Onyx is a Django-based API for managing metadata records, analyses, and other associated data. It provides a flexible system for handling projects with different metadata requirements, and has built-in access control, data validation, sensitive identifier anonymisation, and a granular query system.
As part of CLIMB-TRE, Onyx serves as the central metadata repository for the following projects:
- mSCAPE (Metagenomics Surveillance Collaboration and Analysis Programme): A collaborative initiative led by UKHSA, involving a consortium of NHS and academic partners, to deliver a pilot surveillance network trialling the use of metagenomic data for public health surveillance and pathogen analysis.
- PATH-SAFE (Pathogen Surveillance in Agriculture, Food and Environment): Led by the FSA, PATH-SAFE piloted the development of a national surveillance network to improve the detection and tracking of foodborne human pathogens and AMR within agriculture.
- synthSCAPE (Synthetic dataset for mSCAPE)
- openMGS (Open Meta-Genomic Surveillance)
Different pieces of Onyx (the backend, project definitions and frontend apps) are defined in the following repositories:
| Repository | Description |
|---|---|
| onyx | Backend API and database for Onyx. |
| onyx-client | Command-line interface and Python API for interacting with Onyx. |
| onyx-gui | Graphical user interface for browsing Onyx records/analyses, and producing graphs of aggregated data. |
| onyx-extension | Wraps the interface provided by onyx-gui and provides additional logic to convert it into a JupyterLab extension, making it accessible from CLIMB Jupyter notebook servers. |
| onyx-projects (private) | Contains the Django apps that define each active project in CLIMB-TRE, as well as configurations for sites and which projects they have access to. |
Documentation can be found here.