https://github.com/cnag-biomedical-informatics/clarid-tools

https://github.com/cnag-biomedical-informatics/clarid-tools

Last synced: 9 months ago
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• Host: GitHub
• URL: https://github.com/cnag-biomedical-informatics/clarid-tools
• Owner: CNAG-Biomedical-Informatics
• Created: 2025-09-02T14:24:38.000Z (9 months ago)
• Default Branch: main
• Last Pushed: 2025-09-03T09:59:07.000Z (9 months ago)
• Last Synced: 2025-09-03T10:23:21.012Z (9 months ago)
• Language: Perl
• Size: 55 MB
• Stars: 1
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          


  





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



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**📘 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

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# 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.

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## 🔬 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 

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## 🚀 Getting Started

### 🛠️  Installation

We offer two modes of installation:

1. [Non-Containerized](non-containerized/README.md)

2. [Containerized](docker/README.md)

### 📘 Example Usage

1. [Quickstart](https://cnag-biomedical-informatics.github.io/clarid-tools/usage/quickstart/)

2. Use Cases:

 

  * [Biosample](https://cnag-biomedical-informatics.github.io/clarid-tools/use-cases/biosample.md)

  * [Subject](https://cnag-biomedical-informatics.github.io/clarid-tools/use-cases/subject.md)

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## 🧠 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_.

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## 👤 Author 

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

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## 📄 License

ClarID-Tools is released under the Artistic License. See the [LICENSE](LICENSE) file for details.