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
This code can be installed with pip3 install git+https://github.com/bio2bel/wikipathways.git
Note that the Bio2BEL HGNC should be installed and loaded in order to map ENTREZ identifiers to HGNC Symbols and populate the database:
You can load Bio2BEL HGNC by running the following command in your terminal: python3 -m bio2bel_hgnc populate
Functionalities and Commands
Following, the main functionalities and commands to work with this package:
Populate local database with WikiPathways info
python3 -m bio2bel_wikipathways populateRun 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
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Source Distribution
Hashes for bio2bel_wikipathways-0.0.2.tar.gz
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| MD5 | f9eb721679cc823d8170040139d7f246 |
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| BLAKE2b-256 | 4acaa450a8a21be96b081f94f82fa12654f1dde157db6edcd97a8e3efe8b4f42 |
