Research team developing amphibian anatomy ontology

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On December 19, 2007

A group of faculty and students in the biological and computer sciences
departments at the University of Missouri-Rolla are working with experts from
around the world to develop a formal vocabulary, called an ontology, to
describe the anatomy of more than 6,200 species of amphibians.

The group has been awarded a grant for $1.1 million over three years from
the National Science Foundation (NSF) to develop the ontology, which marks the
first attempt to develop a comprehensive warehouse of information for an entire
class of animals, rather than a single species.

“Essentially, we’re coming up with an agreed-upon set of terms that
researchers will use when refer to amphibian anatomy,” says Dr. Anne Maglia,
assistant professor of biological sciences at UMR, who is working on the
project with Dr. Jennifer Leopold, assistant professor of computer sciences at
UMR, and Analía Pugener, a postdoctoral researcher in biological sciences at

Maglia said hundreds of years of anatomical research has led to the use of
multiple terms to describe the morphology, or form and structure, of
amphibians, with detailed descriptions dating as far back as the early 1800s.
The usage of many terms also has changed during the years and varies across

“This limits researchers’ ability to integrate the results of gene
expression and anatomy studies, or studies of one kind of amphibian to
another,” Maglia says. “We have hundreds of years of people describing and
naming things and sometimes not realizing that the anatomical part they are
referring to already has been described in a different species. We’re now
trying to get all of the camps together to decide on a common terminology.” To
develop the ontology, the UMR team is seeking input from experts around the
world. At, experts
can create an account and log on to submit comments about the developing
ontology. The website also contains information about the project that can be
viewed by the public.

Part of the grant funding also is being used to organize yearly workshops
where experts from around the world can gather to discuss the ontology as it

“We’ve really developed a consortium of anatomists worldwide who are working
on this project,” Maglia says. “This is allowing the world’s experts to come
together, and it is helping to modernize and synthesize our science.”

Information extraction technology also is being used in the ontology’s
development. Another investigator on the project, Dr. Susan Gauch, head of the
department of computer science at the University of Arkansas, has designed
software that reads online scientific literature and scans the contents for
terminology. The information then is sent back and stored in a database at UMR
that Leopold and her team developed.

Maglia says the team at UMR hopes to have a draft of the ontology completed
by the end of the three-year grant. The goal is to have the groundwork laid so
that, with support, the project can continue until a comprehensive ontology is

The ontology could contain as many as 100,000 terms, and also will include
ancillary information for the terms, such as cited literature, dates of the
terms’ publication and pictures.

Amphibians were chosen for the project because they often are used in
embryology studies, drug research and gene expression, Maglia says.

On Jan. 1, 2008, UMR will become Missouri University of Science and

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On December 19, 2007. Posted in Research