An earth-system RO-Crate

name: inverse
layout: true
class: center, middle, inverse

</span></div>

</span></div>

---

# An earth-system RO-Crate

<div class="contributors-line">
		
	
<ul class="text-list">
			
			<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>
</ul>

</div>

<div class="footnote" style="bottom: 8em;">
  <i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated:   
  <i class="fas fa-fingerprint" aria-hidden="true"></i><span class="visually-hidden">purl</span><abbr title="Persistent URL">PURL</abbr>: <a href="https://gxy.io/GTN:S00127">gxy.io/GTN:S00127</a>
</div>

<div class="footnote" style="bottom: 5em;">

<i class="far fa-play-circle" aria-hidden="true"></i><span class="visually-hidden">video-slides</span> <a href="/training-material/videos/watch.html?v=/fair/tutorials/earth_system_rocrate/slides">Video slides</a> |

<i class="fas fa-file-alt" aria-hidden="true"></i><span class="visually-hidden">text-document</span><a href="slides-plain.html"> Plain-text slides</a> |

</div>

<div class="footnote" style="bottom: 2em;">
    <strong>Tip: </strong>press <kbd>P</kbd> to view the presenter notes
    | <i class="fa fa-arrows" aria-hidden="true"></i><span class="visually-hidden">arrow-keys</span> Use arrow keys to move between slides

</div>

???
Presenter notes contain extra information which might be useful if you intend to use these slides for teaching.

Press `P` again to switch presenter notes off

Press `C` to create a new window where the same presentation will be displayed.
This window is linked to the main window. Changing slides on one will cause the
slide to change on the other.

Useful when presenting.

---

### <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 ?

---

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

## 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)
---

## 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)
---

### From workflow to RO-Crate

![From workflow to RO-Crate](./images/workflow_rocrate.png)
---

### The RO-Crate folder and architecture

![From workflow to RO-Crate](./images/all_tree_structure.png)
---

### Let's dive into the ro-crate-metadata.json

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

### Description of the RO-Crate structure

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

### Galaxy Provenance

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

### Title and workflow details

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

### Dates

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

### Data

![Data uploaded for the workflow and produced by it](./images/rocrate6.png)
---

### First tool Prodigal

![Details on Prodigal](./images/rocrate7.png)
---

### Second tool Regex Find and Replace

![Details on Regex Find and Replace](./images/rocrate8.png)
---

### Third tool InterProScan

![Details on InterProScan](./images/rocrate9.png)
---

### Fourth tool SanntiS to build Genbank

![Details on SanntiS to build Genbank](./images/rocrate10.png)
---

### Fourth tool SanntiS to annotate biosynthetic gene clusters

![Details on SanntiS to annotate biosynthetic gene clusters](./images/rocrate11.png)
---

### Details on the different files in the RO-Crate

![Details on the different files in the RO-Crate](./images/rocrate12.png)
---

### 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)
---

### Thank you!

Try to do the same on your workflow!

---
### <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

---

## 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!

<div class="contributors-line">
		
<table class="contributions">
	
	<tr>
		<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>

</table>

</div>

</div>

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/>