VirJenDB RDM and bioinformatics support resource for virus research

Recent advances in sequencing technologies have led to a dramatic increase in virus sequence submissions, particularly for SARS-CoV-2, to global repositories such as INSDC [1] and GISAID [2]. However, the data and accompanying metadata can contain errors which can propagate to downstream analyses, hampering provenance and reproducibility [3]. As part of the NFDI4Microbiota initiative [4], we have established the VirJenDB database, based at FSU Jena [5], to enable the management, analysis, sharing, and reuse of virus sequences and metadata, following the FAIR [6] and Open Science [7] principles. The additional aim is to increase, enrich and improve virus metadata and sequence deposition to ENA/INSDC. Here, we report updates introduced with the v0.2 beta release freely available at https://www.virjendb.org. Virus sequences and metadata were aggregated from ENA [8], BV-BRC [9], NCBI Virus [10], ICTV [11], and ViralZone [12]. The data were curated, harmonized, and stored in a MySQL database and indexed using ElasticSearch [13]. In v0.2, the VJDB metadata schema was expanded by 55 fields for a total of 95 based on GSC MIxS standards [14] and ENA sample checklists. A pilot submission tool was also developed to support sequence deposition to ENA, incorporating feedback from early users. The VJDB web portal offers semantic search, a taxonomy browser, summary plots, table and card views, and downloads for 12 million virus sequences and up to 95 metadata fields. Metadata schema templates for specific viruses are being developed in collaboration with experts, with the goal of contributing to GSC and bioschemas.org [15]. Templates are available in XML, JSON, and CSV formats and formalization of the metadata is planned. Future plans for VirJenDB include a metadata correction and quality control pipeline. Further, bioinformatics workflows for (meta)genomic and (meta)transcriptomic analyses, protein and host prediction, and improved summary visualizations will be integrated. A secure workbench is also being developed to enable users to manage, analyze, and share interdisciplinary virus datasets. VirJenDB aims to provide a comprehensive platform combining large-scale virus datasets with user-centered tools to support virus researchers.