The report of a National Taxonomy Forum, held in October 2007 at the
Australian Museum, has just been released-
http://www.environment.gov.au/biodiversity/abrs/workshop-forum/pubs/ntf-proc
eedings.pdf
While the report is national in scope, the issues addressed and the
associated recommendations should (noting recent taxacom postings) have
wide applicability. Sober reading.
Lee
Lee Belbin
TDWG Secretariat
lee(a)tdwg.org
PanAmerican Advanced Studies Institute
Cyberinfrastructure for International Collaborative Biodiversity and
Ecological Informatics
La Selva Biological Station, Costa Rica
May 31 -- June 12, 2008
The University of Kansas and Florida International University, working
with the University of Costa Rica and the Organization for Tropical
Studies (OTS), are hosting a two-week course in biodiversity and
ecological informatics at OTS's La Selva Biological Station in
northeastern Costa Rica from May 31 through June 12. Thanks to a
PanAmerican Advanced Studies Institute Award from the Office of
International Science and Engineering at the US National Science
Foundation, full scholarships plus airfare are available for US and
Latin American graduates. All participation costs will be covered by the
award. The program will be in English.
Graduate students, postdocs and early-career faculty are strongly
encouraged to apply. About 25 participants, half from the U.S. and half
from Latin America will be accepted. Only students/researchers from
Latin America and from the United States are eligible to apply.
The online application and further information, including a draft
curriculum is available at: www.ciara.fiu.edu/eco/index.htm
Please note that the application date is rapidly approaching, potential
participants need to act quickly.
There is also some opportunity for additional resource faculty from the
U.S. and from Latin America in the area of bioinformatics who could join
the course for various periods during the two week schedule.
Please contact Jim Beach, University of Kansas, beach(a)ku.edu, or Julio
Ibarra, Florida International University, julio(a)fiu.edu, for more
information but see the web site for details.
Dear TDWGians
There are a number of issues that I'd like to raise-
1. As you may be aware, Ricardo has setup an Events Calendar at
http://www.tdwg.org/events/ to advertise Biodiversity Informatics related
meetings, grants and awards. I've seeded it with some events but I know
there are more out there. This system complements the Biodiversity
Informatics related Projects database (http://www.tdwg.org/biodiv-projects/)
and the Biodiversity Informatics Networks database
(http://www.tdwg.org/biodiv-networks/) If you are aware of other 'events'
for 2008 or 2009, please either add them yourself (you must be logged in) or
send me a URL and I'll add them. A related issue: I have produced a 'glossy'
poster (see
http://www.tdwg.org/fileadmin/executive/movies/TDWG_Poster_BioData_A1.pdf)
and brochure (see
http://www.tdwg.org/fileadmin/documentation/outreach/TDWG_Brochure.pdf) I
have high-quality printed version of both resources available if any of you
are planning to attend a conference/meeting and would like to help promote
TDWG. Note: There are other related resources (PowerPoints, videos etc)
available at http://www.tdwg.org/about-tdwg/resources-for-outreach/. BTW: A
general TDWG video clip is currently being produced.
2. Attached is a v.preliminary draft program for TDWG 2008 in Fremantle. Few
sessions are fixed at the moment and there are a number of free slots. If
you have ideas for a session (or four) on one or more issues, please let me
know ASAP. Input is always appreciated. We hope to get more information
regards costs, recommended accommodation and excursion options and dates to
the web site next week.
3. If you haven't already done so, please consider renewing your TDWG
membership, taking out TDWG membership or making a donation to TDWG (see
http://www.tdwg.org/membership/) . TDWG has a small (but enthusiastic!)
membership and relies on your membership fees for basic operational costs.
We would therefore appreciate any support you can provide.
Best Wishes
Lee
Lee Belbin
TDWG Secretariat
This is a live application based on TDWG standards and those under
discussion (eg Taxonx for literature). It is making use of LSIDs.
PLAZI.ORG - THE DIGITAL REPOSITORY FOR SPECIES DESCRIPTIONS.
Knowledge of the actual number of species on planet Earth is one of the
last frontiers in science. It is not known exactly how many species have
been identified and described, much less the number of as yet undescribed
species.
However, the species we do know are documented in well over hundred
million pages of printed scientific books and journals. This knowledge
is hidden in libraries, and no single library holds all this knowledge.
The species descriptions are very rich in data, essentially a quality
controlled summary of what is known at any specific time about a
particular species. In best cases, this information includes a detailed
morphological description, drawings and images, a summary on behavior and
ecology and a detailed list of all the specimens studied. In more recent
publications, links to DNA sequences or video documentation among other
forms of data may be provided. Recently e-publications have become
available, but many of these are copyrighted and thus not generally
available open to the public for perusal or use. Nor are they easily
machine-searchable for discovery and re-use of contents.
Recently, the Biodiversity Heritage Library as a large scale operation to
digitize this biodiversity literature has been launched. Currently, it
includes major US and UK natural history libraries, with the ultimate goal
of including the entire global literature. All publications will be openly
accessible to the public, unless they are copyrighted -- thus most of the
recent publications are still out of reach. The BHL thus falls short of
optimizing the potential uses of these publications.
Tagging the boundaries of a species description and identifying the
species dealt with, supports discovery and retrieval of data not possible
through Google. Mark-up of species descriptions permits queries, such as
which are the "red ant in London", a very common form of query.
Under some national copyright legislation like the Swiss, descriptions can
not be copyrighted because they are through historical constraints (there
are tens of millions of descriptions) and peer review standardized and
listing factual, in most cases morphological data describing species, and
thus they can all be made readily accessible.
Plazi.org is a new Web based service that offers access to descriptions of
species and an archive to store the publications as marked up documents.
GoldenGate, a dedicated editor has been developed to mark up the
publications supporting the extraction of descriptions, based on a TaxonX,
an XML schema modeling the logic content of these publications. The Plazi
Search and Retrieval Server, building on this systematic mark-up of texts,
allows powerful search functions to find species descriptions, or even
simple mention of species, permitting users to answer questions like:
Which species occur together?
Plazi.org includes already more than 3,700 description of 3,000 taxa with
a goal of archiving all the forthcoming new descriptions and, contingent
upon additional funding, all the descriptions of the known 12,278 ant
species listed in the Hymenoptera Name Server/ antbase.org, enhanced with
globally unique species numbers (LSIDs: Life Science Identifiers). While
ants provide the original test case, the service is not restricted to ants
but is potentially open to all groups, from Bacteria to Plants, and will
support most major languages. All descriptions are machine readable and
thus can be picked up for mash-ups or individual Websites.
Plazi.org is run and developed by Donat Agosti, Terry Catapano, Christiana
Klingenberg and Guido Sautter, its development is supported by Grants from
the US National Science Foundation (to the American Museum of Natural
History), the German Deutsche Forschungsgemeinschaft (to University of
Karlsruhe) and the Global Biodiveristy Facility (GBIF; to Plazi.org and
Zootaxa), and is collaborating with the Hymenoptera Name Server at Ohio
State University (Norm Johnson), Zoobank (Richard Pyle), University of
Massachusetts (Robert Morris), antweb.org (Brian Fisher) and Zootaxa
(Zhi-Qiang Zhang).
Plazi.org has been released to the public at the EDIT "IPR and the web:
challenges for taxonomy" meeting in London, Feb. 20, 2008
(http://www.editwebrevisions.info/content/ipr-and-web)
Related Links:
First descriptions of the first ant described (Linnaeus, 1758)
http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=79860…
recent publications with fine grained mark-up allowing extraction of
specimen data and plotting automatically maps
http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=4CED5…
Description in Russian:(please set encoding=utf-8 in your browser.
http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=AE3F8…
Description in Chinese
http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=5F64B…
Fish
http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=30E2A…
Bacterium
http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=A4EA4…
Plant
http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=59DE9…
Fungi
http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=C9BDF…
Donat
--
Dr. Donat Agosti
Research Associate, American Museum of Natural History and Smithsonian
Institution
Email: agosti(a)amnh.org
Web: http://antbase.org
CV: http://research.amnh.org/entomology/social_insects/agosticv_2003.html
Dalmaziquai 45
3005 Bern
Switzerland
+41-31-351 7152
--
Dr. Donat Agosti
Research Associate, American Museum of Natural History and Smithsonian
Institution
Email: agosti(a)amnh.org
Web: http://antbase.org
CV: http://research.amnh.org/entomology/social_insects/agosticv_2003.html
Dalmaziquai 45
3005 Bern
Switzerland
+41-31-351 7152
Dear list subscribers,
The TDWG Secretariat and the TDWG Globally Unique Identifiers (GUID) Task
Group announce the availability of the LSID Authority Setup Guides-
http://www.tdwg.org/activities/guid/documents/lsid-setup-guides/
These guides were written by Richard Pyle, Kevin Richards and myself to help
system administrators avoid common pitfalls in setting up their own LSID
authorities. We hope that they will be useful to those interested in
assigning LSIDs to their biodiversity information data records. Any feedback
would be appreciated.
Best regards,
Ricardo Pereira
Software Engineer
TDWG Globally Unique Identifiers Task Group
Dear TDWG'ians
I have just added some basic information about the TDWG 2008 conference in
Fremantle, Western Australia: http://www.tdwg.org/conference2008/. The
information is preliminary and will be added to over the next few months.
Information about accommodation, travel, presentations, sponsors, excursions
and program will be loaded as soon as possible. I'd be keen to know if there
are other things that would be useful to know.
A REMINDER: Discounted institutional membership of TDWG (2008) is only
available until the end of February. Individual membership is also open and
we would appreciate all renewals as soon as possible. Please see
http://www.tdwg.org/membership/.
Best Wishes
Lee
Lee Belbin
TDWG Secretariat
[This is a summary of an idea discussed on the Taxacom mailing list; it
has also been posted on the microformats wiki:
<http://microformats.org/wiki/rel-tag-feedback#UIDs>]
Many links on the TDWG's LSID resolver, for instance those on:
<http://lsid.tdwg.org/summary/urn:lsid:ubio.org:namebank:11815>
are marked up thus
<a href="/summary/urn:lsid:ubio.org:classificationbank:1909656">
urn:lsid:ubio.org:classificationbank:1909656
</a>
If TDWG would simply add rel="tag" to all such links, thus:
<a rel="tag" href="...
then all their pages would be "tagged" with the relevant LSIDs (i.e.
everything to the right of the final slash), using the "rel-tag"
microformat:
<http://microformats.org/wiki/rel-tag>
and then people could use those tags to find the equivalent tag on pages
about (in blogs, for example) or pictures of (on, say Flickr) the
organism concerned, thereby adding discoverability, without reducing or
changing any of the current uses of LSIDs.
--
Andy Mabbett
* Are you using Microformats, yet: <http://microformats.org/> ?
Dear all,
apologies for cross-posting.
EDIT will hold a workshop on IPR and web publication to be held 20th
Feb 2008 in the Royal Botanic Gardens, Kew. The topics will include
both building content and the development of credit-metrics for
contributors.
Details can be found at
http://www.editwebrevisions.info/content/ipr-and-web
A booking form is accessible from the site.
The morning symposium is open to all. The afternoon workshop
sessions will be limited to 12 people per workshop. Participation in
the workshops will basically be first-come-first-served, but we will
seek to balance attendance between institutions.
Travel funds for this meeting has already been distributed to partner
Institutions as part of the first funding tranche. No further
funding is available from EDIT. There is no registration fee.
Cheers, Dave
--
Dr D.McL. Roberts, Tel: +44 (0)20 7942 5086
European Distributed Institute of Taxonomy Project,
Ccordinator WorkPackage 6 (Unifying Revisionary Taxonomy),
Dept. Zoology,
The Natural History Museum,
Cromwell Road,
London SW7 5BD
Great Britain Email: dmr(a)nomencurator.org
Web page: http://www.editwebrevisions.info/
Web page: http://www.e-taxonomy.eu/
--
In general, it is easier to get forgiveness than to get permission.
--
The National Museum of Natural History, Smithsonian Institution (NMNH)
is planning a new version of its biological collections database web
interface. NMNH needs your help in understanding how you might use our
collections databases (see at
http://www.mnh.si.edu/rc/db/databases.html) The survey should take
less than 15 minutes and will help ensure that your needs are
incorporated in a future upgrade. We would like to close the survey by
30 January 2008.
Note: NMNH has approximately 10-15% of its 126 million specimens
represented in electronic form. Some of the records have minimal data,
while a growing subset have literature, archival materials, photographs,
illustrations, specimen images, attached. This survey will help us
improve access to the data, images, etc., according to your needs.
Thank you for taking a few minutes to help us improve our web database
interface!
Thomas Orrell & Anna Weitzman
Smithsonian Institution PO Box 37012
National Museum of Natural History MRC-136
Washington, DC 20013-7012
Dear colleagues,
Institute of Botany, Průhonice & Faculty of Science, Charles University
Prague are hosting the 5th European Conference on Biological Invasions
NEOBIOTA. The organizing committee is pleased to invite all those who
are interested in invasive plants and animals, to register and submit an
abstract for either an oral or poster presentation at the conference
homepage www.ibot.cas.cz/neobiota, where you will find more detailed
information about the conference venue, topics accommodation, etc.
The conference will take place on 23.-26 September 2008 in Prague, Czech
Republic, starting with an invited evening keynote lecture presented by
Marcel Rejmánek from the University of California, Davis, USA.
The registration is now opened. Please note that the deadline for
registration and submission of abstracts is 30 April 2008.
Everyone interested in Biological Invasions is invited to participate
and share thoughts, opinions and new results. All professions
(ecologists, conservation agencies, and stake-holders), all organisms
(plants, animals, pathogens, fungi) and ecosystems (marine, freshwater,
and terrestrial) will be considered.
For sharing the information with your colleagues interested in
biological invasions, you may want to use the attached conference flyer.
If you have any questions, please, please do not hesitate to contact us.
Looking forward to see you next year in Prague
Petr Pysek and Vojtech Jarosik
(on behalf of the organizing committee)
