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A wraper around the KEGG RESTful API

Project description

This package allows the enrichment of BEL networks with KEGG 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/kegg.git

Functionalities and Commands

Following, the main functionalities and commands to work with this package:

  • Populate local database with KEGG info python3 -m bio2bel_kegg populate
  • Run an admin site for simple querying and exploration python3 -m bio2bel_kegg web (http://localhost:5000/admin/)
  • Export gene sets for programmatic use python3 -m bio2bel_kegg export

Citation

  • Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361 (2017).
  • Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
  • Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

Project details


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