[Taxacom] New taxonomy in Nature's Scientific Reports

Richard Pyle deepreef at bishopmuseum.org
Sun Oct 2 19:49:21 CDT 2016


When any duplicate record is discovered in ZooBank, the two records are evaluated and merged, with the most correct information persisting in the resulting merged record.

As best I can determine from this thread, the duplicate Journal records are for "Scientific Reports", published by the Nature Publishing Group.  In this case, the duplicate record was registered as urn:lsid:zoobank.org:pub:79C28F63-F2D0-415C-996F-C3DD03982835, and the correct record was registered as urn:lsid:zoobank.org:pub:13A0B80D-EB17-4E16-839E-BF03CFFC994A.

Records in ZooBank are NEVER deleted.  They are either correct, identified as a duplicate, or suppressed because they do not represent an actual entity.  In the latter two categories, the records are maintained in the database, but hidden from the website.  This is important because if a record is thought to represent a duplicate or non-entity, then later is discovered to be legitimate, we need to be able to resurrect the original record.  Moreover, EVERY record in ZooBank maintains an "audit" trail of edits, tracking what field of each record was altered from what previous value to what new value, by whom and when.  This allows us to investigate any/all edits and "walk back" records in cases where edits were not correct.  Much of this information is not yet visible on the Public ZooBank website, but plans are in place to add this information in a future version of the site.

In the case of duplicate records that are merged, the duplicate identifiers still resolve on the ZooBank website, but are redirected to the correct record.  For example, if you got to the link for the duplicate "Scientific Reports" journal registration (http://zoobank.org/References/79C28F63-F2D0-415C-996F-C3DD03982835), you will see the correct record displayed (urn:lsid:zoobank.org:pub:13A0B80D-EB17-4E16-839E-BF03CFFC994A).

Now, getting to Stephen's question: Yes, if someone views a record linked to a duplicate Journal, before the duplication is discovered, they will see an incorrect record. Once the error or duplicate is discovered, it is corrected (as I have already done for the journal in question).  But this is no different than any other error discovered on the ZooBank website.
 
Currently, there is no formal ZooBank policy to assess or address the accuracy of information presented on any given ZooBank record. The Commission has long discussed ideas about how to implement a record verification process, but as yet no viable model for record verification has been proposed, let alone implemented.  Presumably it would incorporate some sort of third-party evaluation of each record by a "trusted" source, then flagged as accurate once the details are verified against the associated publication.  Once verified, a record would then be subject to more restrictive editing policies.  But that's just a general outline for how such a system might work.  As with all things nomenclatural (and especially when ZooBank is concerned), the devil is in the details.

I hope that answers the question.  If not, please let me know.

Aloha,
Rich

Richard L. Pyle, PhD
Database Coordinator for Natural Sciences | Associate Zoologist in Ichthyology | Dive Safety Officer
Department of Natural Sciences, Bishop Museum, 1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef at bishopmuseum.org
http://hbs.bishopmuseum.org/staff/pylerichard.html




> -----Original Message-----
> From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
> Sent: Sunday, October 2, 2016 10:10 AM
> To: gread at actrix.gen.nz; deepreef at bishopmuseum.org
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] New taxonomy in Nature's Scientific Reports
> 
> Geoff,
> What you say brings up an issue in need of clarification (Rich): If there are two
> or more records for the same journal (which haven't been merged), only one of
> which has a stated archive, what happens if an article is registered with the
> other record for the journal (i.e. the one without an archive)? If the duplicate
> journal records are subsequently merged, then presumably it then looks like the
> article was registered with a stated archive, but this poses something of a
> potential problem: anyone trying to determine Code compliance before merger
> of the duplicate journal records will see no stated archive on the article record
> and so will determine that it is not Code compliant. Anyone doing this after the
> merger will see what appears to be Code compliance. Is that right, Rich?
> Cheers,
> Stephen
> 
> --------------------------------------------
> On Sun, 2/10/16, Geoffrey Read <gread at actrix.gen.nz> wrote:
> 
>  Subject: Re: [Taxacom] New taxonomy in Nature's Scientific Reports
>  To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
>  Cc: gread at actrix.gen.nz, taxacom at mailman.nhm.ku.edu
>  Received: Sunday, 2 October, 2016, 7:12 PM
> 
>  Stephen,
> 
>  There are two registrations
>  for the journal. It seems you were looking at  the second (unnecessary) one.
> The first one has  had a PMC archive since  2013. But it was an  author initiated
> registration.
> 
>  At least two of the articles published in 2014  seem to comply with the  Code in
> including a  LSID in the pdf and have registrations.  So why  compliance is
> intermittent since, and  hit-and-miss I have no idea.  It  seems  however, that
> with this journal it is up to the authors to  be savvy  about the Code, do the
> registration  work, and make sure a nomenclature  statement  is included.
> 
>  Rather less
>  worrying overall on author ignorance / journal  intransigence  than initially
> appeared from  the story on Twitter.
> 
>  Geoff
> 
> 
>  On Sun, October 2, 2016 5:22 pm, Stephen Thorpe
>  wrote:
>  > PS: Even if the articles had
>  cited the ZooBank LSIDs, it still wouldn't  > count until very recently, as there is
> no  stated archive for the journal  > before  May 30, 2016 (unless it was added
> for the specific  article)!
>  >
>  > BTW,
>  another issue that sometimes comes up with these "high  impact"
>  > journals is that they
>  sometimes relegate the taxonomy to supplementary  > word files, which don't
> count as Code  compliant!
>  >
>  >
>  Stephen
>  >
>  >
>  --------------------------------------------
>  > On Sun, 2/10/16, Geoffrey Read <gread at actrix.gen.nz>
>  wrote:
>  >
>  >  Subject:
>  Re: [Taxacom] New taxonomy in Nature's Scientific  Reports  >  To: "Stephen
> Thorpe" <stephen_thorpe at yahoo.co.nz>  >  Cc: gread at actrix.gen.nz,
> taxacom at mailman.nhm.ku.edu  >  Received: Sunday, 2 October, 2016, 5:03
> PM  >  >  Hi  Stephen,  >  >  Time  fixes the  >  efirst-then-print  problem.  Those
> journals don't have  >  to  >  register  papers and if they do not  >  acknowledge
> problems they create for  >  others  >  in the interim (taxa can be a year or  more
> in limbo)  >  there's  >  nothing to be done, other than  >  chip away at them
> when the occasion  arises  >  to complain.
>  >
>  >  Scientific Reports
>  has about 12 papers
>  >  registered in
>  ZooBank (by
>  >  somebody). As
>  >  ZooBank doesn't display a date or
>  author for edit
>  >  actions it
>  >  is not possible for the public to
>  >  know when an entry arrived and who
>  did
>  >  it.Â
>  >
>  One article has two entries - so something odd there.
>  >
>  >  However, I checked
>  the pdfs of
>  >  three of those articles
>  at random and they
>  >  all lacked any
>  mention of ZooBank or LSIDS.Â
>  >  The
>  paper with the
>  >  Code-unpublished
>  new
>  >  family isn't there in
>  ZooBank.  Those authors
>  >  published
>  a corrigendum last month, but
>  >
>  it's not about the ZooBank issue.
>  >
>  >  Geoff
>  >
>  >  On Sun,
>  >  October 2, 2016 11:43 am, Stephen Thorpe
>  wrote:
>  >  > Hi Geoff,
>  >  > Well,
>  >
>  I'm not sure about "major high-profile
>  ones",
>  >  as it doesn't
>  really
>  >  > matter to me
>  >  which journals are involved. I think  though that there  >  are  >  > ample
> problems with many of the  >  "usual efirst-then-print  ones". Many  >  >
> journals appear  to (rather opaquely)  >  publish in 3
>  steps: (1) efirst
>  >  > without
>  >  allocation to an issue; followed by (2)  efirst publication  >  of  >  > final print
> version; followed by
>  (3)
>  >  actual physical printing of
>  final
>  >  > print
>  >  version. It is (3) which is
>  nomenclaturally the most
>  >  important
>  if
>  >  > the ZooBank
>  >  preregistration hasn't been done
>  properly (often due to
>  >  lack
>  >  > of a stated archive in the
>  ZooBank
>  >  record, which hardly anyone
>  bothers to
>  >  >
>  >  check!), but it is also the hardest date  to determine,  >  particularly since  >  >
> there will be fewer  >  subscriptions for print editions as most  libraries  >  >
> slowly go digital  only. Potentially, it  >  also creates  another problem  >  >
> whereby it  >  may still be necessary to pay for hard  copy subscriptions  >  just
> >  > to determine true publication  >  dates, even though everything else might
> be  >  > already paid for open access  and available  >  digitally!
>  >  > Cheers,
>  >
>  >
>  >  Stephen
>  >
>  >
>  >  >
>  >
>  --------------------------------------------
>  >  > On Sat, 1/10/16, Geoffrey Read
>  <gread at actrix.gen.nz>
>  >  wrote:
>  >  >
>  >  >Â  Subject:
>  >
>  Re: [Taxacom] New taxonomy in Nature's Scientific  >  Reports  >  >Â
>  To: "Stephen
>  >  Thorpe" <stephen_thorpe at yahoo.co.nz>  >  >Â  Cc:
> taxacom at mailman.nhm.ku.edu,  >  gread at actrix.gen.nz  >  >Â  Received:
> Saturday, 1 October,  2016,  >  6:31 PM  >  >  >  >  >  >Â  Stephen,  >  >
> >  >  Can  >  >  you name  >  those journals?  I'm interested if there are  >
> >Â  other major  >  >Â  >  online-only high-profile  >  >Â  ones.The  >  usual efirst-
> then-print ones (Hello  >  >Â  >  JMBA UK) I don't care  about, although
> >  >Â  they're  a pain in the butt to  >  track  >  >Â  when  >  >Â  the  >  articles are
> really  published, and the names become  >  >Â  available.
>  >  >
>  >  >Â  As evident from
>  >  >Â
>  >  the
>  thread yes indeed there are people who don't know  >  >Â  what  >
> >Â  constitutes  >  Code-valid  publication.
>  >  >Â  But Nature
>  >  staff should know.
>  >  >
>  >  >Â
>  Yes, the web site seems to have a pdf
>  >
>  >Â  invisibility problem at the moment -  >  >Â  I used  >  >Â  >  ResearchGate
> instead.
>  >  >
>  >  >Â
>  Geoff
>  >  >
>  >
>  >Â  On Sat,
>  >  >Â  October
>  >  1, 2016 6:11 pm, Stephen Thorpe
>  wrote:
>  >  >Â  > This isn't a
>  big deal! There
>  >  are only
>  >  >Â  less than a handful of
>  >  articles with
>  >
>  >Â  >
>  >  >Â  new taxa. It
>  was up to the authors to
>  >  ensure
>  Code
>  >  >Â  compliance. The
>  >  website
>  >  >Â
>  > seems odd,
>  >  >Â  though, and
>  I can't seem to find a
>  >  way to get
>  a pdf of
>  >  >Â  any of
>  >  >Â  > the articles! Anyway,
>  there are
>  >  >Â  plenty of other
>  journals publishing
>  >  more
>  >  >Â  > new taxa than this one,
>  all
>  >  without valid
>  >  >Â  ZooBank
>  >
>  preregistration!
>  >  >Â  >
>  >  >Â  > Stephen
>  >  >Â
>  >  >
>  >  >Â  >
>  >
>>  >
>  --------------------------------------------
>  >  >Â  > On Sat, 1/10/16, Geoff
>  Read <gread at actrix.gen.nz>
>  >  >Â  wrote:
>  >
>  >Â  >
>  >  >  >ÂÂ
>  Subject:
>  >  >Â
>  >  [Taxacom] New taxonomy in Nature's
>  Scientific Reports
>  >  >Â
>  >  To: Taxacom at mailman.nhm.ku.edu
>  >  >  >  Received:
>  Saturday, 1 October,
>  >  2016,
>  >  >Â  5:57 PM
>  >
>>  >  >
>  >
>  >  >  Has
>  >  >Â
>  anyone here published taxonomy in
>  >
>  >  >ÂÂ
>  >  >Â
>  >  "Scientific Reports",
>  Nature's
>  >  >  >ÂÂ
>  online-only open access
>  >
>  journal?  Why
>  >
>  >Â  aren't
>  >  they
>  >  >  >  registering new
>  taxa
>  >  >Â  in
>  >  >  >ÂÂ
>  >  ZooBank for authors?
>  >  >Â  >
>  >
>  >  >  Twitter thread
>  >
>  >Â  about the issue:
>  >  >Â
>  >  >
>  >  >Â
>  >ÂÂ
>  >  >Â
>  >  https://twitter.com/BioInFocus/status/734870944330731520
>  >  >Â  >
>  >
>  >  >ÂÂ
>  >  Geoff
>  >  >  >  --
>  >  >  >  Geoffrey B.
>  >  >Â  Read, Ph.D.
>  >  >Â
>  >
>  >  Wellington, NEW
>  >
>  >Â  ZEALAND
>  >  >Â
>  >  gread at actrix.gen.nz
>  >  >
>  >  >
>  >  >
>  >  >
>  >
>  >
>  >  --
>  >  Geoffrey B.
>  >  Read, Ph.D.
>  >  8
>  Zaida Way, Maupuia
>  >  Wellington, NEW
>  ZEALAND
>  >  gread at actrix.gen.nz
>  >
>  >
>  >
> 
> 
>  --
>  Geoffrey B. Read, Ph.D.
>  8 Zaida Way, Maupuia
>  Wellington, NEW ZEALAND
>  gread at actrix.gen.nz
> 
> 




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