[Taxacom] are early online publications code-compliant?

Richard Pyle deepreef at bishopmuseum.org
Thu Apr 9 12:03:15 CDT 2015


Hi Daphne,

The automatic registration system requires that content be submitted from the Publisher to ZooBank in a structured way -- so that the computer can break apart the information and enter it directly in the database (the same way that a human breaks apart the information and enters it in a form on the ZooBank website).  On the web, structured information is represented as XML.  Fortunately, there is an XML standard that has been developed (mostly by the people at PLAZI) for XML markup of publications to capture taxonomic and nomenclatural information in a structured way.  This standard, called "TaxPub" is a formal extension to the Journal Article Tag Suite (JATS; http://jats.nlm.nih.gov/).

Pensoft (very wisely) has adopted this international standard when producing the XML versions of their published articles, and for this reason, we are able to automatically harvest content from those XML files and perform automatic registration from them.

Unfortunately, most journals do not conform to the TaxPub extension of JATS in their XML versions of articles (some don't even conform to JATS).  That leaves us with two options:
1) Encourage journals to adopt the international JATS/TaxPub XML standard; or
2) Build a custom automatic registration routine for every individual Journal, to match whatever XML structure they happen to be using.

We could write a grant proposal to pay for developers to do option number 2 (it would be pretty expensive, but within the scope of a large NSF grant).  However, it would require an enormous ongoing maintenance cost to keep each of those custom routines updated whenever a journal changes its XML schema, or whenever a new Journal wants to be able to submit content automatically.  But the real problem is that most of the XML schemas currently used by Journals do not actually tag the information that ZooBank needs.  In other words, even if we did have the resources to build custom XML import routines for each individual journal, most of them wouldn't work because the necessary information for ZooBank information is not tagged.

Given that advantages for journals to produce XML versions of their articles in an international markup standard like JATS/TaxPub are HUGE (the ability to perform automatic registrations through ZooBank is just a tiny, tiny, tiny part of the benefits of conforming to such a standard), I think it makes MUCH more sense to commit the resources to helping Journals conform to the standard.  If we spend money to develop custom import routines for ZooBank for each Journal, then we've built a largely unsustainable/non-scalable system that allows selected journals to perform one task with one system (ZooBank).  Conversely, if we instead devoted those resources to helping Journals conform to the standards in producing XML versions of their works, the entire community benefits, the Journals benefit, and the structured XML versions of those journals become enormously more powerful and useful for a potentially wide range of data services (of which ZooBank is only one).

If you have any ideas for other ways to lower the inertial barriers for automatic registration, I'd love to hear them.  For example, one thing I think that could help everyone is to put more emphasis on retrospective name capture within ZooBank.  I'm sure there are other things we can do as well, if we were creative and if we had the resources.  But building custom automatic registration systems for individual Journals doesn't seem like a wise use of our (VERY) limited resources.

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: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
> Fautin, Daphne G.
> Sent: Thursday, April 09, 2015 5:42 AM
> To: Lyubomir Penev
> Cc: gread at actrix.gen.nz; taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] are early online publications code-compliant?
> 
> I did not say the difficulties are insurmountable -- I wrote that publishers "may
> find it impractical to comply."  On the Commission, we have talked of making
> the process as easy as possible to encourage compliance.  Here, it seems, is an
> opportunity to lower the inertial barriers.
> 
> 
> 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: Lyubomir Penev [lyubo.penev at gmail.com]
> Sent: Thursday, April 09, 2015 2:51 AM
> To: Fautin, Daphne G.
> Cc: gread at actrix.gen.nz; Michael Heads; taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] are early online publications code-compliant?
> 
> Well, Daphne, it is more a matter of willingness and commitment rather than
> of insurmountable difficulties.
> 
> To answer the question of Frank - yes, since two years ZooKeys and all other
> Pensoft journals that publish new names submit to and get data from ZooBank
> via XML, normally a few hours before publication, when the actual metadata
> are fixed. It takes seconds but saves a great amount of effort for the authors
> and reduces the probability of errors.
> 
> Cheers,
> Lyubo
> 
> On Thu, Apr 9, 2015 at 6:02 AM, Fautin, Daphne G.
> <fautin at ku.edu<mailto:fautin at ku.edu>> wrote:
> 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<tel:1-785-864-3062>
> fax 1-785-864-5321<tel:1-785-864-5321>
> skype user name daphne.fautin
> cv:
> www.nhm.ku.edu/inverts/daphne.html<http://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<http://hercules.kgs.ku.ed
> u/Hexacoral/Anemone2/index.cfm>
> 
> ________________________________________
> From: Taxacom [taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-
> bounces at mailman.nhm.ku.edu>] on behalf of Geoffrey Read
> [gread at actrix.gen.nz<mailto:gread at actrix.gen.nz>]
> Sent: Wednesday, April 08, 2015 9:55 PM
> To: Michael Heads
> Cc: gread at actrix.gen.nz<mailto:gread at actrix.gen.nz>;
> taxacom at mailman.nhm.ku.edu<mailto: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<mailto: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<mailto:Frank.Krell at dmns.org>
> >> > Phone: (+1) (303) 370-8244<tel:%28%2B1%29%20%28303%29%20370-
> 8244>
> >> > Fax: (+1) (303) 331-6492<tel:%28%2B1%29%20%28303%29%20331-6492>
> >> > 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<mailto:taxacom-
> bounces at mailman.
> >> > nhm.ku.edu>> on behalf of Geoff
> >> Read
> >> > <gread at actrix.gen.nz<mailto:gread at actrix.gen.nz>>
> >> > Sent: Monday, April 6, 2015 11:01 PM
> >> > To:
> taxacom at mailman.nhm.ku.edu<mailto: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<mailto:taxacom-
> bounces at m
> >> > ailman.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<mailto: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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> 
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