Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.1%) to scientific vocabulary
Repository
API for Pathogen Metadata
Basic Info
- Host: GitHub
- Owner: CLIMB-TRE
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://climb-tre.github.io/onyx/
- Size: 4.1 MB
Statistics
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 9
- Releases: 69
Metadata Files
README.md
Onyx
Overview
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.
Projects
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)
Structure
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
Documentation can be found here.
Owner
- Name: CLIMB-TRE
- Login: CLIMB-TRE
- Kind: organization
- Repositories: 2
- Profile: https://github.com/CLIMB-TRE
GitHub Events
Total
- Create event: 19
- Issues event: 1
- Release event: 9
- Delete event: 8
- Issue comment event: 2
- Push event: 102
- Pull request review comment event: 7
- Pull request review event: 13
- Pull request event: 42
Last Year
- Create event: 19
- Issues event: 1
- Release event: 9
- Delete event: 8
- Issue comment event: 2
- Push event: 102
- Pull request review comment event: 7
- Pull request review event: 13
- Pull request event: 42
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 6
- Total pull requests: 172
- Average time to close issues: 5 months
- Average time to close pull requests: 4 days
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 1.17
- Average comments per pull request: 0.08
- Merged pull requests: 124
- Bot issues: 0
- Bot pull requests: 49
Past Year
- Issues: 1
- Pull requests: 23
- Average time to close issues: about 1 hour
- Average time to close pull requests: 4 days
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.09
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 3
Top Authors
Issue Authors
- tombch (4)
- rmcolq (2)
Pull Request Authors
- tombch (122)
- dependabot[bot] (49)
- warrickball (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- pip