IMIS - Marine Research Groups

Ocean Sampling Day was a project that began in 2014 (see https://doi.org/10.1594.PANGEA.854419 for the data from that year), and in 2018 the OSD network was picked up by the Horizon 2020 project ASSEMBLE Plus, within the Joint Research Activity "Genomics Observatories", and with the support of EMBRC ERIC. Following standardised protocols, water samples were taken and shipped to a centralised location for processing, this being coordinated by the Institute of Marine Biology and Biotechnology (IMBBC) of the Hellenic Centre for Marine Research. Environmental measurements were recorded, following protocols, and those logsheets also processed by IMBCC. DNA metabarcoding data on 16S and 18S rRNA were produced on the Illumina MiSeq system, at HCMR. Metagenomic shotgun sequencing was performed by Genoscope on the Illumina NovaSEq 6000 system. Curation, quality control and FAIRification of the data have been achieved by a team involving researchers from HCMR (Dimitra Mavraki, Dr. Melanthia Stavroulaki, Dr. Jon Ben Kristoffersen) for digetisation of logsheets and metadata QC, VLIZ (Katrina Exter) and GFBio (Dr. Ivailo Kostadinov) for additional metadata QC and adding of semantics and machine-interoperability. In this dataset you will find the documentation used in 2019 (SOPs, Handbook, logsheet templates); a data spreadsheet (CSV format) containing the sampling and event details, collected environmental measurements, and the accession numbers of the sequences in the European Nucleotide Archive; and a metadata spreadsheet (CSV format) in which descriptions, units, and the used vocabularies are given. In version 2 of these data (the current record) an additional flagging of the environmental measurements has been added, to make users aware of potential discrepancies in the reported units. The data provided via the Marine Data Archive (MDA) are human-understandable, while additionally machine-accessible data formats are provided via the OSD Github space (see data links).