{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31837602", "kind": "science-record", "revision": 8, "content_hash": "sha256:7b532f688a5793070ea01e9e7547a807caa30a5768336cbdac866045ebee3943", "created_at": "2026-11-01T15:40:53Z", "updated_at": "2026-11-01T22:44:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "LncRNA MAGI2-AS3 Is Regulated by BRD4 and Promotes Gastric Cancer Progression via Maintaining ZEB1 Overexpression by Sponging miR-141/200a.", "doi": "10.1016/j.omtn.2019.11.003", "pmid": "31837602", "authors": ["Dandan Li", "Jingjie Wang", "Meixin Zhang", "Xinhui Hu", "Jiajun She", "Xuemei Qiu", "Xudong Zhang", "Li Xu", "Ying Liu", "Shanshan Qin"], "journal": "Molecular therapy. Nucleic acids", "year": 2020, "abstract": "Long non-coding RNAs (lncRNAs) play critical roles in tumorigenesis and tumor progression. However, the biological function of most lncRNAs remains unknown in human gastric cancer. This study here aims to explore the unknown function of lncRNA MAGI2-AS3 in gastric cancer. First, bioinformatics analysis showed that lncRNA MAGI2-AS3 was overexpressed in gastric cancer tissues, and the overexpression of MAGI2-AS3 has been shown to be associated with poor prognosis in all three independent gastric cancer cohorts (The Cancer Genome Atlas stomach cancer [TCGA_STAD], GEO: GSE62254 and GSE15459). The multivariate analysis indicated that lncRNA MAGI2-AS3 was an independent prognostic factor for both overall survival and disease-free survival of gastric cancer patients. Moreover, MAGI2-AS3 was identified to be an epithelial-mesenchymal transition (EMT)-related lncRNA and was highly co-expressed with ZEB1/2 in both gastric cancer tissues and normal stomach tissues. Loss-of-function and gain-of-function studies showed that lncRNA MAGI2-AS3 could positively regulate ZEB1 expression and the process of cell migration and invasion in gastric cancer. Subcellular location assay showed that lncRNA MAGI2-AS3 was mainly located in the cytoplasm of gastric cancer cells. Bioinformatics analysis and functional experiments revealed that lncRNA MAGI2-AS3 was negatively correlated with miR-141/200a expression and negatively regulated miR-141/200a-3p expression in gastric cancer. Therefore, we speculate that lncRNA MAGI2-AS3 promotes tumor progression through sponging miR-141/200a and maintaining overexpression of ZEB1 in gastric cancer. Nevertheless, we identified that BRD4 is a transcriptional regulator of lncRNA MAGI2-AS3 in gastric cancer. Additionally, our findings highlight that lncRNA MAGI2-AS3 is an ideal biomarker and could be a potential therapeutic target for gastric cancer.", "claims": [{"id": "claim-method", "statement": "Survival curves were calculated using the Kaplan-Meier method, and differences between the curves were analyzed using the log rank test. A Cox proportional hazards model was used for multivariate survival analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31837602", "locator": "sections[19] \"Statistical Analysis\" paragraph 2", "quote": "Survival curves were calculated using the Kaplan-Meier method, and differences between the curves were analyzed using the log rank test. A Cox proportional hazards model was used for multivariate survival analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA-seq data of 407 gastric cancer samples, miRNA-seq data of 491 gastric cancer samples, and the correlated clinical information of 443 gastric cancer samples were downloaded from The Cancer Genome Atlas (TCGA) by using SangerBox software (http://sangerbox.com/) developed by ShengXinRen (https://shengxin.ren/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31837602", "locator": "sections[13] \"RNA-Seq Data Analysis of Stomach Cancer in TCGA\" paragraph 2", "quote": "RNA-seq data of 407 gastric cancer samples, miRNA-seq data of 491 gastric cancer samples, and the correlated clinical information of 443 gastric cancer samples were downloaded from The Cancer Genome Atlas (TCGA) by using SangerBox software (http://sangerbox.com/) developed by ShengXinRen (https://shengxin.ren/)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:31837602"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31837602", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.omtn.2019.11.003", "sha256": "sha256:b34795a2fe5bd173c4829c2b1c4ad8fa020009f1728e4260d0d55a93fde2907d", "bytes": 48403, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.omtn.2019.11.003", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6920306", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:31837602:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:efd4f6f006450275ffba9807ff42290ff52f16adb611608cf911708b24f7ea85", "bytes": 1305, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#tbl1", "version": null, "note": "The Cox Regression Analysis for Overall Survival (OVS) and Disease-free Survival (DFS) in TCGA Gastric Cancer Cohort", "structure": {"pmcid": "PMC6920306", "section_index": 4, "section_title": "MAGI2-AS3 Overexpression Predicts Poor Prognosis of Patients from TCGA Gastric Cancer Cohort", "row_count": 10, "column_count": 13}, "table": {"label": "Table 1", "caption": "The Cox Regression Analysis for Overall Survival (OVS) and Disease-free Survival (DFS) in TCGA Gastric Cancer Cohort", "rows": [["Factors", "OVS", "DFSa"], ["Univariate Cox", "Multivariate Cox", "Univariate Cox", "Multivariate Cox"], ["HR", "95% CI", "p Value", "HR", "95% CI", "p Value", "HR", "95% CI", "p Value", "HR", "95% CI", "p Value"], ["MAGI2-AS3", "1.18", "1.04–1.34", "0.0102b", "1.24", "1.07–1.42", "0.0031b", "2.54", "1.21–5.29", "0.0133b", "2.51", "1.17–5.38", "0.0181b"], ["Sex", "0.81", "0.57–1.15", "0.2442", "N/A", "N/A", "N/A", "1.22", "0.56–2.66", "0.6096", "N/A", "N/A", "N/A"], ["Age", "1.64", "1.16–2.32", "0.0051b", "1.98", "1.38–2.83", "0.0002b", "1.01", "0.97–1.05", "0.6087", "N/A", "N/A", "N/A"], ["T stage", "1.39", "1.14–1.71", "0.0014b", "1.28", "1.02–1.59", "0.0297b", "0.9", "0.55–1.49", "0.6907", "N/A", "N/A", "N/A"], ["N stage", "1.3", "1.13–1.49", "0.0002b", "1.26", "1.09–1.45", "0.0018b", "0.9", "0.67–1.23", "0.5159", "N/A", "N/A", "N/A"], ["M stage", "1.44", "1.05–1.99", "0.0237b", "1.36", "0.99–1.86", "0.0555b", "0.56", "0.08–4.15", "0.5731", "N/A", "N/A", "N/A"], ["Histological type", "0.95", "0.64–1.41", "0.7936", "N/A", "N/A", "N/A", "0.93", "0.44–1.98", "0.8502", "N/A", "N/A", "N/A"]], "row_count": 10, "column_count": 13, "numeric_cells": 64, "header_rows": 3, "locator": "section[4]/table-wrap[1]#tbl1"}}, {"id": "asset:table:pmid:31837602:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9328d5521f8d842da3818941e27ab36a4254577805fd1ce51fb15b6d62691b24", "bytes": 1353, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#tbl2", "version": null, "note": "The Cox Regression Analysis for Overall Survival (OVS) and Disease-free Survival (DFS) in the GSE62254 Gastric Cancer Cohort", "structure": {"pmcid": "PMC6920306", "section_index": 5, "section_title": "MAGI2-AS3 Overexpression Predicts a Poor Prognosis of Gastric Cancer Patients in the ACRG Cohort", "row_count": 10, "column_count": 13}, "table": {"label": "Table 2", "caption": "The Cox Regression Analysis for Overall Survival (OVS) and Disease-free Survival (DFS) in the GSE62254 Gastric Cancer Cohort", "rows": [["Factors", "OVS", "DFS"], ["Univariate Cox", "Multivariate Cox", "Univariate Cox", "Multivariate Cox"], ["HR", "95% CI", "p Value", "HR", "95% CI", "p Value", "HR", "95% CI", "p Value", "HR", "95% CI", "p Value"], ["MAGI2-AS3", "6.73", "2.43–18.66", "0.0002a", "3.67", "1.19–11.33", "0.0235a", "8.33", "2.71–25.55", "0.0002a", "4", "1.15–13.92", "0.0293a"], ["Sex", "1.11", "0.79–1.55", "0.5587", "N/A", "N/A", "N/A", "1.04", "0.72–1.51", "0.8303", "N/A", "N/A", "N/A"], ["Age", "1.01", "1–1.03", "0.1812", "N/A", "N/A", "N/A", "1.47", "1.03–2.09", "0.0331a", "N/A", "N/A", "N/A"], ["T stage", "1.78", "1.43–2.22", "0.0000a", "1.29", "1.01–1.65", "0.0438a", "1.75", "1.37–2.22", "0.0000a", "1.24", "0.95–1.62", "0.1094"], ["N stage", "1.96", "1.63–2.34", "0.0000a", "1.72", "1.42–2.09", "0.0000a", "2.08", "1.71–2.53", "0.0000a", "1.81", "1.46–2.23", "0.0000a"], ["M stage", "3.84", "2.48–5.94", "0.0000a", "2.29", "1.45–3.6", "0.0003a", "4.04", "2.51–6.51", "0.0000a", "2.11", "1.28–3.47", "0.0034a"], ["Lauren", "0.58", "0.42–0.8", "0.0010a", "0.87", "0.61–1.24", "0.4354", "0.59", "0.41–0.85", "0.0041a", "0.9", "0.61–1.34", "0.6090"]], "row_count": 10, "column_count": 13, "numeric_cells": 76, "header_rows": 3, "locator": "section[5]/table-wrap[1]#tbl2"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Survival curves were calculated using the Kaplan-Meier method, and differences between the curves were analyzed using the log rank test. A Cox proportional hazards model was used for multivariate survival analysis."}}, {"id": "method-2", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann-Whitney"}}, {"id": "method-3", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-4", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-5", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log rank"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": "R4", "reachable": false, "accessions": ["GEO: GSE79973", "GEO: GSE54129", "GEO: GSE62254", "GEO: GSE26595", "GEO: GSE15459", "GEO: GSE26596", "GEO: GSE22377", "GEO: GSE51105"], "resolved_accessions": [], "statements": ["RNA-seq data of 407 gastric cancer samples, miRNA-seq data of 491 gastric cancer samples, and the correlated clinical information of 443 gastric cancer samples were downloaded from The Cancer Genome Atlas (TCGA) by using SangerBox software (http://sangerbox.com/) developed by ShengXinRen (https://shengxin.ren/)."], "basis": "The paper names GEO: GSE79973, GEO: GSE54129, GEO: GSE62254, GEO: GSE26595, GEO: GSE15459, GEO: GSE26596, GEO: GSE22377, GEO: GSE51105, but the accession does not resolve in the repository (no reason recorded, no reason recorded, no reason recorded, no reason recorded, no reason recorded, no reason recorded, no reason recorded, no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:31837602", "asset:table:pmid:31837602:1", "asset:table:pmid:31837602:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:32Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 39949, "completion_tokens": 2942, "cached_tokens": 656}}, "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:31837602", "type": "paper", "label": "pmid:31837602"}, {"id": "source:pmid:31837602", "type": "manuscript", "label": "PMID 31837602 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31837602", "type": "paper", "label": "pmid:31837602"}, {"id": "source:pmid:31837602", "type": "manuscript", "label": "PMID 31837602 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31837602", "type": "extraction", "used": ["source:pmid:31837602"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:31837602", "parent_hash": "sha256:ba143e272e351b50d2c34fd29c091b3068411241d4081695082c4442c7a6e275", "fork_of": null, "generation": 7}, "gaps": ["execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ed a comprehensive transcriptome analysis of RNA-seq data from 373 gastric cancer tissues with co", "t available.aP < 0.05. Materials and Methods RNA-Seq Data Analysis of Stomach Cancer in TCGA RNA-", "gastric cancer, we performed a comprehensive transcriptome analysis of RNA-seq data from 373 gastric ca", "-Seq Data Analysis of Stomach Cancer in TCGA RNA-seq data of 407 gastric cancer samples, miRNA-se"], "order_basis": "paper_text_order:2244", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["http://www.cbioportal.org/).37 Cell Culture, Transfection, and Treatment The human gastric cancer cell", "0.03% glutamine at 37°C in 5% CO2. For siRNA transfection: the siRNAs were designed and synthesized by", "ncer cells were grown in six-well plates and transfected by Lipofectamine 2000 (Invitrogen) according", "he manufacturer’s instructions. At 48 h post-transfection, cells were harvested for qPCR analysis. For"], "order_basis": "paper_text_order:10380", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["(Shanghai, China). All of the gastric cancer cell lines were cultured in DMEM containing 10% fetal bovine serum (F", "). All of the gastric cancer cell lines were cultured in DMEM containing 10% fetal bovine serum (FBS)"], "order_basis": "paper_text_order:10643", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["post-transfection, cells were harvested for qPCR analysis. For lncRNA MAGI2-AS3 overexpressio", "d DMSO. After 24 h, cells were harvested for qPCR analysis. Statistical Analysis For gene expr"], "order_basis": "paper_text_order:11403", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Survival curves were calculated using the Kaplan-Meier method, and differences between the curves were analyzed using the log rank test. A Cox proportional hazards model was used for multivariate survival analysis."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"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":"2026-11-04T03:47:24+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}}}