Linking pixels, proteins and populations: Integrating Data Across Life Science Domains

National Bioinformatics Infrastructure Sweden (NBIS) is a Swedish national research infrastructure that provides advanced informatics support for biomolecular life science research that also builds and maintains infrastructure for computational biology, omics and sensitive data while providing training/guidance on bioinformatics and data management related topics. NBIS is hosted by Uppsala University and has staff distributed and employed at departments across all major universities in Sweden as well as at the Swedish Museum of Natural History. NBIS also coordinates the Swedish Node of ELIXIR that, an ESFRI Landmark RI with a long and successful track record of bringing together large-scale information resources and computational tools for life science research.

NBIS also serves as the bioinformatics platform of the broader national life science infrastructure Science for Life Laboratory (SciLifeLab), where NBIS together with 9 other platforms covers three strategic and cross-disciplinary areas: Planetary Biology, Translation to Healthcare and Pandemic Laboratory Preparedness. Some major infrastructure projects related to the Common European Data Spaces where NBIS is engaged include the European Genomic Data Infrastructure (GDI), European Rare Diseases Research Alliance (ERDERA), EOSC-ENTRUST, and the European Reference Genome Atlas (ERGA).

NBIS bioinformatics support is organised into 5 research area teams focusing on 1) Health & Clinical research, 2) Evolution & Biodiversity, 3) Microbiology, Immunology & Structural biology, 4) Cell & Molecular biology, and 5) BioImage Informatics. Our portfolio of projects (see related publications) offers an overview of where we would be in a good position to support integrations of data across community resources for EOSC, here NBIS staff have been involved in designing the analysis and writing code (bioinformatics) and/or brokering data submissions to specialised databases.

Current priorities include:

• Integration of health and biomolecular research—promote interoperability across EOSC and the Common European Data Space for health.

• Biomolecular dimensions of biodiversity—support the national Data Science Node in Evolution and Biodiversity as part of the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS).

• Multi-modal data sharing and integration—continue to improve community practices across experiment and data types (e.g. imaging, structural, genomic, and other life science data types) and ensure that these are embodied in the thematic EOSC Life Science Research Node, in data services across all SciLifeLab platforms, and in research infrastructure more broadly.

Repositories/data resources at NBIS include:

• FEGA Sweden – a repository for sensitive data that is part of a federated network of nodes with national operations.

• Genomic Data Infrastructure (GDI) – a repository and analysis infrastructure for human genomic information with nodes distributed across Europe to support the 1+ Million Genomies Initiative.

• Human Protein Atlas – a Global Core Biodata Resource that aims to map all human proteins, using various technologies like antibody-based imaging, mass spectrometry, and transcriptomics.

• AIDA Data Hub – a resource for research and clinical innovation in data driven precision health, with a base in multi-modal diagnostics and medical imaging AI.

• NBIS also has close ties to repositories hosted at EMBL-EBI and offers data submission services to broker contributions on behalf of Swedish research projects.