{"schema_version":"1.0","hypothesis_id":40994,"triple":{"drug":"exenatide","drug_canonical":"exenatide","mediator":"MMP-3","mediator_canonical":"mmp-3","outcome":"rheumatoid arthritis","outcome_canonical":"rheumatoid arthritis"},"domain":{"domain":"cross_domain","source":"type_2_diabetes","target":"rheumatoid_arthritis"},"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":"10.1186/s13075-025-03541-8","pmid":"40140918","year":2025,"roles":["mediator_outcome"],"title":"Predicting rheumatoid arthritis progression from seronegative undifferentiated arthritis using machine learning: a deep learning model trained on the KURAMA cohort and externally validated with the ANSWER cohort","journal":"Arthritis Res Ther","work_id":288305,"publication_date":"2025-03-26"},{"doi":"10.1021/acsbiomaterials.9b00084","pmid":"33405657","year":2019,"roles":["mediator_outcome"],"title":"Fluorogenic Probe for Detecting Active Matrix Metalloproteinase-3 (MMP-3) in Plasma and Peripheral Blood Neutrophils to Indicate the Severity of Rheumatoid Arthritis","journal":"ACS Biomater Sci Eng","work_id":300757,"publication_date":"2019-05-10"},{"doi":"10.17219/acem/94065","pmid":"30740946","year":2019,"roles":["mediator_outcome"],"title":"Matrix metalloproteinase-3 levels in relation to disease activityand radiological progression in rheumatoid arthritis","journal":"Adv Clin Exp Med","work_id":289026,"publication_date":"2019-02-08"},{"doi":"10.1002/iub.2031","pmid":"30897288","year":2019,"roles":["drug_mediator"],"title":"Exenatide ameliorates inflammatory response in human rheumatoid arthritis fibroblast‐like synoviocytes","journal":"IUBMB Life","work_id":239213,"publication_date":"2019-03-21"}],"source_paper_count":4,"extracted_claims":[{"side":"drug_mediator","object":"MMP-3","context":"in primary human rheumatoid arthritis fibroblast-like synoviocytes","subject":"exenatide","work_id":239213,"claim_id":181808,"polarity":"positive","predicate":"downregulates","confidence":0.8,"extraction_run_id":27},{"side":"mediator_outcome","object":"rheumatoid arthritis","context":"progression from seronegative undifferentiated arthritis","subject":"MMP-3","work_id":288305,"claim_id":212717,"polarity":"positive","predicate":"associated_with","confidence":0.7,"extraction_run_id":29},{"side":"mediator_outcome","object":"rheumatoid arthritis","context":"in patients","subject":"MMP-3","work_id":289026,"claim_id":216154,"polarity":"positive","predicate":"associated_with","confidence":0.95,"extraction_run_id":29},{"side":"mediator_outcome","object":"rheumatoid arthritis","context":"in plasma and peripheral blood neutrophils for indicating severity","subject":"MMP-3","work_id":300757,"claim_id":257505,"polarity":"positive","predicate":"correlates_with","confidence":0.75,"extraction_run_id":29}],"extracted_claim_count":4,"extraction":{"model":"deepseek-v4-flash","model_source":"configured","prompt_version":"v1_2026_05_07","run_ids":[27,29]},"bridge":{"a_to_b_predicate":"downregulates","b_to_c_predicate":"associated_with","a_to_b_evidence_count":1,"b_to_c_evidence_count":3,"edge_support_log_ab":0.6931471805599453,"edge_support_log_bc":1.3862943611198906,"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":0.20794415416798356,"score":0.20794415416798356,"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":"2026-05-12T21:43:41.695630+00:00"}