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Galaxy hosts a vast array of tools, tutorials, and workflows, with the exact number of workflows remaining uncertain. To address the challenge of enhancing tool visibility within this expansive ecosystem, a pipeline called the Galaxy Tool Metadata Extractor was created during the BioHackathon Europe 2023. This pipeline aggregates Galaxy tool suites from various sources, automatically extracts metadata such as bio.tools identifiers and EDAM ontology, and presents the information in an interactive table. Users can filter this table to find tools relevant to their research community. Throughout development, it was noted that many tools lack EDAM annotations. An effort of the microGalaxy community was started to update 50+ microbial-related Galaxy tools, link them to their respective bio.tools entries, and collectively peer-review the results. However, that was far from enough to properly annotate all Galaxy tools and other types of Galaxy resources like training material and workflows. In addition to tools, the community offers other resources that are not properly annotated using ontologies like EDAM. Annotating all mentioned resources would improve their findability but also allow for aggregation and display of resources covering similar topics. To facilitate this work and work on a proof-of-concept for other communities, the microGalaxy community organized an online hackathon in April 2024. During this hackathon, 41 new bio.tools have been created, 85 Galaxy tool suites linked to bio.tools and EDAM terms, and 33 tutorials annotated with EDAM terms. Some microbial-related Galaxy tools have been improved. In addition, new features and improvements have been added to Galaxy Tool Metadata Extractor. The hackathon was successful with outcomes beyond the initial expectations.
Batut et al. (Tue,) studied this question.
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