{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30258285", "kind": "science-record", "revision": 4, "content_hash": "sha256:3f56fb2a89fbe3e9e65d90549bfd1d891c6665d06240ccb68d8a0e4653c8e852", "created_at": "2026-11-01T15:40:37Z", "updated_at": "2026-11-01T21:21:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Key elements involved in Epstein-Barr virus-associated gastric cancer and their network regulation.", "doi": "10.1186/s12935-018-0637-5", "pmid": "30258285", "authors": ["Jing-Jing Jing", "Ze-Yang Wang", "Hao Li", "Li-Ping Sun", "Yuan Yuan"], "journal": "Cancer cell international", "year": 2018, "abstract": "BACKGROUND: The molecular mechanism of Epstein-Barr virus (EBV)-associated gastric cancer (EBVaGC) remains elusive. A collection of molecular regulators including transcription factor and noncoding RNA (ncRNAs) may affect the carcinogenesis of EBVaGC by regulating the expression and function of key genes. In this study, integration of multi-level expression data and bioinformatics approach was used to identify key elements and their interactions involved in mechanism of EBVaGC and their network regulation.\nMETHODS: Data of the gene expression profiling data sets (GSE51575) was downloaded from GEO database. Differentially expressed genes between EBVaGC and normal samples were identified by GEO2R. Gene ontology and pathway enrichment analyses were performed using R packages Cluster profiler. STRING database was used to find interacting proteins between different genes. Transcription factors in differentially expressed genes were obtained from TF Checkpoint database. Using Cytoscape, we built transcription factor regulation network. miRNAs involved in the gene-interacting proteins and the miRNA-targeted lncRNA were predicted through miRWalk. Using ViRBase, EBV related miRNA regulation network was built. Overlapping genes and regulators of the above three networks were further identified, and the cross network was constructed using Cytoscape software. Moreover, the differential expressions of the target genes and transcription factors in the cross network were explored in different molecular subtypes of GC using cBioPortal. By histological verification, the expression of two main target genes in the cross network were further analyzed.\nRESULTS: A total of 104 genes showed differential expressions between EBVaGC and normal tissues, which were associated with digestion, G-protein coupled receptor binding, gastric acid secretion, etc. Pathway analysis showed that the differentially expressed genes were mainly enriched in gastric acid secretion and protein digestion and absorption. Using STRING dataset, a total of 54 proteins interacted with each other. Based on the transcription factor network, the hub transcription factors IRX3, NKX6-2, PTGER3 and SMAD5 were identified to regulate their target genes SST and GDF5, etc. After screening and matching in miRwalk datasets, a ceRNA network was established, in which the top five miRNAs were hsa-miR-4446-3p, hsa-miR-5787, hsa-miR-1915-3p, hsa-miR-335-3p and hsa-miR-6877-3p, and the top two lncRNAs were RP5-1039K5.19 and TP73-AS1. According to the EBV related miRNA regulation network, CXCL10 and SMAD5 were found to be regulated by EBV-miR-BART1-3p and EBV-mir-BART22, respectively. By overlapping the three networks, CXCL10, GDF5, PTGER3, SMAD5, miR-6877-3p, RP5-1039K5.19, TP73-AS1, EBV-miR-BART1-3p and EBV-mir-BART22 were found to be key elements of regulation mechanism of EBVaGC. CXCL10, GDF5, PTGER3 and SMAD5 were also differentially expressed among the four molecular subtypes of GC. The histological verification experiment showed differential expressions of the two main target genes GDF5 and CXCL10 between EBVaGC and non-tumor tissues as well as EBVnGC.\nCONCLUSION: In the current study, our results revealed key elements and their interactions involved in EBVaGC. Some hub transcription factors, miRNAs, lncRNAs and EBV related miRNAs were observed to regulate their target genes. Overlapping genes and regulators were observed in diverse regulation networks, such as CXCL10, GDF5, PTGER3, SMAD5, miR-6877-3p, RP5-1039K5.19, TP73-AS1, EBV-miR-BART1-3p and EBV-mir-BART22. Moreover, CXCL10, GDF5, PTGER3 and SMAD5 were also differentially expressed among the four molecular subtypes of GC. The histological verification experiment showed differential expressions of the two main target genes GDF5 and CXCL10 between EBVaGC and non-tumor tissues as well as EBVnGC. Therefore, the identified key elements and their network regulation may be specifically involved in EBVaGC mechanisms.", "claims": [{"id": "claim-method", "statement": "As an interactive online tool, GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) can be used to compare two or more sets of samples to determine differentially expressed genes in the GEO series [20]. In order to ensure the accuracy of the results, we used GEO2R to filter differentially expressed genes between EBVaGC and normal samples separately in each of the data sets. FDR < 0.05 and |logFC| > 4 were considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30258285", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "As an interactive online tool, GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/) can be used to compare two or more sets of samples to determine differentially expressed genes in the GEO series [20]. In order to ensure the accuracy of the results, we used GEO2R to filter differentially expressed genes between EBVaGC and normal samples separately in each of the data sets. FDR < 0.05 and |logFC| > 4 were considered statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors declare that the data supporting the findings of this study are available within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30258285", "locator": "sections[28] \"Availability of data and materials\" paragraph 2", "quote": "The authors declare that the data supporting the findings of this study are available within the article."}], "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:30258285"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE51575"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE51575"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30258285", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-018-0637-5", "sha256": 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"GSM1248665"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "13607", "taxon": "Homo sapiens", "title": "mRNA Expression Profiling in EBV-postive Gastric Carcinoma and EBV-negative GC in comparison with their normal mucosa tissue", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30258285:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9a35b5da93d3d99df9456aea317c02a6e8ed6dd87fb221808c0238a03ecf3013", "bytes": 572, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab1", "version": null, "note": "KEGG enrichment analysis for the differential expressed genes", "structure": {"pmcid": "PMC6151003", "section_index": 14, "section_title": "GO and KEGG pathway functional enrichment analyses", "row_count": 3, "column_count": 9}, "table": {"label": "Table 1", "caption": "KEGG enrichment analysis for the differential expressed genes", "rows": [["ID", "Description", "Gene ratio", "Bg ratio", "P value", "P adjust", "q value", "Gene ID", "Count"], ["hsa04971", "Gastric acid secretion", "6/54", "75/7383", "1.58E−05", "0.0012128", "0.0010942", "495/496/6750/3773/9992/887", "6"], ["hsa04974", "Protein digestion and absorption", "6/54", "90/7383", "4.48E−05", "0.0017241", "0.0015556", "643834/1280/1358/6564/10136/23436", "6"]], "row_count": 3, "column_count": 9, "numeric_cells": 16, "header_rows": 1, "locator": "section[14]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:30258285:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:76e854c003210f7412de269f84bfca43fbe30d7d3bd87974cd17d437dc7dd554", "bytes": 1492, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#Tab2", "version": null, "note": "The mRNA expressions of target genes and TFs in the cross network in different molecular subtypes of GC by cBioPortal database", "structure": {"pmcid": "PMC6151003", "section_index": 19, "section_title": "Differential expressions of the target genes and transcription factors in the cross network in different molecular subtypes of GC", "row_count": 30, "column_count": 5}, "table": {"label": "Table 2", "caption": "The mRNA expressions of target genes and TFs in the cross network in different molecular subtypes of GC by cBioPortal database", "rows": [["Gene", "Tpye of GC", "Sample number", "mRNA expression"], ["Mean ± SD", "P value"], ["GDF5", "EBVaGC", "29", "2.11 ± 2.52", "Ref"], ["EBVnGC", "311", "5.16 ± 9.55", "< 0.001"], ["", "", "", "< 0.001*"], ["EBVaGC", "29", "2.11 ± 2.52", "Ref"], ["GS-GC", "47", "10.46 ± 12.75", "< 0.001"], ["MSI-GC", "62", "2.12 ± 2.68", "0.995"], ["CIN-GC", "202", "4.85 ± 9.57", "0.120"], ["CXCL10", "EBVaGC", "30", "6061.34 ± 6.56", "Ref"], ["EBVnGC", "346", "759.53 ± 1.21", "< 0.001"], ["", "", "", "< 0.001*"], ["EBVaGC", "30", "6061.34 ± 6.56", "Ref"], ["GS-GC", "50", "352.97 ± 412.44", "< 0.001"], ["MSI-GC", "73", "1523.12 ± 2.11", "< 0.001"], ["CIN-GC", "223", "600.72 ± 743.04", "< 0.001"], ["SMAD5", "EBVaGC", "30", "1165.21 ± 557.37", "Ref"], ["EBVnGC", "346", "1446.01 ± 459.22", "0.002"], ["", "", "", "< 0.001*"], ["EBVaGC", "30", "1165.21 ± 557.37", "Ref"], ["GS-GC", "50", "1638.22 ± 483.08", "< 0.001"], ["MSI-GC", "73", "1355.35 ± 330.26", "0.058"], ["CIN-GC", "223", "1432.59 ± 479.20", "0.003"], ["PTGER3", "EBVaGC", "30", "78.20 ± 91.63", "Ref"], ["EBVnGC", "346", "191.35 ± 235.51", "< 0.001"], ["", "", "", "< 0.001*"], ["EBVaGC", "30", "78.20 ± 91.63", "Ref"], ["GS-GC", "50", "405.75 ± 309.97", "< 0.001"], ["MSI-GC", "73", "101.47 ± 108.61", "0.610"], ["CIN-GC", "223", "172.69 ± 218.64", "0.021"]], "row_count": 30, "column_count": 5, "numeric_cells": 69, "header_rows": 2, "locator": "section[19]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:30258285:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:be6d8f6f7f0a27e112616df47e28ba9a8e77e8c9efdf3b624365378ba2bfef2a", "bytes": 666, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#Tab3", "version": null, "note": "Histological verification of the mRNA expressions of GDF5 and CXCL10", "structure": {"pmcid": "PMC6151003", "section_index": 20, "section_title": "Verification of the target genes expression in the cross network", "row_count": 8, "column_count": 4}, "table": {"label": "Table 3", "caption": "Histological verification of the mRNA expressions of GDF5 and CXCL10", "rows": [["Gene", "Group", "mRNA expression"], ["Mean ± SD", "P value"], ["GDF5", "EBVaGC vs CON", "0.025 ± 0.038 vs 0.254 ± 0.418", "0.043"], ["EBVnGC vs CON", "0.096 ± 0.096 vs 0.118 ± 0.199", "0.893"], ["EBVaGC vs EBVnGC", "0.025 ± 0.038 vs 0.096 ± 0.096", "0.076"], ["CXCL10", "EBVaGC vs CON", "0.867 ± 1.440 vs 0.205 ± 0.281", "0.080"], ["EBVnGC vs CON", "0.206 ± 0.138 vs 0.154 ± 0.164", "0.686"], ["EBVaGC vs EBVnGC", "0.867 ± 1.440 vs 0.206 ± 0.138", "0.047"]], "row_count": 8, "column_count": 4, "numeric_cells": 13, "header_rows": 2, "locator": "section[20]/table-wrap[1]#Tab3"}}], "gaps": ["asset:data:geo:GSE51575 not downloaded", "asset:data:geo:GSE51575 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "family": null, 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In order to ensure the accuracy of the results, we used GEO2R to filter differentially expressed genes between EBVaGC and normal samples separately in each of the data sets. FDR < 0.05 and |logFC| > 4 were considered statistically significant."}}], "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE51575"], "resolved_accessions": ["GSE51575"], "statements": ["The authors declare that the data supporting the findings of this study are available within the article."], "basis": "The paper names GSE51575 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pathway_enrich"], "assets": ["source:pmid:30258285", "data:geo:GSE51575", "asset:table:pmid:30258285:1", "asset:table:pmid:30258285:2", "asset:table:pmid:30258285:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE51575"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:24Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 32678, "completion_tokens": 1024, "cached_tokens": 784}}, "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:30258285", "type": "paper", "label": "pmid:30258285"}, {"id": "source:pmid:30258285", "type": "manuscript", "label": "PMID 30258285 full text"}, {"id": "data:geo:GSE51575", "type": "dataset", "label": "GEO GSE51575"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30258285", "type": "paper", "label": "pmid:30258285"}, {"id": "source:pmid:30258285", "type": "manuscript", "label": "PMID 30258285 full text"}, {"id": "data:geo:GSE51575", "type": "dataset", "label": "GEO GSE51575"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30258285", "type": "extraction", "used": ["source:pmid:30258285"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE51575", "type": "accession_resolution", "used": ["data:geo:GSE51575"], "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:30258285", "parent_hash": "sha256:d02e7a7f3bc683226f3edfbdbfb7908887c1da111ef9f963d3c16ef19a03eb50", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE51575 licence not read", "asset:data:geo:GSE51575 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["pathway enrichment"], "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. 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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}}}