# Design and production of a plug-in tool facilitating the submission of microbial meta-omics data to an international repository

Baptiste Rousseau, Véronique Jamilloux, Thomas Denecker, Hélène Chiapello, Ariane Bize

► To cite this version:

Baptiste Rousseau, Véronique Jamilloux, Thomas Denecker, Hélène Chiapello, Ariane Bize. Design and production of a plug-in tool facilitating the submission of microbial meta-omics data to an international repository. JOBIM 2023, Jun 2023, Nancy, France. . hal-04139284

HAL Id: hal-04139284

https://hal.inrae.fr/hal-04139284

Submitted on 23 Jun 2023

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RÉPUBLIQUE
FRANÇAISE

Liberté
Égalité
Fraternité

INRAE

PROSE

PRocédés biOtechnologiques
au Service de l'Environnement

université
PARIS-SACLAY

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INSTITUT FRANÇAIS DE BIOINFORMATIQUE

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Baptiste Rousseau<fnref n="1" />
Véronique Jamilloux<fnref n="1" />
Thomas Denecker<fnref n="3" />
Hélène Chiapello<fnref n="2" />,<fnref n="3" />
Ariane Bize<fnref n="1" />

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# DeepOmics Submission, a plug-in tool to facilitate the submission of meta-omics data to the ENA

## DeepOmics

* **Storage** and interrogation of project data and metadata, from laboratory reactors and pilots or industrial plants

* **Import** and **export** data in standard formats (biom, fastq, fasta, CSV...)

* **Statistical analysis** and **data visualization** of 16S metabarcoding and metagenomic data thanks to coupling with the user-friendly application Easy16S - [genome.jouy.inra.fr/shiny/easy16S/](https://genome.jouy.inra.fr/shiny/easy16S/)

## Technological choices

### Shiny:

* Easy and fast to develop, suited for a POC

* Does not need extra knowledge of DeepOmics architecture

* Facilitates the deployment with an INRAE in-house solution, SK8

### Metark:

* Data-brokering requires specific skills and a precise expertise

* Ensures the quality of the data and metadata submitted to the ENA

* Guarantees process stability by absorbing potential changes in the submission process

## Development best practices

### Versioning

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git → [https://forgemia.inra.fr/prose/deepomics-submission](https://forgemia.inra.fr/prose/deepomics-submission)

### Virtual environments and dependency

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### Development tools

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Center
Jouy-en-Josas - Antony

## Context

INRAE PROSE has coordinated the development of **DeepOmics**, an information system dedicated to **meta-omics** datasets in the field of **environmental biotechnology**. DeepOmics offers the possibility to upload, query and export **16S metabarcoding data** from several environmental biotechnologies, together with many relevant associated metadata, especially regarding operating conditions and process design. To date, DeepOmics has all the data and metadata necessary for submission of the datasets to international repositories such as the European Nucleotide Archive (**ENA**), but submission remains a manual and rather complex process.

In collaboration with the French Institute of Bioinformatics (**IFB**), we designed and developed a R-shiny plug-in application, **DeepOmics Submission**, to prepare and automate raw sequencing data submission to the ENA. We will also guarantee the quality of the associated metadata with an IFB data brokering application prototype.

## DeepOmics Submission

A proof-of-concept (POC) application plugging into DeepOmics to cover:

* Mapping of DeepOmics concepts onto ENA checklists;

* Extracting the architecture of a DeepOmics project;

* Enabling the selection of biological samples;

* Extracting and transmitting to ENA the raw sequence files for these samples;

* Extracting and transmitting to Metark the metadata for these samples;

* Managing errors and comments from ENA;

* Finalizing the submission and retrieving the ENA submission identifier.

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## Conclusion

Most objectives of the **POC** have been **completed**. DeepOmics is currently in the pre-production phase and is now entering **production**. DeepOmics Submission works with the development version of DeepOmics and will thus need some modifications to work with the production version, especially regarding user account management. DeepOmics Submission will also need to be **deployed**, by relying on **SK8** at this stage. The realization of this POC raised many **conceptual** and **technological challenges**, from **concept mapping** to developing a **headless** and **stateless application**. All in all, it gives rise to **optimism** regarding the prospects of **FAIR data** and contributing to **Open Science**.

<footnote n="1">¹ Université Paris-Saclay, INRAE, PROSE, 92761 Antony, France</footnote>

<footnote n="2">² Université Paris-Saclay, INRAE, MalAGE, 78350 Jouy-en-Josas, France</footnote>

<footnote n="3">³ CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Évry, France</footnote>

<footnote>→ ariane.bize@inrae.fr
thomas.denecker@france-bioinformatique.fr</footnote>