Interoperability of Bioconductor packages within the ELIXIR Research Software Ecosystem using the EDAM ontology

Bioconductor packages are currently annotated using the biocViews controlled vocabulary (Carey et al., 2024), structured as a graph with nearly 500 terms, of which 175 are meant for software annotation. In order to ensure the consistency of the annotations, an automated validation is performed by BiocCheck upon submission of a new package. This ensures that packages include valid biocViews terms and meet the minimum requirement of at least two non-top-level terms. However, it lacks the formal structure of an ontology and is specific to the Bioconductor project, thereby limiting both the semantic search capabilities as well as the interoperability of the packages . EDAM (Ison et al., 2013) is a domain ontology specialised in data analysis and management concepts in biosciences, making it a good candidate for the annotation of Bioconductor software packages. Furthermore, EDAM is a key component for the Findability, Accessibility, Interoperability, and Reusability (FAIR principles) within ELIXIR resources, including the ELIXIR Research Software Ecosystem (RSEc) (Ienasescu et al. 2023) and the bio.tools registry (Ison et al., 2019). bio.tools holds a collection of more than 30,000 entries, curated and annotated using EDAM terms, and provides enhanced search capacities through an API for easy programmatic access to the database. In order to increase the visibility and interoperability of Bioconductor packages, as well as the coverage and validity of Bioconductor in the RSEc, we aim to use the EDAM ontology to describe Bioconductor package metadata, and to automate their integration into the bio.tools registry. Our first results towards these objectives include mapping the biocViews vocabulary to EDAM, initiating the curation of a reference set of packages with manual annotations to be used as a gold standard, 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 refinement of Bioconductor package descriptions. It will also consequently improve their integration within the Galaxy toolshed through the bio.tools registry of software. Beyond advancing the FAIRification of resources for life science research, this initiative builds a collaborative bridge between the Bioconductor, ELIXIR and Galaxy communities.