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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":"10.1038/s41598-025-15370-5","pmid":"40849565","year":2025,"roles":["mediator_outcome"],"title":"Aging associated immunosenescence in rheumatoid arthritis identified by machine learning and single cell profiling","journal":"Sci Rep","work_id":299570,"publication_date":"2025-08-23"},{"doi":"10.1186/s12967-025-07015-y","pmid":"41131607","year":2025,"roles":["mediator_outcome"],"title":"Integrated analysis of single-cell RNA-seq and bulk RNA-seq reveal macrophage subpopulation characteristics and the role of STAT1 in rheumatoid arthritis","journal":"J Transl Med","work_id":293907,"publication_date":"2025-10-23"},{"doi":"10.1111/sji.13424","pmid":"39545481","year":2024,"roles":["drug_mediator"],"title":"Expression of <scp>STAT</scp>‐ and T‐cell‐related genes in women with first‐line treatment of relapsing‐remitting multiple sclerosis","journal":"Scand J Immunol","work_id":207332,"publication_date":"2024-11-15"},{"doi":null,"pmid":"36247278","year":2022,"roles":["mediator_outcome"],"title":"Identification and validation of potential hub genes in rheumatoid arthritis by bioinformatics analysis.","journal":"Am J Transl Res","work_id":301576,"publication_date":"2022-01-01"},{"doi":"10.3892/mmr.2018.9677","pmid":"30483789","year":2018,"roles":["mediator_outcome"],"title":"Identification of potential biomarkers for differential diagnosis between rheumatoid arthritis and osteoarthritis via integrative genome‑wide gene expression profiling analysis","journal":"Mol Med Rep","work_id":289347,"publication_date":"2018-11-20"}],"source_paper_count":5,"extracted_claims":[{"side":"drug_mediator","object":"STAT1","context":"in blood of women with RRMS treated with first-line drugs","subject":"teriflunomide","work_id":207332,"claim_id":157635,"polarity":"positive","predicate":"upregulates","confidence":0.8,"extraction_run_id":25},{"side":"mediator_outcome","object":"rheumatoid arthritis","context":"in synovial tissue from RA vs OA patients","subject":"STAT1","work_id":289347,"claim_id":217520,"polarity":"positive","predicate":"associated_with","confidence":0.9,"extraction_run_id":29},{"side":"mediator_outcome","object":"rheumatoid arthritis","context":"in rheumatoid arthritis","subject":"STAT1","work_id":293907,"claim_id":235926,"polarity":"positive","predicate":"associated_with","confidence":0.9,"extraction_run_id":29},{"side":"mediator_outcome","object":"rheumatoid arthritis","context":"in rheumatoid arthritis","subject":"STAT1","work_id":299570,"claim_id":253572,"polarity":"positive","predicate":"treats","confidence":0.6,"extraction_run_id":29},{"side":"mediator_outcome","object":"rheumatoid arthritis","context":"in human microarray datasets and rat synovial tissue","subject":"STAT1","work_id":301576,"claim_id":259400,"polarity":"positive","predicate":"associated_with","confidence":0.7,"extraction_run_id":29}],"extracted_claim_count":5,"extraction":{"model":"deepseek-v4-flash","model_source":"configured","prompt_version":"v1_2026_05_07","run_ids":[25,29]},"bridge":{"a_to_b_predicate":"upregulates","b_to_c_predicate":"associated_with","a_to_b_evidence_count":1,"b_to_c_evidence_count":4,"edge_support_log_ab":0.6931471805599453,"edge_support_log_bc":1.6094379124341003,"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"}