Planning for Field Based Biological Sample Collection: Using the Genomic Observatories Metadatabase Project Interface

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). The GeOMe project interface enables administrators to plan and execute field based sample collection efforts. GeOMe projects specify a core set of sample metadata fields based on community standard vocabularies and also includes plugins for associating samples with photos, subsamples, NextGen sequence metadata, and permits. Users can upload their own expedition-specific metadata, which contributes to the overall project dataset while providing the user a convenient method for updating and refining their contributed data.  GeOMe provides connection points to the Global Biodiversity Information Facility and archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA), linking specimens and seqeuences via unique persistent identifiers.