The goal of this package is to facilitate the evaluation of pathway knowledge across three of the major pathway databases by harmozing and consolidating different formats.
PathMe does that by converting KEGG, Reactome, and WikiPathways to Biological Expression Language (BEL). Once the three databases are harmonized into BEL, we can evaluate the consensus and gaps in pathway knowledge. For that, PathMe is complemented with a web application (PathMe Viewer) that enables the exploration of all the pathways from these three resources. PathMe is the follow-up of the ComPath web application which is aimed at exploring, analyzing, and curating pathway knowledge in a more simplistic, gene-centric view.
pathmecan be installed with the following commmands:
python3 -m pip install git+https://github.com/ComPath/PathMe.git@master
or in editable mode with:
git clone https://github.com/ComPath/PathMe.git
python3 -m pip install -e .
How to use¶
PathMe first requires to download the raw files from the original pathway databases.
python3 -m pathme download
Generate BEL Graphs
python3 -m pathme populate
Alternatively, you can do any of these two steps for a particular database by the following command:
python3 -m pathme database_name action
python3 -m pathme kegg download