MetaHQ Documentation¶

MetaHQ is a hub for high-quality annotations for biomedical data of all types.

The construction of the MetaHQ database would not be possible without efforts from the greater biomedical research community. All of our annotations come from fellow researchers interested in using publicly available biomedical data that understand the difficulty in finding samples and studies of interest.

We encourage researchers to submit their high-quality, manually curated annotations to be included in the MetaHQ database! See our documentation for information on how to contribute.

Features¶

• 🔍 Annotation Retrieval: Query standardized and harmonized biomedical annotations
• 🧠 ML-Ready Outputs: Retrieve labels for classification tasks
• 🖥️ CLI Interface: User-friendly command-line tools

Quick Links¶

• Installation
• Quick Start
• User Guide

Paper¶

The preprint for MetaHQ can be found at https://arxiv.org/abs/2602.07805.

Terms and Conditions¶

Before using MetaHQ, please read our full Terms and Conditions.

The MetaHQ database is released under CC BY-NC 4.0 (Creative Commons Attribution-NonCommercial 4.0 International) because several source datasets carry NonCommercial restrictions.

For commercial use: You must either:

1. Obtain permissions from sources with NonCommercial restrictions
2. Use only annotations from sources with commercial-compatible licenses (CC0, CC BY)

Our software is released under the BSD 3-Clause.

Getting Help¶

Open an issue on GitHub if you encounter any issues or have questions: