[Taxacom] New taxonomy in Nature's Scientific Reports

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Sun Oct 2 20:04:52 CDT 2016


Rich said: "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".

Hmm, well I'm not sure about that final sentence. It seems a wee bit contrived to claim that a registration linked to a duplicate journal record is an "incorrect record". Bear in mind that the first record for a journal might be the one *lacking* archive info, and a subsequent "duplicate" may already have an archive. It seems to me that if an article record is linked to a journal record without a specified archive (and no archive is specified in the article record itself), then the article straightforwardly fails Code compliance for electronic publication, even though there was another record for the same journal, with an archive, which could have been linked to instead. What I am worried about is if subsequent merging of the duplicate journal records makes it retrospectively look like the article was linked to an archived journal record in the first place. That would mean that we cannot simply look at the record for an article to see if it is Code compliant for electronic publication from the date it was published online. What we see might change. This is quite important because a authors who preregister their publications on ZooBank sometimes start by creating a new record for the journal (with no specified archive) and then link the article registration to that journal record.

Stephen

--------------------------------------------
On Mon, 3/10/16, Richard Pyle <deepreef at bishopmuseum.org> wrote:

 Subject: RE: [Taxacom] New taxonomy in Nature's Scientific Reports
 To: "'Stephen Thorpe'" <stephen_thorpe at yahoo.co.nz>, gread at actrix.gen.nz
 Cc: taxacom at mailman.nhm.ku.edu
 Received: Monday, 3 October, 2016, 1:49 PM
 
 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:
 > 
 >  >
 >  >  > 
 Subject:
 >  >
 > 
 Re: [Taxacom] New taxonomy in Nature's Scientific 
 >  Reports  >  >Â
 >  To:
 "Stephen
 >  >  Thorpe"
 <stephen_thorpe at yahoo.co.nz> 
 >  >  Cc:
 > taxacom at mailman.nhm.ku.edu, 
 >  gread at actrix.gen.nz 
 >  >  Received:
 > Saturday, 1
 October,  2016,  >  6:31 PM  >  >  > 
 >  >  >  Stephen,  >  >
 > >  >  Can  >  >  you
 name  >  those journals?  I'm interested if
 there are  >
 > >  other major 
 >  >  >  online-only high-profile  > 
 >  ones.The  >  usual efirst-
 > then-print ones (Hello  >  > 
 >  JMBA UK) I don't care  about, although
 > >  >  they're  a pain in
 the butt to  >  track  >  >  when  > 
 >  the  >  articles are
 >
 really  published, and the names become  >  > 
 available.
 >  >  >
 >  >  >  As evident from
 >  >  >Â
 > 
 >  the
 >  thread yes indeed there
 are people who don't know  >  >  what 
 >
 > >  constitutes  > 
 Code-valid  publication.
 >  > 
 >  But Nature
 >  >  staff
 should know.
 >  >  >
 >  >  >Â
 > 
 Yes, the web site seems to have a pdf
 > 
 >
 >  >  invisibility problem at
 the moment -  >  >  I used  >  > 
 >  ResearchGate
 > instead.
 >  >  >
 > 
 >  >Â
 >  Geoff
 >  >  >
 > 
 >
 >  >  On Sat,
 >  >  >  October
 >  >  1, 2016 6:11 pm, Stephen
 Thorpe
 >  wrote:
 > 
 >  >  > This isn't a
 > 
 big deal! There
 >  >  are only
 >  >  >  less than a handful
 of
 >  >  articles with
 >  >
 >  > 
 >
 >  >  >  new taxa. It
 >  was up to the authors to
 >  >  ensure
 > 
 Code
 >  >  >  compliance.
 The
 >  >  website
 >  >  >Â
 > 
 > seems odd,
 >  >  > 
 though, and
 >  I can't seem to find
 a
 >  >  way to get
 >  a pdf of
 >  > 
 >  any of
 >  >  >  >
 the articles! Anyway,
 >  there are
 >  >  >  plenty of other
 >  journals publishing
 >  >  more
 > 
 >  >  > new taxa than this one,
 >  all
 >  > 
 without valid
 >  >  > 
 ZooBank
 >  >
 > 
 preregistration!
 >  >  > 
 >
 >  >  >  > Stephen
 >  >  >Â
 > 
 >  >
 >  >  >  >
 >  >
 >  >Â
 >  >
 > 
 --------------------------------------------
 >  >  >  > On Sat, 1/10/16,
 Geoff
 >  Read <gread at actrix.gen.nz>
 >  >  >  wrote:
 >  >
 >  > 
 >
 >  >  >  >ÂÂ
 >  Subject:
 >  > 
 >Â
 >  >  [Taxacom] New taxonomy
 in Nature's
 >  Scientific Reports
 >  >  >Â
 > 
 >  To: Taxacom at mailman.nhm.ku.edu
 >  >  >  > 
 Received:
 >  Saturday, 1 October,
 >  >  2016,
 > 
 >  >  5:57 PM
 >  >
 >  >Â
 >  > 
 >
 >  >
 > 
 >  >  Has
 >  > 
 >Â
 >  anyone here published taxonomy
 in
 >  >
 > 
 >  >ÂÂ
 >  >  >Â
 >  >  "Scientific
 Reports",
 >  Nature's
 >  >  >  >ÂÂ
 >  online-only open access
 >  >
 > 
 journal?  Why
 > 
 >
 >  >  aren't
 >  >  they
 > 
 >  >  >  registering new
 >  taxa
 >  > 
 >  in
 >  >  > 
 >ÂÂ
 >  >  ZooBank for
 authors?
 >  >  >  >
 >  >
 >  > 
 >  Twitter thread
 >  >
 >  >  about the issue:
 >  >  >Â
 > 
 >  >
 >  >  >Â
 >  >ÂÂ
 > 
 >  >Â
 >  >  https://twitter.com/BioInFocus/status/734870944330731520
 >  >  >  >
 >  >
 >  > 
 >ÂÂ
 >  >  Geoff
 >  >  >  >  --
 >  >  >  >  Geoffrey
 B.
 >  >  >  Read, Ph.D.
 >  >  >Â
 > 
 >
 >  >  Wellington, NEW
 >  >
 >  > 
 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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