ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration

📘 Documentation: https://cnag-biomedical-informatics.github.io/clarid-tools

📓 Google Colab tutorial: https://colab.research.google.com/drive/1smS42yzL7qYV1kCz34baTWLRr_AAap-r

📦 CPAN Distribution: https://metacpan.org/pod/ClarID::Tools

🐳 Docker Hub Image: https://hub.docker.com/r/manuelrueda/clarid-tools/tags

ClarID-Tools

📝 Description

ClarID-Tools is a flexible, schema-driven toolkit for generating and parsing structured identifiers for subject and biosample data. The objective is to standardize how subject and biosample metadata are encoded into compact, informative IDs for downstream integration and tracking.

🔬 Key Features

• 🧬 Biosample and Subject ID generation from structured metadata
• 🩺 Support for clinical and experimental metadata, including species, tissue, assay, condition, and more
• 📄 Human-readable and stub-formatted modes for compact or verbose identifiers
• 🧪 Bulk and single-record encoding/decoding
• ✅ Schema validation using JSON Schema and YAML codebooks
• 📦 Command-line interface

🚀 Getting Started

🛠️ Installation

We offer two modes of installation:

1. Non-Containerized

2. Containerized

📘 Example Usage

1. Quickstart

2. Use Cases:

• Biosample
• Subject

🧠 Citation

If you use ClarID-Tools in your work, please cite:

Manuel Rueda and Ivo G. Gut (2025). ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration. Submitted.

👤 Author

Written by Manuel Rueda, PhD. Info about CNAG can be found at https://www.cnag.eu.

📄 License

ClarID-Tools is released under the Artistic License. See the LICENSE file for details.