identifications.

I want all my data to be consistent. I'd rather enforce formula A sp. (so
that no genus-only IDs can be made without the 'sp.') but that seems too
difficult so for the sake of consistency and simplicity having all
genus-only IDs be formula A is my preference.

-Derek

On Wed, Oct 16, 2019 at 4:08 PM Carla Cicero [e-mail]
wrote:

This is a long thread. What is the main reason to get rid of 'A sp.' ?

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Professor of Entomology
University of Alaska Museum
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Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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[campmlc]

What about Teresa's suggestion? This seems preferable as means of enforcing
consistency:

Or we could add sp. to any name that has a rank of genus?

On Wed, Oct 16, 2019 at 6:14 PM DerekSikes [e-mail] wrote:

Because techs can't be consistent and sometimes enter a genus only ID as
formula A and sometimes as formula A sp.

This leads to 2 separate identifications that have the same meaning and
screw up any summary of the data that hopes to list a minimal number of
unique identifications.

I want all my data to be consistent. I'd rather enforce formula A sp. (so
that no genus-only IDs can be made without the 'sp.') but that seems too
difficult so for the sake of consistency and simplicity having all
genus-only IDs be formula A is my preference.

-Derek

On Wed, Oct 16, 2019 at 4:08 PM Carla Cicero [e-mail]
wrote:

This is a long thread. What is the main reason to get rid of 'A sp.' ?

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[email protected]

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[DerekSikes]

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.')

-D

On Wed, Oct 16, 2019 at 6:13 PM Mariel Campbell [e-mail]
wrote:

What about Teresa's suggestion? This seems preferable as means of enforcing
consistency:

Or we could add sp. to any name that has a rank of genus?

On Wed, Oct 16, 2019 at 6:14 PM DerekSikes [e-mail]
wrote:

Because techs can't be consistent and sometimes enter a genus only ID as
formula A and sometimes as formula A sp.

This leads to 2 separate identifications that have the same meaning and
screw up any summary of the data that hopes to list a minimal number of
unique identifications.

I want all my data to be consistent. I'd rather enforce formula A sp. (so
that no genus-only IDs can be made without the 'sp.') but that seems too
difficult so for the sake of consistency and simplicity having all
genus-only IDs be formula A is my preference.

-Derek

On Wed, Oct 16, 2019 at 4:08 PM Carla Cicero [e-mail]
wrote:

This is a long thread. What is the main reason to get rid of 'A sp.' ?

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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

University of Alaska Museum - search 400,276 digitized arthropod records
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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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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[campmlc]

Sounds like getting rid of it makes sense, but only if we make sure that go
through existing names to make sure all names have an assigned taxon rank.
Otherwise we end up with a whole lot more beetles when iDigBio turns our
Aves into Avus. Also, we need good documentation and perhaps interface
prompts to let people know to use A {string}.

On Wed, Oct 16, 2019 at 8:22 PM DerekSikes [e-mail] wrote:

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.')

-D

On Wed, Oct 16, 2019 at 6:13 PM Mariel Campbell [e-mail]
wrote:

What about Teresa's suggestion? This seems preferable as means of
enforcing
consistency:

Or we could add sp. to any name that has a rank of genus?

On Wed, Oct 16, 2019 at 6:14 PM DerekSikes [e-mail]
wrote:

Because techs can't be consistent and sometimes enter a genus only ID
as
formula A and sometimes as formula A sp.

This leads to 2 separate identifications that have the same meaning and
screw up any summary of the data that hopes to list a minimal number of
unique identifications.

I want all my data to be consistent. I'd rather enforce formula A sp.
(so
that no genus-only IDs can be made without the 'sp.') but that seems
too
difficult so for the sake of consistency and simplicity having all
genus-only IDs be formula A is my preference.

-Derek

On Wed, Oct 16, 2019 at 4:08 PM Carla Cicero <[email protected]

wrote:

This is a long thread. What is the main reason to get rid of 'A sp.'
?

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

[email protected]

phone: [phone]
FAX: [phone]

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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Professor of Entomology
University of Alaska Museum
1962 Yukon Drive
Fairbanks, AK 99775-6960

[email protected]

phone: [phone]
FAX: [phone]

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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[dustymc]

Yep what Derek said, plus whatever impossibility would have to happen to allow you to edit (or block you from editing, or something) names that are genus and used in IDs. (Imagine: "Arctos has magically changed the thing where you allegedly record what the collector wrote because someone made an arbitrary and possibly controversial change regarding the categorization of a name!" notifications.)

The last sentence in https://github.com/ArctosDB/arctos/issues/1304#issuecomment-542899224 is a few links to names that are sometimes used as genus. There are at least a few thousand of them in Arctos, and who knows how many more that we'll eventually accumulate.

It's easy to find records without taxon rank, but I'm not sure that was ever the problem at iDigBio.

[Jegelewicz]

GBIF and other aggregators strip the 'sp.' off at their end anyhow.

I think this is one of the better arguments for getting rid of A sp. along with:

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.

[...]

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. - @DerekSikes

Traditions are nice, but sometimes they get in the way of progress. A sp. was necessary when you couldn't decide if a monomial was a family or a species, but we shouldn't NEED that in the world of biodiversity data. The associated rank in DWC does this for us and I think we should stop trying to make it hard on ourselves and let that system work. Of course, that means that we each need to make sure our names have associated classifications... see #1761

If A sp. was really that important - wouldn't all of our Genus names really be species names, with the specific epithet being "sp."?

And finally, see also #2172

[ccicero]

we need good documentation and perhaps interface prompts to let people know to use A {string}.

I'm ok with stripping off the 'sp.' but re-iterate what Mariel said above.

It seems like the same issue with ssp. but maybe that's just not used as much and inconsistency is less of a concern there? However, I wouldn't want to strip off the 'ssp.' because that means (to me) that we tried identifying to subspecies but couldn't. So are we ok with just having A for genus but A ssp. for polytypic genus+species where subspecies is not identified?

[Jegelewicz]

I wouldn't want to strip off the 'ssp.' because that means (to me) that we tried identifying to subspecies but couldn't.

What does it mean to everyone else? Perhaps a better way of saying this is by using the identification remark - "not able to identify to subspecies" or use the new confidence level thingee or an attribute, like "examined for ectoparasites", but "attempted to ID to subspecies".

Any way you cut this, it still seems to me that anything identified to species just wasn't identified down to subspecies. If there is a reason for that and no one else should make the attempt, then that should be spelled out instead of using ssp. which seems a pretty cryptic way of saying "we tried to ID this to subspecies, but couldn't".

[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 [e-mail] wrote:

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

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

[email protected]

phone: [phone]
FAX: [phone]

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
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[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 [e-mail]
Sent: Wednesday, November 6, 2019 11:07 AM
To: ArctosDB/arctos [e-mail]
Cc: Prondzinski, Mary Beth [e-mail]; Comment [e-mail]
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 <[email protected][e-mail]> wrote:

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

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

[email protected][e-mail]

phone: [phone]
FAX: [phone]

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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[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 [e-mail]
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.

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[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.