Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research

Cynthia Riginos; Eric D Crandall; Libby Liggins; Michelle R Gaither; Rodney B Ewing; Christopher Meyer; Kimberly R Andrews; Peter T Euclide; Benjamin M Titus; Nina Overgaard Therkildsen; Antonia Salces-Castellano; Lucy C Stewart; Robert J Toonen; John Deck

doi:10.1111/1755-0998.13269

Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research

Mol Ecol Resour. 2020 Nov;20(6):1458-1469. doi: 10.1111/1755-0998.13269. Epub 2020 Oct 27.

Authors

Affiliations

¹ School of Biological Sciences, The University of Queensland, St Lucia, Qld, Australia.
² Department of Biology and Chemistry, California State University, Seaside, CA, USA.
³ Department of Biology, Pennsylvania State University, University Park, PA, USA.
⁴ School of Natural and Computational Sciences, Massey University, Auckland, New Zealand.
⁵ Department of Biology, Genomics and Bioinformatics Cluster, The University of Central Florida, Orlando, FL, USA.
⁶ Biocode LLC, Junction City, OR, USA.
⁷ Smithsonian Institution, National Museum of Natural History, Washington, DC, USA.
⁸ Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA.
⁹ Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI, USA.
¹⁰ Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
¹¹ Department of Natural Resources, Cornell University, Ithaca, NY, USA.
¹² Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain.
¹³ GNS Science, Lower Hutt, New Zealand.
¹⁴ Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA.
¹⁵ University of California at Berkeley, Berkeley, CA, USA.

PMID: 33031625
DOI: 10.1111/1755-0998.13269

Abstract

Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards-compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.

Keywords: FAIR principles; bioinformatics; ecoinformatics; genomic; open data; reproducible research.

MeSH terms

Biodiversity*
Databases, Nucleic Acid*
Ecology
Genomics*
Information Storage and Retrieval
Metadata*
Research*
Workflow

Abstract

MeSH terms

Grants and funding