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Database of biodiversity offers peek at biologists’ field notes, photographs

Wednesday, June 26, 2013

LAWRENCE — For centuries, biologists have cataloged Earth’s biodiversity, cramming drawers in universities and institutions with meticulously labeled voucher specimens collected in the field. The problem is that much of that precious information has been inaccessible and limited in scope by the standards of today’s interconnected world. These days, many efforts are aimed at bringing such information into the digital age.

But one researcher of aquatic beetles at the University of Kansas believes that merely digitizing information from specimen labels isn’t good enough.

Andrew Short, assistant professor of ecology and evolutionary biology, is leading an effort known as the Collection Resources for Aquatic Coleoptera that combines species data, records of collection efforts, maps, digital photography and scans of biologists’ handwritten field notes into a simple-to-use database available to researchers and the public online.

The effort, dubbed CReAC, focuses on species of aquatic beetles — which outnumber all mammals and birds combined — but could apply to any efforts at cataloging biodiversity on Earth.

Pronounced “creek,” the resource will have its public launch this summer. The unique project bases information around researchers’ trips into the field to collect specimens, resulting in a more accurate accounting of where specimens were located and where they weren’t found.

“It’s a research interface with a different approach,” said Short, who also serves as a curator with the KU Biodiversity Institute. “We record collecting events, then attach specimens to those. Most times there are specimens resulting from time in the field, but sometimes there aren’t. And if we don’t take that approach, a lot of data goes missing. For example, when you collect up in the Andes Mountains, there are very few species living over 3,000 meters. We’ve collected up there in ponds, and we don’t get anything. But how do we put this in a conventional database? We want to show that we’ve collected there, and we haven’t gotten anything — it’s absence data. If we used a specimen-based approach, that data is never going to be present. With CReAC, we use the event-based maps that can show where nothing was found, and compare those with the maps of where specimens were actually found.”

Moreover, the CReAC project allows researchers to scan field notes — usually containing troves of relevant information not found in the labels that are attached with voucher specimens. For example, Short has scanned in a career’s worth of field notes of Paul J. Spangler, a prolific former aquatic beetle researcher at the Smithsonian Institution. Examples are here and here.

“For most biologists, we write out field notes,” said Short. “So instead of starting with the specimens, we scanned in 2,000 pages of his notes. You have a list of what he collected, but also water quality information, how deep the water was, the water temperature, plants that were in the water. You unlock a huge amount of information.”

Further, CReAC will allow contemporary biologists to upload digital photography of their specimens and link the images with the rest of the data. For instance, Short spends much of his time in the field hunting for new species of aquatic beetle in South America, where he takes hundreds of photos of streams and pools where the beetles are found.

“We takes lots of pictures in the field, but they just live on my hard drive,” said Short. “Now, we’ve attached thousands of these images to the database. Not only are you getting the field notes, but also you’re getting thousands of images of where the beetles were collected. It’s basically organizing all of this data which was just living in the offices and computers of the scientists.”

In addition to the collection of aquatic beetles at KU, the CReAC project will incorporate the collections of the Smithsonian Institution, Universidad Central de Venezuela, Universidad del Zulia (Venezuela), National Zoological Collection of Suriname and the Santa Barbara Museum of Natural History.

The National Science Foundation supported the CReAC project.