# The EDAM Framework and Control Room

Claire Rioualen, Alban Gaignard, Matúš Kalaš, Hervé Ménager

## ► To cite this version:

Claire Rioualen, Alban Gaignard, Matúš Kalaš, Hervé Ménager. The EDAM Framework and Control Room: Facing the data deluge, one concept at a time. Journées Ouvertes en Biologie Informatique et Mathématiques JOBIM 2024, Jun 2024, Toulouse, France. hal-04619281

HAL Id: hal-04619281

https://hal.science/hal-04619281

Submitted on 20 Jun 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons CC0 - Public Domain Dedication 4.0 International License
# The EDAM Framework and Control Room

Claire Rioualen, Alban Gaignard, Matúš Kalaš, Hervé Ménager

► To cite this version:

Claire Rioualen, Alban Gaignard, Matúš Kalaš, Hervé Ménager. The EDAM Framework and Control Room. Journées Ouvertes en Biologie Informatique et Mathématiques JOBIM 2024, Jun 2024, Toulouse, France. hal-04619281

HAL Id: hal-04619281

https://hal.science/hal-04619281v1

Submitted on 20 Jun 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons CC0 - Public Domain Dedication 4.0 International License
# The EDAM Framework and Control Room

Facing the data deluge, one concept at a time...

Claire Rioualen<fnref n="1" />, Alban Gaignard², Matúš Kalaš<fnref n="3" />, Hervé Ménager<fnref n="1" />,⁴, and the EDAM community

## What is EDAM?

EDAM is an ontology about data management & analysis in life sciences. Ontologies define **standard terminologies and relationships** between concepts. Those concepts are used to ** annotate resources**: they are semantic metadata. Standard annotations increase the **findability & interoperability** of digital resources.

<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

## Take-home

* EDAM is an ontology about data analysis

* Increases findability & interoperability

* Developed in a participatory manner

* Extends beyond life sciences

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

https://github.com/edamontology

## Community-based development

* EDAM Geo: **earth & environment** sciences

* BioMaging: **image processing and deep learning** concepts

* Systems biology: **annotation of training materials**

<figure><img src="image_7.png" /></figure>

<figure><img src="image_8.png" /></figure>

annotation of packages + bio.tools catalogue [coming soon]

genomic concepts for FAIR genomic tracks [coming soon]

## Continuous integration

* **Quality control** validation with Caseologue

* Continuous integration using GitHub Actions

<figure><img src="image_9.png" /></figure>

## EDAM control room

* **User-friendly** web application

* Overview of the contents in the ontology

* Guides users towards **tailored curation tasks**

<figure><img src="image_10.png" /></figure>

### Long-term goals

* Broaden community

* Credit contributions

* Platform for hackathon events

* Frequency of new releases

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

## Annotating resources

* Numerous content providers use EDAM annotations

* Those resources are interoperable

elixir
bio tools

elixir
textos

<figure><img src="image_13.png" /></figure>

Galaxy
PROJECT

<figure><img src="image_14.png" /></figure>

Bioschemas

<figure><img src="image_15.png" /></figure>

EMBL-EBI

<figure><img src="image_16.png" /></figure>

## Mapping concepts

* Concepts can be visualized with **EDAM popovers** navigator extension

* **EDAM map** allows **text mining** concepts in scientific articles or web resources

## Navigating the ontology

* The **EDAM browser** allows to **navigate current and past versions**

* Suggestions for terms or attributes can be made using GitHub issues

<figure><img src="image_17.png" /></figure>

<figure><img src="image_18.png" /></figure>

## References

Beard N, Bacall F, Nenadic A, Thurston M, Goble CA, Sansone SA, et al. TeSS: a platform for discovering life-science training opportunities. Bioinformatics. 2020 May 15;36(10):3290-1. 1.
Brancotte B, Blanchet C, Ménager H. A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. Journal of Open Source Software. 2018 Jul 22;3(27):698.
Gray AJG, Goble C, Jimenez RC. Bioschemas: From Potato Salad to Protein Annotation. In International Semantic Web Conference (Posters, Demos & Industry Track(s). 2017.
Ison J, Jenasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, et al. The bio.tools registry of software tools and data resources for the life sciences. Genome Biology. 2019 Aug 12;20(1):164.
Lamothe L, Gaignard A, Kierkegaard M, Eldakrouy H, Black M, Brancotte B, et al. EDAM: life sciences ontology for data analysis and management. Zenodo. 2022 Jun 28.
Rioualen, C., Bacall, F., Furlan, C., Kalaš, M., Leskosek, B., Ménager, H., & Szomolay, B. (2024). Synergising ELIXIR resources for training in systems biology. OSF. https://doi.org/10.37044/

<footnote n="1">1. Institut Français de Bioinformatique, CNRS UAR 3601, Évry, France; 2. Nantes Université, CNRS, INSERM, l'Institut du thorax, Nantes F-44000, France;</footnote>

<footnote n="3">3. University of Bergen, 5020 Bergen, Norway; 4. Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France.</footnote>
# The EDAM Framework and Control Room

Facing the data deluge, one concept at a time...

Claire Rioualen<fnref n="1" />, Alban Gaignard², Matúš Kalaš<fnref n="3" />, Hervé Ménager<fnref n="1" />,⁴, and the EDAM community

## What is EDAM?

EDAM is an ontology about data management & analysis in life sciences. Ontologies define **standard terminologies and relationships** between concepts. Those concepts are used to ** annotate resources**: they are semantic metadata. Standard annotations increase the **findability & interoperability** of digital resources.

<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

## Take-home

* EDAM is an ontology about data analysis

* Increases findability & interoperability

* Developed in a participatory manner

* Extends beyond life sciences

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

https://github.com/edamontology

## Community-based development

* EDAM Geo: **earth & environment** sciences

* BioMaging: **image processing and deep learning** concepts

* Systems biology: **annotation of training materials**

<figure><img src="image_7.png" /></figure>

<figure><img src="image_8.png" /></figure>

annotation of packages + bio.tools catalogue [coming soon]

genomic concepts for FAIR genomic tracks [coming soon]

## Continuous integration

* **Quality control** validation with Caseology

* Continuous integration using GitHub Actions

<figure><img src="image_9.png" /></figure>

## EDAM control room

* **User-friendly** web application

* Overview of the contents in the ontology

* Guides users towards **tailored curation tasks**

<figure><img src="image_10.png" /></figure>

### Long-term goals

* Broaden community

* Credit contributions

* Platform for hackathon events

* Frequency of new releases

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

## Annotating resources

* Numerous content providers use EDAM annotations

* Those resources are interoperable

elixir
bio tools

elixir
textos

<figure><img src="image_13.png" /></figure>

Galaxy
PROJECT

<figure><img src="image_14.png" /></figure>

Bioschemas

<figure><img src="image_15.png" /></figure>

EMBL-EBI

<figure><img src="image_16.png" /></figure>

## Mapping concepts

* Concepts can be visualized with **EDAM popovers** navigator extension

* **EDAM map** allows **text mining** concepts in scientific articles or web resources

<figure><img src="image_17.png" /></figure>

## Navigating the ontology

* The **EDAM browser** allows to **navigate current and past versions**

* Suggestions for terms or attributes can be made using GitHub issues

<figure><img src="image_18.png" /></figure>

<figure><img src="image_19.png" /></figure>

## References

Beard N, Bacall F, Nenadic A, Thurston M, Goble CA, Sansone SA, et al. TeSS: a platform for discovering life-science training opportunities. Bioinformatics. 2020 May 15;36(10):3290-1. 1.
Brancotte B, Blanchet C, Ménager H. A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. Journal of Open Source Software. 2018 Jul 22:3(27):698.
Gray AJG, Goble C, Jimenez RC. Bioschemas: From Potato Salad to Protein Annotation. In International Semantic Web Conference (Posters, Demos & Industry Track(s). 2017.
Ison J, Jenasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, et al. The bio.tools registry of software tools and data resources for the life sciences. Genome Biology. 2019 Aug 12;20(1):164.
Lamothe L, Gaignard A, Kierkegaard M, Eldakrouy H, Black M, Brancotte B, et al. EDAM: life sciences ontology for data analysis and management. Zenodo. 2022 Jun 28.

Lamothe L, Gaignard A, Kierkegaard M, Eldakrouy H, Black M, Brancotte B, et al. EDAM: life sciences ontology for data analysis and management. Zenodo. 2022 Jun 28.
Rioualen, C., Bacall, F., Furlan, C., Kalaš, M., Leskosek, B., Ménager, H., & Szomolay, B. (2024). Synergising ELIXIR resources for training in systems biology. OSF. https://doi.org/10.37044/

<figure><img src="image_20.png" /></figure>

<footnote n="1">1. Institut Français de Bioinformatique, CNRS UAR 3601, Évry, France; 2. Nantes Université, CNRS, INSERM, l'Institut du thorax, Nantes F-44000, France;</footnote>

<footnote n="3">3. University of Bergen, 5020 Bergen, Norway; 4. Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France.</footnote>