{"schema_version":"1.0","hypothesis_id":32516,"triple":{"drug":"OPAHs","drug_canonical":"opahs","mediator":"APP","mediator_canonical":"app","outcome":"Alzheimer's disease","outcome_canonical":"Alzheimer disease"},"domain":{"domain":"cross_domain","source":"inflammatory_bowel_disease","target":"alzheimer"},"provenance_completeness":"partial_backfill","completeness_notes":"Backfilled retroactively from DB state on 2026-05-13. The pipeline_run this row references was created by the backfill script, not by the actual generation orchestrator. Source papers, claims, scoring, and embedding config are recovered; generation-time metadata (exact git commit at gen time, host, exact command) is not recoverable.","source_papers":[{"doi":"10.1016/j.ecoenv.2025.119153","pmid":"41038021","year":2025,"roles":["drug_mediator"],"title":"Exploring the mechanisms underlying effects of oxygenated polycyclic aromatic hydrocarbons exposure on inﬂammatory bowel disease","journal":"Ecotoxicol Environ Saf","work_id":278106,"publication_date":"2025-10-01"},{"doi":"10.3233/jad-220683","pmid":"36776048","year":2023,"roles":["mediator_outcome"],"title":"Machine Learning Selection of Most Predictive Brain Proteins Suggests Role of Sugar Metabolism in Alzheimer’s Disease","journal":"J Alzheimers Dis","work_id":62995,"publication_date":"2023-02-07"},{"doi":"10.1038/s41598-021-04027-8","pmid":"34997052","year":2022,"roles":["mediator_outcome"],"title":"Regulation of gene expression by the APP family in the adult cerebral cortex","journal":"Sci Rep","work_id":67208,"publication_date":"2022-01-07"},{"doi":"10.3389/fnins.2021.673684","pmid":"34140878","year":2021,"roles":["mediator_outcome"],"title":"Sunday Driver Mediates Multi-Compartment Golgi Outposts Defects Induced by Amyloid Precursor Protein","journal":"Front Neurosci","work_id":161759,"publication_date":"2021-06-01"},{"doi":"10.3390/cells9112506","pmid":"33228083","year":2020,"roles":["mediator_outcome"],"title":"Amyloid-β Precursor Protein APP Down-Regulation Alters Actin Cytoskeleton-Interacting Proteins in Endothelial Cells","journal":"Cells","work_id":66761,"publication_date":"2020-11-19"},{"doi":"10.1038/s41598-019-43607-7","pmid":"31068645","year":2019,"roles":["mediator_outcome"],"title":"Microvesicles from cerebrospinal fluid of patients with Alzheimer’s disease display reduced concentrations of tau and APP protein","journal":"Sci Rep","work_id":64690,"publication_date":"2019-05-08"},{"doi":"10.3389/fninf.2018.00026","pmid":"29875647","year":2018,"roles":["mediator_outcome"],"title":"Analyzing the Behavior of Neuronal Pathways in Alzheimer's Disease Using Petri Net Modeling Approach","journal":"Front Neuroinform","work_id":69992,"publication_date":"2018-05-23"}],"source_paper_count":7,"extracted_claims":[{"side":"drug_mediator","object":"APP","context":"molecular docking analysis","subject":"OPAHs","work_id":278106,"claim_id":253351,"polarity":"positive","predicate":"binds_to","confidence":0.7,"extraction_run_id":31},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"brain tissue, AD versus control classification","subject":"APP","work_id":62995,"claim_id":43990,"polarity":"positive","predicate":"predicts","confidence":0.8,"extraction_run_id":16},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"in microvesicles from cerebrospinal fluid","subject":"APP","work_id":64690,"claim_id":47965,"polarity":"positive","predicate":"predicts","confidence":0.85,"extraction_run_id":16},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"general","subject":"APP","work_id":66761,"claim_id":52702,"polarity":"positive","predicate":"associated_with","confidence":0.9,"extraction_run_id":16},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"","subject":"APP","work_id":67208,"claim_id":53664,"polarity":"positive","predicate":"associated_with","confidence":0.95,"extraction_run_id":16},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"stochastic Petri net model of Alzheimer's disease","subject":"APP","work_id":69992,"claim_id":59319,"polarity":"positive","predicate":"causes","confidence":0.7,"extraction_run_id":16},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"AD pathogenesis","subject":"APP","work_id":161759,"claim_id":115434,"polarity":"positive","predicate":"associated_with","confidence":0.5,"extraction_run_id":22}],"extracted_claim_count":7,"extraction":{"model":"deepseek-v4-flash","model_source":"configured","prompt_version":"v1_2026_05_07","run_ids":[16,22,31]},"bridge":{"a_to_b_predicate":"binds_to","b_to_c_predicate":"predicts","a_to_b_evidence_count":1,"b_to_c_evidence_count":6,"edge_support_log_ab":0.6931471805599453,"edge_support_log_bc":1.9459101490553132,"novelty_factor":1.0,"direct_a_to_c_count":0},"embedding":{"model":"bge-m3","dim":1024,"max_length":8192,"similarity_scores":{}},"scoring":{"method":"swanson_abc_log_evidence_with_novelty_penalty","formula":"score = min((log(ab+1) + log(bc+1)) * novelty / 10, 1.0); novelty = 1.0 if direct==0 else 0.7 / (direct+1)","score_raw":0.26390573296152586,"score":0.26390573296152586,"quality_tier":"mid","quality_reason":null},"pipeline_run":{"id":4,"run_uuid":"eb8b7730-d92e-4cd5-95dd-95f6c5d62cc2","command":"scripts/backfill_provenance_v2.py:v2_2026_05_12","status":"completed","git_commit":"9996ffaa56e9b7cd5f677bd8203624c2c18aa000","host":"MacBook-Pro-Daniel96.local","started_at":"2026-05-12T21:35:53.363326+00:00","ended_at":"2026-05-12T21:43:41.903387+00:00","notes":"Retroactive provenance backfill on 2026-05-13 for snapshot v2_2026_05_12. Synthetic pipeline_runs row — original generation run records are lost (pre-date provenance schema). All recoverable fields populated from current DB state (claims, works, repurposing_hypotheses); pipeline_run record is synthetic, hence completeness='partial_backfill'.\nBackfilled 1,618 provenance rows. Source papers: avg=3.73, zero=0. Claims matched: avg=4.09, zero=0.\nRefreshed 1,618 provenance rows. Source papers: avg=3.73, zero=0. Claims matched: avg=4.09, zero=0.\nRefreshed 1,618 provenance rows. Source papers: avg=3.73, zero=0. Claims matched: avg=4.09, zero=0.","domains":["als","alzheimer","depression","epilepsy","glioblastoma","inflammatory_bowel_disease","multiple_sclerosis","pancreatic_cancer","rheumatoid_arthritis","type_2_diabetes"]},"generated_at":"2026-05-12T21:43:40.945575+00:00"}