[Taxacom] PygmyBrowse

[Shorthouse, David]

An alternative solution if the tree isn't too large (e.g. for a subset of
taxonomic groups) is to make use of the raw xml with a stylesheet like the
following: http://www.devx.com/getHelpOn/Article/11874/0/page/5 and
available for Nearctic spiders here:
http://canadianarachnology.dyndns.org/data/canada_spiders/xmltree/xmltree2.x
ml. What you might also want to consider Rod is how to have different
branches of the tree expanded at the same time. ZooBank's rather trivial
problem can be solved if they just used << onClick="whatever; return false"
>> to prevent the page from jumping up to the top with every click event.

David P. Shorthouse
------------------------------------------------------
Department of Biological Sciences
CW-403, Biological Sciences Centre
University of Alberta
Edmonton, AB   T6G 2E9
Phone: 1-780-492-3080
mailto:dps1 at ualberta.ca
http://canadianarachnology.webhop.net
http://arachnidforum.webhop.net
------------------------------------------------------

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
Sent: Friday, September 22, 2006 10:28 AM
To: TAXACOM
Subject: [Taxacom] PygmyBrowse

After being so rude about ZooBank, I've decided to try and be a little more
constructive.

One thing which did annoy me about ZooBank's web site was the way the
taxonomic tree was displayed (constructive stuff coming, promise). It
rapidly became huge, and every time the node was clicked on the page
reloaded, and bounced you back to the top. Trying to navigate through
chordates, for example, was a nightmare.

I stumbled across the PygmyBrowse tree browser (see
http://iphylo.blogspot.com/2006/09/pygmybrowse.html for details and links to
the original work), and thought this might be a useful approach to the
difficult problem of navigating large trees.

You can view a demo online at
http://linnaeus.zoology.gla.ac.uk/~rpage/pygmy/ . It's at the toy stage, but
is "live" and is displaying a real classification (in this case the ITIS
animal classification). It has limitations (after all, it was knocked
together in a coffee shop while avoiding actual work). The search only works
for taxa whose name comprises a single word (i.e., you won't find species
names), and not all it's features work in Microsoft Internet Explorer (which
manages to follow most, but not all web standards). It works fine in Firefox
and Safari.

It doesn't actually do much (you'll see the taxon and ITIS tsn number
displayed for each taxon you click on), but what I'm interested in is any
comments on whether this is a useful approach to navigating trees, which is
a common task in our area.

For the technically minded, it's written in PHP, uses AJAX, and ITIS is
stored in a MySQL database. If that means anything to you you'll realise how
easy it is to do this. If, however, it reads like gibberish, then you'll
realise that I'm just trying to show off by drowning you in acronyms.

Regards

Rod

------------------------------------------------------------------------ 
----------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
DEEB, IBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom

Phone:    +44 141 330 4778
Fax:      +44 141 330 2792
email:    r.page at bio.gla.ac.uk
web:      http://taxonomy.zoology.gla.ac.uk/rod/rod.html
iChat:    aim://rodpage1962
reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html

Subscribe to Systematic Biology through the Society of Systematic
Biologists Website:  http://systematicbiology.org
Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species: http://ispecies.org
Rod's rants on phyloinformatics: http://iphylo.blogspot.com
Rod's rants on ants: http://semant.blogspot.com


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