Below some comments
to a press release from PLOS-one regarding yesterday’s online publication
of new ant species (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001787)
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 http://plazi.org:8080/GgSRS/search?214588052.ModsDocID=21401&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, Taiwan.
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 Central.
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 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001787)
.
Donat
Press release:
* * * * * * * * * * * *
Scientists Present a Collaborative
Model for Accelerating Taxonomy
A case study involving 1,700
ant specimens from
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.
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
Sciences and M. Alex Smith
of the
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
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
allowed Fisher and his
colleagues to recommend future conservation areas
on the island, well before a
2008 deadline set by the Malagasy
government.
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). 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) to
enhance their 150 million
specimen records.
Education and Research at
the
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
is in the midst of an
extensive rebuilding project in
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.
Contact:
Stephanie Stone
Email: sstone@calacademy.org
Tel: +1 (415) 321-8119
Andrew Ng
Email: ang@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,
Email: agosti@amnh.org
Web: http://antbase.org
Blog: http://biodivcontext.blogspot.com/
Skype: agostileu
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