{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32802507", "kind": "science-record", "revision": 8, "content_hash": "sha256:cb614918e14d8e34c941fbf58fdef3c7937a8479df4a303ac280fdab597fd105", "created_at": "2026-11-01T15:41:08Z", "updated_at": "2026-11-01T22:45:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection.", "doi": "10.1155/2020/6285987", "pmid": "32802507", "authors": ["Ping Yang", "Junjie Liu", "Tianci Yang", "Lei Zhang", "Peiyou Gong", "Boqing Li", "Xiuzhi Zhou"], "journal": "Biochemistry research international", "year": 2020, "abstract": "BACKGROUND: Helicobacter pylori (H. pylori) is a common human pathogen, which is closely correlated with gastric cancer (GC). However, the mechanism of H. pylori-related GC has not been elucidated. This study aimed to explore the role of H. pylori infection in GC and find biomarkers for early diagnosis of H. pylori-related GC.\nMETHODS: We identified differentially expressed microRNAs (DEMs) and genes (DEGs) from the Gene Expression Omnibus (GEO) dataset, constructed microRNA-(miRNA-)mRNA expression networks, analyzed the function and signal pathway of cross-genes, analyzed the relations between cross-genes and GC prognosis with the Cancer Genome Atlas (TCGA) data, and verified the expression of cross-genes in patients with H. pylori infection.\nRESULTS: 22 DEMs and 68 DEGs were identified in GSE197694 and GSE27411 dataset. 16 miRNAs and 509 genes were involved in the expression network, while the cross-genes of the network were mainly enriched in MAP kinase (MAPK) signaling pathway and TGF-beta signaling pathway. Patients with higher expression of hsa-miR-196b-3p, CALML4, or SMAD6 or lower expression of PITX2 or TGFB2 had better outcomes than those with lower expression of hsa-miR-196b-3p, CALML4, or SMAD6 or higher expression of PITX2 or TGFB2 (P < 0.05). Patients with H. pylori infection had a higher expression of hsa-miR-196b-3p and CALML4 than those without H. pylori infection (P < 0.05).\nCONCLUSION: The study of miRNA-mRNA expression network would provide molecular support for early diagnosis and treatment of H. pylori-related GC.", "claims": [{"id": "claim-data-access", "statement": "The data used to support the findings of this study are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32802507", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are included 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:32802507"], "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:GSE19769"], "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": {"fdr_threshold": "with Benjamini–Hochberg false discovery rate adjustment; source data"}, "inputs": ["data:geo:GSE19769"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32802507", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/6285987", "sha256": "sha256:576e5d829dbacb0034de4414ab1a98189214ec2ac9cc0ddb308389934154c4fa", "bytes": 36653, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/6285987", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7410007", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19769", "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=GSE19769", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19769", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM493633", "GSM493634", "GSM493635", "GSM493636", "GSM493637", "GSM493638", "GSM493639", "GSM493640", "GSM493641", "GSM493642", "GSM493643", "GSM493644", "GSM493645", "GSM493646", "GSM493647", "GSM493648", "GSM493649", "GSM493650", "GSM493651"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "9081", "taxon": "Homo sapiens", "title": "miRNA expression signatures for human stomach biopsy samples, H. pylori positive versus negative", "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:GSE27411", "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=GSE27411", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27411", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM677730", "GSM677731", "GSM677732", "GSM677733", "GSM677734", "GSM677735", "GSM677736", "GSM677737", "GSM677738", "GSM677739", "GSM677740", "GSM677741", "GSM677742", "GSM677743", "GSM677744", "GSM677745", "GSM677746", "GSM677747"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "6255", "taxon": "Homo sapiens", "title": "Transcriptional analysis reveals the molecular details of atrophic gastritis in Helicobacter pylori infected corpus mucosa", "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:32802507:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:15d591098eb1847c8ace3949d16533763d39d07b3bda933b7af97d66cf348587", "bytes": 463, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#tab1", "version": null, "note": "Summary of clinical information of 69 patients.", "structure": {"pmcid": "PMC7410007", "section_index": 8, "section_title": "2.6. Patient Data", "row_count": 13, "column_count": 2}, "table": {"label": "Table 1", "caption": "Summary of clinical information of 69 patients.", "rows": [["Characteristics", "Patients (n)"], ["Age (year)", ""], ["≤60", "31"], [">60", "38"], ["Sex", ""], ["Male", "46"], ["Female", "23"], ["Histopathological type", ""], ["Gastritis", "32"], ["Gastric adenocarcinoma", "37"], ["H. pylori infection", ""], ["Negative", "18"], ["Positive", "51"]], "row_count": 13, "column_count": 2, "numeric_cells": 10, "header_rows": 1, "locator": "section[8]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:32802507:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:151f09184be0dee792afdef54e13851aee5dd8edd8a8a6a46d001d297fdc6578", "bytes": 2123, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tab2", "version": null, "note": "Differential expression of miRNAs of H. pylori-negative and -positive patients.", "structure": {"pmcid": "PMC7410007", "section_index": 13, "section_title": "3.1. Identification of DEMs and DEGs", "row_count": 23, "column_count": 7}, "table": {"label": "Table 2", "caption": "Differential expression of miRNAs of H. pylori-negative and -positive patients.", "rows": [["miRNA ID", "LogFC", "t", "B", "P value", "Adj. P value", "Expression"], ["hsa-miR-455", "−1.29961", "−13.2889", "14.50158", "1.32E − 10", "6.20E − 08", "Down"], ["hsa-miR-223", "2.015725", "7.995567", "7.036115", "2.91E − 07", "5.02E − 05", "Up"], ["hsa-miR-200a-5p", "−1.04839", "−7.29849", "5.792449", "1.02E − 06", "9.54E − 05", "Down"], ["hsa-miR-146b", "1.846493", "7.098055", "5.422075", "1.47E − 06", "0.000115", "Up"], ["hsa-miR-200a-3p", "−1.18346", "−6.46158", "4.208209", "4.97E − 06", "0.000249", "Down"], ["hsa-miR-155", "1.41517", "6.230643", "3.753807", "7.83E − 06", "0.000335", "Up"], ["hsa-miR-411", "−1.54782", "−5.84129", "2.971589", "1.71E − 05", "0.00062", "Down"], ["hsa-miR-551b", "−1.30788", "−5.44908", "2.164424", "3.85E − 05", "0.000994", "Down"], ["hsa-miR-142-3p", "1.67688", "5.430155", "2.12503", "4.00E − 05", "0.000994", "Up"], ["hsa-miR-203", "−1.63669", "−5.12951", "1.494025", "7.54E − 05", "0.001476", "Down"], ["hsa-miR-142-5p", "1.677953", "5.051426", "1.32866", "8.90E − 05", "0.001609", "Up"], ["hsa-miR-153", "−1.47449", "−4.88801", "0.980864", "0.000126", "0.002045", "Down"], ["hsa-miR-204", "−1.55239", "−4.24223", "−0.41065", "0.000513", "0.006184", "Down"], ["hsa-miR-196b", "1.594266", "3.80117", "−1.36658", "0.001355", "0.012736", "Up"], ["hsa-miR-509", "1.069763", "3.765869", "−1.44288", "0.001465", "0.013238", "Up"], ["hsa-miR-326", "−1.20269", "−3.53852", "−1.93239", "0.002417", "0.019915", "Down"], ["hsa-miR-146a", "1.324456", "3.446357", "−2.1296", "0.00296", "0.022082", "Up"], ["hsa-miR-299-5p", "−1.04861", "−3.32334", "−2.39132", "0.003877", "0.027607", "Down"], ["hsa-miR-520e", "1.32247", "3.302749", "−2.43493", "0.004055", "0.028448", "Up"], ["hsa-miR-650", "1.709805", "3.294791", "−2.45177", "0.004127", "0.028522", "Up"], ["hsa-miR-138", "1.114925", "3.195115", "−2.6619", "0.00513", "0.033381", "Up"], ["hsa-miR-368", "−1.02603", "−3.19023", "−2.67214", "0.005185", "0.033381", "Down"]], "row_count": 23, "column_count": 7, "numeric_cells": 132, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tab2"}}, {"id": "asset:table:pmid:32802507:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c848761bdfa67ec835b58a78474ebe0fa93e112d08cf1b81710aa8ea316c064a", "bytes": 2404, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tab3", "version": null, "note": "Top 10 GO functions of the cross-genes in the network.", "structure": {"pmcid": "PMC7410007", "section_index": 15, "section_title": "3.3. GO and KEGG Analysis of Cross-Genes in the Network", "row_count": 33, "column_count": 4}, "table": {"label": "Table 3", "caption": "Top 10 GO functions of the cross-genes in the network.", "rows": [["Category", "Gene terms", "Count", "P value"], ["Biological process", "GO:0003148, outflow tract septum morphogenesis", "10", "1.24E − 09"], ["GO:0003151, outflow tract morphogenesis", "15", "3.98E − 09"], ["GO:0001655, urogenital system development", "30", "6.76E − 09"], ["GO:0003279, cardiac septum development", "17", "1.22E − 08"], ["GO:0060411, cardiac septum morphogenesis", "13", "1.60E − 07"], ["GO:0010632, regulation of epithelial cell migration", "26", "1.74E − 07"], ["GO:0010631, epithelial cell migration", "29", "1.75E − 07"], ["GO:0061564, axon development", "33", "1.77E − 07"], ["GO:0043542, endothelial cell migration", "25", "1.77E − 07"], ["GO:0090132, epithelium migration", "29", "2.09E − 07"], [""], ["Cellular component", "GO:0005667, transcription factor complex", "23", "4.28E − 07"], ["GO:0097060, synaptic membrane", "26", "9.71E − 06"], ["GO:0045211, postsynaptic membrane", "21", "2.70E − 05"], ["GO:0099699, integral component of synaptic membrane", "14", "3.31E − 05"], ["GO:0005912, adherens junction", "28", "7.12E − 05"], ["GO:0099240, intrinsic component of synaptic membrane", "14", "7.62E − 05"], ["GO:0033267, axon part", "22", "0.000108619"], ["GO:0000790, nuclear chromatin", "20", "0.000128584"], ["GO:0099055, integral component of postsynaptic membrane", "11", "0.000162968"], ["GO:0000151, ubiquitin ligase complex", "16", "0.000198327"], [""], ["Molecular function", "GO:0000978, RNA polymerase II proximal promoter sequence-specific DNA binding", "38", "5.75E − 10"], ["GO:0000987, proximal promoter sequence-specific DNA binding", "39", "5.92E − 10"], ["GO:0035326, enhancer binding", "19", "1.24E − 09"], ["GO:0000980, RNA polymerase II distal enhancer sequence-specific DNA binding", "15", "1.89E − 08"], ["GO:0001158 enhancer sequence-specific DNA binding", "16", "5.18E − 08"], ["GO:0003682, chromatin binding", "34", "9.92E − 08"], ["GO:0001228, DNA-binding transcription activator activity, RNA polymerase II-specific", "29", "2.20E − 06"], ["GO:0004714, transmembrane receptor protein tyrosine kinase activity", "9", "7.94E − 06"], ["GO:0003712, transcription coregulator activity", "32", "1.19E − 05"], ["GO:0019199, transmembrane receptor protein kinase activity", "10", "1.30E − 05"]], "row_count": 33, "column_count": 4, "numeric_cells": 90, "header_rows": 1, "locator": "section[15]/table-wrap[1]#tab3"}}, {"id": "asset:table:pmid:32802507:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:569f5007a3362aa53a4316ad2ea4c753057faff632ded54be53d997f9bc0c413", "bytes": 797, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#tab4", "version": null, "note": "Top 10 KEGG pathways of the cross-genes in the network.", "structure": {"pmcid": "PMC7410007", "section_index": 15, "section_title": "3.3. GO and KEGG Analysis of Cross-Genes in the Network", "row_count": 12, "column_count": 3}, "table": {"label": "Table 4", "caption": "Top 10 KEGG pathways of the cross-genes in the network.", "rows": [["KEGG terms", "Count", "P value"], ["MAPK signaling pathway", "25", "3.70E − 06"], ["Axon guidance", "17", "3.89E − 05"], ["Ras signaling pathway", "19", "9.06E − 05"], ["TGF-beta signaling pathway", "11", "0.000134809"], ["cGMP-PKG signaling pathway", "15", "0.000184067"], ["Human cytomegalovirus infection", "18", "0.000186779"], ["Adrenergic signaling in cardiomyocytes", "14", "0.00018806"], ["Hepatocellular carcinoma", "15", "0.000196653"], ["Rap1 signaling pathway", "17", "0.000244921"], ["ErbB signaling pathway", "10", "0.000259955"], ["Growth hormone synthesis, secretion, and action", "12", "0.000281056"]], "row_count": 12, "column_count": 3, "numeric_cells": 22, "header_rows": 1, "locator": "section[15]/table-wrap[2]#tab4"}}], "gaps": ["asset:data:geo:GSE19769 not downloaded", "asset:data:geo:GSE19769 licence not read", "asset:data:geo:GSE27411 not downloaded", "asset:data:geo:GSE27411 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fdr_threshold": "with Benjamini–Hochberg false discovery rate adjustment; source data"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "reordered", "quote": "“The significance analysis of DEGs and DEMs in H. pylori-negative and -positive samples was performed using the R language software (version 3.6.0, https://www.r-project.org/) and a limma R package. The Benjamini and Hochberg false discovery rate (FDR) method was used to adjust the P value to reduce the false-positive risk.” “The miRNA expression profile (GSE19769) [7] and the gene expression profile (GSE27411) [17] were included in this study.”"}}], "targets": [], "gaps": []}, "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: limma_voom."}, "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": ["GSE19769", "GSE27411"], "resolved_accessions": ["GSE19769", "GSE27411"], "statements": ["The data used to support the findings of this study are included within the article."], "basis": "The paper names GSE19769, GSE27411 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:32802507", "data:geo:GSE19769", "asset:table:pmid:32802507:1", "asset:table:pmid:32802507:2", "asset:table:pmid:32802507:3", "asset:table:pmid:32802507:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19769"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:57Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 33850, "completion_tokens": 1835, "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:32802507", "type": "paper", "label": "pmid:32802507"}, {"id": "source:pmid:32802507", "type": "manuscript", "label": "PMID 32802507 full text"}, {"id": "data:geo:GSE19769", "type": "dataset", "label": "GEO GSE19769"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32802507", "type": "paper", "label": "pmid:32802507"}, {"id": "source:pmid:32802507", "type": "manuscript", "label": "PMID 32802507 full text"}, {"id": "data:geo:GSE19769", "type": "dataset", "label": "GEO GSE19769"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32802507", "type": "extraction", "used": ["source:pmid:32802507"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19769", "type": "accession_resolution", "used": ["data:geo:GSE19769"], "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:32802507", "parent_hash": "sha256:b38607fb95f02aff89f2fb8645454d3be7000f7a864df692bacbb5f0a49cebc8", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE19769 licence not read", "asset:data:geo:GSE19769 not downloaded", "asset:data:geo:GSE27411 licence not read", "asset:data:geo:GSE27411 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["“The significance analysis of DEGs and DEMs in H. pylori-negative and -positive samples was performed using the R language software (version 3.6.0, https://www.r-project.org/) and a limma R package. The Benjamini and Hochberg false discovery rate (FDR) method was used to adjust the P value to reduce the false-positive risk.” “The miRNA expression profile (GSE19769) [7] and the gene expression profile (GSE27411) [17] were included in this study.”"], "order_basis": "analysis_only", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:39:24+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}}}