https://github.com/bio2bel/wikipathways
Integration of pathway-related information from WikiPathways in BEL
https://github.com/bio2bel/wikipathways
biological-expression-language pathways systems-biology wikipathways
Last synced: 4 months ago
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Integration of pathway-related information from WikiPathways in BEL
- Host: GitHub
- URL: https://github.com/bio2bel/wikipathways
- Owner: bio2bel
- License: mit
- Created: 2018-01-25T14:36:17.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2020-11-18T16:47:50.000Z (over 5 years ago)
- Last Synced: 2026-01-03T13:44:07.275Z (5 months ago)
- Topics: biological-expression-language, pathways, systems-biology, wikipathways
- Language: Python
- Homepage: http://bio2bel-wikipathways.rtfd.io
- Size: 126 KB
- Stars: 3
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
Bio2BEL WikiPathways |build| |coverage| |documentation| |zenodo|
================================================================
This package allows the enrichment of BEL networks with WikiPathways information by wrapping its RESTful API.
Furthermore, it is integrated in 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 WikiPathways mechanistic
relationships to BEL. That functionality is implemented in the
`PathMe project `_.
Installation |pypi_version| |python_versions| |pypi_license|
------------------------------------------------------------
``bio2bel_wikipathways`` can be installed easily from `PyPI `_ with
the following code in your favorite terminal:
.. code-block:: sh
$ pip install bio2bel_wikipathways
or from the latest code on `GitHub `_ in development mode with:
.. code-block:: sh
$ git clone https://github.com/bio2bel/wikipathways.git
$ cd wikipathways
$ pip install -e .
Setup
-----
WikiPathways can be downloaded and populated from either the Python REPL or the automatically installed command line
utility.
Python REPL
~~~~~~~~~~~
.. code-block:: python
>>> import bio2bel_wikipathways
>>> wikipathways_manager = bio2bel_wikipathways.Manager()
>>> wikipathways_manager.populate()
Command Line Utility
~~~~~~~~~~~~~~~~~~~~
.. code-block:: bash
bio2bel_wikipathways populate
Other Command Line Utilities
----------------------------
- Run an admin site for simple querying and exploration :code:`bio2bel_wikipathways web` (http://localhost:5000/admin/)
- Export gene sets for programmatic use :code:`bio2bel_wikipathways export`
Citation
--------
- Slenter, D.N., et al WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research
Nucleic Acids Research, (2017) doi.org/10.1093/nar/gkx1064
- Kutmon, M., et al. WikiPathways: capturing the full diversity of pathway knowledge Nucl. Acids Res., 44, D488-D494
(2016) doi:10.1093/nar/gkv1024
- Kelder, T., et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012
Jan;40(Database issue):D1301-7
.. |build| image:: https://travis-ci.org/bio2bel/wikipathways.svg?branch=master
:target: https://travis-ci.org/bio2bel/wikipathways
:alt: Build Status
.. |coverage| image:: https://codecov.io/gh/bio2bel/wikipathways/coverage.svg?branch=master
:target: https://codecov.io/gh/bio2bel/wikipathways?branch=master
:alt: Coverage Status
.. |documentation| image:: http://readthedocs.org/projects/bio2bel-interpro/badge/?version=latest
:target: http://bio2bel.readthedocs.io/projects/wikipathways/en/latest/?badge=latest
:alt: Documentation Status
.. |climate| image:: https://codeclimate.com/github/bio2bel/wikipathways/badges/gpa.svg
:target: https://codeclimate.com/github/bio2bel/wikipathways
:alt: Code Climate
.. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_wikipathways.svg
:alt: Stable Supported Python Versions
.. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_wikipathways.svg
:alt: Current version on PyPI
.. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_wikipathways.svg
:alt: MIT License
.. |zenodo| image:: https://zenodo.org/badge/118924155.svg
:target: https://zenodo.org/badge/latestdoi/118924155