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LNG_UB_SUBSTRATE_CHANGED (default off): ubiquitination depletes only the changed partner (deltasignal specs/057) - #113
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… partner it changes, not the ones it carries (deltasignal specs/057) A substrate was any input leaf whose gene reappears in the output. A complex ubiquitinated in place returns every partner, so each was depleted: CBL monoubiquitinating MET depleted free GRB2. Under the flag a substrate's own stId must be absent from the output's leaves. Off is unchanged (tested). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…Ub-X complex member is still the substrate (deltasignal specs/057 amendment 1) Reactome writes some products as a complex of the substrate and Ub (Ub-SMAD2 = SMAD2 + Ub), so the substrate's stId reappears in the output and the changed-stId test called it passed through (24 of 301 removed edges). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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Registered in deltasignal specs/057 before any build.
Bug. The ubiquitin pass of
_emit_substrate_depletion_edgestakes as substrate every input leaf whose gene reappears in the output. A complex ubiquitinated in place returns every partner, so each partner is depleted. Example: "CBL monoubiquitinates activated MET" (R-HSA-8875183) returns GRB2 unchanged, yet free GRB2 was depleted by the p-Y-CBL complex, which inverts every MET/HGF perturbation in Signaling by MET. Census on the canonical build: 301 of 727 depletion edges, 32 pathways.Change. Under
LNG_UB_SUBSTRATE_CHANGED=1a substrate's own stId must also be absent from the output's leaves (it leaves changed). The output query now also returns leaf stIds. Default off: the off path is unchanged (tests/test_ub_substrate.py).Measured by a variant build (
catalog.sh build --variant ubs --env LNG_UB_SUBSTRATE_CHANGED=1) against the canonical build; the default changes only if the deltasignal gate passes and Adam agrees.Tests: new file passes; the full suite has one failure,
test_main_edges_proportional_to_best_matches[Class_I_MHC...], which fails identically on main.🤖 Generated with Claude Code