pcplantdb

[Richard Morris <webmaster@pfaf.org>]

John Howe wrote:
> I have been lurking here for a while now and have been playing around with
> the pfaf mysql db on Linux. 

Cool. Hows it going?

> 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

Great, I can see I'm going to be busy reading.

Also worth having a look at http://www.itis.usda.gov/
and the many databases listed on
        http://www.comp.leeds.ac.uk/pfaf/Links_4.html

In general I think we (Ken) favors the www.ipni.org for
authorative plant names.

> 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. 

Schema? Normilisation? Whats those? ;-)

No we have not really examined such matters. The database
has basically been created by Ken with a few tweeks by me.
Neither of us have any formal training in database design
and the database has never been subjected to these sorts
of considerations.

For the curious Normilisation basically means changing the
design of tables in the database so that repeated information
is removed. If the same item is repeated in two seperate places
it can cause big problems if one item is changed and the other is not.

There are quite a lot of places where the pfaf data does
badly break normilisation rules, particlarly in info related
to shade and habitats and there are inconsistances and gaps
in the data. I'd like to try to fix these things, one day!

> Or is the pfaf just one of many seed sources for the plantdb?

Ideally this would be the case. I'd really like to incorperate
other datasets and find other who like to contribute data.
There are copyright issues to be addressed if we wish to do this.
A lot of networking is really needed to make this more than
a representation of the pfaf data.

My thoughs are to actually have a good schema (which fields
appear in which tables) for the pcplantdb
which follows good normilisation rules. I'm not sure how closly
it should follow the pfaf scheme. I've a few ideas about other
fields which would go in.

Indeed part of the point in the version release a few week back
was to leave the schema open ended. So it is quite easy to
add new sections etc.

I'd like to encourage some more discussion on schema and get
closer to the nitty gritty.

> 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?

If you so wish! Its actually possible to add new types of things
quite easily.
> ----------------------------------------------------------------------------------------------
>
> 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?

Good question. I'd guess it could be distributed, probably with
a central repository or reference dataset. If we keep things
append only then propagating updates is easier.

> How to importing diverse upstream databases into the plantdb schema?

I've a few ideas on how this sort of thing could be done.
Really we need some structure for mapping a particular
DB schema onto ours.

> Moderation/peer review on data entries?

Yep. A long way down the line yet. I've though of
having some sort of editoral board. Keeping things append only
and propper citation of whos added what is a good starting point.

> GIS mapping of observed guilds to entries?

Nice, but could be a lot of work. We do need some
mechanism to describe geological locations. Quite a tricky
problems as sometimes we will want small areas (say a particular plant 
sighting) and other times much larger regions (say a Country).

> 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. )

I see this sort of thing as being quite important. If we are
thinking of a global database we need to address global issues.

> 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.

All these questions seem to point to an extensible scheme.
All ideas seem good to me and it would be nice to let this sort
of info be added easily.
> Display of information appropriate to clients bandwidth ( text
> only/text+images/complex real-time navigatable apps )

Should be quite easy. Seperating data from presentation
allows diffent interfaces to be used.

> 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.

Hum, yes. We could have a 'guild precursor' object.

> How to guilds map to recent phylogenetic research?

Yes linking to external sources, website, papers, books etc.
is important.

> Cheers!

Thanks for a lot of very good questions.

> ----------------------------------------------------------------------------
> John Howe, B.S, M.A., Sr. Systems Administrator
> ----------------------------------------------------------------------------

Out of interest where are you based, whos system to you administer?

        All the best

                Rich

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