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MSMetaEnhancer

MSMetaEnhancer: A Python package for mass spectra metadata annotation - Published in JOSS (2022)

https://github.com/recetox/msmetaenhancer

Science Score: 95.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov, joss.theoj.org
  • ✓
    Committers with academic emails
    1 of 8 committers (12.5%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

annotations hacktoberfest mass-spectrometry python usegalaxy

Keywords from Contributors

gass-chromatography fuzzy-matching fuzzy-search metabolomics similarity-measures

Scientific Fields

Mathematics Computer Science - 84% confidence
Chemistry Physical Sciences - 83% confidence
Last synced: 4 months ago · JSON representation

Repository

Tool for mass spectra metadata annotation.

Basic Info
Statistics
  • Stars: 8
  • Watchers: 6
  • Forks: 10
  • Open Issues: 7
  • Releases: 13
Topics
annotations hacktoberfest mass-spectrometry python usegalaxy
Created over 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License

README.md

MSMetaEnhancer

install with bioconda docs Conda PyPI - Python Version DOI

MSMetaEnhancer is a tool used for .msp files annotation. It adds metadata like SMILES, InChI, and CAS number fetched from the following services: CIR, CTS, PubChem, IDSM, and BridgeDb. The app uses asynchronous implementation of annotation process allowing for optimal fetching speed.

If you use MSMetaEnhancer in your work, please cite the following publication:

Troják et al., (2022). MSMetaEnhancer: A Python package for mass spectra metadata annotation. Journal of Open Source Software, 7(79), 4494, https://doi.org/10.21105/joss.04494

Usage

```python import asyncio

from MSMetaEnhancer import Application

app = Application()

import your .msp file

app.loadspectra('tests/testdata/sample.msp', file_format='msp')

curate given metadata (e.g. fix CAS numbers)

app.curate_metadata()

specify requested services (these are supported)

services = ['CTS', 'CIR', 'IDSM', 'PubChem', 'BridgeDb', 'RDKit']

specify requested jobs

jobs = [('name', 'inchi', 'IDSM'), ('inchi', 'formula', 'IDSM'), ('inchi', 'inchikey', 'IDSM'), ('inchi', 'iupacname', 'IDSM'), ('inchi', 'canonicalsmiles', 'IDSM')]

run asynchronous annotations of spectra data

asyncio.run(app.annotate_spectra(services, jobs))

export .msp file

app.savespectra('tests/testdata/sampleout.msp', fileformat='msp') ```

Installation

Prerequisites:

  • Python 3.9+
  • Anaconda

Install MSMetaEnhancer from Bioconda with:

```

install MSMetaEnhancer in a new virtual environment to avoid dependency clashes

conda create --name MSMetaEnhancer python=3.9 conda activate MSMetaEnhancer conda install --channel bioconda --channel conda-forge MSMetaEnhancer ```

Developer Documentation

Setup

Create your development environment using the provided script via conda to install all required dependencies.

Contributing

We appreciate contributions - feel free to open an issue on our repository, create your own fork, work on the problem and post a PR. Please add your contributions to the changelog and to adhere to the versioning. For more information see here.

Testing

All functionality is tested with the pytest framework.

Owner

  • Name: RECETOX
  • Login: RECETOX
  • Kind: organization
  • Location: Brno, Czechia

At RECETOX we are engaged in research and education in the management of environmental and health risks associated with the chemicals around us.

JOSS Publication

MSMetaEnhancer: A Python package for mass spectra metadata annotation
Published
November 02, 2022
DOI
Volume 7, Issue 79, Page 4494
Authors
Matej Troják ORCID
RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
Helge Hecht ORCID
RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
Martin Čech ORCID
RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
Elliott James Price ORCID
RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic
Editor
Charlotte Soneson ORCID
Tags
mass spectra annotation
View PDF Review Thread Software Archive

GitHub Events

Total
  • Create event: 2
  • Release event: 1
  • Issues event: 7
  • Issue comment event: 1
  • Member event: 4
  • Push event: 2
  • Pull request event: 3
  • Pull request review event: 11
  • Pull request review comment event: 5
  • Fork event: 2
Last Year
  • Create event: 2
  • Release event: 1
  • Issues event: 7
  • Issue comment event: 1
  • Member event: 4
  • Push event: 2
  • Pull request event: 3
  • Pull request review event: 11
  • Pull request review comment event: 5
  • Fork event: 2

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 421
  • Total Committers: 8
  • Avg Commits per committer: 52.625
  • Development Distribution Score (DDS): 0.295
Past Year
  • Commits: 10
  • Committers: 2
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.1
Top Committers
Name Email Commits
Matej Trojak t****k@m****z 297
hechth h****t@r****z 83
maximskorik m****k@g****m 21
acquayefrank a****k@g****m 9
Martin Cech m****n@b****u 8
Egon Willighagen e****n@g****m 1
Charlotte Soneson c****n@g****m 1
Jakub Galgonek j****k@u****z 1
Committer Domains (Top 20 + Academic)
uochb.cas.cz: 1 bx.psu.edu: 1 recetox.muni.cz: 1 mail.muni.cz: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 58
  • Total pull requests: 56
  • Average time to close issues: 2 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 7
  • Total pull request authors: 8
  • Average comments per issue: 0.97
  • Average comments per pull request: 0.63
  • Merged pull requests: 55
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 3
  • Average time to close issues: 22 days
  • Average time to close pull requests: 13 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • hechth (30)
  • xtrojak (18)
  • martenson (3)
  • marshallmcdonnell (3)
  • chryswoods (2)
  • egonw (1)
  • acquayefrank (1)
Pull Request Authors
  • xtrojak (33)
  • hechth (10)
  • maximskorik (5)
  • martenson (3)
  • acquayefrank (3)
  • galgonek (2)
  • egonw (1)
  • csoneson (1)
Top Labels
Issue Labels
bug (4) wontfix (1) documentation (1) enhancement (1)
Pull Request Labels
bug (2) documentation (1)

Dependencies

pyproject.toml pypi
  • flake8 ^7.0.0 develop
  • mock ^5.1.0 develop
  • myst-parser ^2.0.0 develop
  • pytest ^8.0.2 develop
  • pytest-aiohttp ^1.0.5 develop
  • pytest-cov ^4.1.0 develop
  • pytest-dependency ^0.6.0 develop
  • readthedocs-sphinx-ext ^2.2.5 docs
  • sphinx ^7.2.6 docs
  • sphinx-rtd-theme ^2.0.0 docs
  • aiocircuitbreaker ^2.0.0
  • aiohttp ^3.9.3
  • asyncstdlib ^3.12.0
  • frozendict ^2.4.0
  • matchms ^0.14
  • multidict ^6.0.5
  • openpyxl ^3.1.2
  • pandas ^2.2.1
  • python >=3.9,<3.13
  • rdkit ^2023.9.5
  • requests ^2.31.0
  • scipy ^1.12.0
  • tabulate ^0.9.0
  • twine ^5.0.0
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  • github/codeql-action/analyze v2 composite
  • github/codeql-action/init v2 composite
.github/workflows/project_automation.yml actions
.github/workflows/publish_pypi.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
  • pypa/gh-action-pypi-publish release/v1.5 composite
.github/workflows/test-package.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite