[Taxacom] are early online publications code-compliant?

John Noyes j.noyes at nhm.ac.uk
Tue Apr 14 04:41:36 CDT 2015


Hi Rich,

In general I would agree with you, but I fancy it would be hard to convince the majority of taxonomists out there that they must register their taxonomic acts on ZooBank before they become available, even by the time the 5th edition of the Code comes out. At present this is done by a some publishers (not for free) but only very, very few. 

As Stephen has alluded to, registration alone (as you seem to favour) would not work unless it became mandatory for the equivalent of a "published" taxonomic act to be deposited and made freely available on ZooBank at the time if its registration. Otherwise there would be a risk that nomenclatural acts would be made available without any certainty that the details supporting that nomenclatural act would continue to exist into the future; i.e. you could end up with a meaningless list of the entirety of all available names/acts in one easily replicated file without any information being available to support those acts. 

John

John Noyes
Scientific Associate
Department of Life Sciences
Natural History Museum
Cromwell Road
South Kensington
London SW7 5BD 
UK
jsn at nhm.ac.uk
Tel.: +44 (0) 207 942 5594
Fax.: +44 (0) 207 942 5229

Universal Chalcidoidea Database (everything you wanted to know about chalcidoids and more):
www.nhm.ac.uk/chalcidoids 


-----Original Message-----
From: Richard Pyle [mailto:pylediver at gmail.com] On Behalf Of Richard Pyle
Sent: 14 April 2015 10:11
To: John Noyes; 'Frank T. Krell'; 'Sue Gardner'; 'Stephen Thorpe'
Cc: taxacom at mailman.nhm.ku.edu; gread at actrix.gen.nz
Subject: RE: [Taxacom] are early online publications code-compliant?

Well.... ZooBank Registration has been mandatory for all electronic works since 2012, and voluntary for any/all works since 2008.  So far, despite all these issues of pre-publication and dating and such, compliance has been far higher than originally anticipated (2300+ registered users, consistently high rates of registrations, etc.)  

Are we ready right now to abandon the traditional publication model for nomenclatural availability?  ABSOLUTELY NOT!  Could we be ready by the time the 5th Edition is ready?  ABSOLUTELY YES!  At least.... "Yes" from an infrastructural/procedural perspective.  Less certain is the social buy-in, as you and Neal and others have alluded to.

Personally, I believe that a shift of this sort would solve FAR more problems than it creates; and because this is my belief, I will continue to make my best rational case for it.

As for persistence; the concept for GNUB (the database behind ZooBank) is to have replicated copies all over the world.  Currently there are multiple copies on several continents.  These need some fortification, but the concept has been demonstrated.  The copies lag behind the master by about 7-10 seconds.  There is no reason we couldn't extend this "live" replication to dozens or hundreds of simultaneous copies around the world. Additional copies could be generated almost as easily as a PDF file.  The difference is, each PDF file would represent only one published work with its own set of names.  By contrast, the registry database would represent the entirety of all available names in one easily replicated file.

In terms of persistence, my money is on the registry (rather than the totality of zillions of disparate PDFs with varying degrees of archiving and paywalls, etc.)

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: John Noyes [mailto:j.noyes at nhm.ac.uk]
> Sent: Monday, April 13, 2015 10:25 PM
> To: 'deepreef at bishopmuseum.org'; 'Frank T. Krell'; 'Sue Gardner'; 
> 'Stephen Thorpe'
> Cc: taxacom at mailman.nhm.ku.edu; gread at actrix.gen.nz
> Subject: RE: [Taxacom] are early online publications code-compliant?
> 
> Hi Rich,
> 
> Fair enough, but how would you solve this to everyone's satisfaction? 
> At the moment all we have is "publication" as a control of 
> availability. Compulsory registration on ZooBank may be a way but that 
> more than likely would not be universally accepted because of its 
> perceived tenuous nature and other foreseen problems. Printed 
> publications or electronic publications (as PDFs or similar, certainly 
> not HTML etc.) by their nature have many copies and should always be available. Or do you have something else in mind . . . . ?
> 
> John
> 
> John Noyes
> Scientific Associate
> Department of Life Sciences
> Natural History Museum
> Cromwell Road
> South Kensington
> London SW7 5BD
> UK
> jsn at nhm.ac.uk
> Tel.: +44 (0) 207 942 5594
> Fax.: +44 (0) 207 942 5229
> 
> Universal Chalcidoidea Database (everything you wanted to know about 
> chalcidoids and more):
> www.nhm.ac.uk/chalcidoids
> 
> 
> -----Original Message-----
> From: Richard Pyle [mailto:pylediver at gmail.com] On Behalf Of Richard 
> Pyle
> Sent: 13 April 2015 21:32
> To: 'Frank T. Krell'; 'Sue Gardner'; John Noyes; 'Stephen Thorpe'
> Cc: taxacom at mailman.nhm.ku.edu; gread at actrix.gen.nz
> Subject: RE: [Taxacom] are early online publications code-compliant?
> 
> I've generally been staying out of this discussion -- in part because 
> this horse has already been repeatedly beaten to a pulp; and in part 
> because I've just been too busy with other things.  However, I 
> happened to re-read something just now that PERFECTLY captures my own 
> perspective of how to solve all of
> this:
> 
> "...it seems likely, in the longer term, and with the development of 
> new information systems, that the solution will not lie in patching up 
> a definition of publication but, rather, in scrapping it and finding a 
> means of replacing "publication" as a primary determinant of availability."
> 
> Brilliant!  EXACTLY right, in my opinion!
> 
> By the way, here's the source of the quote:
> http://www.nhm.ac.uk/hosted-
> sites/iczn/code/index.jsp?booksection=introduction
> [Second paragraph under the heading "Development of underlying 
> principles"]
> 
> 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: Frank T. Krell [mailto:Frank.Krell at dmns.org]
> > Sent: Monday, April 13, 2015 5:55 AM
> > To: Sue Gardner; John Noyes; 'Stephen Thorpe';
> 'deepreef at bishopmuseum.org'
> > Cc: taxacom at mailman.nhm.ku.edu; gread at actrix.gen.nz
> > Subject: RE: [Taxacom] are early online publications code-compliant?
> >
> > Taxonomists vote already with their feet by choosing where to submit.
> > Many of them are happy with early online publication and don't care 
> > about changing page numbering, some are not. I am afraid there won't 
> > be a unified voice.
> > I have no problems with changing metadata although it is a nuisance 
> > - BUT with increasing single article publishing, I am pretty sure 
> > that the problem will largely go away.
> >
> > 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: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf
> Of
> > Sue Gardner
> > Sent: Monday, April 13, 2015 8:20 AM
> > To: John Noyes; 'Stephen Thorpe'; 'deepreef at bishopmuseum.org'
> > Cc: taxacom at mailman.nhm.ku.edu; gread at actrix.gen.nz
> > Subject: Re: [Taxacom] are early online publications code-compliant?
> >
> > John posed an important question: "Shouldn't the taxonomists be 
> > telling the publishers how to do this and not the other way around?"
> >
> > As an observer off to the side, I have to chime in and say:
> > -absolutely yes-. The publishers should cater to your needs. As 
> > taxonomists, you should not have to adapt to their choices. Be 
> > clear, objective, and preferably unified in your voice on this and, 
> > if one publisher doesn't serve your needs, move along to a publisher that does.
> >
> > Sue Ann Gardner, MLS
> > Scholarly Communications Librarian
> > Discovery and Resource Management
> > 302S Love Library
> > University of Nebraska-Lincoln
> > Lincoln, Nebraska 68588-4100 USA
> > sgardner2 at unl.edu
> > 402-472-8566
> >
> > ________________________________________
> > From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of John 
> > Noyes <j.noyes at nhm.ac.uk>
> > Sent: Monday, April 13, 2015 3:54 AM
> > To: 'Stephen Thorpe'; 'deepreef at bishopmuseum.org'
> > Cc: taxacom at mailman.nhm.ku.edu; gread at actrix.gen.nz
> > Subject: Re: [Taxacom] are early online publications code-compliant?
> >
> > Hi Stephen,
> >
> > I am not being inflexible on this. I am trying to be objective 
> > (which really should be viewed as being more constructive rather than less).
> > It is not a matter of recognising the availability of new names. It 
> > is a matter of the date upon which these names and nomenclatural 
> > acts become available - from the prepub date or from the publication 
> > date of the compiled version. It is also a matter of which 
> > pagination and volume number to use (on occasion there is only a 
> > DOI) when citing the article or its contents. Shouldn't the 
> > taxonomists be telling the publishers how to do this and not the 
> > other way around? I have no argument with publishers who publish 
> > with fixed metadata - it is more with those that publish with 
> > variable metadata. After all if more than one publisher (there are 
> > at least three that I know of) can publish with fixed metadata then they could all could do it very easily.
> > Personally I do not really see there is any wiggle room in the Code 
> > on this if you try to be completely objective about it. It says what 
> > it says irrespective of whether there is any mention of specific 
> > types of prepubications or metadata. If there is any disagreement in 
> > the
> interpretation of what is stated in the Code then it needs to be 
> changed so that there is only one way of interpreting it.
> >
> > John
> >
> > John Noyes
> > Scientific Associate
> > Department of Life Sciences
> > Natural History Museum
> > Cromwell Road
> > South Kensington
> > London SW7 5BD
> > UK
> > jsn at nhm.ac.uk
> > Tel.: +44 (0) 207 942 5594
> > Fax.: +44 (0) 207 942 5229
> >
> > Universal Chalcidoidea Database (everything you wanted to know about 
> > chalcidoids and more):
> > www.nhm.ac.uk/chalcidoids
> >
> >
> > -----Original Message-----
> > From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
> > Sent: 09 April 2015 21:54
> > To: 'deepreef at bishopmuseum.org'; John Noyes
> > Cc: taxacom at mailman.nhm.ku.edu; gread at actrix.gen.nz
> > Subject: RE: [Taxacom] are early online publications code-compliant?
> >
> > Hi John,
> >
> > I have some sympathy with your views, but I don't see it as 
> > constructive to be inflexible on this. The reality is that 
> > e-publication in zoology was largely influenced by one person, who's 
> > publishing company does not prepublish without already fixed metadata.
> > This is largely because that person has complete control over all 
> > stages of publication. Many other publishers are not like this. The 
> > electronic amendment really hasn't taken them into account properly.
> > But given that there is wiggle room in the Code to allow prepubs 
> > without metadata (it is not explicit, but neither is it explicitly 
> > ruled out), I
> think we should run with it rather than fail to recognise a great many 
> new names.
> > New names can fail to be strictly speaking available for all sorts 
> > of subtle reasons, but there is really no harm in continuing to use 
> > those names for taxa that would otherwise be without any name.
> >
> > Cheers,
> >
> > Stephen
> >
> > --------------------------------------------
> > On Thu, 9/4/15, John Noyes <j.noyes at nhm.ac.uk> wrote:
> >
> >  Subject: RE: [Taxacom] are early online publications code-compliant?
> >  To: "'Stephen Thorpe'" <stephen_thorpe at yahoo.co.nz>, 
> > "'deepreef at bishopmuseum.org'" <deepreef at bishopmuseum.org>
> >  Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>, 
> > "gread at actrix.gen.nz" <gread at actrix.gen.nz>
> >  Received: Thursday, 9 April, 2015, 9:15 PM
> >
> >  Hi Stephen,
> >
> >  As you know, I disagree with
> >  you and a few others with regards to the so-called metadata.
> >  I believe that the page numbers and volume numbers are part  of the 
> > article because, as you say, they act as a signpost  to specific 
> > parts of the
> article.
> > Where does  "metadata" start and end? For instance, if for  some 
> > reason, the figure numbers were changed but the actual  content of 
> > the article were not changed then do figure  numbers constitute 
> > metadata as they only point to specific  parts of the article. The 
> > same could be said of other  information. So far as I know there is 
> > no definition of  metadata in the Code and as it stands 
> > prepublications are in conflict with the code if any part of the 
> > article is changed  and that includes pages numbers, volume numbers 
> > etc. Until  such a time that metadata is defined in the code and the  
> > code says that changes in metadata are allowed and do not  make the 
> > prepublication unavailable then I, and others,  shall continue to regards prepubs as unavailable.
> > I hope  there is a change in the Code that defines this one way or 
> > the other, but at the same time I hope this change is not  
> > retrospective as the
> fourth edition was because this causes  all sorts of unseen, unwanted problems.
> >
> >  John
> >
> >  John
> >  Noyes
> >  Scientific Associate
> >  Department of Life Sciences
> >  Natural History Museum
> >  Cromwell
> >  Road
> >  South Kensington
> >  London
> >  SW7 5BD
> >  UK
> >  jsn at nhm.ac.uk
> >  Tel.: +44 (0) 207 942 5594
> >  Fax.: +44 (0) 207 942 5229
> >
> >  Universal Chalcidoidea Database (everything you  wanted to know 
> > about chalcidoids and more):
> >  www.nhm.ac.uk/chalcidoids
> >
> >
> >  -----Original Message-----
> >  From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
> >
> >  Sent: 08 April 2015 21:47
> >  To: 'deepreef at bishopmuseum.org';
> >  John Noyes
> >  Cc: taxacom at mailman.nhm.ku.edu;
> >  gread at actrix.gen.nz
> >  Subject: RE: [Taxacom] are early online  publications code-compliant?
> >
> >  John,
> >
> >  The
> >  prepub and the "compiled" article are *the same
> >  version* (or should be). The metadata isn't part of the  article, 
> > so if two articles differ only in metadata, they  are the same version.
> > Versions differ only if the content  differs. The metadata is useful 
> > for signposting (e.g. the  start page of a description in a long 
> > article), so it makes  sense to use the compiled page numbers when 
> > these are  assigned (and before then, or alternatively, one can use, 
> > e.g. [6] for the sixth page of the article). There may be a  problem 
> > for e-only publications without pagination, but  these are still rare.
> > I do not understand you when you say  [quote] However when the 
> > compiled version is published the  prepublication is no longer 
> > available (or am I wrong here)  only the compiled version, with the 
> > different pagination and  volume number, is available [unquote]. Do 
> > you
> mean  "available" in the nomenclatural sense, or in the  everyday sense?
> >
> >  Cheers,
> >
> >  Stephen
> >
> >  --------------------------------------------
> >  On Wed, 8/4/15, John Noyes <j.noyes at nhm.ac.uk>
> >  wrote:
> >
> >   Subject: RE:
> >  [Taxacom] are early online publications code-compliant?
> >   To: "'deepreef at bishopmuseum.org'"
> >  <deepreef at bishopmuseum.org>,
> >  "'Stephen Thorpe'" <stephen_thorpe at yahoo.co.nz>
> >   Cc: "taxacom at mailman.nhm.ku.edu"
> >  <taxacom at mailman.nhm.ku.edu>,
> >  "gread at actrix.gen.nz"
> >  <gread at actrix.gen.nz>
> >   Received: Wednesday, 8 April, 2015, 11:11  PM
> >
> >   Dear Rich and
> >  others,
> >
> >   I still have this
> >  problem
> >   about prepubs (EarlyView, etc.). I  know that many of you  think 
> > that "metadata" is  not important, but when maintaining a taxonomic 
> > catalogue  it is difficult to know whether one should enter the  
> > pagination of the  prepublication or that of the
> compiled  publication.
> > The  correct pagination is important,  especially where many taxa  
> > are dealt with in the same  publication. There is also the  problem 
> > of volume number which is often omitted from the  prepublication. If 
> > the version of record, in the case of  prepublications, is the  
> > version where the name is first made  available then this  is the 
> > one that has the correct  pagination. However when  the compiled 
> > version is published  the prepublication is no  longer available (or am I wrong
> >   here) only
> >  the compiled version, with the different  pagination and  volume 
> > number, is available. I know it seems  to be a minor  thing but it 
> > becomes important (to me at
> >
> >  least) when cataloguing or maintaining a database, whether  it be 
> > on-line or otherwise. I am glad that Frank is trying  to clear up 
> > the problem, but in my view, we are being  pushed  into this by the 
> > publishers and
> it is unnecessary.
> >  I do not  think that prepublications are necessary in  taxonomy. At 
> > the  moment we have two differing views, one  driven by the 
> > publishers (that prepublications are OK),  and one that is  held by 
> > the majority of taxonomists that I  have discussed  this with (that 
> > prepubs are not OK). If  publishers could include the correct 
> > pagination and volume  number
> with the
> >   (uncompiled) prepublication
> >  (i.e. an exact copy of the  compiled version then I would  have no 
> > problem in accepting  the publication as available,  but as it 
> > stands I find this  difficult because it is  apparently in conflict 
> > with the code  as it
> stands.
> >
> >   John
> >
> >   John Noyes
> >   Scientific
> >  Associate
> >   Department
> >   of
> >  Life Sciences
> >   Natural History Museum
> >   Cromwell Road
> >   South
> >   Kensington
> >   London SW7 5BD
> >   UK
> >   jsn at nhm.ac.uk
> >   Tel.: +44 (0) 207 942 5594
> >
> >  Fax.: +44 (0) 207 942 5229
> >
> >   Universal Chalcidoidea Database (everything  you  wanted to know 
> > about chalcidoids and more):
> >   www.nhm.ac.uk/chalcidoids
> >
> >
> >
> >   -----Original
> >  Message-----
> >   From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
> >   On Behalf Of Richard Pyle
> >
> >  Sent: 07 April
> >   2015 07:39
> >
> >  To: 'Stephen Thorpe'
> >   Cc: taxacom at mailman.nhm.ku.edu;
> >   gread at actrix.gen.nz
> >   Subject: Re: [Taxacom] are early online  publications code-compliant?
> >
> >   > Even that is somewhat unclear. If the  PDF  is reupped with 
> > (previously  >
> > missing)  evidence  of ZooBank preregistration (where "pre-"
> >   means
> >   > "before the
> >  date
> >   reupped"), then it might be
> >  available before the  > print edition, but there are a  lot of  complexities ...
> >
> >
> >  The
> >   general consensus -- at least among  Commissioners I have  
> > discussed this with -- is that a work  becomes available the  moment 
> > it fulfills all requirements  of the Code.  This has  always been 
> > true for printed  works; and there is no reason  to think it should 
> > be any  different for electronic works.
> >   Using your
> >  hypothetical example above, the moment the  "reupped" PDF (with 
> > included evidence for  ZooBank
> >   registration) is obtainable (and
> >  assuming all other criteria  are fulfilled), is the moment  the 
> > work becomes available.  The same would apply to cases  when the 
> > ZooBank record is subsequently updated to include  required 
> > elements, such as the ISSN or indication of an  online Archive.
> >
> >   Not
> >  really all that complex,
> >   actually.
> >
> >   Of course, all of
> >   these problems will vanish when if/when we  adopt the 
> > Registered=Available model of registration  (leaving  "Publication" 
> > to the realm of science;  not part of  the realm of nomenclatural availability).
> >
> >   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
> >
> >
> >
> >
> >  _______________________________________________
> >   Taxacom Mailing List
> >   Taxacom at mailman.nhm.ku.edu
> >   http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >   The Taxacom Archive back to 1992 may be  searched at:
> > http://taxacom.markmail.org
> >
> >   Celebrating 28 years of
> >   Taxacom in 2015.
> >
> >
> > _______________________________________________
> > Taxacom Mailing List
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> > http://taxacom.markmail.org
> >
> > Celebrating 28 years of Taxacom in 2015.
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> >
> > Celebrating 28 years of Taxacom in 2015.




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