BioXend is a new computational framework for submitting Microbial Biotransformation of Xenobiotics data. You can checkout the webpage for BioXend project here: https://zmahnoor14.github.io/BioXend/
- WP1: is to develop minimum reporting standards based on community consensus
- WP2: is to automate the metadata collection
- WP3: is to develop a submission workflow to ChEMBL
- WP4: is to release this framework as part of NFDI4Micropbiota workflow
We welcome community participation especially for developing the minimum standards called Minimum Information about Xenobiotics-Microbiome Biotransformation (MIX-MB).
Minimum Information about Xenobiotics-Microbiome Biotransformation (MIX-MB)
BioXend framework defines community-driven minimum reporting standards for xenobiotic microbial biotransformation data, enabling consistent data deposition to databases such as ChEMBL.
We would like to invite you to participate in this community driven project. The standards are informed by
- already existing standards,
- ChEMBL submission guidelines, and
- an open survey.
Please view the current results from the survey in Standards/MIX-MB_Survey_Analysis.ipynb notebook.
BioXend/
├── .github/ # GitHub Actions workflows, PR and issue templates
├── Standards/ # MIX-MB standards documents and templates
│ ├── Templates/ # Submission templates (Excel, CSV, JSON-LD)
│ ├── MIX-MB_Survey_Analysis.ipynb # Community survey results and analysis
│ ├── MIXMB_Biotransformation.md # MIX-MB(B): Biotransformation process standards
│ ├── MIXMB_Microbes.md # MIX-MB(M): Microorganism standards
│ ├── MIXMB_Standards_main.md # Top-level MIX-MB standards overview
│ ├── MIXMB_Xenobiotics.md # MIX-MB(X): Chemical substrate standards
│ └── Versioning.md # Versioning policy for standards
├── bin/ # Executable scripts and generated ChEMBL output files
├── modules/ # Nextflow DSL2 process modules
├── notebooks/ # Development notebooks (Jupyter + R)
├── versions/ # Independent version tracking per component
├── CODE_OF_CONDUCT.md
├── CONTRIBUTING.md
├── README.md
└── VERSION.md
All participants are expected to follow our Code of Conduct. Also check thelink to the current project board: BioXend Project Board
We welcome contributions to the standards, template, and nf workflow for submission! See our Contributing Guide for details. There are different ways to contribute, either via an issue, via dicussions, via Pull Requests (PR) or via endorsement of the already submitted changes that you can easily view in the BioXend Project Board.
Easy:
- Fill out the open survey using the survery link
- Propose changes by opening an issue
- Discuss ideas in GitHub Discussions
- Endorse proposals by adding 👍 to issues and PRs you support
Requires git knowledge:
- Submit a pull request (PR) targeting the
develbranch
- Download the latest
Template.xlsx - Read the
Template_Descriptionsheet for instructions. This template defines mandatory, recommended and optional fields based on ChEMBL submission guidelines and also the current version of MIX-MB. - Fill in your data — green columns are mandatory, blue are recommended, purple are optional
- Submit feedback on ease of use via issues or discussion -- This template will be used as input to generate ready to submit ChEMBL files.
Each standard document, the template, and the nf workflow are versioned independently. The framework version increments with any component release. See VERSION.md for details.
This project is licensed under the MIT License.