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specs/047: the experimental gap to MP-BioPath, case by case; adapter fix - #99
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…oned pathway list
It required the retired '{name}_R-HSA-...' directory names and a cases file
with pathway_id/pathway_name columns, so on a current catalog it adapted
nothing. Both are accepted now; output dirs use the bare stable id.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ental axis against MP-BioPath's published per-case calls Joins an arm's experimental_cases.tsv with MP-BioPath's MP_BioPathReactomePathwayAccuracy-Tests-updated.tsv (849 cases; reproduces 643 vs 594). A missing case or a label disagreement is an error. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…h (103 only-MPB, 54 only-DS; 41 sign inversions); PTEN overexpression traced to 12 microRNA inhibitors on a siloed mRNA copy Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…PDPK1 inhibitor (added after 2019); candidate pathogen-inert rule Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…10/849 (MPB 643) and matches or beats MPB in 8 of 10 pathways; the experimental gap is network construction (RAF, G1, CCC, TP53), not the propagator Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ed and re-bound (positive carrier loop); MP-BioPath's network lacks the release; candidate: multi-step carrier cycles as balance pools Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ass table Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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{name}_R-HSA-…directory names, so on a current catalog it adapted nothing. It now reads bare stable-id directories and the versioned pathway list (+2 checks).Analysis only; no behaviour change.
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