GEOME is putting genetic data in its place

Records for sequenced mollusk samples along the southern California coast (GEOME)

Infrastructure to make genetic data widely available for research beyond its initial publication has been a theme of the genomics revolution, from GenBank to the Sequence Read Archive. For molecular ecologists, though, genetic data is only half of our field — the other half is the ecological context in which that data is collected. This month, Molecular Ecology Resources highlights an initiative to bring that ecological context to genetic data archiving: the Genomic Observatories Metadatabase, or GEOME.

Led by Cynthia Riginos at the University of Queensland, Eric Crandall at Penn State, Libby Liggins at Massey University, and Michelle Gaither at the University of Central Florida, the GEOME collaborators present the case for creating yet another data deposition service: although there are a number of established databases for public deposition of genetic and ecological data, no one repository linked both types together. GEOME, which launched in 2017, offers a single metadata framework to link DNA sequence or marker data to sample locality and ecological measurements.

GEOME allows researchers to create records linked to sequence data they’ve already posted to a public repository — or, now, to upload samples to the International Nucleotide Sequence Data Collaboration SRA alongside ecological data through a single unified portal. Datasets are then searchable through the GEOME website, which includes multiple levels of search control alongside a useful map visualization, or through a new R package that interacts with the GEOME API.

About Jeremy Yoder

Jeremy B. Yoder is an Assistant Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.
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