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Add batch_confounded quality flag - #72
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Treatment contrast fully confounded with a processing batch (sequencing run, MS acquisition batch, extraction batch). DUPERRET2025_POMS_STARVE (diet vs MS batch) and DECICOMP2025_POMS_AGE (age vs challenge year) both note that AREE had no such flag. Validation reads the vocabulary, so the term validates with no code change. quality_score counts every flag equally (1 - n/5), so it costs the same as low_replication; tests pin both. No registered study declares it yet, so no existing score changes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
batch_confoundedtoregistry/controlled_vocabularies/quality_flags.yaml: the treatment contrast is fully confounded with a processing batch (sequencing run, MS acquisition batch, extraction batch), so the treatment effect can't be separated from batch.DUPERRET2025_POMS_STARVE(fed and starved samples acquired in separate MS batches months apart, see [study] DUPERRET2025_POMS_STARVE (MTBLS13313): reanalyzed from Table S12, QC failed #70) andDECICOMP2025_POMS_AGE(age confounded with challenge year). Both YAMLs say AREE has no such flag.Consumers checked
schemas/study.schema.json:quality_flagsis freestringitems. Nothing to change.src/intake/schema_validate.py: checks flags against the vocabulary, so the new term validates with no code change.src/harmonize/schema.py::compute_quality_flags: passes study-level flags through, so the flag reaches every evidence record from a study that declares it.src/prioritize/scoring.py/cross_species.py:quality_score = 1 - n_flags/5. Every flag weighs the same, sobatch_confoundedcosts exactly as much aslow_replication, including at thequality_score >= 0.4high-priority gate.Scoring effect
No registered study declares the flag yet, so no existing score changes. Documented in
docs/interpreting_candidate_scores.md.Tests
test_batch_confounded_quality_flag_validates: a study that declares the flag validates.test_batch_confounded_costs_at_least_as_much_quality_as_low_replicationruff check src testsclean.Follow-up
Under
check_study_scope, a study PR can't touch shared files, and this PR can't touch study files. Adding the flag toDUPERRET2025_POMS_STARVE.yamlandDECICOMP2025_POMS_AGE.yamlneeds one study PR each after this merges.🤖 Generated with Claude Code