pcplantdb

["John Howe" <warlock@arashi.com>]

> Folks,
> I've had a play about with TouchGraph to see what we could do with it.
Have a
> look at
http://www.ibiblio.org/pfaf/pcplantdb/PlantFamilyTree/PlantFamilies.html
> in which I've put the family tree from Kingdom down to Species as a
TouchGraph.
> (Note for size reasons there are separate graphs for each family).

Hey Rich, All,

I have been lurking here for a while now and have been playing around with
the pfaf mysql db on Linux. I am curious what platform you tested this
TouchGraph on.

I tried accessing this TouchGraph app on a couple of systems, and here are
my results:

MacOS X 10.2.8
~ Mozilla 1.4 ( applet downloaded, then empty node browser window )
~ Firebird 0.6 ( applet downloaded, then empty node browser window )
~ Safari 1.0 ( applet downloaded, then empty node browser window )
~ MS IE 5.2 ( applet download, 37 seconds to load on 640K DSL line, once
parent
node is clicked, the application is basically unusable, as nodes spawn out
too fast and the app stops responding. Can't seem to compress the nodes
either. Information windows can not be rescaled to display info )

Linux Debian "Sid"
~ Mozilla 1.4 ( no java support )
~ Firebird 0.7 ("")

Windows 2000
~ Not tested

There seem to be a couple alternates to TouchGraph that may be kinder to
the web client ( with limited bandwidth, was that jar file 2.6M?  ) and
make caching of information easier to proxies/upstream mirrors. It may be
programatically more complex however to implement.

Specifically:

1. http://www.research.att.com/sw/tools/graphviz/

AT&T's graphviz, accessable via PHP Pear libraries ( PHP
Pear::Image_GraphViz ), requires netpbm as well.

2. http://webesquema.tucajon.com/

Sort of a tree/class browser ( habla espanol? )

Some example php/js/graphviz projects as reference:

http://pathalizer.bzzt.net/
http://erw.dsi.unimi.it/
http://urlgreyhot.com/graphviz/

An alternate delivery mechanism could be using GraphViz and dhtml
mouse-over boxes to image maps ( example @
http://www.knopper.net/knoppix-mirrors/, mouse over items in "Download
von" list ) to the java app in terms of bandwidth/cross-platform broswer
portability.

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I am still researching this project, trying to become more familiar with
the existing upstream projects/standards and tracking biological
taxonomies in general. Some sites I have been looking at:

http://faculty.washington.edu/mandoli/fuzzyfig.html
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
http://tolweb.org/tree/home.pages/techiedetails.html
http://www.treebase.org/treebase/index.html
http://ucjeps.berkeley.edu/bryolab/GPphylo/
http://ucjeps.berkeley.edu/DeepGreen/ScienceMagazine.html
http://wwbota.free.fr/Samples/parsing.htm
http://wwbota.free.fr/UML_diagrams.htm
http://wwbota.free.fr/project-state.html
http://www.bgbm.fu-berlin.de/TDWG/CODATA/SydneyWorkshop.htm
http://www.biogis.huji.ac.il/
http://www.biosis.org.uk/zrdocs/zoolinfo/stn_soft.htm
http://www.ento.csiro.au/biolink/index.html
http://www.hcs.ohio-state.edu/hcs/TMI/HORT234/FirstClass/sld013.htm
http://www.ipni.org/index.html
http://www.rhs.org.uk/research/registerpages/daff7.asp
http://www.speciestoolkit.org/index.jsp
http://www.tdwg.org/index.html

I am curious about how many schema revisions the pfaf has been through and
if there is any thought to running it past a couple of normalization runs?
It appears that most projects try to attain at least 3rd Normal Form ( 3NF
) with their databases. Or is the pfaf just one of many seed sources for
the plantdb?

I also have other questions about Guilds in general. Stepanie talked about
the relationship between plants and insects. I would think that Guilds
would include animals, birds, insects and fungii as well. Will that be
included in mapping Guilds?

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Some high level design questions:

Will this be a distributed application? ( being open source ) or singly
hosted?
If so, how to we replicate data between remote systems?

How to importing diverse upstream databases into the plantdb schema?

Moderation/peer review on data entries?

GIS mapping of observed guilds to entries?

Can X in guild N in location L1:L1 having environmental conditions Y
behave/belong to Guild M in location L2:L2 with environmental conditions
Z? I am thinking about how Rhodederdrons behave here as opposed to their
behaviour in Ireland ( contained in Seattle, invasive in Ireland ). (
Environmental conditions can include avg days of sunlite, rainfall, temp.
etc. )

Are the anti-guild agents? For example, english ivy is invasive in the
parks here and systemically changes the soil structures which guild member
Oregon Grape depends on.

Guild member to environment condition mapping. An old mentor of mine
pinted out that Burdock growing in a field in California was indicative of
underground water flows.

Display of information appropriate to clients bandwidth ( text
only/text+images/complex real-time navigatable apps )

Tracking general pattern observations as a guild precursor. It may be a
guild member, I see plant x, plant y, bird z together at location.

How to guilds map to recent phylogenetic research?

Cheers!

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John Howe, B.S, M.A., Sr. Systems Administrator
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The most beautiful thing we can experience is the
mysterious. It is the source of all true art and science.
 -- Albert Einstein