Skip to main content

Bio2BEL Reactome Build Status Coverage Status Documentation Status zenodo

This package allows the enrichment of BEL networks with Reactome information by wrapping its RESTful API. Furthermore, it is integrated in the ComPath environment for pathway database comparison.

Installation

This code can be installed with pip3 install git+https://github.com/bio2bel/reactome.git

These two resources will be installed together with this package and can be quickly loaded by running the following commands in your terminal:

  • python3 -m bio2bel_hgnc populate

  • python3 -m bio2bel_chebi populate

Installation Current version on PyPI Stable Supported Python Versions MIT License

bio2bel_reactome can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install bio2bel_reactome

or from the latest code on GitHub with:

$ python3 -m pip install git+https://github.com/bio2bel/reactome.git@master

Setup

Reactome can be downloaded and populated from either the Python REPL or the automatically installed command line utility.

The following resources will be automatically installed and loaded in order to fully populate the tables of the database:

Python REPL

>>> import bio2bel_reactome
>>> reactome_manager = bio2bel_reactome.Manager()
>>> reactome_manager.populate()

Command Line Utility

bio2bel_reactome populate

Other Command Line Utilities

  • Run an admin site for simple querying and exploration python3 -m bio2bel_reactome web (http://localhost:5000/admin/)

  • Export gene sets for programmatic use python3 -m bio2bel_reactome export

Citation

  • Fabregat, Antonio et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 44.Database issue (2016): D481–D487. PMC. Web. 6 Oct. 2017.

  • Croft, David et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research 42.Database issue (2014): D472–D477. PMC. Web. 6 Oct. 2017.

Metadata

Release files for bio2bel-reactome 0.2.3

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for bio2bel-reactome 0.2.3
File Size Uploaded Provenance
bio2bel_reactome-0.2.3.tar.gz 34.4 kB Without provenance Details

Release files / bio2bel_reactome-0.2.3.tar.gz

Download URL bio2bel_reactome-0.2.3.tar.gz
Size 34.4 kB
Tags Source
SHA-256 checksum
How to use checksums
eea5822b6bae1b0712ef7d742b1cc7800cfecd7a4398261e08c3067c5205aaae
BLAKE2b-256 checksum
How to use checksums
e06f51a767f5cad75858ac8e19eec476ae7a1aafe917442db8ddf3a8058c7b36
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing?
No
Uploaded via twine/1.11.0 pkginfo/1.4.2 requests/2.19.1 setuptools/39.0.1 requests-toolbelt/0.8.0 tqdm/4.23.0 CPython/3.6.5

Security for bio2bel-reactome 0.2.3

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

No provenance found

None of the files in this release were uploaded with provenance metadata.

A note on package security

PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.

To learn more about protecting yourself from malicious actors, visit our package security documentation.

Anthropic, PBC Visionary sponsor Bloomberg Visionary sponsor Hudson River Trading Visionary sponsor Meta Visionary sponsor NVIDIA Visionary sponsor Microsoft Sustainability sponsor Depot Continuous Integration AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page