[Taxacom] e-publication of EarlyView: clarification needed

Richard Zander Richard.Zander at mobot.org
Wed Sep 12 11:25:30 CDT 2012

Interesting how digitization may affect taxonomic practice.

My understanding is that digitizers do not define the protologue, this
is a considered opinion of the next person who reads the article about
what is relevant to what the author meant in his original paper. If a
paper cited in the bibliography includes information that helps define
the type, that is then part of the protologue. 

I wonder to what extent xml and other formatting are intended to do our
thinking for us. In some instances, this could be a boon and lessen
mistakes, in other instances it is a bias introduced by a third party
who may have no expertise in the group or in the tedious definitions
associated with nomenclatural methods.

Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA  
Web sites: http://www.mobot.org/plantscience/resbot/ and
Modern Evolutionary Systematics Web site:
UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Donat Agosti
Sent: Wednesday, September 12, 2012 11:14 AM
To: 'TAXACOM'; Roderic Page
Subject: Re: [Taxacom] e-publication of EarlyView: clarification needed

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.

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