Download Biota: The Biodiversity Database Manager.—Robert K. Colwell

Review
Syst. Biol. 46(3):574-575, 1997
Biota: The Biodiversity Database Manager.—Robert
K. Colwell. 1996. Sinauer Associates, Sunderland,
Massachusetts, xvi + 574 pp. + software. $125.00.
ISBN 0-87893-128-7.
"Biodiversity" and "information management" are
buzzwords of the 90s, but there has been little intersection of biodiversity concerns and information management. High-level information models exist, such as that
developed by a committee of the Association for Systematics Collections (http:/ /www.ascoll.org/data.htrnl), and
an information reengineering effort is underway at UC
Berkeley (http: / / www.mip.berkeley.edu / mvz / cis.html).
In the meantime, systematists, ecologists, and conservation biologists have muddled along without an effective tool for managing precious data. Rob Colwell
has crafted Biota, a powerful and easy-to-use information management system that fills that need more
than adequately. Biota is a stand-alone application that
was developed with 4th Dimension (4D), a high-end
relational database system by Acius. The first release
of Biota was developed for the Macintosh, but Biota is
now available in a Windows version as well. The Biota
Web site can be accessed at http:/ /viceroy.eeb.uconn.
edu/biota.
Biota makes heavy use of the relational capabilities
of 4D. There are 12 core tables: Specimen, Collection,
Locality, Loans, Personnel, Species, Genus, and five
more higher taxonomic categories. The Specimen table
is the intersection of a geographic hierarchy and a taxonomic hierarchy. The geographic hierarchy includes
Specimen, Collection, and Locality tables, each more
inclusive. Thus, there can be many Specimens in one
Collection and many Collections from one Locality.
The taxonomic hierarchy includes Specimens, Species,
Genus, Family, Order, Class, Phylum, and Kingdom
tables. Colwell is aware of current trends in taxonomic
theory regarding unranked taxa (de Queiroz and Gauthier, 1990). However, current database development
systems offer no efficient way of recursively searching
records linked as tree structures, so Biota retains traditional ranks, each corresponding to a table. Additional ranks (cohort, subfamily) are accommodated in
a clever way as are temporary determinations, such as
when a beetle can only be identified to Chrysomelidae.
Junior and senior synonyms in Species records can
be tracked. The Determination History (changes in genus or species) of Specimen records is carefully archived. Images in PICT format can be stored in records related to Species records (but not to the
Specimen records). I caused a problem by loading an
image file from disk that caused the program to jam
because insufficient memory was allocated to it. I also
caused Biota to crash hard by loading a TIFF image;
only PICT images are allowed by 4D. An unlimited
number of Notes records can be attached to any record in the Specimens, Species, Collection, Locality,
and Loans tables. Data about users can be stored in
the Personnel table, and these records can be associated into groups, such as a team of biologists doing
an inventory. Longitude and latitude can be stored in
several formats. Partial dates can be accommodated.
Default values and choice lists can be defined for
fields. Barcode entry can be used for certain key fields,
such as Specimen identifier.
The design of the Loan table and related tables allows both outgoing loans and specimens loaned from
another institution to be entered into Biota. The loan
system is somewhat limited and seems least suitable
for museum use. For example, one cannot add specimens to an existing loan, and after loans are returned
there is no record of which specimens had been
loaned. These drawbacks could be addressed in future
releases.
In contrast, other aspects of Biota are more flexible
than its information structure suggests (Colwell provides a complete schema in the manual). The Specimen table can be used to track living organisms, as
in a life list, or to create species lists for inventory
sites. Complex relationships between hosts and commensals can be accommodated to several levels as
well. This relationship can be used to track tissue samples or other secondary preparations of a specimen.
All menus in Biota are accessible regardless of
which table is viewed. Each menu item specifies a task
(searching, data entry, printing, etc.) that runs as an
independent process, meaning that many tasks (only
limited by memory) on different tables can be executed simultaneously. There are few command-key
equivalents, a feature I miss. Different selections of
records from the same table can be displayed at once
in different windows. These selections can be saved
and retrieved. Set arithmetic can be performed on selections of records. Searches or sorts of records, including those in related tables, can be executed with
generic search and sort editors or by streamlined tools
for commonly searched fields. Referential integrity
among tables is enforced, with some override allowed
to the user, and tools are available to identify childless
and parentless records. In the current version, menus
and display screens are in English, but the important
dialog screens are available in English or Spanish.
One of the general disadvantages of a precompiled
database is lack of flexibility; once fields are defined
they cannot be changed. However, Colwell has provided some ingenious solutions. Fields in the core tables can be renamed using a system of aliases. For the
Species, Specimen, Collection, and Locality tables, any
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number of auxiliary fields can be defined. These are
not true new fields in the table but rather records in
special tables that function as cells in a sparse matrix.
Auxiliary fields can be used to store and export character data in the NEXUS format used by PAUP and
MacClade.
Preformatted labels can be printed with data from
the Collection, Species, or Specimen tables. They can
be used for insect pins, vials, slides, or herbarium
specimens. Using 4D's built-in label generator, custom
labels can be produced and can include data from related parent tables, but the labels are not stored as
records. Biota has a series of preformatted reports,
and 4D provides a custom report generator as part of
its programming tools. This report generator is functional but is not as intuitive as the rest of Biota; this
is a limitation of 4D. If the flexibility of the report
generator is not sufficient, the results can be output to
a disk file for further manipulation. Data can also be
exported in Web-page format, with embedded HTML
commands.
A password system allows four different access levels to users. Using 4D Server software (available separately), Biota can be run in a true client-server mode
using TCP/IP protocol, but the manual suggests that
most Internet connections are too slow to make this a
viable solution. The newest release of 4D (not presently used for Biota) features a Web server, and future
editions of Biota will likely have this capability. The
574 page manual is well written (unlike many commercial manuals), profusely illustrated, and accurately
indexed.
Of course, I would write some parts of Biota differently. But this is largely a matter of taste, and one can
hardly argue with something that works extremely
well. Why not just use commercial software and develop your own custom database? I have written herpetology collection databases in both Filemaker Pro
and 4D. Filemaker Pro is easy to use and inexpensive
but is somewhat limited when compared with 4D. Unless you simply love to program, purchasing Biota will
save you a lot of grief. Even with several years experience using 4D, I estimate it would take 10-12 months
to duplicate the functions of Biota with my own code.
I recommend Biota very highly to database designers
and programmers if only to see interesting solutions
to common design and implementation problems.
More importantly, Biota is an extremely useful and
perhaps unparalleled software tool for any biologist
who manages biodiversity information.
REFERENCES
DE QUEIROZ, K., AND J. GAUTHIER. 1990.
Phylogeny
as a central principle in taxonomy: Phylogenetic definitions of taxon names. Syst. Zool. 39:307-322.
David C. Cannatella, Texas Memorial Museum and Department of Zoology, University of Texas, Austin, Texas
78712, USA.