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
🗂️ Use Cases I & II GDC Data: https://github.com/CNAG-Biomedical-Informatics/clarid-tools/tree/main/nb/data
📦 CPAN Distribution: https://metacpan.org/pod/ClarID::Tools
🐳 Docker Hub Image: https://hub.docker.com/r/manuelrueda/clarid-tools/tags
ClarID-Tools is a toolkit for working with the ClarID specification, including the reference command-line implementation, preprocessing utilities, and example workflows. The objective is to standardize how subject and biosample metadata are transformed into compact, informative IDs for downstream integration, tracking, and exchange.
- 🧬 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
We offer two modes of installation:
- If you cloned this repository, run commands from the repository root with
bin/clarid-tools. - If you installed ClarID-Tools with CPAN or system-wide, run
clarid-tools. - The packaged default codebook is used automatically, so
--codebookis only needed when you want to use a custom codebook. - The
qrcodesubcommand requiresqrencodeandzbarimgon host installs. The Docker image already includes them.
-
Use Cases:
The documentation site is built with Docusaurus under docs-site/.
cd docs-site
npm install
npm run buildSome Docusaurus pages are generated from repository README files; see docs-site/README.md before editing copied installation or preprocessing pages.
If you use ClarID-Tools in your work, please cite:
Rueda, M. and Gut, I.G. (2026). ClarID: a human-readable and compact identifier specification for biomedical metadata integration. Journal of Biomedical Semantics 17, 9. https://doi.org/10.1186/s13326-026-00349-6
Written by Manuel Rueda, PhD. Info about CNAG can be found at https://www.cnag.eu.
ClarID-Tools is released under the Artistic License. See the LICENSE file for details.