mite-schema

A repository containing the MITE JSON schema and auxiliary files

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

Science Score: 67.0%

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

  • CITATION.cff file
    Found CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
    Found .zenodo.json file
  • DOI references
    Found 1 DOI reference(s) in README
  • Academic publication links
    Links to: zenodo.org
  • Academic email domains
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A repository containing the MITE JSON schema and auxiliary files

Basic Info
  • Host: GitHub
  • Owner: mite-standard
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 65.4 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 13
Created over 1 year ago · Last pushed 9 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

mite_schema

DOI PyPI version

This repository contains the schema of the MITE data standard.

Furthermore, this repository provides functionality to validate files against said schema. It can be used as command line interface or as library. For command line use, see the installation instructions below.

For more information, see the MITE Data Standard Organization page.

Installation

  • pip install mite_schema

Quick Start

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

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

For developers

  • Install hatch using one of the methods described here
  • Download or clone this repository
  • Run hatch -v env create dev. This will download and install the appropriate Python version and any required packages
  • Run hatch run dev:pre-commit install. This will set up pre-commit
  • If necessary, remove the environment 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_schema
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 Zurich, Zurich, Switzerland'
    family-names: Rutz
    given-names: Adriano
    orcid: 'https://orcid.org/0000-0003-0443-9902'
repository-code: 'https://github.com/mite-standard/mite_schema'
abstract: >-
    A repository containing the MITE JSON schema and auxiliary files .
keywords:
  - python
  - tailoring enzymes
  - data standard
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: 13
  • Release event: 7
  • Issues event: 5
  • Delete event: 8
  • Issue comment event: 2
  • Member event: 1
  • Push event: 23
  • Pull request event: 18
Last Year
  • Create event: 13
  • Release event: 7
  • Issues event: 5
  • Delete event: 8
  • Issue comment event: 2
  • Member event: 1
  • Push event: 23
  • Pull request event: 18

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: about 18 hours
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.6
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 5
  • Average time to close issues: N/A
  • Average time to close pull requests: about 18 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.6
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Top Authors
Issue Authors
  • mmzdouc (5)
Pull Request Authors
  • mmzdouc (14)
  • Adafede (1)
Top Labels
Issue Labels
documentation (1) enhancement (1)
Pull Request Labels
enhancement (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 174 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 13
  • Total maintainers: 1
pypi.org: mite-schema

Containing the Minimum Information about a Tailoring Enzymes data standard schema and auxiliary methods

  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 174 Last month
Rankings
Dependent packages count: 10.5%
Average: 34.9%
Dependent repos count: 59.3%
Maintainers (1)
Last synced: 7 months ago

Dependencies

pyproject.toml pypi
  • argparse ~=1.4
  • coloredlogs ~=15.0
  • jsonschema ~=4.23
  • pydantic ~=2.8
  • referencing ~=0.35
  • requests ~=2.32
.github/workflows/ci.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v4 composite
.github/workflows/publish_pypi.yml actions
  • actions/checkout v4 composite
  • actions/download-artifact v4 composite
  • actions/setup-python v5 composite
  • actions/upload-artifact v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite