Frustrated users of BioInformatics, etc.

[christian thompson]

Below is a copy of message I received this morning. I would very much be
interested how TAXACOM people would react to this frustrated user of
taxonomic information. Whether we call it Biodiversity Informatics or what,
they are people who want our help and apparently not getting it
===================================================
From:   "Malcolm Chisholm" <chisholm2 at home.com>
To:     SELMAIL.nmnh_po(cthompso)
Date:   Mon, Feb 12, 2001 11:04 PM
Subject:        Questions on Taxonomy

Dear Dr Thomson,

I was very interested to read your paper in Biodiversity_II for several
reasons.  I did my Ph.D. in studying the practical effects of competition
between insects in cowdung (Diptera & Coleoptera) in the UK.  I found I
could not pursue a career in research so I moved to the US where I became a
data modeler (you can check out my new book at www.refdataportal.com) an
important branch of computing.  My wife and I also have a coffee farm in El
Salvador where we are trying to do something practical about biodiverity
conservation.

... detailed questions about data keys have been deleted here ...

This is of more than passing interest to me because I am trying to design a
database to hold biodiversity information.  Actually my goal is to store
information on the ecomomic and cultural significance of the species on my
coffee farm.  I have built a large number of complex databases (and actually
my taxonomic training has been very useful in my career).  However, this
database is proving practically and conceputally very difficult to build.
Here are some of the problems:

(a) I cannot find any real databases of species lists for trees,
butterflies, birds and orchids _ the groups I want to start with where I can
harvest names and build a taxonomic backbone.  What people call databases
are not what I call databases _ they are usually unstructured text
documents

(b) Taxonomists seem to be in the business of creating confusion.  The
number of synonyms is growing.  I just want to know what a species is, not
several opinions on how it fits in some hypothetical evolutionary scheme.
Why have taxonomy if the number of scientific names for an organism is
greater than the number of names for the same organism in a given human
language?

(c) Following this, taxonomists are not able to match scientific names to
common names.  This is very important for my work in El Salvador where local
people have names for each species of tree.  I sponsored a trip by several
taxonomists from a leading European museum to my farm.  They did a lot of
collecting, and came up with a catalog of names, but at the end of the day
could not provide me with matching local names.

(d) I want to know useful facts about species.  The taxonomic community
does not appear to be interested in this at all.  I can find no conceptual
help on how to connect facts in my data model to the taxonomic backbone.
Creating what I call a "factoid database" is proving to be a very difficult
task.  However, I am inching along, and will get the job done eventually.

If I seem to be bashing taxonomists, please understand that I spent many
years learning how to identify a broad range of British invertebrates and
greatly appeciate the work that was done to create the knowledge I was able
to use.  My frustration comes from seeing an ongoing decline in Central
American biodiversity, and thinking that I have a number of practical
solutions that I can apply on my own property, but which I cannot bring to
fruition.

I would be grateful if you can indicate any approaches to the obstacles I
have found.

Best regards,
Malcolm Chisholm
www.askget.com