An earth-system RO-Crate

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# An earth-system RO-Crate

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			<li>
				<a href="/training-material/hall-of-fame/Marie59/" class="contributor-badge contributor-Marie59"><img src="https://avatars.githubusercontent.com/Marie59?s=36" alt="Marie Josse avatar" width="36" class="avatar" />
    Marie Josse</a></li>
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### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- How to generate a RO-Crate

- How to follow a Marine Omics study

- How to read a RO-Crate ?

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### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- Understand RO-Crate in an earth-system context

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# Workflow context

The workflow used as an example here goes from :
- First, produce a protein FASTA file from a nucleotide FASTA file using (<span class="tool" data-tool="tool_id=toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0" title="Prodigal tool" aria-role="button"><i class="fas fa-wrench" aria-hidden="true"></i> <strong>Prodigal</strong> (<i class="fas fa-cubes" aria-hidden="true"></i> Galaxy version 2.6.3+galaxy0)</span>) (a tool that predicts protein-coding genes from DNA sequences).
- Then, use (<span class="tool" data-tool="toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3" title="InterProscan tool" aria-role="button"><i class="fas fa-wrench" aria-hidden="true"></i> <strong>InterProscan</strong> (<i class="fas fa-cubes" aria-hidden="true"></i> Galaxy version 5.59-91.0+galaxy3)</span>) 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 (<span class="tool" data-tool="toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1" title="SanntiS tool" aria-role="button"><i class="fas fa-wrench" aria-hidden="true"></i> <strong>SanntiS</strong> (<i class="fas fa-cubes" aria-hidden="true"></i> Galaxy version 0.9.3.5+galaxy1)</span>) both to build genbank and especially to detect and annotate biosynthetic gene clusters (BGCs).
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## The workflow itself

## Run the workflow

Import and run the [Biosynthetic Gene Clusters workflow](https://earth-system.usegalaxy.eu/u/marie.josse/w/marine-omics-identifying-biosynthetic-gene-clusters)

To know more on how to do that follow the [tutorial](/training-material/topics/ecology/tutorials/marine_omics_bgc/tutorial.html)
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## Generate the RO-Crate

Once you run the workflow you can generate the RO-Crate. To do so follow the [tutorial](/training-material/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html)
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### From workflow to RO-Crate

![From workflow to RO-Crate](./images/workflow_rocrate.png)
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### The RO-Crate folder and architecture

![From workflow to RO-Crate](./images/all_tree_structure.png)
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### Let's dive into the ro-crate-metadata.json

![Date of RO-Crate creation and other informations](./images/rocrate1.png)
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### Description of the RO-Crate structure

![Description of the RO-Crate structure](./images/rocrate2.png)
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### Galaxy Provenance

![Date of RO-Crate creation and other informations](./images/rocrate3.png)
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### Title and workflow details

![Title and details of the workflow](./images/rocrate4.png)
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### Dates

![Dates of running the workflow and creation of the RO-Crate](./images/rocrate5.png)
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### Data

![Data uploaded for the workflow and produced by it](./images/rocrate6.png)
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### First tool Prodigal

![Details on Prodigal](./images/rocrate7.png)
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### Second tool Regex Find and Replace

![Details on Regex Find and Replace](./images/rocrate8.png)
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### Third tool InterProScan

![Details on InterProScan](./images/rocrate9.png)
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### Fourth tool SanntiS to build Genbank

![Details on SanntiS to build Genbank](./images/rocrate10.png)
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### Fourth tool SanntiS to annotate biosynthetic gene clusters

![Details on SanntiS to annotate biosynthetic gene clusters](./images/rocrate11.png)
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### Details on the different files in the RO-Crate

![Details on the different files in the RO-Crate](./images/rocrate12.png)
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### End of the ro-crate-metadata.json

![Details on the different files in the RO-Crate and end of the ro-crate-metadata.json](./images/rocrate13.png)
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### Thank you!

Try to do the same on your workflow!

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### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points

- RO-Crate in earth-system analysis

- Marine omics workflow

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
		<td>
			<a href="/training-material/hall-of-fame/Marie59/" class="contributor-badge contributor-Marie59"><img src="https://avatars.githubusercontent.com/Marie59?s=36" alt="Marie Josse avatar" width="36" class="avatar" />
    Marie Josse</a>
		</td>
	</tr>

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Tutorial Content is licensed under <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.<br/>