{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33403032", "kind": "science-record", "revision": 9, "content_hash": "sha256:6aa4ac745dc8be6c074b8bbaffd0c3ffe47dd6987dee37f7a8ad9f6d34c0c9cf", "created_at": "2026-11-01T15:41:21Z", "updated_at": "2026-11-01T22:45:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Seven Cell Cycle-Related Genes with Unfavorable Prognosis and Construction of their TF-miRNA-mRNA regulatory network in Breast Cancer.", "doi": "10.7150/jca.48245", "pmid": "33403032", "authors": ["Zhipeng Hong", "Qinglan Wang", "Chengye Hong", "Meimei Liu", "Pengqin Qiu", "Rongrong Lin", "Xiaolan Lin", "Fangfang Chen", "Qiuhuang Li", "Lingling Liu", "Chuan Wang", "Debo Chen"], "journal": "Journal of Cancer", "year": 2021, "abstract": "Breast cancer (BC), with complex tumorigenesis and progression, remains the most common malignancy in women. We aimed to explore some novel and significant genes with unfavorable prognoses and potential pathways involved in BC initiation and progression via bioinformatics methods. BC tissue-specific microarray datasets of GSE42568, GSE45827 and GSE54002, which included a total of 651 BC tissues and 44 normal breast tissues, were obtained from the Gene Expression Omnibus (GEO) database, and 124 differentially expressed genes (DEGs) were identified between BC tissues and normal breast tissues via R software and an online Venn diagram tool. Database for Annotation, Visualization and Integration Discovery (DAVID) software showed that 65 upregulated DEGs were mainly enriched in the regulation of the cell cycle, and Search Tool for the Retrieval of Interacting Genes (STRING) software identified the 39 closest associated upregulated DEGs in protein-protein interactions (PPIs), which validated the high expression of genes in BC tissues by the Gene Expression Profiling Interactive Analysis (GEPIA) tool. In addition, 36 out of 39 BC patients showed significantly worse outcomes by Kaplan-Meier plotter (KM plotter), and an additional Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that seven genes (cyclin E2 (CCNE2), cyclin B1 (CCNB1), cyclin B2 (CCNB2), mitotic checkpoint serine/threonine kinase B (BUB1B), dual-specificity protein kinase (TTK), cell division cycle 20 (CDC20), and pituitary tumor transforming gene 1 (PTTG1)) were markedly enriched in the cell cycle pathway. Analysis of the clinicopathological characteristics of hub genes revealed that seven cell cycle-related genes (CCRGs) were significantly highly expressed in four BC subtypes (luminal A, luminal B, HER2-positive and triple-negative (TNBC)), and except for the CCNE2 gene, high expression levels were significantly associated with tumor pathological grade and stage and metastatic events of BC. Furthermore, genetic mutation analysis indicated that genetic alterations of CCRGs could also significantly affect BC patients' prognosis. A quantitative real-time polymerase chain reaction (qRT-PCR) assay found that the seven CCRGs were significantly differentially expressed in BC cell lines. Integration of published multilevel expression data and a bioinformatics computational approach were used to predict and construct a regulation mechanism: a transcription factor (TF)-microRNA (miRNA)-messenger RNA (mRNA) regulation network. The present work is the first to construct a regulatory network of TF-miRNA-mRNA in BC for CCRGs and provides new insights into the molecular mechanism of BC.", "claims": [{"id": "claim-method", "statement": "We detected and removed batch effects in each dataset (Supplementary Figure S1) and then classified the BC specimens and normal breast specimens in three microarray datasets using R software (version 3.4.4) packages edgeR and limma to identify DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33403032", "locator": "sections[4] \"Data processing and differential analysis\" paragraph 2", "quote": "We detected and removed batch effects in each dataset (Supplementary Figure S1) and then classified the BC specimens and normal breast specimens in three microarray datasets using R software (version 3.4.4) packages edgeR and limma to identify DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray datasets of GSE42568, GSE45827 and GSE54002 were all processed on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and contained 104 BC tissues and 17 normal breast tissues, 130 BC tissues and 11 normal breast tissues, and 417 BC tissues and 16 breast tissues, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33403032", "locator": "sections[3] \"Collection of microarray data information from GEO datasets\" paragraph 2", "quote": "Microarray datasets of GSE42568, GSE45827 and GSE54002 were all processed on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and contained 104 BC tissues and 17 normal breast tissues, 130 BC tissues and 11 normal breast tissues, and 417 BC tissues and 16 breast tissues, respectively."}], "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:33403032"], "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:GSE42568"], "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:GSE42568"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33403032", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.48245", "sha256": 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"GSM1045284", "GSM1045285", "GSM1045286", "GSM1045287", "GSM1045288", "GSM1045289", "GSM1045290", "GSM1045291", "GSM1045292", "GSM1045293", "GSM1045294", "GSM1045295", "GSM1045296", "GSM1045297", "GSM1045298", "GSM1045299", "GSM1045300", "GSM1045301", "GSM1045302", "GSM1045303", "GSM1045304", "GSM1045305", "GSM1045306", "GSM1045307", "GSM1045308", "GSM1045309", "GSM1045310", "GSM1045311"], "sample_count": 121, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Breast Cancer Gene Expression Analysis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE45827", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45827", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45827", "version": null, "note": "Microarray datasets of GSE42568, GSE45827 and GSE54002 were all processed on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and contained 104 BC tissues and 17 normal breast tissues, 130 BC tissues and 11 normal breast tissues, and 417 BC tissues and 16 breast tissues, respectively.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets of GSE42568, GSE45827 and GSE54002 were all processed on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and contained 104 BC tissues and 17 normal breast tissues, 130 BC tissues and 11 normal breast tissues, and 417 BC tissues and 16 breast tissues, respectively.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1116084", "GSM1116085", "GSM1116086", "GSM1116087", "GSM1116088", "GSM1116089", 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"GSM1116232", "GSM1116233", "GSM1116234", "GSM1116235", "GSM1116236", "GSM1116237", "GSM1116238"], "sample_count": 155, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from Breast cancer subtypes", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE54002", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54002", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54002", "version": null, "note": "Microarray datasets of GSE42568, GSE45827 and GSE54002 were all processed on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and contained 104 BC tissues and 17 normal breast tissues, 130 BC tissues and 11 normal breast tissues, and 417 BC tissues and 16 breast tissues, respectively.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets of GSE42568, GSE45827 and GSE54002 were all processed on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and contained 104 BC tissues and 17 normal breast tissues, 130 BC tissues and 11 normal breast tissues, and 417 BC tissues and 16 breast tissues, respectively.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1305324", "GSM1305325", "GSM1305326", "GSM1305327", "GSM1305328", "GSM1305329", "GSM1305330", "GSM1305331", "GSM1305332", "GSM1305333", "GSM1305334", "GSM1305335", "GSM1305336", "GSM1305337", "GSM1305338", "GSM1305339", "GSM1305340", "GSM1305341", "GSM1305342", "GSM1305343", "GSM1305344", "GSM1305345", "GSM1305346", "GSM1305347", "GSM1305348", "GSM1305349", 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"GSM1305705", "GSM1305706", "GSM1305707", "GSM1305708", "GSM1305709", "GSM1305710", "GSM1305711", "GSM1305712", "GSM1305713", "GSM1305714", "GSM1305715", "GSM1305716", "GSM1305717", "GSM1305718", "GSM1305719", "GSM1305720", "GSM1305721", "GSM1305722", "GSM1305723", "GSM1305724", "GSM1305725", "GSM1305726", "GSM1305727", "GSM1305728", "GSM1305729", "GSM1305730", "GSM1305731", "GSM1305732", "GSM1305733", "GSM1305734", "GSM1305735", "GSM1305736", "GSM1305737", "GSM1305738", "GSM1305739", "GSM1305740", "GSM1305741", "GSM1305742", "GSM1305743", "GSM1305744", "GSM1305745", "GSM1305746", "GSM1305747", "GSM1305748", "GSM1305749", "GSM1305750", "GSM1305751", "GSM1305752", "GSM1305753", "GSM1305754", "GSM1305755", "GSM1305756"], "sample_count": 433, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling of LCM captured breast cancer cells", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE42568 not downloaded", "asset:data:geo:GSE42568 licence not read", "asset:data:geo:GSE45827 not downloaded", "asset:data:geo:GSE45827 licence not read", "asset:data:geo:GSE54002 not downloaded", "asset:data:geo:GSE54002 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We detected and removed batch effects in each dataset (Supplementary Figure S1) and then classified the BC specimens and normal breast specimens in three microarray datasets using R software (version 3.4.4) packages edgeR and limma to identify DEGs."}}, {"id": "method-2", "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": "analysis of variance"}}, {"id": "method-3", "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": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "he log-rank p value and hazard ratio (HR) with 95% confidenc", "p_value": "The log-rank p value and hazard ratio (HR) w"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-5", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-6", "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": "PPI"}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: edger."}, "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": ["GSE42568", "GSE45827", "GSE54002"], "resolved_accessions": ["GSE42568", "GSE45827", "GSE54002"], "statements": ["Microarray datasets of GSE42568, GSE45827 and GSE54002 were all processed on the GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) and contained 104 BC tissues and 17 normal breast tissues, 130 BC tissues and 11 normal breast tissues, and 417 BC tissues and 16 breast tissues, respectively."], "basis": "The paper names GSE42568, GSE45827, GSE54002 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:33403032", "data:geo:GSE42568"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE42568"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 40313, "completion_tokens": 1740, "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:33403032", "type": "paper", "label": "pmid:33403032"}, {"id": "source:pmid:33403032", "type": "manuscript", "label": "PMID 33403032 full text"}, {"id": "data:geo:GSE42568", "type": "dataset", "label": "GEO GSE42568"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33403032", "type": "paper", "label": "pmid:33403032"}, {"id": "source:pmid:33403032", "type": "manuscript", "label": "PMID 33403032 full text"}, {"id": "data:geo:GSE42568", "type": "dataset", "label": "GEO GSE42568"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33403032", "type": "extraction", "used": ["source:pmid:33403032"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE42568", "type": "accession_resolution", "used": ["data:geo:GSE42568"], "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:33403032", "parent_hash": "sha256:a13417279c883c942fd1660a653728d4b26d5b7448fd612eeec46aa1f8f09f3e", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE42568 licence not read", "asset:data:geo:GSE42568 not downloaded", "asset:data:geo:GSE45827 licence not read", "asset:data:geo:GSE45827 not downloaded", "asset:data:geo:GSE54002 licence not read", "asset:data:geo:GSE54002 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["a bioinformatics methods. BC tissue-specific microarray datasets of GSE42568, GSE45827 and GSE54002,", "ecimens and normal breast specimens in three microarray datasets using R software (version 3.4.4) pa"], "order_basis": "paper_text_order:409", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["(KM plotter) system contained gene ChIP and RNA-seq data sources from the TCGA, European Genome-"], "order_basis": "paper_text_order:3625", "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": ["mycin. MCF-7 cells and MDA-MB-231 cells were cultured in DMEM (Gibco, Carlsbad, CA, United States) co", "ithelial cell line MCF-10A and BC cell lines MCF-7 and MDA-MB-231 were purchased from the Cell", "e and 1 unit (U)/ml penicillin/streptomycin. MCF-7 cells and MDA-MB-231 cells were cultured in"], "order_basis": "paper_text_order:4149", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e protein expression of CCRGs in BC, we used IHC to compare the protein expression between no", "es via the Human Protein Atlas database. The IHC map of CCRGs is shown in Figure 7 and confir", "f data available in the Human Protein Atlas. IHC analysis and RNA expression analysis of gene"], "order_basis": "paper_text_order:10940", "id": "assay:4"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We detected and removed batch effects in each dataset (Supplementary Figure S1) and then classified the BC specimens and normal breast specimens in three microarray datasets using R software (version 3.4.4) packages edgeR and limma to identify DEGs."], "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":"2026-11-04T01:23:04+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}}}