Veranstaltungsdetails

University of Cologne

Anandhi Iyappan (EMBL), Justine Vandendorpe, Konrad Förstner

The rapid expansion of microbial omics data - from raw sequence reads and assembled genomes to consensus sequences and associated process data offers immense potential for advancing microbiome research. At the same time, there is a growing need to include emerging and underrepresented ones, such as imaging and spatial omics datasets, which are essential for a more comprehensive research data ecosystem.

Realizing the full scientific value of these resources requires that data are not only generated at scale, but also deposited, described, and shared in accordance with FAIR principles [1] . However, the consistent implementation of data and metadata standards across microbiological domains remains uneven, with submissions to public repositories such as the European Nucleotide Archive showing considerable variability in annotation depth, controlled vocabulary usage, and adherence to community standards.

NFDI4Microbiota, as part of the National Research Data Infrastructure (NFDI) addresses these challenges by providing access to metadata standards, training, and analysis services tailored to the full spectrum of microbial research spanning

bacteriology, virology, mycology. [3]. A central focus is the development and promotion of standardized metadata frameworks that capture biological, experimental, and administrative context enabling robust discoverability and cross-study comparability [4] .

In this workshop we present use cases based on publicly available datasets including food microbiology studies (ENA: PRJNA947753) [5], large-scale microbiome sampling(ENA: PRJEB56918) [6]. These examples illustrate the diversity and

complexity of metadata requirements across subdisciplines and reflect three main data classes: raw research data, computationally derived process data, and supporting contextual files.

Participants will explore how current submissions align with FAIR principles and identify gaps in metadata completeness. We highlight practical recommendations for metadata registration at the sample, experimental, and analytical levels, including the use of community standards such as Genomic Standards Consortium checklists and the Environment Ontology, while also addressing areas lacking established ontologies. The workshop is designed for approximately 30 participants and requires only a laptop, ensuring accessibility.