An earth-system RO-Crate

Contributors

Author(s)

Marie Josse

Questions

• How to generate a RO-Crate

• How to follow a Marine Omics study

• How to read a RO-Crate ?

Objectives

• Understand RO-Crate in an earth-system context

Workflow context

The workflow used as an example here goes from :

• First, produce a protein FASTA file from a nucleotide FASTA file using ( Prodigal ( Galaxy version 2.6.3+galaxy0)) (a tool that predicts protein-coding genes from DNA sequences).
• Then, use ( InterProscan ( Galaxy version 5.59-91.0+galaxy3)) to create a tabular. Interproscan is a batch tool to query the InterPro database. It helps identify and predict the functions of proteins by comparing them to known databases.

• Finally, discover ( SanntiS ( Galaxy version 0.9.3.5+galaxy1)) both to build genbank and especially to detect and annotate biosynthetic gene clusters (BGCs).

The workflow itself

Run the workflow

Import and run the Biosynthetic Gene Clusters workflow

To know more on how to do that follow the tutorial

Generate the RO-Crate

Once you run the workflow you can generate the RO-Crate. To do so follow the tutorial

From workflow to RO-Crate

The RO-Crate folder and architecture

Let’s dive into the ro-crate-metadata.json

Description of the RO-Crate structure

Galaxy Provenance

Title and workflow details

Dates

Data

First tool Prodigal

Second tool Regex Find and Replace

Third tool InterProScan

Fourth tool SanntiS to build Genbank

Fourth tool SanntiS to annotate biosynthetic gene clusters

Details on the different files in the RO-Crate

End of the ro-crate-metadata.json

Thank you!

Try to do the same on your workflow!

Key Points

• RO-Crate in earth-system analysis
• Marine omics workflow

Thank you!