[Taxacom] Minimum standards for e-voucher documentation (was Provisions to the Code)

Mon Apr 21 13:43:28 CDT 2014

Being based in one the largest entomological collections of the world (Canadian National Collection of Insects, Ottawa) I second and support Alex' comments 100%. I cannot think of any collection manager (or curator, or researcher) that would work as careless as described in the original message... For the past 4-5 years we have had many summer students doing tissue sampling for DNA (= pulling put a leg in most insect cases), and the overall experience is very positive. Yes, we have found the occasional person that is not careful/skillful/interested enough, but it is the rare exception, not the rule. And then, name one human enterprise where that does not happen... It all comes down to overseeing the work being done by the "barcoders team".

In my opinion, the benefits of having collections sampled for DNA (be it the barcoding region or more than that) are much more important than the occasional specimen lost, broken, misplaced... and here in the CNC we have several dozens of thousands of specimens already barcoded, in all major orders of Insecta, so we have gone down that road for a long time.

Cheers,
Jose

--
Jos? L. Fern?ndez-Triana, PhD.
Research Associate, Canadian National Collection of Insects,
and Biodiversity Institute of Ontario
960 Carling Ave, Ottawa, ON, K1A 0C6
Phone: 613-759-1034 . Email: jftriana at uoguelph.ca, Jose.Fernandez at agr.gc.ca
http://www.canacoll.org/Hym/Staff/Triana/Triana.htm
http://cncbraconidae.blogspot.ca/

----- Original Message -----
From: "Alex Borisenko" <aborisen at uoguelph.ca>
To: "John Grehan" <calabar.john at gmail.com>
Cc: "taxacom" <taxacom at mailman.nhm.ku.edu>
Sent: Monday, April 21, 2014 2:28:21 PM
Subject: Re: [Taxacom] Minimum standards for e-voucher documentation (was Provisions to the Code)

IF the following description is correct, then lack of proper curatorial oversight of the collection in question is an even bigger problem. What kind of a collections manager would let in a bunch of students do free-for-all destructive sampling in their collection without supervision? 
Also, what is the issue with barcoding unidentified/misidentified/tentatively identified specimens or those from undescribed species? Barcoding is a tool designed to help with taxonomic validation, so it is to be expected that the construction of reference libraries is an iterative process that often begins with a mess. Finally, please name one large collection that is not under-resourced... 
AB 

----- Original Message -----

From: "John Grehan" <calabar.john at gmail.com> 
To: "Alex Borisenko" <aborisen at uoguelph.ca> 
Cc: "David Campbell" <pleuronaia at gmail.com>, "taxacom" <taxacom at mailman.nhm.ku.edu> 
Sent: Monday, April 21, 2014 2:05:05 PM 
Subject: Re: [Taxacom] Minimum standards for e-voucher documentation (was Provisions to the Code) 

If the following description is correct then the lack of quality control would seem to be a really major problem: 

?A team from [country omitted] moved in and badly damaged the collection in a massive knock legs off everything project. They confused species put material back in the wrong place and damaged hundreds of specimens. They did not talk to us at all. They bar-coded undescribed species or unplaced specimens or species without a clue as to why they were where they were in the collection. Students did the work so they massively miss interpreted the collection and of course took absolutely no account of the varying degrees of reliability of identifications existing in any large under-resourced collection. 

On Mon, Apr 21, 2014 at 12:25 PM, Alex Borisenko < aborisen at uoguelph.ca > wrote: 

Hi David, 

Your critical comment below relates to two separate issues: 
1. The lack of convenient feedback tools for reporting identification errors in online data portals for DNA barcoding information; 
2. The poor quality of data submitted to such portals. 

With regards to #2, I can only say that the data are as good as we (collectively) make them. E.g., many providers of specimen provenance information do not indicate (and often do not know) the name of the identifier at the time of submission. 

With regards to #1, I must note that such tools are available. For example, the Barcode of Life Data System has an attribution section for each specimen record that denotes the name of the identifier (when available) and the name of the project manager who could be asked to address taxonomic problems within a particular dataset. E.g., see public BOLD record below (bottom right corner): 
http://v3.boldsystems.org/index.php/Public_RecordView?processid«SMS268-06 

Because of privacy/spam concerns, it is not possible to email the identifier or project manager directly from a public specimen record - this functionality is only open to registered BOLD users who are logged in. 
However, if users wish to provide instant feedback, they have the option to annotate the data record by clicking the Add Tags&Comments button just above the taxonomy - this will flag the record for future users. 
They can also add tags on the corresponding BIN page which would annotate all specimens putatively referred to a given species: 
http://v3.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:ACF2193 

I am not sure if I fully understand your remarks about 'proper' or 'correct' identifiers. If you imply that some barcode data records are contributed by people without adequate taxonomic expertise or accreditation, I personally think that it is a strength of such large-scale data projects. 
In most other real world situations, the 'proper' and 'correct' identifiers are those who get acknowledged in specialized taxonomic revisions, whereas many of the the 'incorrect' and 'improper' ones write volumes of ecological assessment and biodiversity survey reports whose baseline data never get digitally annotated, let alone cross-referenced against museum collections or taxonomy databases. Ironically, such reports probably have more weight in environmental decision-making. I think that having information from different sources in one digital system where taxonomic inconsistencies become glaringly visible is a step in the right direction. Thank you for your efforts in trying to clean up the resulting taxonomic issues. 

Best wishes 
Alex 

----- Original Message ----- 

From: "David Campbell" < pleuronaia at gmail.com > 
Cc: taxacom at mailman.nhm.ku.edu 
Sent: Monday, April 21, 2014 10:29:38 AM 
Subject: Re: [Taxacom] Minimum standards for e-voucher documentation (was Provisions to the Code) 

Quality information is critical, but it's difficult to formulate a standard 
when different taxa vary greatly in their key features. For many animals, 
dissection showing reproductive features is critical, and often challenging 
*(e.g*., microscopic). Others have key differences in a specific part. 
Barcodes have great potential for facilitating identification, but only if 
the validity of the barcode is tested for the group in question and 
specimens are carefully identified. 
As with any online compilation, content must be accompanied by appropriate 
curation. There needs to be a quick way to communicate information (such 
as corrected identification) to a responsible party. In the case of 
barcoding, where often large numbers of specimens are quickly processed, 
it's particularly important to have a clearly designated identifier for a 
particular specimen. It's frustrating to notice an error in a barcoding 
project, search through several pages to finally find some contact 
information, and then be told that the submitted identifier (the one used 
in GenBank) was not the proper identifier to enable them to tell which 
specimen had the problem. At least they could have given some sort of clue 
as to what the correct identifier would have been ("the one where you've 
got a photo of something from a different order" wouldn't do, either). 

On Mon, Apr 21, 2014 at 2:15 AM, Schindel, David < schindeld at si.edu > wrote: 

> The Consortium for the Barcode of Life (CBOL) is leading the Barcode of 
> Wildlife Project on endangered species. We will be grappling with the 
> issue of what minimum documentation should be required for occurrence 
> records and BARCODE records in GenBank when there is no traditional voucher 
> specimen (e.g., dead animal bones and skin or a herbarium sheet). This has 
> special significance in the project which is constructing a reference 
> library of barcode records in GenBank that will be used to identify the 
> species of organisms involved in the investigation and prosecution of 
> wildlife crime. We're all familiar with circumstances in which a 
> traditional voucher specimen is either impractical (e.g., endangered whales 
> or other large species) or illegal (endangered/protected species). There 
> was a small literature on 'e-vouchers' a few years ago but as far as I 
> know, it never evolved to the level of a proposed standard for 
> documentation. 
> 
> This is related to the ongoing thread about holotypes but I stress that we 
> are not trying to erect new species without a traditional type specimen. 
> Rather, we want to provide a credible way for someone to verify the 
> species identification of a specimen with a GenBank record when there is no 
> traditional voucher. Tissue samples, photographs, geolocation, 
> measurements and environmental context data are the obvious elements in 
> such a standard. Do any of you know of an effort to formalize these 
> minimum information standards? 
> 
> Thanks and regards, 
> 
> David Schindel 
> 
> -----Original Message----- 
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto: 
> taxacom-bounces at mailman.nhm.ku.edu ] On Behalf Of laurent raty 
> Sent: Wednesday, April 16, 2014 6:23 AM 
> To: taxacom at mailman.nhm.ku.edu 
> Subject: Re: [Taxacom] [iczn-list] provisions to the Code 
> 
> - "Physical specimen" is not a term regulated by the ICZN. In fact, the 
> word "physical" appears exactly zero times in the entire text of the 
> Code; and given the definition of "specimen" there, an "un-physical 
> specimen" (Stephen used the word "ghost" recently) seems to be an 
> impossibility. Specimens are always physical, or they would be no 
> specimens. 
> 
> - What comes closest in the ICZN to what some seem to call "physical 
> specimen" is "extant specimen" ("sp?cimens qui existent toujours" in the 
> French text). 
> 
> - For names published after 1999, Art.16.4.2 gives explicit additional 
> requirements for availability in the special case where the holotype or 
> syntypes are extant specimens. As this is clearly treated as a special 
> case, it is obvious that having extant specimens as types cannot be 
> understood as a general requirement for all species-group names 
> published after 1999. 
> 
> - Again, it is a complete misreading to pretend that: 
> "73.1.4. Designation of an illustration of a single specimen as a 
> holotype is to be treated as designation of the specimen illustrated; 
> the fact that the specimen no longer exists or cannot be traced does not 
> of itself invalidate the designation." 
> ...introduces an exception to a general "rule" that would say that a 
> holotype must be an extant specimen. Should such a "rule" exist, this 
> article would actually not allow any exception to it: the designation of 
> the illustrated specimen would be allowed only if the specimen is 
> extant; the designation of the illustration would have to be treated as 
> the designation of the specimen; thus, should the specimen not be 
> extant, the designation of the illustration would not be allowed. 
> 
> The truth is that there is NO such rule in the Code. 
> 
> My two cents, 
> Laurent - 
> 
> 
> 
> 
> 
> 
> On 04/16/2014 09:48 AM, Paul van Rijckevorsel wrote: 
> > From: "Weakley, Alan" < weakley at bio.unc.edu > 
> > Sent: Wednesday, April 16, 2014 1:38 AM 
> > 
> >> Hi all: here is the current code for algae, fungi, and plants 
> >> ( 
> https://urldefense.proofpoint.com/v1/url?u=http://www.iapt-taxon.org/nomen/main.php?page%3Dtitle&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sá234d69e54d95922d340300d45e3d1719a2e98c46bb13d43b448028992f9e95 
> ) 
> > 
> >> Bottom line: after 2007, physical specimen only (exceptions as noted 
> >> below). 
> > 
> > *** 
> > This is not particularly accurate. Illustrations may be 
> > types, and the date of 1 January 2007 does not change 
> > that; such illustrations as were types before that date will 
> > continue to be so after that date. And new designations 
> > of illustrations as types may still be made after that date. 
> > 
> > What has changed with 1 January is that names of new 
> > species or new infraspecific taxa may not have an 
> > illustration as a type (exceptions excepted). 
> > 
> > Paul 
> > 
> > 
> > _______________________________________________ 
> > Taxacom Mailing List 
> > Taxacom at mailman.nhm.ku.edu 
> > 
> https://urldefense.proofpoint.com/v1/url?u=http://mailman.nhm.ku.edu/mailman/listinfo/taxacom&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sÙf54cf48371af1f22f8c4749482432199c25b34415db3e7d8dba08f199e5f01 
> > The Taxacom Archive back to 1992 may be searched at: 
> https://urldefense.proofpoint.com/v1/url?u=http://taxacom.markmail.org/&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sZ6347632a4f57b5937d5523780efebac85be4516d4c8a98ff9ca27b191e26b2 
> > 
> > Celebrating 27 years of Taxacom in 2014. 
> > 
> 
> _______________________________________________ 
> Taxacom Mailing List 
> Taxacom at mailman.nhm.ku.edu 
> 
> https://urldefense.proofpoint.com/v1/url?u=http://mailman.nhm.ku.edu/mailman/listinfo/taxacom&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sÙf54cf48371af1f22f8c4749482432199c25b34415db3e7d8dba08f199e5f01 
> The Taxacom Archive back to 1992 may be searched at: 
> https://urldefense.proofpoint.com/v1/url?u=http://taxacom.markmail.org/&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r”xk%2BkvyzF5zfdS9tDhVEg%3D%3D%0A&m=BWWddgspb8VyrOJmwD7URzKSH%2BOlLYhcK7fpJhBFDHo%3D%0A&sZ6347632a4f57b5937d5523780efebac85be4516d4c8a98ff9ca27b191e26b2 
> 
> Celebrating 27 years of Taxacom in 2014. 
> 
> _______________________________________________ 
> Taxacom Mailing List 
> Taxacom at mailman.nhm.ku.edu 
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom 
> The Taxacom Archive back to 1992 may be searched at: 
> http://taxacom.markmail.org 
> 
> Celebrating 27 years of Taxacom in 2014. 
> 

-- 
Dr. David Campbell 
Assistant Professor, Geology 
Department of Natural Sciences 
Box 7270 
Gardner-Webb University 
Boiling Springs NC 28017 
_______________________________________________ 
Taxacom Mailing List 
Taxacom at mailman.nhm.ku.edu 
http://mailman.nhm.ku.edu/mailman/listinfo/taxacom 
The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org 

Celebrating 27 years of Taxacom in 2014. 

_______________________________________________ 
Taxacom Mailing List 
Taxacom at mailman.nhm.ku.edu 
http://mailman.nhm.ku.edu/mailman/listinfo/taxacom 
The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org 

Celebrating 27 years of Taxacom in 2014. 

_______________________________________________
Taxacom Mailing List
Taxacom at mailman.nhm.ku.edu
http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org

Celebrating 27 years of Taxacom in 2014.