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.
from pathways2go.
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)
- Review the causal flow between EGFR(s) activity and Src activity
- First step: Import Reactome Pathways for MOD species HOT 6
- Second step: Add existing evidence to imported pathways HOT 1
- Third step: Use Textpresso-like resource to identify papers that could provide evidence for statements that aren't supported by evidence from existing annotations. HOT 1
- Represent enzymatic complex enablers according to GO-CAM spec HOT 12
- Representation of an unknown enabler in Reactome and GO-CAM HOT 6
- Signal/Transit peptides in Reactome (12 confirmed cases) HOT 3
- Suspicious sequence range for UniProtKB:P43251 derived EWASes HOT 1
- Complexes & Sets - info needed for PRO
- Switch on intermediate small molecule instance sharing for Reactome HOT 9
- Sub-sequence termini revisions/review HOT 4
- R-HSA-163765 "ChREBP activates metabolic gene expression" cleanup HOT 1
- GO-CAM reaction labels don't match the Reactome pathway browser
- Reactome: amino acid and PTM mismatches
- To discuss: how to handle Reactome and Yeast Pathways imported GO-CAMs wrt input/output data updates
- Fatty AcylCoA biosynthesis HOT 4
- Only include reactions that are part of a pathway in the GO-CAM imports
- Experiment: Only include chemicals that are causally connected in a model. HOT 2
- Activity node for reaction should be a process if GO BP is curated at Reactome HOT 5
- The direction of transport in model R-HSA-6787639 is backwards HOT 1
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