GBIF

GBIF offers a broad overview and information about biodiversity, encompassing everything from species and their distribution to ecosystems and environmental change. GBIF also provides a variety of services, including data access, visualization, and analysis tools, which help researchers effectively explore and use biodiversity data for groundbreaking research.

The importance of GBIF as a research infrastructure cannot be underestimated. Access to extensive biodiversity data, including data from GBIF Sweden, is essential for understanding and protecting the biodiversity of our planet. This information is used in all research fields External link., but especially in disciplines such as ecology, biogeography, climate studies, and the conservation of endangered species.

GBIF enables global collaboration and knowledge sharing that is necessary to address the complex environmental challenges we face and to ensure the preservation of our world's biological heritage for future generations.

Services

GBIF only support open data and fully adheres to the principles of Open Science, FAIR External link. (Findable, Accessible, Interoperable, Reusable), and CARE External link. (Collective benefit, Authority to control, Responsibility, Ethics).

All data and multimedia are provided with open Creative Commons External link, opens in new window. licenses (CC0, CC-BY, or CC-BY-NC). Datasets and filtered downloads are furthermore, both assigned unique digital identifiers (DOIs) to facilitate easy data citation and traceability.

As a participant country of GBIF, there are opportunities to participate in various collaborative programs and apply for funding for capacity-building activities, such as the Capacity Enhancement Support Programme External link, opens in new window. (CESP). Applications are coordinated through the Swedish node and should include collaboration with at least one other participant country.

GBIF administers annual awards for researchers and developers in the field of biodiversity informatics. Nominations of candidates’ active in Sweden, for the Ebbe Nielsen Challenge External link, opens in new window. and the GBIF Graduate Researchers Award External link, opens in new window., are made through the Swedish node. Information about these calls is posted annually on www.gbif.se External link, opens in new window..

As a participant country, Swedish organizations and stakeholders have the opportunity to apply for support to establish a 'Hosted portal.' It is more or less a filtered data portal of gbif.org, where the filtering can be done at desired level, such as region, country, organization, or taxonomic level. A Hosted portal can be customized technically and visually to suit an organization's needs and preferences. GBIF provides support and technical maintenance resources. Hosted portals can serve as a platform to display and disseminate an organization's biodiversity data to promote global distribution and use of this data. Contact the Swedish Node Manager if your organization is interested in applying for a Hosted biodiversity portal. Learn more at https://www.gbif.org/hosted-portals External link, opens in new window..

Tools

Tools for mobilizing and publishing biodiversity data

GBIF Sweden is responsible for and administers the national instance External link. of GBIF's central data publishing tool, the IPT (Integrated Publishing Toolkit). It is a valuable resource for organizations and researchers who want to share biodiversity data with a broader audience. The IPT is developed as open-source software, which means it is freely available and customizable to various needs. The tool features a user-friendly interface that allows users to easily structure, quality-check, and publish biodiversity data in standardized formats. If data owners need assistance with data publishing via the IPT, we are happy to help.

In summary, GBIF's IPT is a powerful tool that facilitates the dissemination and accessibility of biodiversity data, thereby promoting research, conservation, and sustainable development worldwide. It also enables easy tracking of dataset versions over time and assigns stable digital identifiers (DOIs).

Tools for accessing and analyzing biodiversity data

GBIF’s APIs External link. (Application Program Interfaces) are powerful tools that allow users to retrieve and work with biodiversity data from GBIF's extensive database. These APIs provide programmatic access to data on species, observations, geographic information, and much more. By using GBIF's APIs, developers and researchers can integrate biodiversity data into their own applications, analyses, and projects, enabling more flexible and customized solutions for exploring and leveraging biodiversity information.

GBIF's R package, rgbif External link., is a tool for retrieving and exploring biodiversity data directly within the R programming environment. It provides R users with straightforward and programmatic access to biodiversity data. With the help of rgbif, researchers and data scientists can effectively integrate GBIF data into their analyses, visualizations, and projects within R, allowing for more in-depth and tailored studies of biodiversity and ecosystems. It is a valuable tool, for example, for those working with biodiversity data and statistical analysis in the R environment. A corresponding package is available for Python users and is called pygbif External link..

Databases

Data Access

The data made available by GBIF Sweden can be accessed from several data portals. These include the national website for GBIF Sweden (www.gbif.se External link.), the SBDI data portal (https://tools.biodiversitydata.se/ External link.), and the global GBIF data portal (www.gbif.org External link.).

GBIF's data portal is a central digital platform that enables access to and exploration of biodiversity data from around the world. The portal serves as a comprehensive resource that collects and provides an enormous amount of information about the planet's biological diversity.

The datasets made available by GBIF Sweden are furthermore accessible through the national installation of the GBIF publishing tool, IPT (https://www.gbif.se/ipt/ External link.).

What data are available?

GBIF Sweden provides access to several different types of data. The simplest form consists of metadata, which is descriptive information about a dataset. This format can, for example, be used by researchers when preparing a scientific publication. Scientific journals often require research data to be made available according to FAIR principles. To meet these requirements, descriptive information with a stable DOI can be prepared while waiting for a study to be accepted, after which the dataset can be populated with data and published.

There are several species lists, or checklists, available. These are lists of species names. Some examples include the national checklist Dyntaxa External link., the Swedish Red List External link. of threatened species, and the list of species assessed to be invasive alien species in Sweden External link..

Species observations usually follow the format of occurrence data, which is the broadest and most common data type. GBIF Sweden provides data from Natural History Museums, Universities, Government Agencies, as well as the Private Sector. Some examples of data available include the Swedish Museum of Natural History's bird ringing data External link., herbarium collections External link., and fossil animals External link.. A significant portion of the available data consists of spontaneous observations made by citizen scientists, for example, Artportalen External link. and iNaturalist External link..

Genetic data from e.g. metagenomic sequencing or environmental DNA (eDNA), is currently made available as occurrence data, but work is underway to develop standards and data models to better be able to present this type of data.

The last and most advanced data type made available by GBIF Sweden is structured systematically collected data or sample-based data. This includes surveys or studies using a defined methodology, such as annual monitoring programs or research data. Some examples of data available include the Swedish Malaise Trap Project External link., SMHI's marine surveys (SHARK External link.), Swedish Bird Survey External link., and Swedish Butterfly Monitoring External link..

Collaborations

GBIF Sweden is primarily funded by the Swedish Research Council External link. (Vetenskapsrådet or VR) as part of the national research infrastructure, SBDI, Swedish Biodiversity Data Infrastructure External link. (Grant No: 2019-00242). The Swedish Research Council also administers the membership fee to GBIF on behalf of the Swedish government and holds the role as Head of Delegation of the GBIF Sweden delegation.

SBDI - Swedish Biodiversity Data Infrastructure - is the result of an amalgamation and consolidation process of Swedish e-infrastructures for biodiversity and ecosystem research. SBDI is a national research infrastructure and consortium with contributions from eleven organizations across Sweden: the Swedish Museum of Natural History (NRM; Principal Organization), the Swedish University of Agricultural Sciences (SLU), Karolinska Institute (KI), Linnaeus University (LnU), Lund University (LU), the Royal Institute of Technology (KTH), Stockholm University (SU), the Swedish Meteorological and Hydrological Institute (SMHI), Umeå University (UmU), University of Gothenburg (GU), and Uppsala University (UU). The consortium covers the entire spectrum of biodiversity data sources represented in the Swedish research community.

More information about global collaborations can be found at: https://www.gbif.org/partners External link..

Resources and Links

Links

GBIF data portal: https://www.gbif.org/ External link.

GBIF Sweden: https://www.gbif.se/ External link.

SBDI data portal: https://biodiversitydata.se/ External link.

GBIF data blog: https://data-blog.gbif.org/ External link.

GBIF Community Forum: https://discourse.gbif.org/ External link.

GBIF Data use club: https://www.gbif.org/data-use-club External link.

Resources

Manuals for publishing data and latest best practice: https://docs.gbif.org/documentation-guidelines/en/ External link.

Course material: https://www.gbif.org/training-old External link.

A Quick-guide to Darwin Core standard (DwC) and terms: https://dwc.tdwg.org/ External link.

Strategic Documents

GBIF Strategic framework: https://www.gbif.org/strategic-plan External link.

Events

You can find information about current conferences, workshops, webinars, and other upcoming events at https://www.gbif.se/events/ External link..

Publications

• GBIF produces an annual compilation of research made possible by GBIF-mediated data. The latest Science Review can be found at https://www.gbif.org/science-review External link..
• GBIF 20 years - a compilation by CODATA: https://doi.org/10.35035/ctzm-hz97 External link..
• GBIF's economic valuation - an independent study by Deloitte Access Economics: https://www.deloitte.com/au/en/services/economics/perspectives/total-economic-value-open-access-database-living-world.html External link..
• A compilation of how GBIF data is used in research: Heberling et al. 2021, https://doi.org/10.1073/pnas.2018093118 External link..

Mailing Address

GBIF Sweden
PO Box 500 07
104 05 Stockholm
Sweden

Contact the Infrastructure

For general inquiries and support, please use gbif@nrm.se. It is also possible to reach us through the SBDI support form External link.. If you require advanced user support, such as application development or advanced analysis, please use the SBDI support form.

Contact the Node Manager for GBIF Sweden if you, e.g., need support in organizing a course or workshop, want to nominate candidates for GBIF's awards, apply for support for collaborative projects within CESP, or if you want to apply for setting up a Hosted data portal.

GBIF Sweden Staff