Underwater at Rapture Reef with coral and fish

Rapture Reef in the Northwestern Hawaiian Islands shows high biodiversity. Credit: James Watt

A new publicly available database will catalog metadata associated with biologic samples, making it easier for researchers to share and reuse genetic data for environmental and ecological analyses. The resource, called the Genomic Observatories Metadatabase (GeOMe), was developed by researchers at the University of Hawaiʻi at Mānoa’s Hawaiʻi Institute of Marine Biology (HIMB), California State University Monterey Bay and seven other museums and research institutions.

The database links publicly available genetic data to records of where and when samples were collected, providing contextual information that until now has been missing from widely shared databases. Such information is critical for comparing biodiversity in different locations worldwide and tracking it across time. Despite calls for more data sharing within the research community, researchers have until now lacked the tools to make this information readily available. GeOMe permanently links information about samples’ temporal, environmental, geospatial and scholarly context to genetic sequence data stored by the National Center for Biotechnology Information.

Collaboration aids discovery

GeOMe logo

The developers of the database, described in the journal PLOS Biology, said standardizing and preserving this metadata will greatly enhance the value of the genetic sequence data that researchers are already collecting. With GeOMe, researchers will be able to find and access genetic data collected at specific times and places anywhere in the world, enabling them to ask big questions about the structure and sustainability of life on the planet. For example, they might investigate how the inhabitants of a specific altitude throughout the world have shifted as the planet’s climate has changed.

“Recording and understanding changes to global biodiversity is a collaborative effort that no one can accomplish alone,” said Rob Toonen, a professor at HIMB who helped with the development of GeOMe.

“Our collaborative network of over 65 biodiversity researchers, known as the Diversity of the Indo-Pacific network (DIPnet), was founded in 2012 and has made big steps towards sharing data. GeOMe is part of that effort and will advance both data sharing and discovery for the future,” added Michelle Gaither, post-doctoral researcher at HIMB and coordinator for DIPnet.

Together, the combined efforts of researchers from across the globe collaborating and sharing data through GeOMe will allow the sum of individual scientific endeavors to far exceed any individual research product, they concluded.

Making data publicly available

Toonen and Gaither were part of the development team who worked to ensure that the resource is easy to use and adaptable for a wide range of needs. With the database and toolkit freely available to the research community, scientific journals can now mandate that authors make their metadata available in a searchable and standardized format, just as they have long done for genetic sequence data, they said.

Funding for this study was provided by the National Science Foundation, the Gordon and Betty Moore Foundation and the National Oceanic and Atmospheric Administration.

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