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[Taxacom] Taxonomic Content Management Systems - Responses

Vince Smith vsmithuk at yahoo.co.uk
Sun Aug 27 12:01:07 CDT 2006 

Dear all,

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:// 
circa.gbif.net/Public/irc/gbif/digit/library?l=/ 
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.

Regards,

Vince Smith
NHM, London

_______________________________________________
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.
Yours,
Celio Magalhaes
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/ 
Public/irc/gbif/digit/library?l=/ 
digitization_collections&vm=detailed&sb=Title>.
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.

Cheers
Arthur D. Chapman
(Trading as: Australian Biodiversity Information Services)
______________________________________________
We have a crude system operational right now:

http://www2.bishopmuseum.org/natscidb/

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  
imporve
the function and performance, as well as adding editic capabilities  
(I hope
to migrate all of our internal databases to a web interface).  I'd be  
happy
to answer any questions you may have.

Needless to say, I'm very interested in what you find out.

Aloha,
Rich
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.

Best regards

Sven
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!

Cheers,
Urmas
Prof. Urmas Koljalg
Institute of Botany and Ecology
______________________________________________
As you were interested in work in progress, Taxis (the spftware I am  
working
on) is pretty much what it is - a lot of work in progress. The  
version that
is online at the moment (http://www.bio-tools.net) is seriously  
outdated and
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  
mention them:
Bitoolz Taxis 4 will be .Net Framework v2 based.
There will be Windows and Web interfaces essentially duplicationg all  
the
functions including editing.
Data layer is abstracted from specific database and the app (both win  
and
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  
well.

I will be happy to discuss technical details and provide the access  
to beta
versions as soon as WinForms app is in some shape and WebForms is  
uploaded
to Biotoolz server (I am already experimenting with it on the  
localhost).

There are many other things I didn't mention so, again, I will be  
happy to
answer your questions if there are any.

Evgeniy
Evgeniy Meyke
______________________________________________
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:

http://www.biologie.uni-ulm.de/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.

Regards,
Bob
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

Cheers
Chris Jiggins
Links:
My own lab database used mostly for molecular and sequence data but  
also housing collection and specimen data:
http://heliconius.cap.ed.ac.uk/butterfly/db/index.php
A db for pyralid moths, primarily aimed at being an interactive  
systematic list that can be updated over the web:
http://www.pyraloidea.org/
A butterflies of Ecuador database based on collection and systematics  
by Keith Willmott (not editable I dont think).
http://www.flmnh.ufl.edu/butterflies/neotropica/db/search.asp
A Lepidopteran consortium with more links to databases and lists
www.lepsys.eu
______________________________________________
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  
work.
http://worm.unh.edu/

David Fitch
______________________________________________
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/?leucaena monograph
http://herbaria.plants.ox.ac.uk/bol/?cupressaceae monograph
http://herbaria.plants.ox.ac.uk/bol/?oxford curation
http://herbaria.plants.ox.ac.uk/bol/?nhn curation network
http://herbaria.plants.ox.ac.uk/bol/?seabcin curation network
http://herbaria.plants.ox.ac.uk/bol/?gabon checklist

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,

Denis Filer
______________________________________________
Here is a system that might fit the criteria of what you are reviewing:
http://www.entomology.ualberta.ca/

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

Sincerely,

Felix Sperling
Felix Sperling, Professor
______________________________________________
My name is Gemma Reston and I am working alongside Dr David Montagnes  
at the
University of Liverpool in The Biological Sciences Department. I am  
aware that
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  
may have
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.  
Each
species has a dedicated sheet, with descriptive information and some  
images to
aid identification. We are also in the process of putting three  
separate online
identification keys (available through the 'KEY' link on the HPP  
site) which
will make identification of harmful species much more straight forward.

If you would like myself and Dr David Montagnes to give a brief talk  
about what
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  
we have
at the moment is soon to run out. Therefore, we are also actively  
seeking any
available funding for the site and research associated, do you know  
of anyone
who we could potentially approach?

I look forward to hearing from you.

Yours Sincerely

Gemma Reston
______________________________________________
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.

Best regards,

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,  
interactive keys.
The link to the web site is below.
Regards, Dmitry

-- 
Dmitry A. Dmitriev      Illinois Natural History Survey




_________________________________________________________

Dr. Vincent S. Smith
Cybertaxonomist
The Natural History Museum
Cromwell Road,
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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