Specimen databases

Kathie Hodge kh11 at CORNELL.EDU
Thu Aug 10 14:04:04 CDT 2000

We're using Biota now at CUP.  We work mainly with fungal specimens.
The software is working well for us, although we've had to invent
some hacks to get around a few problems.  It has a nice, relational
structure, which saves typing in the end, and promotes uniformity of
the data. It does a good job of keeping track of determination
histories, and can do loan management adequately (but see below).  We
haven't attempted to put it up on the web, but our colleagues have
put up a Biota-based fungal inventory-in-progress:

We use Filemaker to get around some deficiencies.  This has
occasionally led us to question why we didn't use Filemaker for the
whole thing, but when we look at the relational data structure in
Biota we realize how many complex things we take for granted now, and
how difficult it would be for us non-programmers to successfully
implement these things in Filemaker, and then keep up on them through
software and system upgrades and changing personnel.  So we export
Biota data to Filemaker to generate labels of several different types
(for special subcollections, photographs, etc.--which need different
data on the label), and also use Filemaker for shipping notices.
Filemaker has much prettier output capabilities, and any modestly
computer-aware person can learn to customize it.

Some gripes:
Biota currently doesn't track loan histories--when a specimen is out
you can tell where it is, but once it's back Biota forgets who has
had it in the past and keeps no thorough historical records of loan
activity (useful when justifying one's existence).  We haven't
developed a satisfactory hack for this.

In the data structure, we've developed our own conventions.  "Host"
ends up as "substrate" for us (sometimes a plant name, sometimes
"dung").  The synonymy system uses jargon from zoological
nomenclature ("junior synonym") that we don't see much in mycology,
and we have had to be careful not to let Biota change all taxon names
to the "correct" name until someone has actually looked at the
specimen.  We have also had trouble sometimes trying to export fields
that are indirectly related, and again we have worked up Filemaker
hacks for these instances.

Biota's author, Rob Colwell, has been extremely helpful and
responsive to our questions.  I know he has big plans for the next
version, so perhaps some of our hacks can be discarded in the near

Dr. Kathie T. Hodge
Director, Cornell Plant Pathology Herbarium
Assistant Professor of Mycology
334 Plant Science Bldg.
Cornell University
Ithaca, NY 14853

email: CUP-herbarium at cornell.edu
web: http://ppathw3.cals.cornell.edu/CUPpages/CUP.html
phone: 607-255-1546

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