Research Experience for Undergraduates (REU)
in Biodiversity Informatics
The grant that the MVZ received from NSF in 1996 to
implement a new information management system for its specimen collections
did not address the issue of accessibility to the vast quantity of
intimately-related data that are not contained on specimen labels, e.g., data
in field notebooks and in archival photographs and correspondence. These
ancillary materials document important biotic and abiotic parameters such as
weather, habitat descriptions, and evidence of animals present in a given
locale. Such information is also invaluable as a means to document
environmental perturbation over time, to assess changes in vertebrate community
structure, and as an aid to landscape planning and management. Yet the data
remain relatively difficult to access because of their descriptive form.
In May, 1998 the MVZ received REU support to develop
a prototype treatment for accessing data in ancillary collections electronically,
and for linking that information to specimen records in its database.
One subset of MVZ's resources was chosen for this project, i.e., field
notes and photographs covering the research that Joseph Grinnell, the
first MVZ director, and his staff conducted over a ten-year period in
Yosemite National Park, work that culminated in the 1924 publication,
Animal
Life in the Yosemite. This subset of data was chosen because of
the general interest in wildlife conservation, declining levels of biodiversity,
and natural resources management issues that exist today for Yosemite.
Furthermore, Grinnell's notebooks and photographs of Yosemite had already
been cross-referenced manually to MVZ catalogue numbers of the specimens
collected.
In conceptualizing this project, we assumed that
researchers wishing to access information and photographs from our ancillary
collections would, in general, adopt one of two approaches. Some would link
to this archive via specimen records in the database because they wished
additional information about an individual or its collecting locale. Others
would want to examine all relevant descriptive information about a geographic
region known to have been previously surveyed by MVZ staff, e.g., the San
Jacinto Mts., Yosemite National Park. The latter group should then be able to
link directly to relevant specimen records in the MVZ database from referenced
items in the digital images. Given this framework, we determined that the
development of a robust content-referencing system for digital images was
central to the success of this project. The methods of creation, storage, and
display of large numbers of high-quality images linked to relevant specimen
information also needed to be carefully addressed. Following construction of a
data model, the students were charged with developing three applications:
- Image Data Entry Application - for cataloging images into the database.
-
Image Content Referencing Application - for adding image content
references to the database.
- Image Browsing Application - for viewing images and their referenced data.
The results of the REU developments have been
incorporated in the full MVZ data model. Extremely high quality photographs
and images of field notebook pages that have been scanned to-date are now
linked to specimen data and can be viewed in most java-enabled browsers.
Click
here to query the MVZ Image Database
Documents specific to the MVZ REU projects are available as Adobe Acrobat
(PDF) files:
- REU Tables (10/98)
- REU Fields (10/98)
-
REU ER Diagram -- viewable
version (10/98) (entire ERD on one page)
-
REU ER Diagram -- printable
version (10/98) (broken up into pages)
MVZ Contact: John Wieczorek
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