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.