Island University Helps Remove Research Barriers with Open-Access DNA Database

Published: August 03, 2017

Island University Helps Remove Research Barriers with Open-Access DNA Database

CORPUS CHRISTI, Texas – Dr. Christopher Bird, Assistant Professor of Biology at Texas A&M University-Corpus Christi, started working on an international collaboration with a group of colleagues in 2011 called Diversity of the Indo-Pacific Network. Since then, he has helped build this project into what is now known as the Genomic Observatories Metadatabase (GeOMe) with $500 thousand in funding from the U.S. National Science Foundation. What started as a non-public database specializing in marine genetics in the Indo-Pacific, has now become an open-access database for microbes, flora and fauna across many scientific disciplines that is accessible to the greater scientific community and the general public.

“GeOMe started as the brain-child of Dr. Eric Crandall at California State University-Monterrey Bay and Dr. Cynthia Riginos at the University of Queensland,” said Bird. “GeOMe has grown into a collaboration with a core steering committee of ten international scientists, including representatives from University of California-Berkeley, the Smithsonian, the University of Hawai‘i, the University of Central Florida, Biocode LLC and the Gump Pacific Research Station in French Polynesia.”

The GeOMe team designed, built and maintains the GeOMe database for genetic data and associated environmental metadata collected from biosamples. Researchers will be able to upload data that provides a snapshot of the lives of organisms such as microbes, lionfish, tigers, and water bears. Once in the database, the metadata will let the GeOMe users know the DNA sequence of the organism, where it came from and the conditions it lived in.

“This is not so much of a database of organisms sitting on shelves in preservative. Rather, it is a database of organisms in their natural settings. The database brings the researcher into nature,” said Bird. “GeOMe details exactly where samples were collected and the conditions these individuals experienced, and connects that to their unique genetic code in the U.S. National Institutes of Health GenBank database.”

Due to the open-access nature of GeOMe, the metadata will be available internationally. From the comfort of their labs, researchers can upload and download data. This increases the fiscal efficiency of scientific establishments by facilitating taxpayer-funded data to be more easily recycled, thereby reducing the duplication of effort. 

“GeOMe helps break down geo-political barriers to collaborative research,” said Bird. “By allowing researchers to access and build upon information deposited by numerous laboratories, GeOMe enables new questions to be addressed that were too expensive to be undertaken by a single laboratory. GeOMe also enables increasingly complicated biological research to be rigorously scrutinized and replicated.”

The Gulf of Mexico and the Coastal Bend will also benefit from GeOMe. GeOMe meaningfully combines a variety of data in a flexible manner for cross-study research, which would allow marine and wildlife management to use the data to better understand the processes affecting local ecosystems. For example, researchers could use the database to track the origins of invasive species, define biologically relevant management units and gain other insights previously unavailable. Currently, existing DNA databases do not adequately store and provide easy access to uniformly-formatted environmental data associated with DNA sequences.

“Some of our researchers and professors are already utilizing the database,” said Bird. “Drs. Derek Hogan, Assistant Professor of Biology, and Rebecca Hamner, Postdoctoral Researcher, have uploaded their data in invasive lionfish and Maui dolphins, respectively.”

Several other scientists at Texas A&M-Corpus Christi and world-wide will find the GeOMe database to be an effective vehicle for public data storage and sharing because GeOMe was designed to be customized by different research communities, says Bird.

GeOMe has grown bigger than originally anticipated. According to Bird, the next step is handing the reigns over to a federal agency such as the National Science Foundation or National Institutes of Health. With this, GeOMe will be able to obtain additional funding to collaborate with other research networks and better customize GeOMe for particular research communities and to ensure the GeOMe database is supported in perpetuity.

“There’s been a huge push to properly archive scientific data and make it accessible,” said Bird. “There’s typically little reward for doing this, so some journals are discussing mandating that authors deposit their data into GeOMe before their research is published.”

Bird, along with the following people, have contributed to the publication of the GeOMe database: Dr. Eric D. Crandall, Dr. Neil Davies, Dr. John Deck, Dr. Rodney Ewing, Dr. Michelle R. Gaither, Dr. Christopher Meyer, Dr. Cynthia Riginos and Dr. Robert Toonen. Their manuscript in PLoS Biology, “The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples,” will be published this week. PLoS Biology is an international, open-access and peer-reviewed journal featuring the works of exceptional significance, originality and relevance in all areas of biological science.