Short verdict: Keep, but consider separating phosphorylation from O-GlcNAc if precision matters; phosphorylation is vastly broader and mechanistically distinct.
What the current graph claims
Node definition: Post-translational switching by phosphorylation and O-GlcNAcylation affecting protein conformation, interactions, localization, degradation, and signaling.
What is strongly supported: Kinase/phosphatase systems regulate TFs, Pol II, ISR kinases, mTOR, DNA damage, and degrons; O-GlcNAc is a nutrient-sensitive reversible Ser/Thr mark with crosstalk.
What is context-dependent: Phosphorylation can activate, inhibit, localize, or create degrons depending on substrate and site; O-GlcNAc crosstalk is site- and pathway-specific.
What is weak, controversial, or assay-biased: Combining two very broad PTMs can hide specificity; “switch” is a metaphor, not all phosphorylation is binary.
What may be duplicate biology under another name: Overlaps with ROUTER, KEYS, SCRIBE, BRAKE.
Missing or excessive graph structure
Missing edges: Add SWITCH -> FORGE/mTOR more directly? Already FORGE -> SWITCH but feedback is complex.
Excess edges: FORGE -> SWITCH “mTOR->AKT” direction is biologically awkward: AKT is upstream of mTORC1 in many pathways, while mTORC1 signals downstream to S6K/4E-BP.
Candidate splits: Optional split PHOSPHO and O-GLCNAC.
Candidate merges: No merge.
Candidate renames: PTM-SWITCH.
Recommendation
Concrete graph change, if any: Keep; fix mTOR/AKT directionality and avoid binary switch wording.
Concrete technical-notes/blog wording change, if any: Mirror the graph recommendation in the glossary and relation catalogue, and explicitly mark the confidence/caveat where the claim is context-dependent or assay-sensitive.