A wrapper around Reactome RESTful API

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for cthoyt from gravatar.com cthoyt Avatar for ddomingof from gravatar.com ddomingof

Unverified details

These details have not been verified by PyPI
Project links
Meta

Project description

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.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for cthoyt from gravatar.com cthoyt Avatar for ddomingof from gravatar.com ddomingof

Unverified details

These details have not been verified by PyPI
Project links
Meta

Release history Release notifications | RSS feed

0.2.3

0.2.2

0.2.0

0.1.5

0.1.4

0.1.3

0.1.2

0.1.1

This version

0.1.0

0.0.12

0.0.11

0.0.10

0.0.9

0.0.9.dev0 pre-release

0.0.8

0.0.8.dev0 pre-release

0.0.7

0.0.7.dev0 pre-release

0.0.6

0.0.5

0.0.4

0.0.3

0.0.2

0.0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bio2bel_reactome-0.1.0.tar.gz (32.7 kB view hashes)

Uploaded Source

Built Distribution

bio2bel_reactome-0.1.0-py3-none-any.whl (16.2 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page