https://github.com/bio2bel/reactome
Integration of pathway-related information from Reactome in BEL
https://github.com/bio2bel/reactome
biological-expression-language networks-biology pathways reactome system-biology
Last synced: 4 months ago
JSON representation
Integration of pathway-related information from Reactome in BEL
- Host: GitHub
- URL: https://github.com/bio2bel/reactome
- Owner: bio2bel
- License: mit
- Created: 2017-09-11T13:19:33.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2020-11-18T17:13:55.000Z (over 5 years ago)
- Last Synced: 2026-01-03T13:43:56.625Z (5 months ago)
- Topics: biological-expression-language, networks-biology, pathways, reactome, system-biology
- Language: Python
- Homepage: http://bio2bel-reactome.rtfd.io
- Size: 1.21 MB
- Stars: 5
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
Bio2BEL Reactome |build| |coverage| |documentation| |zenodo|
============================================================
This package handles the nomenclature and membership of chemicals/proteins in Reactome pathways.
It is integrated with the `ComPath environment `_ for pathway database
comparison.
If you find this package useful, please consider citing [domingofernandez2018]_:
.. [domingofernandez2018] Domingo-Fernandez, D., *et al* (2018). `ComPath: an ecosystem for exploring, analyzing,
and curating mappings across pathway databases `_.
*Npj Systems Biology and Applications*, __5__(1), 3.
**Warning** This package creates ``partOf`` relationships in BEL, but does not convert Reactome mechanistic
relationships to BEL. That functionality is implemented in the
`PathMe project `_.
Installation |pypi_version| |python_versions| |pypi_license|
------------------------------------------------------------
``bio2bel_reactome`` can be installed easily from `PyPI `_ with the
following code in your favorite terminal:
.. code-block:: sh
$ pip install bio2bel_reactome
or from the latest code on `GitHub `_ in development mode with:
.. code-block:: sh
$ git clone https://github.com/bio2bel/reactome.git
$ cd reactome
$ pip install -e .
Setup
-----
Reactome can be downloaded and populated from either the Python REPL or the automatically installed command line
utility.
Python REPL
~~~~~~~~~~~
.. code-block:: python
>>> import bio2bel_reactome
>>> reactome_manager = bio2bel_reactome.Manager()
>>> reactome_manager.populate()
Command Line Utility
~~~~~~~~~~~~~~~~~~~~
.. code-block:: bash
bio2bel_reactome populate
Other Command Line Utilities
----------------------------
- Run an admin site for simple querying and exploration :code:`bio2bel_reactome web` (http://localhost:5000/admin/)
- Export gene sets for programmatic use :code:`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.
.. |build| image:: https://travis-ci.com/bio2bel/reactome.svg?branch=master
:target: https://travis-ci.com/bio2bel/reactome
:alt: Build Status
.. |coverage| image:: https://codecov.io/gh/bio2bel/reactome/coverage.svg?branch=master
:target: https://codecov.io/gh/bio2bel/reactome?branch=master
:alt: Coverage Status
.. |documentation| image:: http://readthedocs.org/projects/bio2bel-interpro/badge/?version=latest
:target: http://bio2bel.readthedocs.io/projects/reactome/en/latest/?badge=latest
:alt: Documentation Status
.. |climate| image:: https://codeclimate.com/github/bio2bel/reactome/badges/gpa.svg
:target: https://codeclimate.com/github/bio2bel/reactome
:alt: Code Climate
.. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_reactome.svg
:alt: Stable Supported Python Versions
.. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_reactome.svg
:alt: Current version on PyPI
.. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_reactome.svg
:alt: MIT License
.. |zenodo| image:: https://zenodo.org/badge/103138323.svg
:target: https://zenodo.org/badge/latestdoi/103138323