Comments (4)
To get this converted to GO-CAM, you can try modifying your rule to link the activity that creates the physical entity, rather than the entity itself. So in your example, if physical_entity is an output of reaction_A, then reaction_A directly_negatively_regulates reaction.
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The 'physical entity' involved in regulation of 'function' relations are correct but the UI reverses them in the folded view - see geneontology/noctua#582
These reflect physical controllers from, e.g. Reactome, that are not catalysts but exert some other form of regulatory control.
Leaving this issue open to explore the modification above to produce function regulates function assertions.
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Forgot, this rule is actually already in place. See rule slides 14 and 15 in https://docs.google.com/presentation/d/1_UAQN09WPCA5win5mbMs1ORMALNwiRwMBgZDPuyJEW8/edit?slide=id.g355425beec_0_3#slide=id.g360932a148_0_36
You can see in the reaction linked above that "Beta-catenin is released from the destruction complex" is positively regulated by 'Phosphorylation of LRP5/6 cytoplasmic domain by CSNKI'�
from pathways2go.
This looks like a legacy problem that Reactome has now fixed. It used to be legal to annotate regulation of an entity. We decided that wasn't useful, removed all such annotations, and changed the curation process so no more can be made. However, depending when the BioPax used here was generated, it might have included some old regulation_of_entity instances.
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Related Issues (20)
- Convert chemicals to ChEBI rather than Reacto HOT 7
- Aspartate and asparagine metabolism (R-HSA-8963693)
- Something is weird about the import of Regulation of glycolysis by fructose 2,6-bisphosphate metabolism - imported from: Reactome HOT 4
- Regulation of glycolysis by fructose 2,6-bisphosphate metabolism (R-HSA-9634600)
- Deprecated or suboptimal UniProtKB accessions referenced in Reactome HOT 7
- Same entity?
- Representation questions (more to add later; didn't want to lose the notes)
- Reaction intermediates: out of scope? HOT 1
- Regulation of ChREBP (MLXIPL) ( R-HSA-163765, R-HSA-163680, R-HSA-163358, R-HSA-163767) HOT 1
- Triglyceride biosynthesis (R-HSA-75109) HOT 1
- Reactome proteoforms that point to deleted UniProt entries HOT 4
- Report for missing ChEBI IDs in release 83 work HOT 9
- Orphan gene products are showing up in pathways HOT 2
- Add starting locations for transported molecules HOT 1
- Analysis of missing ChEBI identifiers
- Cleanup of an ChEBI non pH7.3 chemicals
- fix errors in fructose metabolism R-HSA-5652084 HOT 2
- YeastPathways import: "source: null:*pathway-name" instead of "source: SGD:*pathway-name*" HOT 4
- providedBy: URLs inconsistent between users from same group HOT 3
- Header on the "clone evidence" popup has a gomodel: that doesn't match the model title HOT 3
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