Open dustine32 opened 1 year ago
@tmushayahama For the small_molecule_regulator rule we'll need to update the reactome parser to pass a list of controllers for each reaction. Here's an example rxn with multiple controllers in pathway R-HSA-204174:
This reaction ("PDK isoforms phosphorylate lipo-PDH" R-HSA-203946) has multiple entries in it's
pybiopax
object under controlled_of
:
Three of them represent the small molecule regulators that are circled at the top of the GO-CAM above. These use
Control
BioPAX classes. The enabled_by
entity of this reaction is in the Catalysis
BioPAX class. We should have the parser somehow pass these four controlled_of
entries to the GO-CAM data structure used by TransformationStrategy
, maybe just simply pass in all controlled_of
entries. For these entries, we need to retain the Control
and Catalysis
type info (since that's used to determine enabled_by
vs. is_small_mo_regulator
) as well as retain ControlType
.
Thanks @dustine32 this is clearer now. Lemme see the biopax. Where is the model R-HSA-204174 on noctua-dev
Model on noctua-dev: http://noctua-dev.berkeleybop.org/editor/graph/gomodel:R-HSA-204174
Write inference rules that transform BioPAX data into appropriate GO-CAM structure.
First task will be to add
infer_small_molecule_regulators
step.