{"schema_version":"1.0","hypothesis_id":39036,"triple":{"drug":"tofacitinib","drug_canonical":"tofacitinib","mediator":"JAK2","mediator_canonical":"jak2","outcome":"poor prognosis","outcome_canonical":null},"domain":{"domain":"cross_domain","source":"rheumatoid_arthritis","target":"pancreatic_cancer"},"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":"10.1021/acs.jcim.3c01090","pmid":"37906702","year":2023,"roles":["drug_mediator"],"title":"Machine Learning-Based Drug Repositioning of Novel Janus Kinase 2 Inhibitors Utilizing Molecular Docking and Molecular Dynamic Simulation","journal":"J Chem Inf Model","work_id":287537,"publication_date":"2023-10-31"},{"doi":"10.1371/journal.pmed.1004249","pmid":"37384596","year":2023,"roles":["drug_mediator"],"title":"Efficacy and Safety of Tofacitinib in Patients with Polymyalgia Rheumatica (EAST PMR): An open-label randomized controlled trial","journal":"PLoS Med","work_id":287299,"publication_date":"2023-06-29"},{"doi":"10.1021/acsomega.9b02800","pmid":"31956784","year":2020,"roles":["drug_mediator"],"title":"Insights into the Binding Recognition and Susceptibility of Tofacitinib toward Janus Kinases","journal":"ACS Omega","work_id":286698,"publication_date":"2020-01-02"},{"doi":"10.1155/2020/7656031","pmid":"33029256","year":2020,"roles":["mediator_outcome"],"title":"High JAK2 Protein Expression Predicts a Poor Prognosis in Patients with Resectable Pancreatic Ductal Adenocarcinoma","journal":"Dis Markers","work_id":174775,"publication_date":"2020-09-22"},{"doi":"10.1590/s0004-2803.201800000-36","pmid":"30043874","year":2018,"roles":["drug_mediator"],"title":"TOFACITINIB IN THE MANAGEMENT OF ULCERATIVE COLITIS REFRACTORY TO ANTI-TNF AND ANTI-INTEGRIN THERAPIES","journal":"Arq Gastroenterol","work_id":301608,"publication_date":"2018-06-01"}],"source_paper_count":5,"extracted_claims":[{"side":"drug_mediator","object":"JAK2","context":"at ATP-binding site via electrostatic attraction, hydrogen bond formation, and van der Waals interaction; involving residues E930 and L932 in the hinge region","subject":"tofacitinib","work_id":286698,"claim_id":207898,"polarity":"positive","predicate":"binds_to","confidence":0.9,"extraction_run_id":29},{"side":"drug_mediator","object":"JAK2","context":"in CD4+ T cells from PMR patients in vitro","subject":"tofacitinib","work_id":287299,"claim_id":209380,"polarity":"positive","predicate":"suppresses","confidence":0.9,"extraction_run_id":29},{"side":"drug_mediator","object":"JAK2","context":"reference compound in docking","subject":"tofacitinib","work_id":287537,"claim_id":209933,"polarity":"positive","predicate":"inhibits","confidence":0.95,"extraction_run_id":29},{"side":"drug_mediator","object":"JAK2","context":"in vitro","subject":"Tofacitinib","work_id":301608,"claim_id":259554,"polarity":"positive","predicate":"inhibits","confidence":0.7,"extraction_run_id":29},{"side":"mediator_outcome","object":"poor prognosis","context":"in patients with resectable pancreatic ductal adenocarcinoma","subject":"JAK2","work_id":174775,"claim_id":128463,"polarity":"positive","predicate":"predicts","confidence":0.95,"extraction_run_id":23}],"extracted_claim_count":5,"extraction":{"model":"deepseek-v4-flash","model_source":"configured","prompt_version":"v1_2026_05_07","run_ids":[23,29]},"bridge":{"a_to_b_predicate":"inhibits","b_to_c_predicate":"predicts","a_to_b_evidence_count":4,"b_to_c_evidence_count":1,"edge_support_log_ab":1.6094379124341003,"edge_support_log_bc":0.6931471805599453,"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":0.23025850929940456,"score":0.23025850929940456,"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"}