Identification

Alternate Identifier

59d238e5-3f82-45a4-88a9-0e8bdfe4d36a

Publication Date

2019-08-05

Title

Ocean Sampling Day: Data Access

Abstract

Ocean Sampling Day (OSD) is a simultaneous sampling campaign of the world’s oceans, which took place for the first time in 2014 (via the MicroB3 project) and again in 2018 (via the ASSEMBLE Plus project). The OSD samples, which are related in time, space, and collected environmental parameters, provide insights into microbial diversity and function, enriching our understanding of marine biodiversity and contributing to the blue economy through the identification of ocean-derived biotechnologies. We see OSD data as a reference data set for generations of experiments.

The data for OSD2014 were published via PANGAEA. The sampling and event metadata, collected environmental values, documentation (including SOPs) and the ENA accession numbers for the raw sequences (18S, 16S, shotgun metagenomics) can be found there.

There is also a (no-longer maintained) Github repository for Ocean Sampling Day 2014 and 2015 https://github.com/MicroB3-IS/osd-analysis. This includes

Overview and documentation for the sequencing and analysis done (2014, 2015)

Links to raw and (partially-)processed sequence data (2014, 2015)

Links to metagenomic analysis results (2014)

Links to the environmental data (2014)

Scripts used to produce some of these datasets (2014, 2015)

(A page on ODS2016 is also included in the Github repository, however very little was done and no data are provided.)

The activities and data of OSD 2018 to OSD2021 were covered by ASSEMBLE Plus. The sampling, event, environmental, and ENA accession numbers, plus documentation, are published in the IMIS datasets catalogue for OSD2018 and OSD2019. The 2020-21 OSD events were interrupted by Covid-19, but these data will eventually also be published in IMIS. Additionally, one can find the same data, but in a wider range of formats, in the (new) OSD GitHub site (available here for the standard Github site https://github.com/ocean-sampling-day, and here for a webview of the site https://data.ocean-sampling-day.org/).

Developed by:

OSD 2014/5 were coordinated by the MicroB3 project, as was the MyOSD2016 public participation event. The OSD2018/19 events were coordinated by HCMR in Greece and run under ASSEMBLE Plus.

Technology or platform:

The descriptions, code, and links to data are provided on the above-mentioned GitHub sites.

License Information