[Taxacom] PygmyBrowse & myNature
Adorian Ardelean
ardelean at aquaecology.de
Mon Sep 25 09:18:14 CDT 2006
Hi Rod & David,
Concerning trees: coincidentally, at the requests
of some users of myNature portal, I work also on
a similar mini project: a classification browser
that goes through the content of the database.
Of course a big tree loads slow. Here, in this
particular case I wanted to make the tree also
more content sensitive: I wanted to load sister
groups and children nodes only if there is some
content in the database (we do not want hundreds
of nodes for exotic orchid species for example if
we have only data for temperate species from
Romania. Although the source tree is huge (700k
nodes) the thing loads relatively fast because it
loads only the parts that are needed. Basically,
I break the process of tree loading in 3 major
steps: get_tree_path, get_sister_groups, get_children_nodes.
Even in this short form the tree is still
informative and allows browsing downward on
sister clades (without additional clicks).
Next step of course would be some SAXAJ
implementation for both panels: classification
tree and the content panel. This would allow
browsing content, changing filtering conditions,
display options without reloading page every time such a change was made.
http://mybiosis.org/nature/portal.php?pagename=higher_taxon_classify&BLOCKID=3&CHILDID=26324&dataset=PLANTS
http://mybiosis.org/nature/portal.php?pagename=higher_taxon_classify&BLOCKID=5&CHILDID=2&dataset=INVERTEBRATA
NOTE: This is just a very basic prototype.
Potential problems you may see in the tree are
not of the algorithm itself but due to the
mapping of resources on the tree (the mapping
algorithm which is apart from the tree building
algorithm, needs some consideration regarding
homonyms; but this is a different story). I have
to mention that parts of the tree come through
webservice interaction with CU*STAR database
(some speed may be gain there if this would be an in house solution).
All the best,
Adorian
At 12:59 PM 9/22/2006, Shorthouse, David wrote:
>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
>
>
>_______________________________________________
>Taxacom mailing list
>Taxacom at mailman.nhm.ku.edu
>http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
>
>_______________________________________________
>Taxacom mailing list
>Taxacom at mailman.nhm.ku.edu
>http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
>
>
>--
>No virus found in this incoming message.
>Checked by AVG Free Edition.
>Version: 7.1.405 / Virus Database: 268.12.7/454 - Release Date: 9/21/2006
----------
Adorian Ardelean Dr.
AquaEcology
Stresemanstr. 46
27570 Bremerhaven
Germany
phone: 0471-140-475
<http://aquaecology.de>http://aquaecology<http://aquaecology.de>.de
----------
proiectul myNature
str. Rascoala din 1907 nr 12
Timisoara 300325
Romania
<http://mybiosis.org/nature/portal.php?pagename=firstpage>http://mybiosis.org/nature/portal.php?pagename=firstpage
[a biodiversity-database]
<http://mybiosis.org/nature/portal.php?pagename=adorian>http://mybiosis.org/nature/portal.php?pagename=adorian
CV]
<http://mybiosis.org/romanianorchids/>http://mybiosis.org/romanianorchids/
[Romanian Orchids]
<http://greendorf.com/>http://greendorf.com [botanical illustration]
<http://www.ubio.org/>http://www.ubio.org
http://portal.ubio.org
<http://microscope.mbl.edu/>http://microscope.mbl.edu
http://starcentral.mbl.edu/biopedia
http://starcentral.mbl.edu/custar
Yahoo messenger: transylvaniasan
AOL messenger: transylvaniasan
Ne vom întoarce într-o zi...
Si cei de azi cu pasii grei
Nu ne-or vedea, nu ne-or simti,
Cum vom intra încet în ei.
Radu Gyr
----------
-------------- next part --------------
No virus found in this outgoing message.
Checked by AVG Free Edition.
Version: 7.1.405 / Virus Database: 268.12.8/455 - Release Date: 9/22/2006
More information about the Taxacom
mailing list