B-B.06: Advancing FAIR biodiversity genomics with open-source solutions: The Swedish Reference Genome Portal and DivBase
Daniel P. Brink
Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden. Science for Life Laboratory (SciLifeLab), Data Centre, Uppsala University, Uppsala, Sweden.
Rory Crean
Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden. Science for Life Laboratory (SciLifeLab), Data Centre, Uppsala University, Uppsala, Sweden.
Quentin Ågren
Science for Life Laboratory (SciLifeLab), Data Centre, Uppsala University, Uppsala, Sweden. Kungliga Tekniska högskolan, Stockholm, Sweden.
Andreas Wallberg
Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
Hanna Kultima
Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden. Science for Life Laboratory (SciLifeLab), Data Centre, Uppsala University, Uppsala, Sweden.
Johan Rung
Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden. Science for Life Laboratory (SciLifeLab), Data Centre, Uppsala University, Uppsala, Sweden.
Henrik Lantz
National Bioinformatics Infrastructure Sweden (NBIS), Uppsala University, Uppsala, Sweden.
Keywords
Genomics, genome browser, genetic variants, data management, open-source, FAIR, data service, national research infrastructure
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Production and access to genomic data is critical for biological research and biodiversity management. However, the rapid growth of genomics data poses challenges for data management, including fragmentation, limited accessibility and insufficient metadata integration. These issues hinder reproducibility, reuse and compliance with Open Sciences and FAIR (Findable, Accessible, Interoperable, Reusable) principles, particularly in distributed and collaborative research environments involving multiple teams and stakeholders.
Here, we introduce two complementary technical solutions developed by Science for Life Laboratory (SciLifeLab), Sweden's national research infrastructure for life sciences, to address these challenges. First, the Swedish Reference Genome Portal provides an open-access, user-friendly platform for visualizing and disseminating genomes and genomic annotations generated by researchers affiliated with Swedish institutions. By lowering barriers to genomic data access and exploration, the portal enhances discoverability and long-term usability of genomic resources, thereby supporting open science and collaboration.
Second, DivBase (Genomic diversity database) addresses the management of large population genomics datasets and their associated metadata. In collaborative environments, such datasets are often dispersed and poorly linked across teams, increasing risks of data loss and limiting reuse. DivBase serves as a working repository where VCF files and sample metadata are securely stored, shared and queriable among collaborators, until final deposition in a discipline-specific repository. It provides a centralized system with versioning, metadata integration and query capabilities, facilitating collaborative analysis of genetic diversity and downstream submission to long-term archives.
Together, these solutions exemplify how national research infrastructures can operationalize FAIR principles and enable more efficient, transparent, and reproducible genomics research.
Co-authors: Daniel P. Brink, Rory Crean, Quentin Ã…gren, Andreas Wallberg, Hanna Kultima, Johan Rung, Henrik Lantz
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