Integrating Bioconductor packages with the ELIXIR research software ecosystem using EDAM

Résumé fourni par la source

Bioconductor is a global open-source project providing over 2,000 packages for a wide range of bioinformatics applications, and a critical resource for life science research. Bioconductor uses the biocViews controlled vocabulary for the description of package metadata. However, it lacks the formal structure of an ontology and is conceived for internal use only, thereby limiting semantic search capabilities and interoperability of the packages with other software and repositories. EDAM is a domain ontology describing data analysis and management concepts in biosciences, making it a good candidate for the annotation of Bioconductor software packages. EDAM is a key component for the FAIRification of ELIXIR resources, including the ELIXIR Research Software Ecosystem (RSEc) and the bio.tools registry, which holds a collection of more than 30,000 entries, curated and annotated using EDAM terms. In order to FAIRify Bioconductor packages and enhance the RSEc, this project seeks to improve Bioconductor packages metadata by using the EDAM ontology, and automate their integration into the bio.tools registry. Most of this work was initiated as a 2024 ELIXIR BioHackathon project. Key results include mapping the biocViews vocabulary to EDAM, integrating Bioconductor metadata into the RSEc with automated updates, and prototyping a tool for automated EDAM term suggestions. Together, these achievements establish a strong foundation for further integration and metadata refinement of the Bioconductor packages. Beyond advancing the EDAM standard, this initiative builds a collaborative bridge between Bioconductor and ELIXIR, and contributes to ongoing efforts towards a more accessible and interoperable bioinformatics ecosystem.

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.