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New database collecting all species names

  |   July 2, 2002 at 5:10 PM
WOODS HOLE, Mass., July 2 (UPI) -- Researchers at the Universal Biological Indexer and Organizer Project are assembling a new digital database meant to serve as an online "tree of life," a catalog of all living things and the millions of names used to refer to them.

By bringing together in one place the different names of every known plant, animal, bacteria, fungus and assorted other life forms, researchers hope that information gleaned from libraries of all past biological knowledge can assist a wide array of activities, from cutting-edge genetics research to birdwatching.

"It's meeting a need that anyone working in the field of biology has," bioinformatics developer David Remsen, the project's lead researcher, told United Press International.

Over the centuries, an organism can accrue dozens of names for itself. For example, the species of dinosaur known as brontosaurus -- a name that was popularized by "The Flintstones" animated television series of the 1960s -- is now officially called apatosaurus.

"There's a local fish found in Woods Hole I use as an example all the time," Remsen said. "This bluefish has the scientific name Pomatomus saltator. If you go look for articles on that name -- and that's what current authorities would tell you is the name for that fish -- you would only retrieve one article. With our system, it would retrieve 47 articles exactly about that organism."

Remsen explained that even the lowly bluefish has 18 names, something not unusual in biology. In this case, he said, its oldest name dates back to 1766 when famed taxonomist Carl Linnaeus first described it.

"There's a huge problem in biology, not only with dinosaurs and fishes, but in all biology," Remsen explained. "They refer to (it) as 'the names problem' -- the names used to refer to organisms change over time, and you can easily miss information. Or you could have someone catch a fish in Australia, think it's a new species and name it only to find out it also lives somewhere else and has another name."

This scientific dilemma is compounded by the fact that taxonomy -- the science of classifying and naming organisms -- is scattered into dozens of specialties, each with its own often jealously guarded way of handling things. "Fish experts don't really care about sponges and the dinosaurs, and so you have fish-based and ant-based and mammal-based solutions," Remsen said. "Navigating all that information is hard because you have to re-learn the taxonomy every time -- there's no consistency to it."

The new system is gathering all the biological information on every organism as well as its name. After a year's work, the researchers have an operational prototype. "We envision having a public system available sometime before the end of the year," he said. "We're getting close to a million names now, but I expect to have a couple of million by the end of the year."

Tom Moritz, library director at the American Museum of Natural History in New York City, told UPI he thinks the project holds very high promise.

"It's a problem all scientists face and have a clear need for, including those in areas like biotechnology and gene sequencing," he said. Moritz cited the National Institutes of Health's GenBank, which collects all publicly available DNA sequences.

"Unless you have a system to define names, then you're really at a loss for information collected over the last 200 years. This is an absolutely key piece of digital development in general in biology," he said.

(Reported by Charles Choi, UPI Science News, in New York)

© 2002 United Press International, Inc. All Rights Reserved. Any reproduction, republication, redistribution and/or modification of any UPI content is expressly prohibited without UPI's prior written consent.
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