The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples

PLoS Biol. 2017 Aug 3;15(8):e2002925. doi: 10.1371/journal.pbio.2002925. eCollection 2017 Aug.

Abstract

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.

MeSH terms

  • Biodiversity*
  • Databases, Nucleic Acid*
  • Metadata*
  • Metagenomics*

Grant support

National Science Foundation https://www.nsf.gov/ (grant number DEB-1457848; DIPnet RCN). Received by EDC, CR, RT, MRG, CEB, JD, ND. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Gordon and Betty Moore Foundation https://www.moore.org/ (grant number GBMF1619 Moorea Biocode). Received by CM, ND, JD. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. National Oceanic and Atomospheric Administration http://www.noaa.gov/ (grant number NMFS-PIRO-NA15NMF4270330). Received by CEB. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. National Science Foundation https://www.nsf.gov/ (grant number DBI-0956426; Biological Science Collections Tracker). Received by ND, JD, CM. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. National Science Foundation https://www.nsf.gov/ (grant number EF-0905606; NESCent catalysis and working group funding). Received by EDC, CR, RT. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.