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mite-extras

Validation and conversion functionality for reaction SMARTS collected in the scope of MITE

https://github.com/mite-standard/mite_extras

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Validation and conversion functionality for reaction SMARTS collected in the scope of MITE

Basic Info
  • Host: GitHub
  • Owner: mite-standard
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 337 KB
Statistics
  • Stars: 2
  • Watchers: 3
  • Forks: 1
  • Open Issues: 2
  • Releases: 11
Created about 2 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

mite_extras

DOI PyPI version

This package contains functionality to validate entries of the Minimum Information about a Tailoring Enzyme (MITE) repository.

This includes:

  • Validation of the MITE json format (does the entry follow the mite_schema format)
  • 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

When used as CLI, mite_extras can automatically update MITE entries (see below). However, it can also be used as a library (e.g. as done in mite_data).

For more information, see the README of the MITE-Standard organisation page.

Installation

Attention: this program has only been tested with Ubuntu Linux.

With pip from PyPI

  • Install with pip install mite_extras

With hatch from GitHub

  • Install python 3.12.x
  • Install hatch (e.g. with pipx install hatch)
  • Download or clone the repository
  • Run hatch -v env create

Quick Start: Example

Run from command line:

To validate MITE entries or update them to a new schema version (requires mite_extras to be installed via pip).

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

Run with hatch:

Validate MITE entries or update them to a new schema version

  • hatch run mite_extras -i input/ -o output/

For devs

  • Install developer dependencies with hatch -v env create dev
  • Initialize pre-commit with hatch run dev:pre-commit install
  • Run tests with hatch run dev:pytest
  • Run CLI with hatch run dev:mite_extras and the appropriate options
  • If necessary, remove the environment again with hatch env remove dev

Owner

  • Name: MITE Data Standard
  • Login: mite-standard
  • Kind: organization

Governing body for MITE data standard and affiliated repositories

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: mite_extras
message: >-
  If you use this software, please cite the referenced
  paper.
type: software
authors:
  - affiliation: 'Wageningen University and Research'
    family-names: Zdouc
    given-names: Mitja M.
    orcid: 'https://orcid.org/0000-0001-6534-6609'
  - affiliation: 'Institute of Molecular Systems Biology, ETH Zürich'
    family-names: Rutz
    given-names: Adriano
    orcid: 'https://orcid.org/0000-0003-0443-9902'
repository-code: 'https://github.com/mite-standard/mite_extras'
abstract: >-
    Validation and conversion functionality for reaction SMARTS collected in the scope of MITE.
keywords:
  - python
  - tailoring enzymes
  - SMARTS
license: MIT
preferred-citation:
  type: preprint
  authors:
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Zdouc
      given-names: Mitja M.
      orcid: 'https://orcid.org/0000-0001-6534-6609'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Meijer
      given-names: David
      orcid: 'https://orcid.org/0000-0001-6406-4394'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Biermann
      given-names: Friederike
    - address: 'SINTEF Industry, P.O. Box 4760 Torgard, N-7465, Trondheim, Norway'
      affiliation: 'Department of Biotechnology and Nanomedicine'
      family-names: Holme
      given-names: Jonathan
      orcid: 'https://orcid.org/0009-0007-1652-9477'
    - address: 'University of Tübingen, Germany'
      affiliation: 'Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT)'
      family-names: Korenskaia
      given-names: Aleksandra
      orcid: 'https://orcid.org/0000-0003-3002-6458'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Lien
      given-names: Annette
      orcid: 'https://orcid.org/0009-0006-0578-9225'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Louwen
      given-names: Nico L. L.
      orcid: 'https://orcid.org/0000-0002-4431-5499'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Navarro-Muñoz
      given-names: Jorge C.
      orcid: 'https://orcid.org/0000-0003-2992-1607'
    - address: 'SINTEF Industry, P.O. Box 4760 Torgard, N-7465, Trondheim, Norway'
      affiliation: 'Department of Biotechnology and Nanomedicinev'
      family-names: Nguyen
      given-names: Giang-Son
      orcid: 'https://orcid.org/0000-0001-5730-3326'
    - address: 'ETH Zurich, Zurich, Switzerland'
      affiliation: 'Institute of Molecular Systems Biology'
      family-names: Rutz
      given-names: Adriano
      orcid: 'https://orcid.org/0000-0003-0443-9902'
    - address: 'Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland'
      affiliation: 'SIB Swiss Institute of Bioinformatics'
      family-names: Sveshnikova
      given-names: Anastasia
      orcid: 'https://orcid.org/0000-0001-9291-0965'
    - address: 'University of Denmark, Kgs. Lyngby, Denmark'
      affiliation: 'The Novo Nordisk Foundation Center for Biosustainability, Technical'
      family-names: Szenei
      given-names: Judith
    - address: 'Sylviusweg 72, 2333 BE Leiden, The Netherlands'
      affiliation: 'Institute of Biology, Leiden University'
      family-names: Terlouw
      given-names: Barbara
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Torres Ortega
      given-names: Rosina
    - address: 'Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland'
      affiliation: 'SIB Swiss Institute of Bioinformatics'
      family-names: Feuermann
      given-names: Marc
    - address: 'Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland'
      affiliation: 'SIB Swiss Institute of Bioinformatics'
      family-names: Bridge
      given-names: Alan J.
      orcid: 'https://orcid.org/0000-0003-2148-9135'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Hooft
      name-particle: van der
      given-names: Justin J. J.
      orcid: 'https://orcid.org/0000-0002-9340-5511'
    - address: 'University of Denmark, Kgs. Lyngby, Denmark'
      affiliation: 'The Novo Nordisk Foundation Center for Biosustainability, Technical'
      family-names: Weber
      given-names: Tilmann
    - address: 'University of Tübingen, Germany'
      affiliation: 'Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT)'
      family-names: Ziemert
      given-names: Nadine
    - address: 'University of Denmark, Kgs. Lyngby, Denmark'
      affiliation: 'The Novo Nordisk Foundation Center for Biosustainability, Technical'
      family-names: Blin
      given-names: Kai
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Medema
      given-names: Marnix H.
  title: The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis.
  journal: ChemRxiv
  year: 2024
  doi: 10.26434/chemrxiv-2024-78mtl

GitHub Events

Total
  • Create event: 25
  • Issues event: 14
  • Release event: 9
  • Delete event: 14
  • Issue comment event: 8
  • Push event: 56
  • Pull request review event: 2
  • Pull request event: 34
Last Year
  • Create event: 25
  • Issues event: 14
  • Release event: 9
  • Delete event: 14
  • Issue comment event: 8
  • Push event: 56
  • Pull request review event: 2
  • Pull request event: 34

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 7
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 7
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 7 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mmzdouc (13)
  • Adafede (2)
Pull Request Authors
  • mmzdouc (22)
  • Adafede (7)
Top Labels
Issue Labels
development (5) enhancement (3)
Pull Request Labels
development (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 239 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 13
  • Total maintainers: 2
pypi.org: mite-extras

Parsing, conversion, and validation functionality for Minimum Information about a Tailoring Enzyme (MITE) files.

  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 239 Last month
Rankings
Dependent packages count: 10.2%
Average: 33.8%
Dependent repos count: 57.4%
Maintainers (2)
mmzdouc adafede
Last synced: 10 months ago

Dependencies

pyproject.toml pypi
  • argparse ~=1.4.0