[Taxacom] iSpecies with Wikipedia

Tue Apr 1 03:16:18 CDT 2008

I could agree with Doug that we ought to have one or few journals publishing
taxonomic descriptions, all of which are open access.

It might be hard though to change a culture including, to the best of my
knowledge, well over 1,000 journals publishing descriptions, to a few
dedicated "journals" as happened in microbial systematics.

That it could be happen is indicated by Zootaxa who has a huge turnover and
increase of production: 
3600 papers describing 7200 new taxa since 2001. 
The journal has over 130 subject editors and over 4,000 active authors. 
The current output are 50-60 publications per week.
It adopted not a full open access policy, but authors can pay a minimal fair
of US20 per page to make their publications open access, and the
descriptions are explicitly exempt from copyright and can be used for
website (understanding that a citation is attached).

Also, GBIF funded ZooTaxa, Zoobank and Plazi to mark up in TaxonX all their
fish, and platygasteroid publications to demonstrate the power of having xml
versions of the publications, a dedicated server to access the publications
(see eg http://plazi.org:8080/GgSRS/search , journal/publisher =Zootaxa for
how this looks like). The mark-up includes as well enhancements of specific
elements like scientific names, collecting events or bibliographic records
with LSID.

Through a collaboration with the National Library of Medicine and Plazi, a
full publishing NLM XML schema including taxononmic specific elements are
being developed, and funding has been requested to figure out how to change
the journal production workflow of Zootaxa to produce XML during the
production of the article. The more elements like Turbotaxonomy can be
embedded into this production, the more efficient it will be.

If initiatives like EOL would pick up descriptions from such services, it
would be an additional incentive for authors to publish in this fashion: it
is the authors self interest to disseminate their results as widely as
possible! Why rewrite or copy and paste if the original description is
online? Compare for example the descriptions of the fish Chromis abyssus in
Plazi and EOL
http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=30E2AC
E97FCC02A34806994547F8E1F5
with 
http://www.eol.org/taxa/17290368
Right now, there are >5,600 descriptions on plazi, some of it detailed some
very rudimentary, but in many cases, that's all that is known of a
particular species. Another 600 descriptions of new taxa (not mentioning
redescriptions) will be added from the above mentioned Zootaxa mark up.

GoldenGate, our dedicated editor is free and open source, as well as plazi's
search engine.

Besides these increasingly sophisticated new tools, we should not forget
that the easiest way to provide access is through self repositories. Our
community is lagging far behind other areas such as physics. Furthermore, an
increasing number of funding bodies and universities require the deposition
of all publications in self repositories. 
Why aren't we becoming one of the lead players in the field? In fact, to my
knowledge, most of the electronic journals including taxonomic content in
the developing world are open access, whilst our leading publications, eg
Systematic Entomology, are not.
A good introduction for institutions on open access is here
http://cyber.law.harvard.edu/interactive/events/2008/03/suber

and for you as author is here
http://www.earlham.edu/~peters/fos/overview.htm
Also, keep in mind, that we are interested in the content, thus having a
preprint (the version after peer review) online will do.

Finally, the best would be to storm Zoobank with requests to deposit new
names and get LSIDs and at the same to deposit the new descriptions, so they
will be accessible from there.

Donat

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Doug Yanega
Sent: Monday, March 31, 2008 7:29 PM
To: TAXACOM at MAILMAN.NHM.KU.EDU
Subject: Re: [Taxacom] iSpecies with Wikipedia

Paul van Rijckevorsel wrote:

>The issues surrounding the digitization of printed matter are well known,
>copyright figuring heavily among them.
>
>However, the digitization of "neural connections within human brains" comes
>with its own set of issues. Here also, there is the matter of ownership,
not
>only of the person who invested years of work and experience in his human
>brain, but in many cases also of the institute he works for, and the
>government who financed this work.

No one is suggesting that these digital works will not be considered 
publications. ZooTaxa is a journal, but also largely digital. About 
the ONLY differences between ZooTaxa and what folks like Rich and I 
are talking about are (1) ZooTaxa is run by a publisher outside of 
the taxonomic community; myself, I believe the taxonomic community 
needs to organize into a single umbrella society and take 
responsibility for its own publishing, to eliminate copyright as an 
issue once and for all. (2) Even ZooTaxa still relies on small 
numbers of anonymous reviews; the model some of us are advocating 
would be OPEN review - real-time, online, non-anonymous - in the 
fashion of a Wiki. When all the criticisms of a submitted work have 
been dealt with (by accommodating the valid criticisms and dismissing 
the inappropriate ones), the work is then formally "published", and 
any new names proposed therein are formally registered with ZooBank.

>Also, the "without any net cost or encumberance to practicing taxonomists"
>sounds facile. If some bit of information is to be put into words, this is
>not without without "cost or encumberance": it does take precious time and
>considerable effort to be precise (not to mention the fear that once
>something has been digitized, it will then be torn out of context, as by
>Zipcodezoo.com, and distorted). No doubt there exist very many, as yet
>unpublished, photographs in various archives, which would be very useful if
>they could be digitized, but this too may require not-insignificant time
and
>effort, depending on how well-documented they are.

I think the idea here is to supply would-be authors with a template 
and a streamlined interface so that the interface that they use to 
write their descriptions is the same software that is used to SUBMIT 
and REVIEW and PUBLISH those descriptions. That reduces the cost and 
encumbrance of doing taxonomy. One way that this would be especially 
helpful is the following:

Suppose you have what you believe is a new species of beetle you wish 
to describe in genus X, which has 6 known species, and therefore 
needs to be revised. Traditionally, you would need to send separate 
requests to each institution holding the 6 known holotypes, to borrow 
the types for examination, in ADDITION to sending out as many letters 
as you could to whichever institutions you personally believed were 
likely to have additional specimens of those species. That could be 
very time-consuming, and is not a very efficient way of going about 
tracking down all possible specimens of interest. Now, with the 
interface being suggested here, the process would be quite different. 
The template would have slots for habitus photos of the 6 known 
species, and the putative new species. All one would need to do is to 
put up the early draft of the revision that includes these photos and 
check two boxes in the interface that say "REQUEST FOR SPECIMENS" and 
"REQUEST FOR TYPES/IMAGES" and enter details under each box. From 
that instant, (A) every collection manager in the world who logs onto 
the site will see that you have made a request for specimens, and 
this request will include details (what taxa, what global 
distribution, PLUS the habitus photos) so they know whether they 
might have what you're looking for, and (B) the collection managers 
of the institutions holding the types you want will also be notified 
the second they log in that you have made a request for those types, 
which they can respond to by sending the specimens or by sending 
digital images (which may be enough). What does this mean? Well, just 
think: how many of you have encountered a publication describing a 
new taxon which you find you have specimens of in your institution's 
possession, but which the author(s) describing it never saw? That 
would NEVER HAPPEN AGAIN. Additionally, since your request was made 
in public, with a known time-stamp, no unscrupulous and unethical 
individual could try to "steal" your new taxon and pre-emptively 
publish it, without exposing themselves to the absolute condemnation 
of the entire taxonomic community. Theft of other people's taxonomic 
discoveries would NEVER HAPPEN AGAIN.

The crucial concept here is to give a concrete and practical reason 
why every taxonomist, every collection manager, etc., should be 
involved in this effort, and using this one central website and 
interface. If everyone, everywhere, is LITERALLY on the same page, 
that will make *everyone's* work a lot easier. "Cybertaxonomy" should 
not be viewed as simply publishing online, or making character 
matrices available online, but as setting things up so THE ENTIRE 
PROCESS, from early manuscript drafts all the way to completion and 
even beyond (yes, I'm talking about updating publications after their 
initial completion), is all done online.

>So, digitization may be "the key to moving forward with "cybertaxonomy"."
>but this does not necessarily mean it is the key to moving forward with
>taxonomy?

Implemented wisely, I believe the answer is YES.

Sincerely,
-- 

Doug Yanega        Dept. of Entomology         Entomology Research Museum
Univ. of California, Riverside, CA 92521-0314        skype: dyanega
phone: (951) 827-4315 (standard disclaimer: opinions are mine, not UCR's)
              http://cache.ucr.edu/~heraty/yanega.html
   "There are some enterprises in which a careful disorderliness
         is the true method" - Herman Melville, Moby Dick, Chap. 82

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