[Taxacom] Taxonomic Content Management Systems - Responses
vsmithuk at yahoo.co.uk
Sun Aug 27 12:01:07 CDT 2006
A couple of weeks ago I made a request about web based taxonomic
content management systems for the storage and management of
taxonomic data. I received a total of 16 replies, including one
pointing to a previous review conducted in 2003 of 24 systems
conducted by Walter Berendsohn et al. for GBIF (see http://
digitization_collections&vm=detailed&sb=Title). Posted below are the
consolidated results of the messages I received.
Many thanks to all of those who replied.
I would appreciate if you could post or send direct to my e-mail the
replies of your question. The INPA's fish collection is using Specify
and we are currently considering which system to use in our
Invertebrate collections (Insects and 13 other invertebrate groups).
Thank you in advance.
Collection of Invertebrates
Instituto Nacional de Pesquisas da Amazonia
Manaus, AM - Brazil
Are you aware of the list created by Walter Berendsohn et al. for GBIF?
Berendsohn, W., Güntsch, A. and Röpert, D. (2003). Survey of existing
publicly distributed collection management and data capture software
solutions used by the world's natural history collections. Global
Biodiversity Information Facility, Copenhagen. <http://circa.gbif.net/
Note that BioLink is no longer available via the CSIRO Web site.
There was also an exercise by WCMC about 5 or 6 years ago - came out
on Floppy Disk. I am sure I have a copy somewhere.
Arthur D. Chapman
(Trading as: Australian Biodiversity Information Services)
We have a crude system operational right now:
It's little more than a prototype at the moment, but I am just now
emabraking on a complete re-write, updating to .NET, and will vastly
the function and performance, as well as adding editic capabilities
to migrate all of our internal databases to a web interface). I'd be
to answer any questions you may have.
Needless to say, I'm very interested in what you find out.
Richard L. Pyle, PhD
Re your post to Taxacom, The Artedian and the WebArtedian are being
actively developed, and going from Ichthyology will eventually be
more generally useful.
http://artedi.nrm.se/nrmfish/ for the WebArtedian
http://artedi.nrm.se/fishbase_se/software/artedian/ for a now
somewhat dated version of the Artedian
Within GBIF-Sweden we are developing similar web-based tools, but
nothing ready for presentation yet.
Sven O Kullander, PhD, Associate Professor
We are developing web based molecular database for the identification
fungi. Data on specimen, DNA and in some cases descriptions including
pictures are included. Look at http://unite.ut.ee
It would be most interesting to receive consolidated results!
Prof. Urmas Koljalg
Institute of Botany and Ecology
As you were interested in work in progress, Taxis (the spftware I am
on) is pretty much what it is - a lot of work in progress. The
is online at the moment (http://www.bio-tools.net) is seriously
will be replaced next year. I will attach in the end of the message the
latest newsletter sent to Taxis users in April.
Since that message things has changed again and I will briefly
Bitoolz Taxis 4 will be .Net Framework v2 based.
There will be Windows and Web interfaces essentially duplicationg all
functions including editing.
Data layer is abstracted from specific database and the app (both win
web) can connect to the most database systems available.
More interfaces may come next year (for handheld devices for instance)
Web interface will be asp.net (AJAX enabled)
Win interace will of course be able to access the remote database as
I will be happy to discuss technical details and provide the access
versions as soon as WinForms app is in some shape and WebForms is
to Biotoolz server (I am already experimenting with it on the
There are many other things I didn't mention so, again, I will be
answer your questions if there are any.
I am not personally working on a fully integrated Web-based taxonomic
system, but a draft version of "Millipedes of Australia" is
circulating on CD-ROM. This is organised hierarchically a la the
current taxonomy and includes complete synonymies, a bibliography, a
types catalogue and museums list, images and distribution maps. All
information is internally hyperlinked: ca. 9500+ hyperlinks on the
current ca. 400 HTML pages. I hope to have the site online (on CSIRO
Entomology's server) later this year and to add illustrated text
keys, as in my "multipedes" site (see below). The hierarchical
structure will make it easy to add genetic data, more images,
publication PDFs, etc in future. However, the site is not linked to a
specimen database. Separate specimen databases for various Australian
millipede groups are under construction by specialists but there is
no plan yet to make these public due to possible data-ownership
issues for museums.
The most useful external site I've found which overlaps with my own
interests is the wonderful SysTax:
This is database-linked. There is a personnel overlap at SysTax with
German workers who are building a gigantic digital library of
original taxonomic works, but I understand the latter project is sub
rosa for the time being.
Dr Robert Mesibov
We recently had a meeting of Lepidopteran systematists and there was
quite a bit of discussion of the databasing problem. I have a lab
database aimed at looking after mostly genetic data, but it also has
specimen data which would benefit from linking to up to date
taxonomy. The only interactive and updateable database I know for
Leps is the pyralid project (see below). We are hoping to develop
the genetic interactive database with the help of Nescent (http://
www.nescent.org/main/), but it would be great if there were an open-
source modular architecture that could be developed in different ways
by different groups, so as to include everything from taxonomy
through to genomic, biogeographic and phenotypic information. I know
this probably sounds hopelessly ambitious, but if the underlying
database software is made open source and modular then I dont see why
it shouldnt happen eventually. Its something to think about anyway.
See you in London some day
My own lab database used mostly for molecular and sequence data but
also housing collection and specimen data:
A db for pyralid moths, primarily aimed at being an interactive
systematic list that can be updated over the web:
A butterflies of Ecuador database based on collection and systematics
by Keith Willmott (not editable I dont think).
A Lepidopteran consortium with more links to databases and lists
Kelley Thomas and we of the nematode tree of life project are
building a web database. It is by no means up to our standards yet--
it is very much a work in progress, but we have made significant
progress, I think. Most of it is Kelley's brilliant vision and hard
We are in the process of developing online tools to allow the various
categories of BRAHMS users (www.brahmsonline.com) to get their data
online. We made a start on this a few years back with a focus on
specimen data. Examples of various draft databases in Version 1:
http://herbaria.plants.ox.ac.uk/bol/?nhn curation network
http://herbaria.plants.ox.ac.uk/bol/?seabcin curation network
We're working on BOL Version 2 for October this year - this inludes
greater nomenclature content and functionality and a move to SQL
Server. We're being pressed to extend functionality for monographic
data in general.
I hope helpful,
Here is a system that might fit the criteria of what you are reviewing:
The purpose is to provide a seamless merging of species pages (with
images etc) and specimen data, with summaries of the specimen data
being compiled dynamically (e.g. phenology graphs).
If you have any questions about functionality, please contact Jim
Whittome jim.whittome at ualberta.ca
Felix Sperling, Professor
My name is Gemma Reston and I am working alongside Dr David Montagnes
University of Liverpool in The Biological Sciences Department. I am
David collaborates with a few members of staff already (Dave Roberts,
Gianfranco Novarino and Alan Warren).
We are currently developing and maintaining two websites, which you
already come across (they receive over 1000 hits a day):
1. The Planktonic Ciliate Project - www.liv.ac.uk/ciliate/intro.htm
2. The Harmful Plankton Project - www.liv.ac.uk/hab/intro.htm
Both sites, as you will see, are presented in a series of datasheets.
species has a dedicated sheet, with descriptive information and some
aid identification. We are also in the process of putting three
identification keys (available through the 'KEY' link on the HPP
will make identification of harmful species much more straight forward.
If you would like myself and Dr David Montagnes to give a brief talk
we do, then we would be very willing to travel down.
I know this is a bit off topic but the maintenance of the site and data
collection relies solely on funding from external sources. The money
at the moment is soon to run out. Therefore, we are also actively
available funding for the site and research associated, do you know
who we could potentially approach?
I look forward to hearing from you.
I was participated in a European project "FishTrace" whish was
finished on the 30th of June, 2006. FishTrace is a genetic catalogue
assiciated to biological reference collections from more than 200
commercial marine fish. Genetic and taxonomic information is compiled
in on online database : www.fishtrace.org. If you want more
information, please contact our coordinator : José M. Bautisa at
jmbau at vet.ucm.es.
Dr Véronique Verrez-Bagnis
I believe you did not forget my database. For now it does not have an
interface for editing data, but I am thinking about it and I am
interested in results of your survey.
The 3I database stores taxonomic information, distribution, hosts,
literature, images, external links, morphological information,
The link to the web site is below.
Dmitry A. Dmitriev Illinois Natural History Survey
Dr. Vincent S. Smith
The Natural History Museum
London, SW7 5BD, UK
Tel: +44 (0) 207 942 5127
Fax: +44 (0) 207 942 5661
E-mail: v.smith at nhm.ac.uk
Web: http://darwin.zoology.gla.ac.uk/~vsmith/ (THIS WILL CHANGE SOON)
iChat Video Conferencing: vsmithuk at mac.com (invitation only)
Skype: vsmithuk; or SkypeIn London: +44 (0)207 558 8950
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