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SBDI Consortium Partners

SBDI – Swedish Biodiversity Data Infrastructure – is an e-infrastructure providing data and analysis services that offer rich opportunities for innovative, interdisciplinary research on biodiversity and ecosystems.

The SBDI Consortium consists of eleven partner organizations. Below we list the SBDI Consortium partners and describe their responsibilities, contributions and skills.

Swedish Museum of Natural History (NRM)

The Swedish Museum of Natural History (NRM)hosts SBDI, and is the home for key positions in the Executive office, including the SBDI Director and Project Coordinator. NRM is responsible for the core technical infrastructure and leads the Swedish node of the Global Biodiversity Information Facility, GBIF. NRM offers support to data providers in mobilizing data, with particular focus on tools provided by the GBIF and Living Atlases communities. NRM holds some of the largest natural history collections in Europe, and is active in sharing traditional specimen data from these and other collections in Sweden. NRM is also actively involved in developing infrastructure for publishing genetic biodiversity data, and hosts research projects in biodiversity and evolution facilitated by SBDI.

Swedish University of Agricultural Sciences (SLU)

Four departments of SLU takes active part in SBDI; SLU Swedish Species Information Centre (SLU Adb), Dept. of Aquatic Resources (SLU Aqua), Dept. of Wildlife, Fish and Environmental Studies, and Dept. of Forest Resource Management (SLU SRH). SLU Adb is the home of SBDI Deputy Director as well as a Support officer and Communicator. Adb provides parts of the SBDI data flow infrastructure, the Species Observation System (SOS) and contributes with Dyntaxa exports to the taxonomic backbone used by SBDI. Dept. of Wildlife, Fish and Environmental Studies manages the national biotelemetry sensor data e-infrastructure WRAM (Wireless Remote Animal Monitoring). All SLU partners contribute significant amounts of data from their respective field of expertise, from citizen science observations to systematically collected monitoring data (read more about our data providers).

Karolinska Institute (KI)

Karolinska Institute (KI) is, together with SU, KTH, LnU and UU, responsible for the integration of sequence-based species observations into SBDI. More specifically, SU/KI develop and maintain the Swedish ASV portal which includes a database of Amplicon Sequence Variants (ASVs), and a web interface e.g. for accessing ASVs and corresponding SBDI Bioatlas occurrence records via the Basic Local Alignment Search Tool (BLAST). We also provide a guide for submitting raw sequence data from metabarcoding studies to the European Nucleotide Archive (ENA).

KTH Royal Institute of Technology (KTH)

The Royal Institute of Technology coordinates the work of integrating sequence-based species observations into SBDI, which includes services for denoising and taxonomic classification of metabarcoding data, for submitting processed data to SBDI, and for searching and downloading metabarcoding data from SBDI. KTH also maintain BalticMicrobDB, an interface for metagenomics data of the Baltic Sea, and contribute expertise on bioinformatics and analysis of meta-omics data.

Linnaeus University

The EEMiS centre at the Linnaeus University is part of the molecular module team of SBDI. LnU particularly focuses on development of the Nextflow amplicon denoising pipeline nf-core/Ampliseq. LnU also contributes expertise about marine microbial diversity and ecology.

Lund University (LU)

Lund University is responsible for developing and maintaining the Living Atlases tool for handling systematic monitoring data, BioCollect.  LU publishes data from long-term nationwide monitoring of a large number of animal species in Sweden with focus on birds, butterflies, mammals, and amphibians. LU is together with SLU responsible for making animal movement and sensor data available through SBDI. These are data that mainly originates from basic research projects from Swedish universities, where LU since many years hosts a world-leading group of researchers working on migration, movement and related behavior in animals (https://www.canmove.lu.se).

Stockholm University (SU)

Stockholm University (SU) is, together with KI, KTH, LnU and UU, responsible for the integration of sequence-based species observations into SBDI. More specifically, SU/KI develop and maintain the Swedish ASV portal which includes a database of Amplicon Sequence Variants (ASVs), and a web interface e.g. for accessing ASVs and corresponding SBDI Bioatlas occurrence records via the Basic Local Alignment Search Tool (BLAST). We also provide a guide for submitting raw sequence data from metabarcoding studies to the European Nucleotide Archive (ENA).

Swedish Meteorological and Hydrological Institute (SMHI)

SMHI operates Sweden’s National Oceanographic Data Centre, which receives data from national and regional marine monitoring programs. SMHI carries out quality control of data and publishes data through the web site SHARKweb and through the API SHARKdata. SMHI is responsible for making these marine biological data accessible in SBDI. In addition, SMHI maintains and develops an information system on aquatic microalgae. The system includes the Nordic Microalgae  with taxonomic information and images of microalgae provided by the users, i.e. microalgae experts. SMHI also works on making automated image- and video-based data and DNA-data available to the infrastructure, primarily plankton data.

Umeå University (UmU)

Umeå University is responsible for making the palaeoecological data accessible to the SBDI. The data are mapped from the ‘Strategic Environmental Archaeology Database’ (SEAD) and include fossil insects, zooarchaeological (archaeological mammals and fish bone data) and plant macrofossils data.

University of Gothenburg (GU)

University of Gothenburg is responsible for the central SBDI Support office and organizes SBDI training events, courses and workshops. These services are provided by the Gothenburg Global Biodiversity Centre (GGBC), an organization with 16 national academic and public partners who actively collaborate in the field of biodiversity. GU is also responsible for making marine biological data accessible to the infrastructure and helping marine scientists to use this information. GU also works on making marine genetic data available, such as e.g. data originating from Genomic observatories and genetic monitoring programs in Sweden. Finally, GU also publishes biodiversity image and media data from marine environments and develops tools to analyze these.

Uppsala University (UU)

Uppsala University is, together with KI, KTH, LnU and SU, responsible for the integration of sequence-based species observations into SBDI. UU also contributes with expertise on soil micro-eukaryote diversity. The Museum of Evolution at UU provides taxonomical expertise to SBDI and is also responsible for the Bioatlas Crowdsourcing project.