specs/047: the experimental gap to MP-BioPath, case by case; adapter fix by adamjohnwright · Pull Request #99 · reactome/deltasignal

mpbiopath_network_adapter: read bare R-HSA catalog dirs and the versioned pathway list

adamjohnwright

and

claude

committed

62a7a2f

bench/analysis/experimental_gap.py: case-by-case split of the experimental axis against MP-BioPath's published per-case calls

adamjohnwright

and

claude

committed

d5e1ec6

specs/047: experimental gap decomposed case by case against MP-BioPath (103 only-MPB, 54 only-DS; 41 sign inversions); PTEN overexpression traced to 12 microRNA inhibitors on a siloed mRNA copy

adamjohnwright

and

claude

committed

b16ba7a

specs/047: trace 2 - PDPK1 knockout inverts through a SARS-CoV-2 N:M:PDPK1 inhibitor (added after 2019); candidate pathogen-inert rule

adamjohnwright

and

claude

committed

3a8d59d

specs/047: control - our propagator on MP-BioPath's networks scores 610/849 (MPB 643) and matches or beats MPB in 8 of 10 pathways; the experimental gap is network construction (RAF, G1, CCC, TP53)…

adamjohnwright

and

claude

committed

d8e9fa4

specs/047: trace 3 - RAF readouts driven by a curated scaffold released and re-bound (positive carrier loop); MP-BioPath's network lacks the release; candidate: multi-step carrier cycles as balance…

adamjohnwright

and

claude

committed

85eccb4

specs/047: trace 4 (G1 released E2F copies silo) and the mechanism-class table

adamjohnwright

and

claude

committed

b941cde

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specs/047: the experimental gap to MP-BioPath, case by case; adapter fix - #99

specs/047: the experimental gap to MP-BioPath, case by case; adapter fix#99
adamjohnwright merged 7 commits into
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fix/mpb-adapter-bare-ids

Commits on Oct 10, 2026

mpbiopath_network_adapter: read bare R-HSA catalog dirs and the versioned pathway list

bench/analysis/experimental_gap.py: case-by-case split of the experimental axis against MP-BioPath's published per-case calls

specs/047: experimental gap decomposed case by case against MP-BioPath (103 only-MPB, 54 only-DS; 41 sign inversions); PTEN overexpression traced to 12 microRNA inhibitors on a siloed mRNA copy

specs/047: trace 2 - PDPK1 knockout inverts through a SARS-CoV-2 N:M:PDPK1 inhibitor (added after 2019); candidate pathogen-inert rule

specs/047: control - our propagator on MP-BioPath's networks scores 610/849 (MPB 643) and matches or beats MPB in 8 of 10 pathways; the experimental gap is network construction (RAF, G1, CCC, TP53)…

specs/047: trace 3 - RAF readouts driven by a curated scaffold released and re-bound (positive carrier loop); MP-BioPath's network lacks the release; candidate: multi-step carrier cycles as balance…

specs/047: trace 4 (G1 released E2F copies silo) and the mechanism-class table