Documentation & Data

The Underlying Data

We are incredibly grateful to the researchers who have generated and shared these data. This project would not be possible without their commitment to open science. Below is a summary of the datasets currently integrated into the Open Pathogen Kinetics Commons.

Data Selection

The datasets included in OPKC were identified through a comprehensive literature search focusing on studies with longitudinal pathogen load measurements. We are continuously working to expand this library by bringing in new papers and datasets as they become available.

All underlying data are either open access or used with specific permission from the authors. Our inclusion criteria prioritize studies that meet the "bare minimum" requirement of providing pathogen load measurements over time (see our Data Standard for details). We filter and clean these datasets to ensure they can be meaningfully compared, but we strive to preserve the original structure and intent of the data wherever possible.

Data Visualization

The Sample Explorer is a tool designed to provide immediate, visual insight into the contents of the database. It allows users to:

• Filter by study, pathogen, sample source, and more.
• Visualize kinetic trajectories to understand the density and duration of sampling.
• Compare data across different studies and units (e.g., Ct values vs. pathogen load).

This visualization is intended as a "helper" tool—a way to quickly assess which datasets might be relevant for your specific research question before downloading the full dataset for detailed analysis.

Web Development

The Open Pathogen Kinetics Commons is built using open-source tools to ensure transparency and reproducibility.

• Backend: Django (Python)
• Frontend: Tailwind CSS and Plotly.js
• Code Assistance: Google Gemini was used to assist with writing the underlying code for this platform.