RE: [AntCat] NEW FEATURE: Verbatim type location

[Philip Ward]

Hi Mark,

Do you mean "verbatim type locality", i.e., the geographical place(s) where the type specimens are
reported from in the original description? I think "type locality" is a better understood phrase--
unless I am misunderstanding and you mean the location (i.e., museum collection) where the type
specimen(s) is/are stored.

Cheers, Phil



> There is now a field for "verbatim type location" in AntCat for
> species-group taxa. The contents of the field are displayed on the taxon's
>
> catalog page. Let me know if you see other places where it should also be
> displayed.
>
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Philip S. Ward
Department of Entomology
University of California
Davis, CA 95616

[Mark Wilden]

Yes, you're right, Phil. It is indeed "verbatim type locality" everywhere in AntCat - except this announcement.

[Michael Branstetter]

Apologies if this has been discussed already, but what information should be entered into the "verbatim type locality" field when adding new species (this is not described in the directions yet)? Should it be the entire type string? Just the collection information? Or Just the locality information? 

For example, in the recent publication by Ortiz & Fernández (2014), the following is the entire type string for the species Brachymyrmex delabiei: 

Holotype worker (MZSP) [USNM ENT 00757718] and Paratypes 3 workers (CPDC [USNM ENT 00757719], ICN [USNM ENT 00757720], USNM [USNMENT 00757721]): Brazil, São Paulo, Tapiraí, 24°01'55.5"S 47°27'56"W, 08–14 Jan 2001, col. R.R. Silva & Eberhardt, Transecto 1 Winkler 23.

Should I copy this entire type string into the field, or just the part starting following "Brazil..."

Thanks,

Michael

**********************************************

Michael G. Branstetter, Ph.D.

Postdoctoral Fellow

National Museum of Natural History

Smithsonian Institution

Office: (202) 633-1002

Email: mgbran...@gmail.com

Websites:

Project LLAMA

Smithsonian Profile

[Phil Ward]

Since we are just talking about the type locality (“location” is a bit of a misnomer) then this would be:

Brazil, São Paulo, Tapiraí, 24°01'55.5"S 47°27'56"W

 

Ultimately we would like to characterize the type locality of each species name by recording information in several fields: country, primary administrative division, locality name, coordinates, etc.

But some (especially older) names cannot be so pigeon-holed (e.g., old Emery names where the type locality is “New Guinea”), so verbatim type locality is a useful fallback. And if we capture the information in verbatim type locality now it can always be parsed out later, to the extent possible.

 

Mark, Stan: am I getting the intention right?

 

Phil

 

 

Phil

 

Philip S. Ward

Department of Entomology & Nematology

University of California at Davis

One Shields Avenue

Davis, CA 95616, USA

psw...@ucdavis.edu

[Marek Borowiec]

Good point Michael.

I have been copying the entirety of the collection data associated with the holotype which, of course, varies a lot from description to description.

I think that at least type deposition is an important piece of information and often included in catalogs. Do we need another field for that, or should we just paste this into the verbatim locality field?

Marek L. Borowiec
Ward Lab, 381 Briggs Hall
Department of Entomology
University of California, Davis

One Shields Avenue
Davis, CA 95616

https://sites.google.com/site/marekborowiecmyrmecologist/

[Mark Wilden]

I'm deferring to Brian and Stan on this one - however, Phil is correct that information can be reparsed at a later date, as long as everything needed is captured in this field.

[Phil Ward]

Certainly another desirable feature (down the line) would be a field for the place of deposition of the type specimen(s) of any given name. This will require considerable additional researching for most of the names in antcat. And remember that many of the older names are represented by syntypes so there will not necessarily be a single place of deposition. Also we would need to  decide on an approved list of acronyms for collections.

 

Maybe for now we should throw type deposition information in the “Verbatim type location” field, recognizing that it is a serving an interim hold-all function?

 

Phil

 

Philip S. Ward

Department of Entomology & Nematology

University of California at Davis

One Shields Avenue

Davis, CA 95616, USA

psw...@ucdavis.edu

 

From: ant...@googlegroups.com [mailto:ant...@googlegroups.com] On Behalf Of Marek Borowiec
Sent: Friday, January 17, 2014 1:23 PM
To: ant...@googlegroups.com
Subject: Re: [AntCat] NEW FEATURE: Verbatim type location

 

Good point Michael.

[Brian L. Fisher]

If we are going with just one field, I suggest we get all the
information we can.

If we just want "locality" then I think we need all the locality and
collection data. In this case:

Brazil, São Paulo, Tapiraí, 24°01'55.5"S 47°27'56"W, 08–14 Jan 2001,
col. R.R. Silva & Eberhardt, Transecto 1 Winkler 23.

Locality and collection data are both useful to figure out which
specimen(s) are part of the type series.

On Fri, Jan 17, 2014 at 1:18 PM, Phil Ward <psw...@ucdavis.edu> wrote:

Brian Fisher
Curator
California Academy of Sciences
San Francisco, CA 94118, USA
www.antweb.org

[Blum, Stan]

RE Verbatim type locality:

 

A little background.  There are usually two available sources for type locality information to the general user (not the collector, and not the describer).  Those are the label on the type specimen(s), and the published original description.  At the workshops in August, I think we came to the consensus that the locality data on the label should be the purview of specimen databases, and the published data should be the purview of the taxonomic catalog, which should focus on published information. 

 

So, the Verbatim Type Locality field in AntCat should contain the information about place contained in the original description.  In this case, it would be exactly as Phil said.  Is it important to exclude the other information about date, collectors, transect, and winkler number?  I don’t have a strong opinion about that.  It could be very helpful to a human user trying to track down information in ancillary sources (field notes and specimen labels), but extraneous information could impede machine parsing.  I would err on the side of inclusion in this case.

 

Yes, we have talked about (asked for) reference to holotype in the catalog, just as a text field, which could hold a reference to the depository name if the holotype is not cataloged (numbered).  Mark, that’s still a high priority item for us.

 

Best,

 

-Stan

[Phil Ward]

And just a reminder: we are not talking about putting information about the entire "type series" in the Verbatim Type Locality (Location) field. We are talking about the primary type or types (“name-bearing types”, in ICZN parlance). The only primary types are holotypes, lectotypes, neotypes, and syntypes. Paratypes and paralectotypes are not primary types.

 

Cheers, Phil

 

Philip S. Ward

Department of Entomology & Nematology

University of California at Davis

One Shields Avenue

Davis, CA 95616, USA

psw...@ucdavis.edu

 

[Blum, Stan]

Agreed (strongly).   Locality of only primary type(s).

[Phil Ward]

This also applies to the “Locality” field. So, for example, the recent entry Yantaromyrmex mayrianum listed the Locality as “Baltic and Rovno ambers”. But the holotype is from Baltic amber (with an additional paratype from Rovno amber) so I edited the entry to read “Baltic amber” only.

[Mark Wilden]

I'm sorry if I dropped the ball on this field. What should its name be, and could it contain more than 255 characters?

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Philip S. Ward
Department of Entomology
University of California
Davis, CA 95616

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[Blum, Stan]

I think  "Primary Type(s)" would be a good label.  I don't think it needs to be longer than 255.  Are there big functional differences between varchar(255) and longer text fields?  I don't think we need to sort on the these contents, but it would be good to search on them (show all records where types contains "CAS" or "USNM").  We should use this list of collection codens :  http://hbs.bishopmuseum.org/codens/codens-inst.html

We should also have a field for URL to type specimen data that is available on line, e.g., from AntWeb.

This is what I recorded in the Editorial Workshop notes:

• for species group names (species, subspecies):

  • Type material:  a text box for a human readable  identifiers/indicators of primary type specimens

  • URL to type specimen for cases where the information about a type specimen is served from an online resource (i.e., AntWeb or a collection database)

Thanks, Mark!

-Stan

[Michael Branstetter]

Based on what everyone has stated so far I suggest the following:

1) "Verbatim type locality" be renamed "Primary type locality" or "Primary type(s)" or "Primary collection locality" and that it include the entire verbatim collection string (most easily entered by copying and pasting from the pdf file). 

AND

2) A new field be created called "Primary type repository" that will be used to list the collection(s) where the primary type(s) is located. Note: I'm not sure if this should be the verbatim repository, or one of the standardized names from the bishop list.

Using the Brachymyrmex example again (repeated below), one would enter the following into fields 1 and 2:

Holotype worker (MZSP) [USNM ENT 00757718] and Paratypes 3 workers (CPDC [USNM ENT 00757719], ICN [USNM ENT 00757720], USNM [USNMENT 00757721]): Brazil, São Paulo, Tapiraí, 24°01'55.5"S 47°27'56"W, 08–14 Jan 2001, col. R.R. Silva & Eberhardt, Transecto 1 Winkler 23.

1) Brazil, São Paulo, Tapiraí, 24°01'55.5"S 47°27'56"W, 08–14 Jan 2001, col. R.R. Silva & Eberhardt, Transecto 1 Winkler 23.

2) MZSP

If we decide to combine 1 and 2 into a single field, how would this be done for the Brachymyrmex example? How would it be standardized? Also, what about the specimen code? Is it important to have that linked to the primary type(s) as well?

Best,

Michael

**********************************************

Michael G. Branstetter, Ph.D.

Postdoctoral Fellow

National Museum of Natural History

Smithsonian Institution

Office: (202) 633-1002

Email: mgbran...@gmail.com

Websites:

Project LLAMA

Smithsonian Profile

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[Philip Ward]

Hi Michael et al.,

Yes, good ideas. I think we can stick with "Verbatim Type Locality" for the name of the first field.
"Primary type locality" would be redundant. According to the ICZN, the type locality is the locality (or
sometimes, in the case of syntypes, the localities) where the primary type(s) is/are from. But until
we parse out type locality information in multiple controlled fields, "Verbatim Type Locality" is a
convenient place to put the type locality information as a text string, taken from the original
publication.

The second field could be called Primary Type Repository. And, as Stan said, one could restrict the
acronyms to a controlled list.

Until we have this second field in AntCat I suggest that we include information about the type
repository in Verbatim Type Locality.

Note that we do already have a "Type Locality" field in AntCat, and that is for the name of the
country of the type locality.

Cheers, Phil

> 1) "Verbatim type locality" be renamed "Primary type locality" or "Primary
> type(s)" or "Primary collection locality" and that it include the entire
> verbatim collection string (most easily entered by copying and pasting
> from
> the pdf file).
>
> AND
>
> 2) A new field be created called "Primary type repository" that will be
> used to list the collection(s) where the primary type(s) is located. Note:
> I'm not sure if this should be the verbatim repository, or one of the
> standardized names from the bishop list.
>

> Using the *Brachymyrmex *example again (repeated below), one would enter

> the following into fields 1 and 2:
>
> Holotype worker (MZSP) [USNM ENT 00757718] and Paratypes 3 workers (CPDC
> [USNM ENT 00757719], ICN [USNM ENT 00757720], USNM [USNMENT 00757721]):

> Brazil, S�o Paulo, Tapira�, 24�01'55.5"S 47�27'56"W, 08�14 Jan 2001, col.

> R.R. Silva & Eberhardt, Transecto 1 Winkler 23.
>

> 1) Brazil, S�o Paulo, Tapira�, 24�01'55.5"S 47�27'56"W, 08�14 Jan 2001,

> col. R.R. Silva & Eberhardt, Transecto 1 Winkler 23.
> 2) MZSP
>
> If we decide to combine 1 and 2 into a single field, how would this be
> done

> for the *Brachymyrmex *example? How would it be standardized? Also, what

> about the specimen code? Is it important to have that linked to the
> primary
> type(s) as well?
>
> Best,
> Michael
>
>
>
>
>
> **********************************************
> Michael G. Branstetter, Ph.D.
> Postdoctoral Fellow
> National Museum of Natural History
> Smithsonian Institution
> Office: (202) 633-1002
> Email: mgbran...@gmail.com
>
> Websites:

> Project LLAMA <https://sites.google.com/site/longinollama/>
> Smithsonian Profile
> <http://entomology.si.edu/StaffPages/Branstetter.html>

>
>
>
> On Sat, Jan 18, 2014 at 2:01 PM, Blum, Stan <SB...@calacademy.org>
> wrote:
>
> > I think "Primary Type(s)" would be a good label. I don't think it
> > needs to be longer than 255. Are there big functional differences
> between
> > varchar(255) and longer text fields? I don't think we need to sort on
> the
> > these contents, but it would be good to search on them (show all records
> > where types contains "CAS" or "USNM"). We should use this list of
> > collection codens : http://hbs.bishopmuseum.org/codens/codens-inst.html
> >
> > We should also have a field for URL to type specimen data that is
> > available on line, e.g., from AntWeb.
> >
> >
> > This is what I recorded in the Editorial Workshop notes:
> >
> >
> >

> > * - for species group names (species, subspecies): - Type material: a

> > text box for a human readable identifiers/indicators of primary type

> > specimens - URL to type specimen for cases where the information about a

> > type specimen is served from an online resource (i.e., AntWeb or a

> > collection database) *

[Blum, Stan]

I agree with Phil about Verbatim Type Locality. It fits well with other
DarwinCore term names.

I think the field for Type Specimen(s) Repository, though, needs a little
more discussion. My intention was to have one field that can hold a
human readable reference to the primary type(s), and another to hold a URL
(should be clickable). The human readable reference should not be just a
name or code for the holding collection, but also a catalog number, if one
is available.

Other numbers can be applied to specimens that can help in their
identification, but can also cause confusion or at least inconsistency in
where we record specific information. I would suggest that we record any
numbers that identify the specimen in the type specimen reference, but
numbers that identify the collecting-event be recorded with the verbatim
type locality (e.g., a collector's field number which could apply to 10s,
100s, or even 1,000s of specimens). The example we've been talking about
(below) contains:

1) a repository code and USNM catalog number: [USNM ENT 00757718], which
should go with the Type Specimen Reference;
2) date, collectors, and sample numbers, [ 08-14 Jan 2001, col.R.R. Silva
& Eberhardt, Transecto 1 Winkler 23 ], which should go in the Verbatim
Type Locality field.

Does that rub anyone the wrong way?

-Stan

[Marek Borowiec]

Sounds good to me. Can we post a standardized list of repository acronyms somewhere on AntCat?

Also, how do we deal with cases where the geographical locality  (or similar info) is not given directly under material examined sections? This would mostly be the case with fossils, I guess. For example, the description of Pheidole rasnitsyni Dubovikoff, 2011 contains a verbatim type locality string that goes like this:  Holotype: worker no. DD 8/5; Late Eocene, Baltic amber; 

From the paper we further discover that this specimen is in the Zoological Institute of the Russian Academy of Sciences (ZISP), but this information is not under the material examined section of the description.

Furthermore, from the introduction we learn that 'this material was mostly collected in Königsberg (now Kaliningrad) (...)'.

I saw that Vincent Perrichot put 'Baltic amber, Kaliningrad, Russia' in the type locality field, but should we have this information there if we're not sure if this is the physical locality of where these specimens were collected?

However, we have three separate pieces of information that are obviously of use to the future users of the catalog and ideally we'd be able to store all of them. I arbitrarily decided to put 'Baltic amber' as the type locality, 'Likely from Kaliningrad, Russia' under notes, and Holotype: worker no. DD 8/5; Late Eocene, Baltic amber; Zoological Institute of the Russian Academy of Sciences (ZISP) under Verbatim type locality fields.

Right now the way this is displayed in AntCat is not ideal (see below).

Any thoughts?

†Pheidole rasnitsyni Dubovikoff, 2011: 255, figs. 1-5 (w.) Likely from Kaliningrad, Russia Dubovikoff, 2011: 255 BALTIC AMBER. Verbatim type locality: Holotype: worker no. DD 8/5; Late Eocene, Baltic amber; Zoological Institute of the Russian Academy of Sciences (ZISP). 

Marek L. Borowiec
Ward Lab, 381 Briggs Hall

Department of Entomology
University of California, Davis

One Shields Avenue
Davis, CA 95616

https://sites.google.com/site/marekborowiecmyrmecologist/

[Mark Wilden]

Tell me how to make it ideal, and I will make it so! 

Everything that's been discussed is eminently doable. I'm waiting for Stan to drop the hammer on the fields and labels you all think are useful.

[Flávia Esteves]

So, does Verbatim Type Locality contain date, collectors, and sample numbers?

Flávia Esteves

Postdoctoral Fellow
Entomology
California Academy of Sciences
Golden Gate Park
55 Music Concourse Drive
San Francisco, CA 94118, U.S.A.

[Flávia Esteves]

Never mind, I just understood "I would err on the side of inclusion in this case."