mite_schema

Contents

• Overview
• Documentation
• System Requirements
• Installation Guide
• Quick Start
• Attribution
• For Developers

Overview

MITE (Minimum Information about a Tailoring Enzyme) is a community-driven database for the characterization of tailoring enzymes. These enzymes play crucial roles in the biosynthesis of secondary or specialized metabolites, naturally occurring molecules with strong biological activities, such as antibiotic properties.

This repository contains the data schema in JSON Schema format followed by the entries of the MITE data repository mite_data.

For more information, visit the MITE Data Standard Organization page or read our publication.

Documentation

This repository is the single source of truth for the formatting of entries of the MITE data repository mite_data.

It contains a data model in form of a JSON Schema file and provides CLI functionality to validate files against said schema. Furthermore, this repository can also be used as a library. For examples, see mite_data, mite_extras or mite_web.

For feature requests and suggestions, please refer to the MITE Schema thread in the MITE Discussion forum.

System Requirements

OS Requirements

Local installation was tested on:

• Ubuntu Linux 20.04 and 22.04 (command line)

Python dependencies

Dependencies including exact versions are specified in the pyproject.toml file.

Installation Guide

With pip

• pip install mite_schema

Quick Start

To validate your MITE-formatted .json-file(s), run:

• mite_schema -i <input1.json input2.json ... inputN.json>

Attribution

License

mite_schema is an open source tool licensed under the MIT license (see LICENSE).

Publications

See CITATION.cff or MITE online for information on citing MITE.

Acknowledgements

This work was supported by the Netherlands Organization for Scientific Research (NWO) KIC grant KICH1.LWV04.21.013.

For Developers

Nota bene: for details on how to contribute to the MITE project, please refer to CONTRIBUTING.

Package Installation

Please note that the development installation is only tested and supported on (Ubuntu) Linux.

With uv from GitHub

Note: assumes that uv is installed locally - see the methods described here

git clone https://github.com/mite-standard/mite_schema
uv sync --extra dev
uv run pre-commit install

All tests should be passing

uv run pytest

CI/CD and Deployment

CI/CD via GitHub Actions runs on every PR and push to the main branch.

A new release created on the mite_schema GitHub page will automatically relay changes to PyPI and Zenodo.