[Taxacom] New taxonomy in Nature's Scientific Reports
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Sun Oct 2 20:31:07 CDT 2016
2016
Actually, this might make things clearer:
Suppose that an article is preregistered on ZooBank on 1 Jan 2016, but linked to a record for the journal which lacks a stated archive, and no archive is stated for the article. Suppose also that there is another record for the same journal which had an archive specified since 1 Jan 2015. If these two duplicate records for the journal get merged (say on 1 Feb 2016), then does the article record then show a date when an archive was added, and if so what date? By my reckoning the date should be 1 Feb 2016, but I'm just a bit worried it might show as 1 Jan 2016, as if the article record was created with the other journal record (i.e. the one with an archive).
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:
>
> >
> > >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, > >
> > >Â Can > >Â 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
> >
>
--------------------------------------------
> > >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
> > > >ÂÂ
Received:
> Saturday, 1 October,
> > 2016,
>
> >Â 5:57 PM
> >
> >Â
> >
>
> >
>
> > 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
> > >Â
>ÂÂ
> > ZooBank for
authors?
> > >Â >
> >
> >Â
> Twitter thread
> >
> >Â about the issue:
> > >Â
>
> >
> > >Â
> >ÂÂ
>
> >Â
> > https://twitter.com/BioInFocus/status/734870944330731520
> > >Â >
> >
> >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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