biodumpy: A Comprehensive Biological Data Downloader

Overview

biodumpy is a powerful and versatile Python package designed to simplify the process of retrieving biological information from several public databases. With biodumpy, researchers can easily download and manage data from multiple sources, ensuring access to the most up to date and comprehensive biological information available.

Note: This package is currently under development.

Key Features

biodumpy offers dedicated modules for each supported database, with each module featuring functions specifically designed for retrieving information from its respective source. The modules implemented so far are:

• Barcode of life data system v4 (BOLD)
• Catalogue of life (COL)
• Crossref
• Global biodiversity information facility (GBIF)
• iNaturalist
• International union for the conservation of nature (IUCN)
• National center for biotechnology information (NCBI)
• Ocean biodiversity information system (OBIS)
• World register of marine species (WoRMS)
• ZooBank

This list can be expanded, thus suggestions and feedback are greatly appreciated.

Main functionalities and workflow

Before using biodumpy, users need to install the package in their Python environment with the following command:

pip install biodumpy

Usage

To simplify the use of biodumpy, we create a general structure common among the modules:

1. Load the package. Import biodumpy into your Python environment.
2. Load the desired modules. Import one or more specific modules needed to retrieve the data.
3. Set up the configuration of one or more modules. Configure the biodumpy function/s with the required parameters.
4. Start the download. Execute the function to begin retrieving the data.

Here, we provide two examples illustrating the general structure of a biodumpy script:

In detail, we described:

• Single Module Example: This example demonstrates how to use a single biodumpy module (for example, GBIF).
• Multiple Modules Example: This example shows how to use multiple biodumpy modules (for example, GBIF and IUCN).

Example N.1

    # Import biodumpy package
    from biodumpy import Biodumpy

    # Import GBIF module
    from biodumpy.inputs import GBIF

    # Create a list of taxa
    taxa = ['Alytes muletensis (Sanchíz & Adrover, 1979)', 'Bufotes viridis (Laurenti, 1768)',
            'Hyla meridionalis Boettger, 1874', 'Anax imperator Leach, 1815']

    # Set the Biodumpy function with the specific parameters
    bdp = Biodumpy([GBIF(sleep=3, bulk=False, accepted_only=True)])

    # Start the download
    bdp.start(taxa, output_path='./downloads/{date}/{module}/{name}')

Example N.2

    # Import biodumpy package
    from biodumpy import Biodumpy

    # Import GBIF and IUCN modules
    from biodumpy.inputs import GBIF, IUCN

    api_key = 'YOUR_IUCN_API_KEY'

    # Create a list of taxa
    taxa = ['Alytes muletensis', 'Bufotes viridis', 'Hyla meridionalis', 'Anax imperator']

    # Set the Biodumpy functions with the specific parameters
    bdp = Biodumpy([GBIF(bulk=False, accepted_only=True),
                    IUCN(api_key=api_key, bulk=True, region=['Global'])])

    # Start the download
    bdp.start(taxa, output_path='./downloads/{date}/{module}/{name}')

Documentation and Support

For detailed documentation and tutorials, please visit the biodumpy Read the Docs documentation.

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 in our GitHub repository or contact with the support team ✉️ 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.

Acknowledgments

The project is developed by the "Centre Balear de Biodiversitat" (CBB) at the University of the Balearic Islands, with support from MCIN and funding from the European Union—NextGenerationEU (PRTR-C17.I1), as well as the Government of the Balearic Islands.

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