An R shiny interactive application that provides an automated and user-friendly workflow for generating species occurrence cubes from user-provided datasets. Users can upload their biodiversity occurrence data in CSV or TSV format and configure the cube generation process. The user can additionally merge generated cubes with occurrence cubes obtained from GBIF or any other compatible source. This graphical interface supports datasets with different formats and structures, reducing the technical expertise required to generate standardized occurrence cubes.
For further information on how to use Cubit, navigate to the B-Cubed documentation website or the GitHub repository ,where comprehensive documentation for this application is available. Additionally, if you want to execute this workflow for larger datasets or simply don’t want to upload sensitive data, there is a locally installable version here.
Traditional biodiversity monitoring programmes usually generate well-curated species occurrence data, with high spatial and temporal resolutions but often only for restricted areas. In recent years, technological developments along with online digital platforms have increased the amount of information available on species occurrences, both from the scientific community as well as from community-based contributions such as citizen science. The increase in data availability and accessibility poses the challenge of integrating such highly heterogenous data sets on species occurrencesm datasets.
B-Cubed addressed this challenge by transforming biodiversity monitoring into an agile and responsive process. It leverages the concept of data cubes to standardise access to biodiversity data using the Essential Biodiversity Variables framework. These cubes are the basis for developing models and indicators to assess past, current and future biodiversity.
Cubit was created to address the need to convert and integrate data from different sources into standardized species occurrence cubes, allowing users to make the most of all the information available.
This application is provided as a tool to assist in the generation of cubes from biodiversity occurrence datasets. While every effort is made to ensure the accuracy of the underlying mapping logic and transformation scripts, the outputs are provided "as is" without any guarantees of completeness, accuracy, or fitness for a specific purpose.
Pinto, R., Estupinan-Suarez, L., Trekels, M., Golivets, M., Hillaert, J., Preda, P., Machado, A. L., Lobos, R. C., Teixeira, H. (2026). Cubit - Integrating open and private data sources into Species Occurrence Cubes (Version 1.0). This work is available under an MIT License.
Technical support: If you encounter any bugs or functional glitches, please report them by opening a new issue in the GitHub repository.
This application was created in the scope of the B-Cubed project, funded by the European Union under the Horizon Europe Programme with Grant Agreement No. 101059592 ( 10.3030/101059592 : Biodiversity Building Blocks for policy).