[Taxacom] e-publication of EarlyView: clarification needed

Donat Agosti agosti at amnh.org
Wed Sep 12 11:13:45 CDT 2012

There is also a further development, that is the use of XML to semantically enhance and link an article. This way a structure is given to an article, that for example defines where a protologue or other treatments begins and ends, what the nomenclatorial elements are, what the descricption etc. The structure is thus more than the traditional html but semantic mark up, defining the content within an element. Though there is no use of doi or aquivalent assigned to the treatments, this could, and in my view should, be done and linked to during the registration process. Right  now, a link from the treatment is included for a Zoobank LSID that is obtained during the registration process. Why not assign a doi/equivalent and add this during the registration?

All the elements for this are here and in use for several years. Zookeys (and their sisters like Phytokeys, Mycokeys, Journal of Hymenoptera Research, adopted the National Library of Medicine Archiving and Publishing Tagset that has been extended to include taxonomy domain specific elements (TaxPub NLM DTD) which allows not just publishing hard copies, html and pdf but also xml as well as automatically export particular parts of the article.
New descriptions are directly harvested by EOL, all the articles by Plazi which is the source for other harvesters. In this process, for each of the treatment a unique identifier is issues for each treatment - a process that could be done during the journal production workflow, and with that, the discussion of pagination, discovering a treatment would be resolved. It would also allow to create direct links not just to the paper, but the right content in the referred source.

Technology is here - we must make best use of it, even if this is a bit more complex then writing a html page.


P.S. A further advantage of going the NLM DTD avenue is the possibility to register the journal at PubMedCentral and with that having most likely the best guarantee for long term archiving.

From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of David Campbell
Sent: Wednesday, September 12, 2012 8:18 PM
Subject: Re: [Taxacom] e-publication of EarlyView: clarification needed

> Why the obsession with pagination? If an article is online and has a DOI then it's published. Use the DOI to refer to the article. CrossRef has tools which can take a DOI and tell you when the article went online (and, indeed, when it was printed if that's applicable), and also whether the article has been updated (see http://www.crossref.org/crossmark/ ).
> Much of the discussion about digital publication seems to have the 
> cart before the horse. Publishers are going digital only, physical 
> pagination is less and less relevant, and articles are being given 
> unique identifiers (such as DOIs) that provide many of the services we 
> need. I guess we're still working this thing out, but it's time to 
> stop treating digital publication as if it worked the same way as 
> print.<

The difficulty here is largely a matter of adjusting from existing tradition-does the journal that I'm writing for have a good system for bibliographic citation of online publications?  how do I convey the location of something within an online text in a way that is useful to a human reader?  It should not be hard to do this, but it needs to be done in a way that is both human and computer friendly.

Although I would expect that the vast majority of publishers are using DOI's, etc., relying on them as the sole way to refer to an article depends on it being a universal, consistent, and persistent reference.
 Not knowing much about the programming end of bioinformatics, I don't know how thoroughly those issues have been addressed in any given system, though no doubt they have been considered.

The flexibility of online publication makes it potentially difficult to identify what is an official final version of a publication.  The example of online early publication of non-final drafts is a particularly conspicuous version, but more generally there's always the urge to go back and make corrections or, among the less ethical, to make it look as though you published more earlier than you actually did.  These issues affect print as well-multiple printings of taxonomic books often have unheralded changes between editions, and poor-quality, hastily published material can be found on paper.  A handful of freshwater mussel genera and type designations come from the corrigenda to Frierson, which was apparently issued separately from the main text as it's not present in all copies and pasted into either the front or the back in the copies that have it.  Thus, I can't pin down the date more precisely than between the original printing and the first subsequent mention of the new names, two years later (Zoological Record was rather late in noticing them).  In a way, online has an advantage, because files should have some sort of dates on them, if you know where to look.  The difficulty is that the ease of producing multiple versions is much higher, and it may not be easy to determine how many versions there are and which one you happened to read.

Dr. David Campbell
Visiting Professor
Department of Natural Sciences
Gardner-Webb University
Boiling Springs NC 28017


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