Pathway Importer

This is a Python package that converts pathways from KEGG and WikiPathways into JSON format. These files can then be used with biowc-pathwaygraph.

Installation

• Clone this repository:

git clone https://github.com/jmueller95/pathway-importer.git
cd pathway-importer

• Install and activate the conda environment:

a) On Windows:

conda env create -f ./environment_windows.yml

b) On Unix:

conda env create -f ./environment_unix.yml

Then

conda activate pathway_importer

(or install the dependencies yourself)

Usage

• Run the main script as follows:

cd pathway_database_importer
python main.py --download

This will create a folder raw next to pathway_database_importer and download the latest versions of all pathway diagrams from KEGG and WikiPathways. The raw pathways are in KGML (KEGG) and GPML (WikiPathways) format. Pathway Importer downloads automatically downloads diagrams of ten organisms:

• Homo sapiens (hsa)
• Escherichia coli (eco)
• Saccharomyces cerevisiae (sce)
• Caenorhabditis elegans (cel)
• Drosophila melanogaster (dme)
• Arabidopsis thaliana (ath)
• Danio rerio (dre)
• Mus musculus (mmu)
• Mycobacterium tuberculosis (mtu)
• Oryza sativa (osa)

If you don't want to download all of them, delete the respective line from constants.py.

Pathway Importer then converts the pathways in the raw directory into JSON and stores the output in a folder json.
If you have already obtained the raw pathway diagrams before and don't want to run the download, omit the --download parameter.