search

UCDenver-ccp / Cartoomics

0 stars 0 forks source link

78 use wikipathways node metadata #80

Closed bsantan closed 8 months ago

bsantan commented 8 months ago

Add support for:

  1. Using wiki pathways node metadata file for node ID matching
  2. Using node normalizer API for id mapping
lagillenwater commented 8 months ago

Ignore the last comment, I was using creating_subgraph_from_KG not wikipathways_creating_subgraph_from_KG.py

lagillenwater commented 8 months ago

Ok, I am getting a new error now with the proper script call (I think): image

lagillenwater commented 8 months ago

Sometimes I get this error:

image

I think this stems from the database being 'WikiPathways', as seen with MAPK

image

lagillenwater commented 8 months ago

Could Wikipathways be added to constants? PKL doesn't use wikipathways, does it?

bsantan commented 8 months ago

I would skip that one, updating to skip Unknown or Wikipathways. I don't think this exists in node normalizer and it feels circular to index to another WP?

lagillenwater commented 8 months ago

I think if it's not in the metadata file, we should then try to index it in the KG based on label. This may be how you're doing it already? The example here is MAPK signaling, which I think would have an analog in PKL.