mite-extras

mite_extras

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 functionality to validate MITE entries in JSON format.

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

Documentation

This repository provides validation functionality for verifying files following the MITE JSON Schema format, such as the files in the MITE data repository mite_data.

The validation functionality includes:

• Calling the mite_schema functionality
• Validation of reaction SMARTS (does the reaction SMARTS lead to the expected product when applied to a specified substrate)
• Sanitation of SMILES and reaction SMARTS
• Fetching of NCBI GenPept/UniProtKB IDs

mite_extras can be used as a CLI to automatically update MITE entries. Furthermore, this repository can also be used as a library. For examples, see mite_data or mite_web.

For errors, feature requests, and suggestions, please open an Issue or start a discussion 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

• Install with pip install mite_extras

Quick Start

To validate MITE entries or update them to a new schema versiom, run:

• mite_extras -i <input/> -o <output/>

Attribution

License

mite_extras 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_extras
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_extras GitHub page will automatically relay changes to PyPI and Zenodo.