[Taxacom] are early online publications code-compliant?

David Campbell pleuronaia at gmail.com
Fri Apr 10 10:36:11 CDT 2015


There's actually appreciable confusion related to GenBank registration as
well.  Journals that aren't particularly on GenBank's radar (which includes
many taxonomic publications) do not get automatically updated when a
sequence is published.  GenBank considers it up to the author to send in
notifications, but authors often don't realize that.  This is not to
disparage GenBank, but to bring up an issue to think about for our efforts
to improve ZooBank and similar efforts.  Perhaps an automated "you sent
this in a year ago -is it still unpublished?" type of message would be
possible.  As with any system, there's the issue of staff funding - can we
pay someone (or design an automatic system) to search for status updates?

On Thu, Apr 9, 2015 at 12:59 PM, Frank T. Krell <Frank.Krell at dmns.org>
wrote:

> Dear Daphne et al.,
>
> I agree that automated registration should be the goal, but this needs
> engagement of the publishers, too, because the markup procedure is
> integrated into the publishers' workflow, that ZooBank will not control, of
> course. While I do not know the technicalities, I am pretty sure that
> publishers are interested in markups of their papers or do this already for
> different purposes. It is hopefully a matter of time (and good will and
> collaboration), and automated registration will be established at some
> point.
>
> Currently, only the registration of works is mandatory, and only for
> electronic works. Manual registration of a work takes one minute or two.
> This is not too burdensome, neither for an author nor for a publisher (even
> if he or she publishes 20 paper per day).
>
> Authors register sequences in GenBank without complaint. This is not done
> by the publisher, but by the authors. It is required by journals. It is
> probably more burdensome, given the number of sequences per paper, than
> just registering the paper (and a few names). I don't see the burden if
> journals require registration in ZooBank, but I see that journals doing it
> for the authors have a competitive advantage with a probably increasing
> number of authors.
>
> Cheers
>
> Frank
>
>
> Dr. Frank-T. Krell, Chair, ZooBank Committee
> http://zoobank.org
> Commissioner, International Commission on Zoological Nomenclature
> Curator of Entomology
> Department of Zoology
> Denver Museum of Nature & Science
> 2001 Colorado Boulevard
> Denver, CO 80205-5798 USA
> Frank.Krell at dmns.org
> Phone: (+1) (303) 370-8244
> Fax: (+1) (303) 331-6492
> http://www.dmns.org/science/museum-scientists/frank-krell
> lab page: http://www.dmns.org/krell-lab
>
>
>
>
>
> -----Original Message-----
> From: Fautin, Daphne G. [mailto:fautin at ku.edu]
> Sent: Thursday, April 09, 2015 10:02 AM
> To: Frank T. Krell; gread at actrix.gen.nz; Michael Heads
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] are early online publications code-compliant?
>
> Dear Frank,
>
> The statement that inspired my comment was from Geoff:  "It's been a
> surprise many authors and publishers just aren't bothering with it."  My
> question did not have to do with problems individual authors may have,
> practical or psychological.  It had to do with publishers.  As I wrote, it
> seems it is not that easy for publishers to automate registration.  On the
> Commission, we have discussed this as a step that would mean authors would
> not have to do it -- so names created even those who would not have
> registered them in in ZooBank will be in ZooBank if they were to be
> published in a journal that, as a matter of routine, registered its names.
> It was my understanding that that is what Zookeys does.  But perhaps I am
> wrong on both counts?
>
> My point was that it may be that publishers "aren't bothering with it"
> because it is considered burdensome.  There may come a time registration
> will be as routine as any other step in the nomenclatural process, but if
> we want to encourage registration, it is in our interests to make it as
> simple as possible.  It seems not to be simple enough yet.
>
>
> Sincerely,
> Daphne
>
> Daphne G. Fautin
> Professor, Ecology and Evolutionary Biology University of Kansas
> 1200 Sunnyside Avenue
> Lawrence, Kansas 66045 USA
>
> telephone 1-785-864-3062
> fax 1-785-864-5321
> skype user name daphne.fautin
> cv: www.nhm.ku.edu/inverts/daphne.html
>
>     database of hexacorals, including sea anemones
>        most recent version released 2 January 2013
> hercules.kgs.ku.edu/Hexacoral/Anemone2/index.cfm
>
> ________________________________________
> From: Frank T. Krell [Frank.Krell at dmns.org]
> Sent: Wednesday, April 08, 2015 10:19 PM
> To: Fautin, Daphne G.; gread at actrix.gen.nz; Michael Heads
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] are early online publications code-compliant?
>
> I thought that ZooKeys still registers manually - Lyubo?
> Registration of works (papers) before publication is fast and easy. No
> burden at all.
> Establishing an automated registration system with xml markup etc. is
> certainly more elegant, but more complicated to establish. Manually it is
> no problem.
> Has anybody ever had a problem to register a work in ZooBank?
>
> Frank
>
> Dr. Frank-T. Krell
> Curator of Entomology
> Commissioner, International Commission on Zoological Nomenclature Chair,
> ICZN ZooBank Committee Department of Zoology Denver Museum of Nature &
> Science
> 2001 Colorado Boulevard
> Denver, CO 80205-5798 USA
> Frank.Krell at dmns.org
> Phone: (+1) (303) 370-8244
> Fax: (+1) (303) 331-6492
> http://www.dmns.org/science/museum-scientists/frank-krell
> lab page: http://www.dmns.org/krell-lab
>
>
>
> ________________________________________
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Fautin,
> Daphne G. <fautin at ku.edu>
> Sent: Wednesday, April 8, 2015 9:02 PM
> To: gread at actrix.gen.nz; Michael Heads
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] are early online publications code-compliant?
>
> I was stunned to learn that a major publisher that wanted to emulate
> ZooKeys and have new names be registered by the publisher (to be sure it
> happens -- and lessen the responsibilities of the authors, as well as
> minimize errors) found it is so difficult the IT division of this publisher
> could not handle it.  I am pursuing details, but this route has been
> proposed to increase users and it may be too difficult.  So it may not be
> that publishers are unaware or do not care -- they may find it impractical
> to comply.
>
>
> Daphne
>
> Daphne G. Fautin
> Professor, Ecology and Evolutionary Biology University of Kansas
> 1200 Sunnyside Avenue
> Lawrence, Kansas 66045 USA
>
> telephone 1-785-864-3062
> fax 1-785-864-5321
> skype user name daphne.fautin
> cv: www.nhm.ku.edu/inverts/daphne.html
>
>     database of hexacorals, including sea anemones
>        most recent version released 2 January 2013
> hercules.kgs.ku.edu/Hexacoral/Anemone2/index.cfm
>
> ________________________________________
> From: Taxacom [taxacom-bounces at mailman.nhm.ku.edu] on behalf of Geoffrey
> Read [gread at actrix.gen.nz]
> Sent: Wednesday, April 08, 2015 9:55 PM
> To: Michael Heads
> Cc: gread at actrix.gen.nz; taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] are early online publications code-compliant?
>
> Hi Michael,
>
> Yes, that's true. Usages are happening of these names that are in limbo
> before print. Once released out in the wild there's no going back.
> However, under the Zoo Code they're not yet available.  They're sort of
> interim nomina nuda and don't yet enter formal nomenclature. There is a
> risk for authors that actions in other fully compliant taxonomic papers may
> gain priority over them.
>
> WoRMS is about recording all aquatic names & evaluating their Code status.
> My own practice for WoRMS polychaete edits is to record limbo new names in
> the usual detail, but with an appropriate warning.  I'll think hard before
> implementing new synonymies before they're in print, although I can mention
> they are pending.  I'd rather not be doing this extra work, but I am
> because a simple new Code recording mechanism isn't being adhered to by
> various parties.
>
> Long term the ZooBank requirement may fail to take hold, but we aren't
> there yet.  It's been a surprise many authors and publishers just aren't
> bothering with it.  Ignorance or don't care? Suspect both. I've done my bit
> talking about the need for ZooBank registration to peers.  The paper in
> prep on electronic works Frank Krell mentioned surely will raise awareness.
>
> Geoff
>
> On Thu, April 9, 2015 12:41 pm, Michael Heads wrote:
> > Geoff,
> >
> > As you emphasized earlier, if the article was publically available on
> > the net in 2014, in this day and age it's de facto published in 2014.
> > It's natural that the author of the 2014 'internet names',  doesn't
> > see a problem, especially if they have grown up with the internet. If
> > it is a problem for WoRMS then WoRMS need to change their rules. It is
> > quite possible that I and other biogeographers, systematists,
> > ecologists, conservationists etc. have already used the 'unpublished'
> 'internet names'
> > from the Cladistics 2014 paper in our own publications - this is now
> > standard practice.
> >
> > Michael
> >
> > On Thu, Apr 9, 2015 at 11:59 AM, Geoffrey Read <gread at actrix.gen.nz>
> > wrote:
> >
> >> Today I'm looking at an example of non-availability in Wiley's
> >> 'Cladistics'.  The article has been online unaltered since mid July
> >> 2014, nine months ago, and is still unassigned to an issue. The pdf
> >> has no publication date, and (of course) is unregistered in ZooBank.
> >> The author is quite oblivious of any problem I might have in
> >> including his intended four new genera, correctly formally defined,
> >> as valid names in WoRMS.
> >>
> >> I shall watch this one with interest to see what date the publisher
> >> finally puts on it. Currently the apparent version of record is just
> >> copyright 2014, which is obviously not going to be correct for
> >> nomenclature.
> >>
> >> This scenario is so easily avoided. However, conversely we know what
> >> happens to rules more ignored than complied with.
> >>
> >> Geoff
> >>
> >> On Tue, April 7, 2015 5:14 pm, Frank T. Krell wrote:
> >> > Geoff,
> >> > yes, if there is no evidence for ZooBank registration in an
> >> > electronic paper, it is not available for nomenclatural purposes.
> >> > The
> >> nomenclatural
> >> > acts will be available from the paper publication.
> >> > My paper just dealt with the publication models, assuming that all
> >> other
> >> > criteria for availabilities are fulfilled.
> >> > It now becomes increasingly obvious that a large number of editors
> >> > is agnostic towards the criteria of availability. With
> >> > co-commissioners Thomas Paper and Rich Pyle, I am currently
> >> > preparing a paper
> >> explaining
> >> > what the "Works" are that need to be registered in order to be
> >> available
> >> > in electronic form.
> >> > Electronic publication for nomenclatural purposes is still new. It
> >> > is expected that everybody needs some time to adapt, and we do what
> >> > we
> >> can
> >> to
> >> > help.
> >> > Cheers
> >> >
> >> > Frank
> >> >
> >> > Dr. Frank-T. Krell
> >> > Curator of Entomology
> >> > Commissioner, International Commission on Zoological Nomenclature
> >> > Chair, ICZN ZooBank Committee Department of Zoology Denver Museum
> >> > of Nature & Science
> >> > 2001 Colorado Boulevard
> >> > Denver, CO 80205-5798 USA
> >> > Frank.Krell at dmns.org
> >> > Phone: (+1) (303) 370-8244
> >> > Fax: (+1) (303) 331-6492
> >> > http://www.dmns.org/science/museum-scientists/frank-krell
> >> > lab page: http://www.dmns.org/krell-lab
> >> >
> >> >
> >> > ________________________________________
> >> > From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of
> >> > Geoff
> >> Read
> >> > <gread at actrix.gen.nz>
> >> > Sent: Monday, April 6, 2015 11:01 PM
> >> > To: taxacom at mailman.nhm.ku.edu
> >> > Subject: Re: [Taxacom] are early online publications code-compliant?
> >> >
> >> > Dear Frank,
> >> >
> >> > I refer to your p25 "Cambridge’s FirstView articles are available
> >> for the
> >> > purposes of zoological nomenclature.".  The problem one for me and
> >> others
> >> > at WoRMS is 'Journal of the Marine Biological Association of the
> >> United
> >> > Kingdom' but I glanced at their 'Bulletin of Entomological Research'.
> >> The
> >> > 'publication model' at Cambridge may potentially conform as regards
> >> > version of record, but as there is no ZooBank registration done by
> >> > the editors, there is no availability until print unless authors
> >> > are sufficiently aware to do it themselves and put it in the MS.
> >> > Yet to
> >> see
> >> > one of those for JMBAUK.
> >> >
> >> > Cheers,
> >> >
> >> > Geoff Read
> >> >
> >> >
> >> > -----Original Message-----
> >> > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf
> >> > Of Frank T. Krell
> >> > Sent: Tuesday, 7 April 2015 9:49 a.m.
> >> > To: Taxacom (taxacom at mailman.nhm.ku.edu)
> >> > Subject: [Taxacom] are early online publications code-compliant?
> >> >
> >> > Hi all,
> >> > In the last issue of the Bulletin of Zoological Nomenclature I
> >> published
> >> a
> >> > paper scrutinizing major publishers' models for early online
> >> publications,
> >> > i.e. paper published on the web before they get integrated into a
> >> journal
> >> > issue. I suggested a solution based on the NISO guidelines for
> >> publishers
> >> > on journal article versions. In short, I suggest that if the early
> >> online
> >> > publication is the Version of Record, it should be considered the
> >> final
> >> > version and nomenclaturally available. The paper can be downloaded
> >> here
> >> > (line two from below):
> >> >
> >> http://www.dmns.org/science/museum-scientists/frank-krell/krell-lab-e
> >> ntomology-program/updates/online-pre-publications-and-nomenclature/
> >> >
>
>
>
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> Celebrating 28 years of Taxacom in 2015.
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>



-- 
Dr. David Campbell
Assistant Professor, Geology
Department of Natural Sciences
Box 7270
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