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https://github.com/damourchris/metabolicqueries.jl

A Julia package for accessing data from metabolic databases.

https://github.com/damourchris/metabolicqueries.jl

Science Score: 26.0%

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    Found 10 DOI reference(s) in README
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    Low similarity (10.9%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

A Julia package for accessing data from metabolic databases.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed over 2 years ago
Metadata Files
Readme Contributing License

README.md

MetabolicQueries.jl

Project Status: WIP - This project is a work in progress. Docs-stable Docs-dev Github License
Satisfy you metabolic data and models needs in Julia.

Features

Installation

To use this package, add it to you environment:

julia using Pkg Pkg.add("https://github.com/damourChris/MetabolicQueries.jl") using MetabolicQueries

or via the REPL

julia (@v1.8) pkg> add https://github.com/damourChris/MetabolicQueries.jl julia> using MetabolicQueries

Databases

BiGG

BiGG-website BiGG-DOI

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more).

For details about updates to the BiGG Models website and database, see the updates page and the GitHub repository.

KEGG

KEGG-website KEGG-DOI
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.

MetabolicAtlas

metabolic_atlas-website metabolic_atlas-DOI

Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis. Their goal is to collect curated GEMs, and to bring these models closer to FAIR principles. The website provides visualisations and comparisons of the GEMs, and links to resources, algorithms, other databases, and more general software applications. Their vision is to create a one-stop-shop for everything metabolism related.

Documentation

Docs Docs

Documentation for the package is available here.

Contribution

If you want to help developing and maintaining this package, here a rough guideline:

  • Open up an issue:

    • if you encounter a bug while using this package
    • if you find a mismatch between the version of the database listed here and the one on the official page.

  • Pull request:

    • Adding a new feature set
    • Adding support for a new database
    • Documentation improvements

Acknowledgement

This package would not be possible without the support from the databases. If you end up using this package in your research, please make sure to properly cite all the resources that you have used!

License

This package is licensed under the MIT License.

Owner

  • Name: Christopher Damour
  • Login: damourChris
  • Kind: user
  • Location: Maastricht

My public student profile

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Dependencies

.github/workflows/docs-deployment.yml actions
  • actions/checkout v4 composite
  • actions/deploy-pages v4 composite
  • actions/upload-pages-artifact v3 composite
  • awalsh128/cache-apt-pkgs-action v1 composite
  • julia-actions/cache v1 composite
  • julia-actions/julia-runtest latest composite
  • julia-actions/setup-julia latest composite
.github/workflows/TagBot.yml actions
  • JuliaRegistries/TagBot v1 composite
.github/workflows/run-tests.yml actions
  • actions/checkout v4 composite
  • awalsh128/cache-apt-pkgs-action v1 composite
  • julia-actions/cache v1 composite
  • julia-actions/julia-runtest latest composite
  • julia-actions/setup-julia latest composite