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mite_data

Repository containing entries following the MITE data standard

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

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 (9.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Repository containing entries following the MITE data standard

Basic Info
  • Host: GitHub
  • Owner: mite-standard
  • License: cc0-1.0
  • Language: Python
  • Default Branch: main
  • Size: 37.4 MB
Statistics
  • Stars: 2
  • Watchers: 3
  • Forks: 0
  • Open Issues: 2
  • Releases: 16
Created over 1 year ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

Overview

DOI

This repository contains the "ground truth" dataset of the Minimum Information about a Tailoring Enzyme (MITE) data repository (mite_data/data).

Furthermore, the repository contains auxiliary files and scripts to automatically update them:

  • Metadata files summarizing information of all MITE entries in a single file (mite_data/metadata)
  • Protein FASTA-files for all active (i.e. non-retired) MITE entries (mite_data/fasta)

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

For developers

Nota bene: This installation will only work on (Ubuntu) Linux and assumes a Python installation.

commandline pip install hatch hatch env create hatch run pre-commit install hatch run pytest

Adding/modifying entries

  • (Create a new branch)
  • Update version in pyproject.toml, add changelog to CHANGELOG.md
  • Reinstall the package to update version metadata: hatch env remove && hatch env create
  • Add new/modify existing entries (N.B. for new entries, change accession and status)
  • Pre-commit will automatically validate and update metadata files upon committing
  • If pre-commit was not installed, these steps need to be performed manually:

commandline hatch run python ./mite_data/main.py hatch run python .github/mite_validation.py

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_data
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_data'
abstract: >-
   Repository containing entries following the MITE data standard.
keywords:
  - python
  - tailoring enzymes
  - data standard
license: CC0-1.0
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: 39
  • Issues event: 107
  • Release event: 14
  • Watch event: 1
  • Delete event: 25
  • Member event: 13
  • Issue comment event: 122
  • Push event: 156
  • Gollum event: 13
  • Pull request review event: 3
  • Pull request event: 48
Last Year
  • Create event: 39
  • Issues event: 107
  • Release event: 14
  • Watch event: 1
  • Delete event: 25
  • Member event: 13
  • Issue comment event: 122
  • Push event: 156
  • Gollum event: 13
  • Pull request review event: 3
  • Pull request event: 48

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 29
  • Total pull requests: 22
  • Average time to close issues: 22 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.32
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 29
  • Pull requests: 22
  • Average time to close issues: 22 days
  • Average time to close pull requests: 6 days
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.32
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mite-bot (44)
  • mmzdouc (13)
  • cthoyt (1)
Pull Request Authors
  • mmzdouc (19)
  • mite-bot (16)
  • Adafede (8)
Top Labels
Issue Labels
reviewed (15) development (3) enhancement (2) added to repository (1) documentation (1)
Pull Request Labels
reviewed (5) development (1)

Dependencies

pyproject.toml pypi
  • AlphaFetcher ~=0.2
.github/workflows/ci.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v4 composite