Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/damourchris/metabolicqueries.jl
A Julia package for accessing data from metabolic databases.
https://github.com/damourchris/metabolicqueries.jl
Last synced: 5 days ago
JSON representation
A Julia package for accessing data from metabolic databases.
- Host: GitHub
- URL: https://github.com/damourchris/metabolicqueries.jl
- Owner: damourChris
- License: mit
- Created: 2024-02-11T15:42:40.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2024-02-20T17:19:37.000Z (10 months ago)
- Last Synced: 2024-11-05T13:26:53.738Z (about 2 months ago)
- Language: Julia
- Homepage: https://damourchris.github.io/MetabolicQueries.jl/
- Size: 874 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
MetabolicQueries.jl
Satisfy you metabolic data and models needs in Julia.
---
Features
- Querying, downloading, and working with data and models from databases such as [BiGG](http://bigg.ucsd.edu/), [KEGG](https://www.kegg.jp/) or the [MetabolicAtlas](https://metabolicatlas.org/).
- Integrated with metabolic packages in the julia ecosystem such as [COBREXA.jl](https://github.com/LCSB-BioCore/COBREXA.jl), [SBMLToolkit.jl](https://docs.sciml.ai/SBMLToolkit/stable/),[SMBL.jl](https://github.com/LCSB-BioCore/SBML.jl),[Catalyst.jl](https://docs.sciml.ai//stable/) and [ReactionNetworkImporters.jl](https://docs.sciml.ai/ReactionNetworkImporters/stable/)
---
- [Installation](#installation)
- [Databases](#databases)
- [BiGG](#bigg)
- [KEGG](#kegg)
- [MetabolicAtlas](#metabolicatlas)
- [Documentation](#documentation)
- [Contribution](#contribution)
- [Acknowledgement](#acknowledgement)
- [License](#license)
## 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 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](http://bigg.ucsd.edu/updates) and the [GitHub repository](https://github.com/SBRG/bigg_models/releases).
### KEGG
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 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
Documentation for the package is available [here](https://damourChris.github.io/MetabolicQueries.jl).
## 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](https://github.com/damourChris/MetabolicQueries.jl/blob/main/LICENSE).