Proceedings of TDWG : Conference Abstract
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Conference Abstract
The Genomic Observatories Metadatabase
expand article infoJohn Deck‡,§, Michelle Gaither|, Rodney Ewing§, Christopher Bird, Neil Davies#,¤,«, Christopher Meyer», Cynthia Riginos˄, Robert Toonen˅, Eric Crandall¦
‡ Berkeley Natural History Museums, University of California at Berkeley, Berkeley, United States of America
§ Biocode, LLC, Junction City, United States of America
| Hawai‘i Institute of Marine Biology, Kaneohe, United States of America
¶ Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, United States of America
# University of California Berkeley, Berkeley, United States of America
¤ Gump South Pacific Research Station, University of California Berkeley, Moorea, French Polynesia
« Berkeley Institute for Data Science, University of California, Berkeley, United States of America
» Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, United States of America
˄ School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia, Queensland, Australia
˅ University of Hawaii at Manoa, Kane’ohe, United States of America
¦ Division of Science and Environmental Policy, California State University, Seaside, United States of America
Open Access

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. It contributes to the informatics stack – Biocode Commons – of the Genomic Observatories Network (https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-3-2). While public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. These metadata are especially important for process oriented, time-series research, as for example, at Long Term Ecological Research (LTER) sites or longitudinal public health studies. 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 standards-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 publically archived genetic sequence data in a structured manner, GeOMe provides an important linchpin across all levels of biodiversity.

Keywords

Genomic Observatories, genomics, metadata

Presenting author

John Deck

Presented at

TDWG 2017