This week we decided to work on testing the GPML uploader feature of GraphSpace.
For this we downloaded all the pathways from the WikiPathways website and uploaded them to GraphSpace using the REST API. The script to do this can be found here. https://gist.github.com/MridulS/2a406ed5c2a465531b5e924af41e3eca
The preliminary results suggest that a total of 970 pathways were able to pass the API call out of 2857. The ones which weren’t able to pass had properties like ‘mitochondria’ for shape and some interactions missed the GraphId, which should be present according to the schema (that’s why the assumption that GraphId is required for all interactions) The uploader will be updated to throw an error in these cases.
Out of the 970 that passed the API call 518 were successfully uploaded on the GraphSpace website and and 452 failed the tests for presence of GraphRefs for interaction. The output can be seen here. https://gist.github.com/MridulS/bbdf0de7b6cec55d00e509e688f40075 it is a dictionary with the API return message keyed by the Pathway ID.
The uploader will be improved further on the results of this test.
This activity helped us discover things like different shapes that wasn’t possible to catch manually.