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

Background The Bioconductor community provides an open collection of more than 2,000 software packages for users worldwide. They are broadly used and downloaded from its repository, and are also available on many other platforms and through a variety of services, such as Bioconda, Galaxy, nf-core pipelines, and WorkflowHub, among others. The visibility of those carefully documented tools could be further expanded by implementing additional metadata conventions. The ELIXIR Research Software Ecosystem (RSEc) aims to enhance software discoverability across projects and platforms by extracting and standardizing package and software metadata, and centralizing those through the ELIXIR bio.tools repository. The bio.tools repository, which currently contains more than 30,000 curated entries, aims to improve visibility and findability, benefiting both users and developers. It also offers centralized software metadata curation efforts and cross-linking of software using bio.tools identifiers and associated metadata. Objectives This project aims to further improve Bioconductor package annotations and FAIRness by synchronizing their metadata within the RSEc. This is achieved by leveraging existing, extensively used standards for schema markup, ontologies, and semantic specifications. By increasing metadata interoperability, those shared principles allow to further integrate resources, improve their visibility, and reach yet a wider range of users worldwide. By implementing those shared conventions, this project also contributes to consolidating interactions between the Bioconductor community and the ELIXIR infrastructure, two major international organisations promoting good practices and open source resources in the domain of bioinformatics. Results This collaboration allowed to import Bioconductor software package metadata into the ELIXIR RSEc. About 1,500 existing Bioconductor software descriptions were updated, and another 700 package entries were newly created. By using the ELIXIR bio.tools registry as a hub for metadata uniformization, the RSEc contributes to assisting software metadata curation efforts and enhancing software visibility across platforms. We are also using AI agents and developing a Model Context Protocol server that can facilitate metadata suggestions or aid software metadata curators with decision support backed by standard ontologies such as the EDAM ontology. Perspectives This project aims to foster mutual interactions between package developers, curators and users. Consequently, our next steps include working on guidelines to promote these standards, and facilitate their use in close collaboration with package developers.