EUREMAP Data Management

A short guide to how data are managed when using the EUREMAP Marine Bioprospecting Pipeline.

This material is intended to be read in 20 minutes, give or take... If you have any questions or comments please leave an “Issue” in the book’s GitHub repository.

Introduction¶

The EUREMAP project aims to optimise the marine bioprospecting workflow within the European research community, enabling state-of-the-art research and enhanced capacity for academia and industry. The EUREMAP Bioprospecting Pipeline was developed as part of the EU Commission Horizon Europe programme.

The data management workflow adopted by the project relies heavily on services provided by EMBL-EBI as part of the ELIXIR Research Infrastructure’s contribution to European Open Science Cloud (EOSC) infrastructure. All (meta)data artifacts of a EUREMAP-based project are linked to a single BioProject/Study accession, that itself sits below the EUREMAP BioProject Umbrella Study. Metadata describing samples (e.g. DNA samples, culture samples, etc) from which data are collected are registered in BioSamples. Data created by using a “step” with the EUREMAP pipeline are published in an appropriate repository (e.g. sequence data in EMBL-ENA, metabolomic data in Metabolights, etc) and linked to the BioProject Accession and the BioSamples accession. The figure below shows this data linking for a sequence based experiment.

Linking the data this way allows multiple data sets to be linked to a single BioSample, and multiple BioSamples and data set types (in different data repositories) to be linked under a single BioProject/Study.

Finally, the BioProject, BioSamples, and data repository accessions are linked to a BioStudies accession. The BioStudies accession describes the experiment and can also contain additional data files (e.g. CSV tables) that could not be included in data-specfic repositories.

Quick Start¶

1. Open Science Principles¶

General background information about the importance of data management

2. Data Management Plan (DMP)¶

Create a DMP using the OpenAIRE Argos platform

3. EMBL ENA Webin Submission Portal¶

Create an account in the ENA Webin Submission Portal

4. BioProject/Study¶

Create a BioProject/Study accession from the Webin Portal

5. BioSamples¶

Submit sample metadata to BioSamples through the Webin Portal

6. Data deposition¶

Submit your data to an appropriate data repository, referencing both the relevant
BioSamples and BioProject accessions

7. BioStudies¶

Create a BioStudies accession using the BioStudies Submission Tool and link BioProject,
BioSamples, additional data files, and all data repository accessions to your
BioStudies accession