Welcome to biodumpy: A Comprehensive Biological Data Downloader
Overview
In recent years, public biodiversity platforms and their associated datasets have grown significantly, driven by advancements in research, institutional efforts, expanded data storage capabilities, and the availability of powerful computational tools. These developments have provided unprecedented access to ecological and biological data, covering extensive geographic regions, long time periods, and a wide array of taxonomic groups. Such resources have become essential in ecological research, enabling scientists to undertake more thorough analyses and explore hypotheses that were previously unfeasible due to data constraints. These constraints include issues such as inconsistent data quality, low data quantity, and the heterogeneity of sources.
As these databases have expanded, so too has the number of programming libraries aimed at facilitating data access and interaction, making data retrieval more straightforward. However, most of these tools have been designed to work with a single database, posing difficulties for researchers who need to integrate information from multiple sources.
To overcome this limitation, we developed biodumpy, a Python library that simplifies the retrieval, management, and integration of biological data across various public databases. biodumpy grants users access to a broad range of up-to-date datasets, including genetic, distributional, taxonomic, and bibliographic information. Its modular design enables efficient data retrieval tailored to specific taxa, with support for processing multiple modules concurrently.
Note
This project is under active development.
Key Features
biodumpy offers dedicated modules for each supported database. Each module comes with specific parameters tailored to retrieve information from its respective source. Explore the Modules section to learn about the currently supported modules.
Contribution
biodumpy is an open-source project, and contributions are welcome! If you have ideas for new features, bug fixes, or improvements, please submit an issue or pull request on our GitHub repository or contact our support ✉️ here.
License
biodumpy is licensed under the MIT License for its software components. Additionally, any creative works associated with this project—such as documentation, visual assets, or other non-code materials—are licensed under the Creative Commons Attribution (CC BY 4.0) license. See the LICENSE file for full details.
Disclaimer
The data retrieved and downloaded using this package is sourced from external databases. We do not take responsibility for the accuracy, completeness, or currency of the data. Users are advised to verify the information independently. By using this package, you agree that the authors and contributors are not liable for any errors, omissions, or potential consequences arising from the use of the data.
If you encounter any bugs or issues using the package, please contact the developers for support.
Acknowledgments
This package has been partially sponsored and promoted by the Comunitat Autonoma de les Illes Balears through the Conselleria d’Educació i Universitats and by the European Union- Next Generation EU/PRTR-C17.I1.