How to reuse Dryad data

Dryad hosts a vast collection of curated datasets across a wide range of scientific disciplines. We enable researchers to share, access, and reuse high-quality data. This guide helps researchers make the most of data on Dryad.

Understanding usage rights

All datasets on Dryad are published under the CC0 (Creative Commons Zero) Public Domain Dedication. This means:

• No restrictions: You can reuse, modify, share, and even redistribute the data for both commercial and non-commercial purposes without asking for permission.
• Attribution: While you are not legally required to provide attribution under CC0, we strongly recommend as a scholarly courtesy to cite any data you reuse in your work. This ensures proper credit to the data creators and supports academic integrity. Dryad provides a recommended citation for each dataset, which follows this format:
  Author(s). Year. Dataset Title [Dataset]. Publisher. DOI: Dataset DOI.

Finding data to reuse

Dryad provides a user-friendly search interface to help you locate datasets relevant to your interests. Here’s how to get started:

1. Navigate to the search bar on Dryad’s homepage or the Explore data page.
2. Enter keywords or phrases related to your research topic. For example, “climate change impacts on biodiversity” or “gene expression in cancer.”
3. Filter options are available on the left-hand side, allowing you to narrow your results by:
   1. Subject area: Select from common keywords that describe the topics or disciplines relevant to the dataset.
   2. Journal name: To find datasets associated with studies published in specific journals.
   3. Institution name: To find datasets associated with researchers from specific academic organizations.
   4. Geographical location: To find datasets associated with a certain region or country.
   5. Funder: To find datasets financially supported by a certain funding organization.
   6. File extension: To identify datasets of a certain file type such as CSV or fasta.
4. Once you find a dataset of interest, clicking on it will lead you to the dataset’s landing page. Key components of a dataset landing page include:
   • Abstract: A brief description of the data.
   • README: Starting with datasets published in 2023, you’ll find an embedded README file describing data collection and processing methods, term definitions, a file inventory, and other useful context for reusing the data.
   • Data citation and DOI: Dryad provides a recommended citation for each dataset so you can give appropriate credit to the original creators. The DOI is a unique digital identifier that makes the dataset persistently accessible and citable.
   • Download options: Links to download the data files, which may come in different formats like CSV, Excel, or other specialized formats depending on the field.
   • Related works: Research objects, such as articles, software, additional datasets, and data management plans that provide context for interpreting the data.

Accessing data via our API

Dryad offers an API (Application Programming Interface) for programmatic access to datasets, which is useful for large-scale data gathering, integration with software tools, or analyses that require multiple datasets. Visit the API documentation page for detailed information on the available endpoints and usage examples.

Common API use cases

1. Programmatic dataset retrieval: Access metadata or download files directly without manual searching.
2. Dataset harvesting: Researchers conducting large meta-analyses or reviews can pull in numerous datasets in an automated fashion.
3. Integrating Dryad data with custom tools: Use the API to fetch and integrate data into software platforms, visualization tools, or machine learning pipelines.

Example API request:

To access a list of datasets, you can make a request to the /search endpoint. For example:

GET https://datadryad.org/api/v2/search?q=evolution&per_page=10

This request fetches datasets related to “evolution,” limited to the first 10 results.

Ideas for reusing Dryad data

The possibilities for reusing data are vast. Here are a few key ways you can leverage the Dryad for your research:

1. Meta-analysis: Aggregate datasets from multiple studies to increase statistical power and provide more robust conclusions. This is common in fields like ecology, medicine, and environmental science.
2. Secondary analysis: Perform new analyses on existing datasets to answer different research questions or look for different patterns and relationships than those explored in the original study.
3. Comparative studies: Use datasets from different regions, species, or time periods to conduct comparative studies. For instance, you could examine climate change's effects on biodiversity across different ecosystems.
4. Data validation: Cross-validate your experimental results by comparing them with similar datasets available on Dryad. This can strengthen the reliability of your findings.
5. Machine learning and AI training: Dryad datasets are an excellent resource for training machine learning models, especially when large, labeled datasets are needed. Researchers in bioinformatics, genomics, and image recognition can utilize datasets for predictive modeling or algorithm development.
6. Teaching and learning: Datasets from Dryad can be valuable teaching tools in undergraduate or graduate courses. Students can use real-world data to practice statistical analysis, coding, or data visualization techniques.

Tips for maximizing data reuse

1. Check for updates: Dryad allows data versioning. Published datasets can be updated or revised over time. Be sure to check back for new versions if it’s been a while since you first accessed a dataset.
2. Collaborate with original authors: If your work significantly expands on the dataset or involves complex questions, consider reaching out to the original authors for collaboration or clarification. Dryad provides contact information for the corresponding author on the dataset landing page.
3. Take advantage of tabular data previews: For data in tabular formats such as TSV, CSV, and XLSX, Dryad lets you preview the contents of the file before downloading, helping you evaluate the relevance of the data for your goals.
4. Check file sizes: Data packages on Dryad can be up to 300GB. Make sure you have the appropriate computational resources to handle and analyze these data before downloading.
5. Review the metadata and README: The README and methods information will include information about how the data was collected, any known limitations, and explanations of variables. A thorough understanding of the dataset’s context will improve the accuracy and interpretation of your analyses.
6. Verify data integrity and quality: Before integrating the dataset into your research, perform data quality checks. This might include assessing missing data, identifying outliers, or confirming consistency across related variables. It ensures that the data you are using is reliable and ready for your specific analysis.
7. Combine multiple datasets for broader insights: One of the advantages of Dryad is the availability of diverse datasets. You can combine multiple datasets to perform meta-analyses, cross-study comparisons, or integrate data from different geographical areas or species. Just ensure that data formats and variables are consistent across studies before merging.
8. Explore different data formats: Dryad datasets may come in a variety of formats (e.g., CSV, fasta, JSON). Be prepared to work with different data formats by converting them or writing scripts that can handle multiple formats. Tools like R, Python, or specialized software can be helpful for analyzing data in various formats.
9. Create derived datasets for further research: If your research results in new data or modifications of an existing Dryad dataset, consider sharing your derived datasets on Dryad. This can contribute to an ongoing cycle of data reuse, allowing future researchers to build upon your work and the original data.
10. Engage with the Dryad community: We offer regular educational webinars, tips, and resources for data sharing and reuse. Visit our blog, subscribe to our newsletter, or follow us on social media to make sure you’re getting the latest updates.