WikiPathways Curation Template

Template repository to set up pathway curation for the subset of WikiPathways, as specified in the pathways.txt file. Second, update the website.txt file (create if needed) to contain the link where the reports (particularly the JSON) files are published.

Step 1. Requirements

You need the following programs and experience with a Makefile:

• curl
• git
• zip
• java
• javac
• bash

You also need four Java archives in the libs/ folder that you can download (and update) with:

make install

Step 2: Update the GPML files

First, make sure the pathways.txt files is updated to list the pathways you want to curate.

Then, do:

make fetch

Step 3: Make sure to have the BridgeDb ID mapping databases

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.

Step 4: Create the RDF (Turtle)

make

Make sure that the GPML and the .rev files are under version control to track the history of the pathway.

Step 5: Run the validation tests

make check

The tests.txt file contains the list of tests that are run. By default it runs all tests, identified with the all methods, from the generic tests and community-specific tests are commented out (by starting the line with an #). By commenting out the the all lines, you can uncomment specific tests in that class.

Step 6: (optional) Publish everything online

For this, enable GitHub Pages and add the files in reports/ to the revision control, including the index.md in the root folder.