Generalize modifier-isoform collapse beyond the hardcoded ubiquitin list - #50
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…biquitin list Replaces the hardcoded 6-entry _UBIQUITIN_ENTITY_SET_IDS check with a query-derived modifier_isoform_set_ids(): human EntitySets whose members are ALL modifier proteins (ubiquitin/SUMO/NEDD8/ISG15/UFM1/ATG8, identified by reference-gene identity), so E3-ligase/enzyme sets are correctly excluded. Falls back to the hardcoded ubiquitin seed when Neo4j is unavailable (offline/tests). Discovers 46 sets vs the 6 previously listed — self-maintaining across Reactome versions instead of an arbitrarily-incomplete hand list. Correctness/maintainability only, not a benchmark lever: the 9 experimental pathways regenerate byte-identical, and DB-wide only 11 reactions take a newly-covered set as a decomposable input. Full non-Neo4j suite passes (922). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Replaces the hardcoded 6-entry
_UBIQUITIN_ENTITY_SET_IDScheck with a query-derivedmodifier_isoform_set_ids(): human EntitySets whose members are all modifier proteins (ubiquitin / SUMO / NEDD8 / ISG15 / UFM1 / ATG8, identified by reference-gene identity). E3-ligase and enzyme sets are correctly excluded because their members aren't modifier genes. Falls back to the hardcoded ubiquitin seed when Neo4j is unavailable (offline / tests).Why
The old list collapsed only 6 "Ub [compartment]" sets, but there are ~40 pure-ubiquitin EntitySets (linkage-specific chains K48/K63/…, other compartments, activated forms) plus SUMO/NEDD8/ATG8 families — all functionally-identical modifier copies that should be atomic, not decomposed into per-gene members. Discovering them by member-gene identity is self-maintaining across Reactome versions instead of an arbitrarily-incomplete hand list.
Impact (measured)
Correctness/maintainability, not a benchmark lever:
Verification
Full non-Neo4j suite passes (922); the 8 pre-existing failures require a live Reactome Neo4j and are unaffected. Live query confirms discovery of 46 modifier-isoform sets vs the 6 previously hardcoded.
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