WikiPathways Pathway Validation Reports

The WikiPathways Pathway validations report are found in this repository. We currently have the following indexes:

• Validation tests that fail for one or more pathways

Report generation

Some scripts to create a list of pathways.

Depedencies

The following tools are needed:

• make
• curl
• jq

Setting up BridgeDb

Create a folder /tmp/OPSBRIDGEDB where you create a config.properties file. To download the BridgeDb identifier mapping files, download them from here and save them in the /path/to/where/the/bridge/files/are folder, mathching what you entered in the config.properties file above with the bridgefiles= parameter. You also want to download the identifier mapping database for coronavirus genes and proteins.

How to run

make updateGPMLS
make -B pathways.txt
nice -20 make -j 4 rdf check