A package for converting Wikipathways to BEL
Project description
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.
Installation 
bio2bel_wikipathways can be installed easily from PyPI with the following code in your favorite terminal:
$ python3 -m pip install bio2bel_wikipathwaysor from the latest code on GitHub with:
$ python3 -m pip install git+https://github.com/bio2bel/wikipathways.git@masterSetup
WikiPathways 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_wikipathways
>>> wikipathways_manager = bio2bel_wikipathways.Manager()
>>> wikipathways_manager.populate()Command Line Utility
bio2bel_wikipathways populateOther Command Line Utilities
Run an admin site for simple querying and exploration
python3 -m bio2bel_wikipathways web(http://localhost:5000/admin/)Export gene sets for programmatic use
python3 -m 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
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file bio2bel_wikipathways-0.1.2.dev0.tar.gz.
File metadata
- Download URL: bio2bel_wikipathways-0.1.2.dev0.tar.gz
- Upload date:
- Size: 25.4 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/1.11.0 pkginfo/1.4.2 requests/2.19.1 setuptools/40.0.0 requests-toolbelt/0.8.0 tqdm/4.24.0 CPython/3.7.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | f50b55cfd2a731203a951d9ce22181a37f563e5c3f9d4f7c8abc8699dbaa287d |
|
| MD5 | 91aeccfcb2d73938741a4dca730ca36c |
|
| BLAKE2b-256 | 1acf5d92b388679163b58bdb29e0bed4aa47b0b20aae0abd260c6f8162b6f40f |
Provenance
File details
Details for the file bio2bel_wikipathways-0.1.2.dev0-py3-none-any.whl.
File metadata
- Download URL: bio2bel_wikipathways-0.1.2.dev0-py3-none-any.whl
- Upload date:
- Size: 12.2 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/1.11.0 pkginfo/1.4.2 requests/2.19.1 setuptools/40.0.0 requests-toolbelt/0.8.0 tqdm/4.24.0 CPython/3.7.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | e2d546972c3e704ffcb0876056cbc05b25bedf6743c63b0733de44c11687ac0e |
|
| MD5 | 6f8ee818da05423262425cead61f623a |
|
| BLAKE2b-256 | 86fd4f2996328abc8281ce15bf5bc508477a6bff0c672fd58b4c223f073952b8 |
