{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31703725", "kind": "science-record", "revision": 7, "content_hash": "sha256:fd5e100216235b2fb6019af39d9712c22701a3b05677a136017519c4894dbb45", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T22:00:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic values and prospective pathway signaling of MicroRNA-182 in ovarian cancer: a study based on gene expression omnibus (GEO) and bioinformatics analysis.", "doi": "10.1186/s13048-019-0580-7", "pmid": "31703725", "authors": ["Yaowei Li", "Li Li"], "journal": "Journal of ovarian research", "year": 2019, "abstract": "BACKGROUND: Ovarian carcinoma (OC) is a common cause of death among women with gynecological cancer. MicroRNAs (miRNAs) are believed to have vital roles in tumorigenesis of OC. Although miRNAs are broadly recognized in OC, the role of has-miR-182-5p (miR-182) in OC is still not fully elucidated.\nMETHODS: We evaluated the significance of miR-182 expression in OC by using analysis of a public dataset from the Gene Expression Omnibus (GEO) database and a literature review. Furthermore, we downloaded three mRNA datasets of OC and normal ovarian tissues (NOTs), GSE14407, GSE18520 and GSE36668, from GEO to identify differentially expressed genes (DEGs). Then the targeted genes of hsa-miR-182-5p (TG_miRNA-182-5p) were predicted using miRWALK3.0. Subsequently, we analyzed the gene overlaps integrated between DEGs in OC and predicted target genes of miR-182 by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. STRING and Cytoscape were used to construct a protein-protein interaction (PPI) network and the prognostic effects of the hub genes were analyzed.\nRESULTS: A common pattern of up-regulation for miR-182 in OC was found in our review of the literature. A total of 268 DEGs, both OC-related and miR-182-related, were identified, of which 133 genes were discovered from the PPI network. A number of DEGs were enriched in extracellular matrix organization, pathways in cancer, focal adhesion, and ECM-receptor interaction. Two hub genes, MCM3 and GINS2, were significantly associated with worse overall survival of patients with OC. Furthermore, we identified covert miR-182-related genes that might participate in OC by network analysis, such as DCN, AKT3, and TIMP2. The expressions of these genes were all down-regulated and negatively correlated with miR-182 in OC.\nCONCLUSIONS: Our study suggests that miR-182 is essential for the biological progression of OC.", "claims": [{"id": "claim-method", "statement": "The overall survival of patients with OC was analyzed using a Kaplan–Meier plot.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31703725", "locator": "sections[6] \"Survival analysis\" paragraph 2", "quote": "The overall survival of patients with OC was analyzed using a Kaplan–Meier plot."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31703725", "locator": "sections[25] \"notes\" paragraph 1", "quote": "The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31703725"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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"identifier": "section[10]/table-wrap[1]#Tab2", "version": null, "note": "Overview of the 6 studies selected from literature", "structure": {"pmcid": "PMC6839211", "section_index": 10, "section_title": "Literature review of miR-182 expression profiles in OC versus NOTs", "row_count": 8, "column_count": 9}, "table": {"label": "Table 2", "caption": "Overview of the 6 studies selected from literature", "rows": [["Author", "Year", "Country", "Case", "Control", "Result", "Detection methods"], ["Source name", "n", "Source name", "n"], ["Wei Lu", "2016", "China", "OC", "12", "NOTs", "8", "Down-regulation", "qRT-PCR"], ["Barbara Marzec-Kotarska", "2016", "Poland", "EOC", "47", "NOTs", "26", "Up-regulation", "microRNA microarrays"], ["Lin Wang", "2014", "China", "OC", "41", "NOTs", "15", "Up-regulation", "Real-time PCR"], ["Bente Vilming Elgaaen", "2014", "Norway", "HGSC", "35", "NOTs", "9", "Up-regulation", "qRT-PCR"], ["Zhaojian Liu", "2012", "USA", "HG-PSC", "56", "FT", "21", 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"column_count": 4}, "table": {"label": "Table 3", "caption": "Top 10 hsa-miR-182-5p-related differentially expressed genes in ovarian cancer tissues compared with normal ovarian tissues according to data from Gene Expression Omnibus (GSE14407)", "rows": [["DEG", "logFC", "P.Value", "adj. P.Value"], ["up-regulated genes"], ["MECOM", "4.902333971", "9.81E-08", "1.99E-05"], ["TFAP2A", "4.745918435", "1.88E-08", "6.04E-06"], ["DEPDC1", "4.032946443", "5.66E-09", "3.03E-06"], ["AIF1L", "3.868411982", "3.79E-08", "9.54E-06"], ["BIRC5", "3.7736042", "8.61E-09", "3.89E-06"], ["BCL11A", "3.534029736", "1.11E-06", "1.13E-04"], ["L1CAM", "3.279255511", "1.66E-06", "1.49E-04"], ["HMMR", "3.262907245", "2.33E-06", "1.95E-04"], ["NCAPG", "3.229344903", "1.07E-08", "4.36E-06"], ["DTL", "3.208682435", "1.51E-10", "3.76E-07"], ["down-regulated genes"], ["PDE7B", "−5.031930277", "6.84E-09", "3.37E-06"], ["TCEAL7", "−4.928868798", "4.70E-09", "2.66E-06"], ["DCN", "−4.886965887", "1.16E-08", "4.61E-06"], ["GPM6A", "−4.799779935", "2.81E-08", "7.77E-06"], ["PGR", "−4.345763842", "2.85E-08", "7.83E-06"], ["PPM1E", "−4.270922539", "1.43E-08", "5.13E-06"], ["TMOD2", "−4.108261122", "5.21E-10", "7.49E-07"], ["NKX3–1", "−3.851343755", "1.34E-07", "2.48E-05"], ["TACC1", "−3.745549626", "5.00E-08", "1.18E-05"], ["FGF13", "−3.684968538", "2.31E-09", "1.78E-06"]], "row_count": 23, "column_count": 4, "numeric_cells": 63, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:31703725:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cbbb9396fdaa45df966a24de243c32669e438d0893a55b45484bb10184d131c5", "bytes": 910, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab4", "version": null, "note": "Functional and pathway enrichment analysis of hsa-miR-182-5p-related differentially expressed genes in ovarian cancer", "structure": {"pmcid": "PMC6839211", "section_index": 13, "section_title": "Functional analysis of miR-182-related DEGs in OC", "row_count": 13, "column_count": 5}, "table": {"label": "Table 4", "caption": "Functional and pathway enrichment analysis of hsa-miR-182-5p-related differentially expressed genes in ovarian cancer", "rows": [["Term", "Description", "Count", "P-Value", "FDR"], ["Cellular components"], ["GO:0005634", "nucleus", "120", "4.67E-08", "6.23E-05"], ["GO:0005737", "cytoplasm", "108", "1.38E-05", "1.85E-02"], ["Molecular function"], ["GO:0005515", "protein binding", "173", "1.58E-07", "2.23E-04"], ["GO:0043565", "sequence-specific DNA binding", "23", "1.18E-05", "1.67E-02"], ["Biological processes"], ["GO:0030198", "extracellular matrix organization", "14", "1.00E-05", "1.70E-02"], ["KEGG pathway"], ["hsa05200", "Pathways in cancer", "22", "1.93E-06", "2.41E-03"], ["hsa04510", "Focal adhesion", "15", "8.20E-06", "1.02E-02"], ["hsa04512", "ECM-receptor interaction", "10", "1.38E-05", "1.72E-02"]], "row_count": 13, "column_count": 5, "numeric_cells": 32, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:31703725:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:587225a4f2883024808024d9ecaf424a43301e66052348dfe6a563a7543de7c7", "bytes": 1558, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab5", "version": null, "note": "Correlation between hsa-miR-182-5p (miR-182) and target genes in patients with ovarian cancer(n = 376)", "structure": {"pmcid": "PMC6839211", "section_index": 15, "section_title": "Survival analysis", "row_count": 22, "column_count": 5}, "table": {"label": "Table 5", "caption": "Correlation between hsa-miR-182-5p (miR-182) and target genes in patients with ovarian cancer(n = 376)", "rows": [["miRNA", "Target gene", "r", "p-value", "FDR"], ["hsa-miR-182-5p", "TPM1", "−0.143", "5.61E-03", "1.99E-02"], ["hsa-miR-182-5p", "COL1A1", "−0.154", "2.74E-03", "1.14E-02"], ["hsa-miR-182-5p", "PDGFRA", "−0.18", "4.40E-04", "2.87E-03"], ["hsa-miR-182-5p", "UBE2B", "−0.149", "3.87E-03", "1.49E-02"], ["hsa-miR-182-5p", "MEF2C", "−0.201", "8.70E-05", "8.01E-04"], ["hsa-miR-182-5p", "SNAI2", "−0.154", "2.84E-03", "1.18E-02"], ["hsa-miR-182-5p", "CACNA2D1", "−0.104", "4.44E-02", "1.01E-01"], ["hsa-miR-182-5p", "RECK", "−0.153", "2.93E-03", "1.21E-02"], ["hsa-miR-182-5p", "FOXO1", "−0.115", "2.57E-02", "6.58E-02"], ["hsa-miR-182-5p", "FBN1", "−0.139", "6.81E-03", "2.33E-02"], ["hsa-miR-182-5p", "ANTXR2", "−0.187", "2.62E-04", "1.90E-03"], ["hsa-miR-182-5p", "NKX3–1", "−0.136", "8.32E-03", "2.70E-02"], ["hsa-miR-182-5p", "TIMP2", "−0.194", "1.51E-04", "1.23E-03"], ["hsa-miR-182-5p", "AKT3", "−0.205", "6.28E-05", "6.32E-04"], ["hsa-miR-182-5p", "RBPMS", "−0.17", "9.57E-04", "5.21E-03"], ["hsa-miR-182-5p", "EGLN3", "−0.113", "2.83E-02", "7.09E-02"], ["hsa-miR-182-5p", "DERL1", "−0.164", "1.41E-03", "6.98E-03"], ["hsa-miR-182-5p", "PRKD1", "−0.177", "5.57E-04", "3.44E-03"], ["hsa-miR-182-5p", "SLC2A13", "−0.115", "2.57E-02", "6.58E-02"], ["hsa-miR-182-5p", "MAF", "−0.268", "1.26E-07", "5.19E-06"], ["hsa-miR-182-5p", "DCN", "−0.236", "3.68E-06", "6.45E-05"]], "row_count": 22, "column_count": 5, "numeric_cells": 86, "header_rows": 1, "locator": "section[15]/table-wrap[1]#Tab5"}}], "gaps": ["asset:data:geo:GSE14407 not downloaded", "asset:data:geo:GSE14407 licence not read", "asset:data:geo:GSE18520 not downloaded", "asset:data:geo:GSE18520 licence not read", "asset:data:geo:GSE23338 not downloaded", "asset:data:geo:GSE23338 licence not read", "asset:data:geo:GSE36668 not downloaded", "asset:data:geo:GSE36668 licence not read", "asset:data:geo:GSE47841 not downloaded", "asset:data:geo:GSE47841 licence not read", "asset:data:geo:GSE53829 not downloaded", "asset:data:geo:GSE53829 licence not read", "asset:data:geo:GSE83693 not downloaded", "asset:data:geo:GSE83693 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "meta_analysis", "specific": "random_effects", "label": "Meta-analysis / evidence synthesis", "dsl_operations": ["random_effects_pool"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["study_level_effect_estimates"], "evidence": {"score": 0.8, "band": "high", "quote": "random effects"}}, {"id": "method-2", "family": "meta_analysis", "specific": "fixed_effects", "label": "Meta-analysis / evidence synthesis", "dsl_operations": [], "missing_operations": ["fixed_effects_pool"], "expressible": false, "parameters": {}, "data_shapes": ["study_level_effect_estimates"], "evidence": {"score": 0.8, "band": "high", "quote": "fixed-effect"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-4", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-5", "family": null, "specific": null, "label": "Kaplan–Meier survival analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The overall survival of patients with OC was analyzed using a Kaplan–Meier plot."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["random_effects_pool"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: random_effects."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE47841", "GSE83693", "GSE53829", "GSE23338", "GSE14407", "GSE18520", "GSE36668"], "resolved_accessions": ["GSE47841", "GSE83693", "GSE53829", "GSE23338", "GSE14407", "GSE18520", "GSE36668"], "statements": ["The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE47841, GSE83693, GSE53829, GSE23338, GSE14407, GSE18520, GSE36668 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["random_effects_pool"], "assets": ["source:pmid:31703725", "data:geo:GSE14407", "asset:table:pmid:31703725:1", "asset:table:pmid:31703725:2", "asset:table:pmid:31703725:3", "asset:table:pmid:31703725:4", "asset:table:pmid:31703725:5", "asset:table:pmid:31703725:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14407"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:07Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25662, "completion_tokens": 2582, "cached_tokens": 16640}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:31703725", "type": "paper", "label": "pmid:31703725"}, {"id": "source:pmid:31703725", "type": "manuscript", "label": "PMID 31703725 full text"}, {"id": "data:geo:GSE14407", "type": "dataset", "label": "GEO GSE14407"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31703725", "type": "paper", "label": "pmid:31703725"}, {"id": "source:pmid:31703725", "type": "manuscript", "label": "PMID 31703725 full text"}, {"id": "data:geo:GSE14407", "type": "dataset", "label": "GEO GSE14407"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31703725", "type": "extraction", "used": ["source:pmid:31703725"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14407", "type": "accession_resolution", "used": ["data:geo:GSE14407"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:31703725", "parent_hash": "sha256:0b3ff2358f948a334e6f4b31908966de2da05d2eaff6584ef91b85a4a72eb89c", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE14407 licence not read", "asset:data:geo:GSE14407 not downloaded", "asset:data:geo:GSE18520 licence not read", "asset:data:geo:GSE18520 not downloaded", "asset:data:geo:GSE23338 licence not read", "asset:data:geo:GSE23338 not downloaded", "asset:data:geo:GSE36668 licence not read", "asset:data:geo:GSE36668 not downloaded", "asset:data:geo:GSE47841 licence not read", "asset:data:geo:GSE47841 not downloaded", "asset:data:geo:GSE53829 licence not read", "asset:data:geo:GSE53829 not downloaded", "asset:data:geo:GSE83693 licence not read", "asset:data:geo:GSE83693 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "meta_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["random_effects_pool"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["random effects"], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:41:59+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}