# Integrating Bioconductor packages with the ELIXIR research software ecosystem using EDAM

Claire Rioualen, Maria Doyle, Alban Gaignard, Vincent J. Carey, Hervé Ménager

► To cite this version:

Claire Rioualen, Maria Doyle, Alban Gaignard, Vincent J. Carey, Hervé Ménager. Integrating Bioconductor packages with the ELIXIR research software ecosystem using EDAM. ELIXIR All Hands Meeting, 2025, Jun 2025, Thessalokini, Greece. F1000 Research Limited, F1000Research 2025, 14(ELIXIR):524 (poster), 2025, 10.7490/f1000research.1120184.1. [http://hal-05098338](http://hal-05098338)

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Submitted on 5 Jun 2025

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Distributed under a Creative Commons Attribution 4.0 International License
# The bridges of EDAM county
## Integrating Bioconductor packages with the ELIXIR Research Software Ecosystem using EDAM

Claire RIOUALEN¹, Maria DOYLE², Alban GAIGNARD¹,³, Vincent CAREY⁴, Hervé MENAGER¹,⁵

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## Bioconductor packages for bioinformatics

* Bioconductor is an open-source projectᵃ with a collection of 2,000 software packages

* Package metadata is annotated with the biocViewsᵇ controlled vocabulary

* However, the biocViews vocabulary is not formally defined & is intended for internal use only, thereby limiting its interoperability with other resources

→ Need for standardised metadata to ensure the interoperability of the Bioconductor package collection

→ Ontologies can help achieve this standardisation

## The EDAM ontology

* Definition of concepts for the annotation of data analysis and management resources in the field of life sciencesᶜ

* 4 main classes of concepts: topic, operation, data, format

* EDAM is currently a key component for ELIXIR resources and services interoperability

→ EDAM could be used as a bridge between the Bioconductor package collection & the ELIXIR ecosystem

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A. Most used biocViews terms in Bioconductor package metadata

B. Top-level EDAM topics (green), operations (blue) and data types (red)

## Building interoperable bridges

### Vocabulary mapping

* Mapping of biocViews terms to EDAM topics using the text2term python libraryᵉ

* Resulting matches manually curated and non-relevant matches revised (Figure C.)

→ 250 mapped and curated terms, 181 matches (72.4%) including 53 modified matches (21.2%)

→ 29 new EDAM concepts suggested for 31 biocViews terms with no current match (12.4%)

### Metadata synchronisation

* Automated weekly synchronisation of Bioconductor metadata with both the bio.tools registryf and the ELIXIR Research Software Ecosystem (RSEc)d (Figure D.)

→ 1,565 updated entries and 724 new entries in RSEc (soon in bio.tools)

→ More detail and results in our recently published 2024 ELIXIR BioHackathon project preprinti

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C. Mapping & curation of biocViews terms to EDAM concepts

D. Synchronisation of Bioconductor package metadata with the RSEc

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## Conclusion & perspectives

→ Together, our results establish bridges between the Bioconductor project and the RSEc, with further interoperability with many resources (Figure E.)

* Aim 1: Further develop LLM-based approaches to automate package annotation

* Aim 2: Extend metadata with EDAM operations, data and formats

* Aim 3: Initiate the vocabulary switch in concertation with Bioconductor developers

→ Project submitted for the 2025 ELIXIR BioHackathon with the Metabolomics community

E. Overview of some of the main interoperable resources and services within the ELIXIR ecosystem

### Author affiliations

1. IFB-core, Institut Français de Bioinformatique (IFB), CNRS, INSERM, INRAE, CEA, 94800 Villejuif, France

2. Limerick Digital Cancer Research Centre, School of Medicine, University of Limerick, V94 T9PX, Ireland

3. Nantes Université, CNRS, INSERM, l'institut du thorax, Nantes F-44000, France

4. Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School, Boston MA, 02115 USA

5. Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France

### Acknowledgements

The Institut Français de Bioinformatique (IFB, UAR 3601) is funded by the Programme d'Investissements d'Avenir subsidised by the Agence Nationale de la Recherche, number ANR-11-INBS-0013. Ce travail a bénéficié d'une aide de l'Etat gérée par l'Agence Nationale de la Recherche au titre de France 2030 relatifs aux équipements structurants pour la recherche / EQUIPEX+ portant la référence ANR-21-ESRE-0048.

This project has been made possible in part by grants'Software for Science (Cycle 6): Ontological resource tagging and discovery for Bioconductor"ID: EOSS6-0000000067), 2024-342819 and 2024-342820 from the Chan Zuckerberg InitiativeDAF, an advised fund of Silicon Valley Community Foundation.

The authors of this work also thank all of the contributors to the 2024 BioHackathon project and published report.

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Inserm

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ELIXIR ALL HANDS 2025

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Bioconductor
OPEN SOURCE SOFTWARE FOR BIOINFORMATICS

### References

a. Bioconductor project. Huber et al. (2015), doi.org/10.1038/nmeth.3252

b. biocViews vocabulary. Carey et al. (2024), bioconductor.org/packages/biocViews.

c. EDAM ontology. Ison et al (2013), doi.org/10.1093/bioinformatics/btt113

d. ELIXIR Reasearch Software Ecosystem. github.com/research-software-ecosystem

e. Text2term library. rsgoncalves.com/text2term

f. bio.tools registry. Ison et al. (2019), doi.org/10.1186/s13059-019-1772-6

g. Lobentanzer et al. (2025), doi.org/10.1038/s41587-024-02534-3

h. Biochatter module. https://github.com/biocipher/biochatter

i. BioHack24 report. Rioualen et al. (2025), QRcode on the right

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