This tutorial aims to teach how to use the interactive tool MetaShRIMPS, available on Galaxy Ecology, to produce Data Papers drafts and FAIR quality assessment reports from metadata using EML standard. This tutorial purpose is also to explain why it is needed to improve the overall FAIR quality of metadata and how this tool responds to this necessity.

Comment: What does FAIR mean?

FAIR stand for Findable, Accessible, Interoperable, Reusable.

These principles were to improve the access and usabiliy of data by the machine and to help making data reusable and shareable for users. Metadata is the data used to describe and explain all the context behind the production of data. It is necessary to produce a rich and FAIR metadata in order to permit external users to understand and reuse data for their own studies.

Agenda

In this tutorial, we will cover:

1. How can this tool improve the metadata quality?
2. Get data
3. Upload Data in MetaShRIMPS
4. Outputs
   1. Draft of Data Paper
   2. Fair Quality Assessment report
5. Conclusion

How can this tool improve the metadata quality?

The purpose of this tool is to help the user improve their metadata quality in order to increase its value to the scientific community and to help highlighting the work of all the producers of the data. To respond to this objective, this tool aims to give an easy access to a quality assessment report of EML metadata which could guide the producers of data/metadata to the production of a metadata with high degree of FAIRness. The other objective of this tool is to highlight the work of all of the people that helped in producing this data by giving the access of a draft of Data Paper that is reuseable either in a non editable HTML file, that can represent the metadata in a more ergonomic way facilitating its understanding and shareability, or in an editable docx file. Having an editable Data Paper draft will allow the producer to complete/modify the draft of Data Paper so that it could become publishable as a real Data Paper giving recognition to all the people that helped producing the data.

Comment: What is a Data Paper?

According to the GBIF (Global Biodiversity Information Facility), A data paper is a peer reviewed document describing a dataset, published in a peer reviewed journal. It takes effort to prepare, curate and describe data. Data papers provide recognition for this effort using a scholarly article.

Get data

Hands-on: Data Upload

1. Create a new history for this tutorial
2. Import this metadata file from Zenodo to test it -> Training Data for “Creating Quality FAIR assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS”:

   https://zenodo.org/record/8130567/files/Kakila_database_marine_mammal.xml
   

   Tip: Importing via links

   • Copy the link location

   • Click galaxy-upload Upload Data at the top of the tool panel

   • Select galaxy-wf-edit Paste/Fetch Data

   • Paste the link(s) into the text field

   • Press Start

   • Close the window

Upload Data in MetaShRIMPS

When opening MetaShRIMPS, you will have an interface looking like this :

To upload data on MetaShRIMPS, if you was selecting the xml file as input of the tool, it is already launched, if not, you have to click on the browse button and select in your local folders, the file you want to use.

Warning: Select the right format

The file uploaded in this tool must be a metadata in XML format using EML metadata standard.

After uploading the file, or if you have indicated it as input data in the tool form, you just have to click on Execute to launch MetaShRIMPS jobs with the file.

Outputs

After clicking the Execute button, 2 new tabs called “Draft of Data Paper” and “Fair Assessment” will appear. You can access all of the tool outputs by clicking on each tab (it can take a little time for your results to be displayed).

Draft of Data Paper

By clicking on the “Draft of Data Paper” tab, you will have access to the draft of Data Paper presented in an HTML format. You can either navigate through the Data Paper with the tabs or with the scrollbar on the right and access different elements.

You can at the top of the page download the draft in either an HTML format or an editable docx format.

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Fair Quality Assessment report

By clicking on the “Fair Assessment” tab, you will access the FAIR Quality report of the metadata uploaded. You will have access to different figures such as a table displaying the results of all checks tested for your metadata.

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You will also have acces to a graph presenting scores of Quality for each of the FAIR principles tested (Findable, Acessible, Interoperable, Reusable) on a 100 point scale.

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Conclusion

Here is the end of this short tutorial aiming in explaining the purpose of MetaShRIMPS and how to use it. Don’t hesitate to contact us if you have any questions :)

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• This tool aims to improve FAIR quality of metadata

• Creating metadata as FAIR as possible is a must

• Be carefull of the format and standard of metadata used only EML metadata will work

Frequently Asked Questions

Useful literature

Further information, including links to documentation and original publications, regarding the tools, analysis techniques and the interpretation of results described in this tutorial can be found here.

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Citing this Tutorial

1. Tanguy Genthon, Yvan Le Bras, Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{ecology-Metashrimps_tutorial,
author = "Tanguy Genthon and Yvan Le Bras",
	title = "Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Funding

These individuals or organisations provided funding support for the development of this resource

FNSO

This project (AAPFNSO2019OpenMetaPaper-14026) is funded with the support of the national Fund for Open Science programme of the French Minister of Higher Education, Research and Innovation. Their funding has supported development of data/metadata management tools and related tutorial for Ecology and FAIR topics.

PNDB

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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