Poster De Conférence Année : 2025

Annotating Bioconductor packages using the EDAM ontology

Résumé

Background. EDAM is an ontology defining and standardising terms for the analysis and management of data in life sciences, including topics, operations, data types and formats. It allows the annotation of digital resources, improving their FAIRification. Bioconductor, an open-source project providing 2,000 packages for a wide range of bioinformatics applications, uses the biocViews vocabulary for the description of package metadata. However it is not defined and structured like an ontology and is made for internal use only, limiting the interoperability of the packages with other resources. In order to increase the visibility and interoperability of Bioconductor packages, we aim for their metadata annotation using the EDAM ontology, and their automated integration into the ELIXIR bio.tools registry and Research Software Ecosystem. Results. In order to shift from biocViews annotations to EDAM annotations, we mapped the existing vocabulary against the ontology and manually curated the results, mostly consisting of “topics” and “operations”. We developed scripts that extract Bioconductor package metadata and automatically incorporate them into the ELIXIR Research Software Ecosystem and bio.tools registry. Finally, we are working on the automated annotation of packages using LLM-based methods in order to further describe their input and output data types, to be synchronised with the ecosystem as well. Conclusions. This project improves the FAIRification of software resources for life science, and further extends the ELIXIR ecosystem. Beyond advancing the EDAM standard, this initiative builds a collaborative bridge between the Bioconductor and ELIXIR communities.

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Cite 10.37044/osf.io/dsgnw_v1 Autre Rioualen, C., Barre, A., Dartigues, B., Carey, V. J., Kalas, M., Lobentanzer, S., MENAGER, H., Neumann, S., Nishida, K., Schwämmle, V., Vu, A. N., Willighagen, E., & Doyle, M. A. (2025). BioHackEU24 report: Integrating Bioconductor packages with the ELIXIR Research Software Ecosystem using EDAM. Center for Open Science. https://doi.org/10.37044/osf.io/dsgnw_v1

Dates et versions

hal-05142802 , version 1 (03-07-2025)

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  • HAL Id : hal-05142802 , version 1

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Claire Rioualen, Maria Doyle, Alban Gaignard, Vincent J. Carey, Hervé Ménager. Annotating Bioconductor packages using the EDAM ontology. Journées Ouvertes en Biologie Informatique et Mathématiques JOBIM 2025, Jul 2025, Bordeaux, France. ⟨hal-05142802⟩
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