Skip to content

Onyx - API for Pathogen Metadata

Introduction

This is the documentation for Onyx, a database and API for managing sample metadata, their analyses, and other associated data.

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)

Contents

CLI & Python API
Learn how to use the Onyx command-line interface and Python API.

JupyterLab Extension
Learn how to use the Onyx JupyterLab extension and graphical user interface.

Types
Learn about the different field types available in Onyx.

Lookups
Learn about the different field lookups available in Onyx.