[tdwg-lit] plos one taxonomic publication

Donat Agosti agosti at amnh.org
Thu May 29 16:16:45 CEST 2008


Below some comments to a press release from PLOS-one regarding yesterday's
online publication of new ant species
complemented by semantically enhanced XML versions. This means, that the
taxonomic domain specific XML mark up schema (TaxonX) has been used to mark
up the content of the publication. Enhanced in the context that elements
such as taxonomic names or materials citations have been amended with
additional information.


For names, that means LSIDs from either Zoobank and or the Hymenoptera Name
Server have been added, for materials citation, if available, each record
has been amended with a collection code form the supporting information
available through the publication, and if available with the BenBank
accession number, when the specimen has been used for barcoding. This file
is in appendix S2. A further file, including an experimental mark up
containing PLoS One schema complemented with Taxonx is available here
(http://hdl.handle.net/10199/15447  : see  pone.0001787_enhanced.xml).


The value of this step is, that the XML can be read by machine and imported
into other projects. Our implementation on plazi.org is here
n> &indexId=0&subIn  . The content of this publication has been imported
into SRS on plazi, where it resides on a dedicated database that allows
exporting it in various versions. In the above link, an html version of each
of the treatments is available, that includes links to the Name Servers
(HNS, Zoobank), the specimens (CAS in this case, which provides for each
specimen a dedicated Webpage), parts of specimens that has been used for DNA
analysis, allowing to monitor the whereabout of material used for genetic
analysis (in this case linked to CAS), plus the GenBank reocord (GB)


Plazi can be harvested using for example a dedicated TAPIR service. Once
GBIF harvests this particular data, it will be available on their database
as well (http://data.gbif.org/datasets/provider/241 ) from where hopefully
soon links will be set up to get back to the original record.


Availability of the names: Deposition of CD-Rom and printed material


In accordance with section 8.6 of the ICZN's International Code of
Zoological Nomenclature, printed copies, and a pdf version of the article
have been sent to be deposited at the following six publicly accessible
libraries: Natural History Museum, London, UK; American Museum of Natural
History, New York, USA; Smithsonian National Museum of Natural History,
Washington DC, USA; Museum National d'Histoire Naturelle, Paris, France;
Russian Academy of Sciences, Moscow, Russia; Academia Sinica, Taipei,


Furthermore, which is not relevant for Art. 8.6, but an option to be
considered for the purpose of providing a permanent scientific record (Art.
8(a.1) a digital copy has been deposited at the Public Archive at PubMed


Additionally, XML versions of the publication are also available at
plazi.org (http://hdl.handle.net/10199/15447).


The value of this experimental publication is, that the content, especially
descriptions, are immediately open access and, could potentially harvested
by machines, like Zoobank, that would automatically add the original
descriptions. A similar publication has been posted on Zootaxa
(http://www.mapress.com/zootaxa/2008/f/zt01671p031.pdf and
http://plazi.org:8080/dspace/handle/10199/15417 .


There are many issues involved in implementing such systems, not least
sustainable business models. But it seems to be the only way forward so that
this information is shared and distributed the widest possible.

Adoption of XML based production workflow will become most efficient, if we
begin to used editing tools to create our publications from begin with as
XML (or similar kind of) documents.


The mark up has been a collaboration between PloS-One and Plazi.


Any comments are welcome, especially on the publications Web Site at
PloS-one to improvie this process





Press release:

* * * * * * * * * * * *


Scientists Present a Collaborative Model for Accelerating Taxonomy


A case study involving 1,700 ant specimens from Madagascar demonstrates

how a combination of DNA barcoding, traditional morphology, and

Web-based tools can help scientists quickly and accurately process large

groups of specimens and make the results immediately available so that

other researchers can readily incorporate the results into their work.


SAN FRANCISCO (May 28, 2008) - Two hundred and fifty years after the

publication of Linnaeus' Systema Naturae, which represents the official

start of modern zoological nomenclature, an article published this week

in PLoS ONE provides a glimpse of what the future of taxonomy could be

in this brave new world of affordable DNA sequencing and the Internet. 


In the article, entomologist Brian Fisher of the California Academy of

Sciences and M. Alex Smith of the University of Guelph, Richard Pyle

from Zoobank, and Terry Catapano and Donat Agosti from Swiss-based Plazi

present a collaborative approach to taxonomy in which collectors,

morphologists, and DNA barcoders combine forces to accelerate the

process of species identification and description. Their publication is

openly accessible on the World Wide Web and offers not only the

descriptions but also the primary specimen and genetic data upon which

they are based. Such accelerated and openly accessible work is necessary

to keep pace with climate change and other human-induced threats to

biodiversity, which may eradicate species from the Earth before they are

even recognized as rare or valuable.


Insects contribute enormously to the biodiversity of most habitats, but

often they are too numerous and too time-consuming to identify using

only morphology-based methods. In the PLoS ONE article, Fisher and Smith

were faced with the gargantuan task of identifying 1,700 ant specimens

collected in Madagascar from 1992 through 2006. To tackle the problem

with speed and efficiency, they employed DNA barcoding-in which they

sequenced 600 base pairs of the cytochrome c oxidase 1 (CO1) gene-on a

representative sample of 501 specimens, and measured the morphological

characters of 209 specimens. 


With this combined data set, they were able to group the ants into five

species of Anochetus (three of which are new species) and three species

of Odontomachus. While the morphological data was useful in determining

the species boundaries between specimens, the results from DNA

barcoding-fast, inexpensive, and relatively easy to produce-were what

allowed the authors to identify the specimens at a useful scale and

speed, especially when members of the same species showed wildly

different morphologies.            


This collaborative approach, anchored by DNA barcoding, will allow

scientists to make more timely recommendations to conservation

policymakers, the authors argue. For example, the ant data was used as

part of a multi-taxon analysis of biodiversity in Madagascar that

allowed Fisher and his colleagues to recommend future conservation areas

on the island, well before a 2008 deadline set by the Malagasy



The publishing model set forth in the PLoS ONE article also leverages

the digital age-the traditional descriptive text is complemented with

links to the underlying data, such as the gene sequences at GenBank,

descriptions and images of specimens at AntWeb (www.antweb.org), and

naming information at Zoobank, the registry of animal names.

Furthermore, the authors have allowed open access to the publication,

and offer enhanced machine- (XML-based) and human-readable versions on

Plazi, a taxonomy website (http://plazi.org <http://plazi.org/> ). Plazi
provides tools to

convert and enhance existing publications and provides standardized,

searchable access to taxonomic literature. It is already used by data

harvesters like the Global Biodiversity Facility (http://gbif.org
<http://gbif.org/> ) to

enhance their 150 million specimen records. 


Education and Research at the California Academy of Sciences:

The Academy is an international center for scientific education and

research and is at the forefront of efforts to understand and protect

the diversity of Earth's living things. The Academy has a staff of over

50 professional educators and Ph.D.-level scientists, supported by more

than 100 Research and Field Associates and over 300 Fellows. It conducts

research in 11 scientific fields: anthropology, aquatic biology, botany,

comparative genomics, entomology, geology, herpetology, ichthyology,

invertebrate zoology, mammalogy and ornithology.

The California Academy of Sciences is home to Steinhart Aquarium,

Morrison Planetarium and the Kimball Natural History Museum. The Academy

is in the midst of an extensive rebuilding project in Golden Gate Park.

Pritzker Prize-winning architect Renzo Piano designed the new Academy,

which is scheduled to open on September 27, 2008. www.calacademy.org

(415) 379-8000.


Stephanie Stone

California Academy of Sciences

Email: sstone at calacademy.org

Tel: +1 (415) 321-8119


Andrew Ng

California Academy of Sciences

Email: ang at calacademy.org

Tel: +1 (415) 321-8121


Citation: Fisher BL, Smith MA (2008) A Revision of Malagasy Species of

Anochetus Mayr and Odontomachus Latreille (Hymenoptera: Formicidae).

PLoS ONE 3(5):e1787. doi:10.1371/journal.pone.0001787


















Dr. Donat Agosti

Science Consultant

Research Associate, American Museum of Natural History and Naturmuseum der
Burgergemeinde Bern

Email: agosti at amnh.org

Web:  <http://antbase.org/> http://antbase.org

Blog:  <http://biodivcontext.blogspot.com/>

Skype: agostileu

CV <http://antbase.org/agosticv_2003.html> 

Current Location <http://antbase.org/agosti_loc_bern.kmz> 

Dalmaziquai 45

3005 Bern


+41-31-351 7152

+1-202-558 0330


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