{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32292720", "kind": "science-record", "revision": 8, "content_hash": "sha256:22063d3488890aeb579b63c5bb4ba978f6fbf9a67ee3514debde96b292b8d5a4", "created_at": "2026-11-01T15:40:59Z", "updated_at": "2026-11-01T22:44:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene Expression Profiles Identified Novel Urine Biomarkers for Diagnosis and Prognosis of High-Grade Bladder Urothelial Carcinoma.", "doi": "10.3389/fonc.2020.00394", "pmid": "32292720", "authors": ["Yuxuan Song", "Donghui Jin", "Ningjing Ou", "Zhiwen Luo", "Guangyuan Chen", "Jingyi Chen", "Yongjiao Yang", "Xiaoqiang Liu"], "journal": "Frontiers in oncology", "year": 2020, "abstract": "Bladder urothelial carcinoma (BC) has been identified as one of the most common malignant neoplasm worldwide. High-grade bladder urothelial carcinoma (HGBC) is aggressive with a high risk of recurrence, progression, metastasis, and poor prognosis. Therefore, HGBC clinical management is still a challenge. We performed the present study to seek new urine biomarkers for HGBC and investigate how they promote HGBC progression and thus affect the prognosis based on large-scale sequencing data. We identified the overlapped differentially expressed genes (DEGs) by combining GSE68020 and The Cancer Genome Atlas (TCGA) datasets. Subsequent receiver operating characteristic (ROC) curves, Kaplan-Meier (KM) curves, and Cox regression were conducted to test the diagnostic and prognostic role of the hub genes. Chi-square test and logistic regression were carried out to analyze the associations between clinicopathologic characteristics and the hub genes. Ultimately, we performed gene set enrichment analysis (GSEA), protein-protein interaction (PPI) networks, and Bayesian networks (BNs) to explore the underlying mechanisms by which ECM1, CRYAB, CGNL1, and GPX3 are involved in tumor progression. Immunohistochemistry based on The Human Protein Atlas and quantitative real-time polymerase chain reaction based on urine samples confirmed the downregulation and diagnostic values of the hub genes in HGBC. In conclusion, our study indicated that CRYAB, CGNL1, ECM1, and GPX3 are potential urine biomarkers of HGBC. These four novel urine biomarkers will have attractive applications to provide new diagnostic methods, prognostic predictors and treatment targets for HGBC, which could improve the prognosis of HGBC patients, if validated by further experiments and larger prospective clinical trials.", "claims": [{"id": "claim-method", "statement": "To identify DEGs in GSE68020 and TCGA BLCA datasets between BC patients and non-tumor healthy controls, we utilized limma R package (12).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32292720", "locator": "sections[5] \"RNA Data Processing and Identification of Differentially Expressed Genes\" paragraph 2", "quote": "To identify DEGs in GSE68020 and TCGA BLCA datasets between BC patients and non-tumor healthy controls, we utilized limma R package (12)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. The data can be found in Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/geo/), The Cancer Genome Atlas (TCGA: http://tcga-data.nci.nih.gov/tcga/), and The Human Protein Atlas (THPA: http://www.proteinatlas.org/). GSE68020 dataset was from GEO; BLCA (Bladder Urothelial Carcinoma) dataset was from TCGA; and immunohistochemistry was from THPA. All the data are open access. Summarized detailed characteristics of immunohistochemistry data from THPA are in Supplementary Table 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32292720", "locator": "sections[25] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. The data can be found in Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/geo/), The Cancer Genome Atlas (TCGA: http://tcga-data.nci.nih.gov/tcga/), and The Human Protein Atlas (THPA: http://www.proteinatlas.org/). GSE68020 dataset was from GEO; BLCA (Bladder Urothelial Carcinoma) dataset was from TCGA; and immunohistochemistry was from THPA. All the data are open access. Summarized detailed characteristics of immunohistochemistry data from THPA are in Supplementary Table 1."}], "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:32292720"], "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:GSE68020"], "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:GSE68020"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32292720", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2020.00394", "sha256": "sha256:6ad125e342732646ffb126f150ea9fbbca4e5f46d174b38c72ca9cce992c04d4", "bytes": 51190, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2020.00394", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7118735", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE68020", "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=GSE68020", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68020", "version": null, "note": "Publicly available datasets were analyzed in this study. The data can be found in Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/geo/), The Cancer Genome Atlas (TCGA: http://tcga-data.nci.nih.gov/tcga/), and The Human Protein Atlas (THPA: http://www.proteinatlas.org/). GSE68020 dataset was from GEO; BLCA (Bladder Urothelial Carcinoma) dataset was from TCGA; and immunohistochemistry was from THPA. All the data are open access. Summarized detailed characteristics of immunohistochemistry data from THPA are in Supplementary Table 1.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. The data can be found in Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/geo/), The Cancer Genome Atlas (TCGA: http://tcga-data.nci.nih.gov/tcga/), and The Human Protein Atlas (THPA: http://www.proteinatlas.org/). GSE68020 dataset was from GEO; BLCA (Bladder Urothelial Carcinoma) dataset was from TCGA; and immunohistochemistry was from THPA. All the data are open access. Summarized detailed characteristics of immunohistochemistry data from THPA are in Supplementary Table 1.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1661253", "GSM1661254", "GSM1661255", "GSM1661256", "GSM1661257", "GSM1661258", "GSM1661259", "GSM1661260", "GSM1661261", "GSM1661262", "GSM1661263", "GSM1661264", "GSM1661265", "GSM1661266", "GSM1661267", "GSM1661268", "GSM1661269", "GSM1661270", "GSM1661271", "GSM1661272", "GSM1661273", "GSM1661274", "GSM1661275", "GSM1661276", "GSM1661277", "GSM1661278", "GSM1661279", "GSM1661280", "GSM1661281", "GSM1661282", "GSM1661283", "GSM1661284", "GSM1661285", "GSM1661286", "GSM1661287", "GSM1661288", "GSM1661289", "GSM1661290", "GSM1661291", "GSM1661292", "GSM1661293", "GSM1661294", "GSM1661295", "GSM1661296", "GSM1661297", "GSM1661298", "GSM1661299", "GSM1661300", "GSM1661301", "GSM1661302"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Identification of gene expression biomarkers in urine for the non-invasive detection of bladder cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32292720:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:66d9922e67f97994348e7bed128832476525112b36424043d337b4c8f2b5790b", "bytes": 969, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#T5", "version": null, "note": "Comparison of immunohistochemistry expression level between normal bladder and HGBC by Fisher's Exact test from The Human Protein Atlas.", "structure": {"pmcid": "PMC7118735", "section_index": 11, "section_title": "Immunohistochemistry From the Human Protein Atlas", "row_count": 12, "column_count": 8}, "table": {"label": "Table 5", "caption": "Comparison of immunohistochemistry expression level between normal bladder and HGBC by Fisher's Exact test from The Human Protein Atlas.", "rows": [["Gene name", "", "N", "Immunohistochemistry expression level", "P-value"], ["", "", "", "Negative (–)", "Weakly positive (+)", "Positive (++)", "Strongly positive (+++)", ""], ["GPX3", "Normal bladder tissue", "2", "0", "2", "0", "0", "0.016"], ["", "HGBC tissue", "8", "7", "1", "0", "0", ""], ["ECM1", "Normal bladder tissue", "2", "0", "2", "0", "0", "0.001"], ["", "HGBC tissue", "9", "9", "0", "0", "0", ""], ["CRYAB", "Normal bladder tissue", "5", "5", "0", "0", "0", "0.439"], ["", "HGBC tissue", "9", "8", "0", "0", "1", ""], ["CGNL1", "Normal bladder tissue", "3", "3", "0", "0", "0", "0.569"], ["", "HGBC tissue", "10", "9", "1", "0", "0", ""], ["CRNN", "Normal bladder tissue", "4", "2", "2", "0", "0", "0.477"], ["", "HGBC tissue", "7", "5", "2", "0", "0", ""]], "row_count": 12, "column_count": 8, "numeric_cells": 55, "header_rows": 2, "locator": "section[21]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:32292720:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:843930f2864b7a6b42df17293939de17d46028a632ba996f9c7bfa849cffa218", "bytes": 892, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "Primer sequences used to amplify target genes by quantitative real-time polymerase chain reaction (qRT-PCR).", "structure": {"pmcid": "PMC7118735", "section_index": 12, "section_title": "Urine Samples in Tianjin Validation Cohort, RNA Extraction and Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR)", "row_count": 13, "column_count": 3}, "table": {"label": "Table 1", "caption": "Primer sequences used to amplify target genes by quantitative real-time polymerase chain reaction (qRT-PCR).", "rows": [["Gene name", "Primer sequences"], ["GPX3", "Forward", "5′-GAAGGCTCCCCGCCAGAT-3′"], ["", "Reverse", "5′-TCAATGGTGAGGGCTCCGTA-3′"], ["ECM1", "Forward", "5′-AGCACCCCAATGAACAGAAGG-3′"], ["", "Reverse", "5′-CTGCATTCCAGGACTCAGGTT-3′"], ["CRYAB", "Forward", "5'-TGGATAGAAGGGGGACAAGGAG-3′"], ["", "Reverse", "5′-CATGGAGACTTGTGATCCGGG-3′"], ["CGNL1", "Forward", "5'-TACGGTGTCAGTATTCGGGTC-3′"], ["", "Reverse", "5′-GCTGGGCGTATGGGTTTTC-3′"], ["CRNN", "Forward", "5′-GGGATCATCGAGGCCTTCAG-3′"], ["", "Reverse", "5′-CTGGATCGTGGGGTTTCACA-3′"], ["GAPDH", "Forward", "5′-AGAAGGCTGGGGCTCATTTG-3′"], ["", "Reverse", "5′-AGGGGCCATCCACAGTCTTC-3′"]], "row_count": 13, "column_count": 3, "numeric_cells": 12, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32292720:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:297453fd3a7b1ede543ed28571341e57d45521466fbb5e36606608195a65da45", "bytes": 4298, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#T2", "version": null, "note": "Relationship between expression of the five DEGs and clinicopathological characteristics in BC patients from TCGA.", "structure": {"pmcid": "PMC7118735", "section_index": 17, "section_title": "Correlations Between Expression Levels of the 5 Hub Genes and Clinical Outcomes in TCGA BLCA Dataset", "row_count": 30, "column_count": 17}, "table": {"label": "Table 2", "caption": "Relationship between expression of the five DEGs and clinicopathological characteristics in BC patients from TCGA.", "rows": [["Clinical characteristics", "Total (N)", "CRYAB expression", "P-value", "ECM1 expression", "P-value", "GPX3 expression", "P-value", "CGNL1 expression", "P-value", "CRNN expression", "P-value"], ["(A)", "", "High", "Low", "", "High", "Low", "", "High", "Low", "", "High", "Low", "", "High", "Low", ""], ["Histological grade"], ["High grade", "380", "198 (52.1%)", "182 (47.9%)", "<0.001", "199 (52.4%)", "181 (47.6%)", "<0.001", "196 (51.6%)", "184 (48.4%)", "0.006", "190 (50.0%)", "190 (50.0%)", "0.383", "192 (50.5%)", "188 (49.5%)", "0.176"], ["Low grade", "20", "2 (10.0%)", "18 (90.0%)", "", "1 (00.3%)", "19 (05.0%)", "", "4 (20.0%)", "16 (80.0%)", "", "8 (40.0%)", "12 (60.0%)", "", "7 (35.0%)", "13 (65.0%)", ""], ["UICC stage"], ["Stage I+II", "130", "43 (33.1%)", "87 (66.9%)", "<0.001", "47 (12.4%)", "83 (21.8%)", "<0.001", "52 (40.0%)", "78 (60.0%)", "0.006", "57 (43.8%)", "73 (56.2%)", "0.094", "71 (54.6%)", "59 (45.4%)", "0.189"], ["Stage III+IV", "271", "158 (58.3%)", "113 (41.7%)", "", "153 (40.3%)", "118 (31.1%)", "", "148 (54.6%)", "123 (45.4%)", "", "143 (52.8%)", "128 (47.2%)", "", "129 (47.6%)", "142 (52.4%)", ""], ["pT stage"], ["T1", "4", "0 (0.0%)", "4 (100.0%)", "0.052", "1 (00.3%)", "3 (00.8%)", "0.356", "2 (50.0%)", "2 (50.0%)", "1.000", "2 (50.0%)", "2 (50.0%)", "1.000", "3 (75.0%)", "1 (25.0%)", "0.623"], ["T2+T3+T4", "367", "193 (52.6%)", "174 (47.4%)", "", "191 (50.3%)", "176 (46.3%)", "", "189 (51.5%)", "178 (48.5%)", "", "184 (50.1%)", "183 (49.9%)", "", "184 (50.1%)", "183 (49.9%)", ""], ["pM stage"], ["No (M0)", "193", "78 (40.4%)", "115 (59.6%)", "0.988", "72 (18.9%)", "121 (31.8%)", "0.409", "77 (39.9%)", "116 (60.1%)", "0.215", "84 (43.5%)", "109 (56.5%)", "0.686", "91 (47.2%)", "102 (52.8%)", "0.485"], ["Yes (M1)", "11", "5 (45.5%)", "6 (54.5%)", "", "6 (01.6%)", "5 (01.3%)", "", "7 (63.6%)", "4 (36.4%)", "", "6 (54.5%)", "5 (45.5%)", "", "4 (36.4%)", "7 (63.6%)", ""], ["pN stage"], ["No (N0)", "234", "108 (46.2%)", "126 (53.8%)", "<0.001", "109 (28.7%)", "125 (32.9%)", "0.029", "116 (49.6%)", "118 (50.4%)", "0.430", "103 (44.0%)", "131 (56.0%)", "0.002", "125 (53.4%)", "109 (46.6%)", "0.106"], ["Yes (N1+N2+N3)", "128", "84 (65.6%)", "44 (34.4%)", "", "75 (19.7%)", "53 (13.9%)", "", "69 (53.9%)", "59 (46.1%)", "", "78 (60.9%)", "50 (39.1%)", "", "57 (44.5%)", "71 (55.5%)", ""], ["Age (years)"], ["≤ 60", "106", "39 (36.8%)", "67 (63.2%)", "0.002", "48 (12.6%)", "58 (15.3%)", "0.271", "44 (41.5%)", "62 (58.5%)", "0.045", "50 (47.2%)", "56 (52.8%)", "0.516", "58 (54.7%)", "48 (45.3%)", "0.246"], [">60", "297", "162 (54.5%)", "135 (45.5%)", "", "153 (40.3%)", "144 (37.9%)", "", "157 (52.9%)", "140 (47.1%)", "", "151 (50.8%)", "146 (49.2%)", "", "143 (48.1%)", "154 (51.9%)", ""], ["gender"], ["Female", "105", "55 (52.4%)", "50 (47.6%)", "0.551", "55 (14.5%)", "50 (13.2%)", "0.551", "55 (52.4%)", "50 (47.6%)", "0.551", "51 (48.6%)", "54 (51.4%)", "0.756", "57 (54.3%)", "48 (45.7%)", "0.293"], ["Male", "298", "146 (49.0%)", "152 (51.0%)", "", "146 (38.4%)", "152 (40.0%)", "", "146 (49.0%)", "152 (51.0%)", "", "150 (50.3%)", "148 (49.7%)", "", "144 (48.3%)", "154 (51.7%)", ""], ["(B)", "", "OR (95%CI)", "", "OR (95%CI)", "", "OR (95%CI)", "", "OR (95%CI)", "", "OR (95%CI)", ""], ["Histological grade (high vs. low)", "400", "9.79 (2.77, 62.14)", "0.002", "20.89 (4.27, 377.21)", "0.003", "4.26 (1.53, 15.08)", "0.011", "1.50 (0.61, 3.91)", "0.386", "2.38 (0.90, 7.43)", "0.100"], ["UICC stage (III+IV vs. I+II)", "401", "2.83 (1.83, 4.41)", "0.000", "2.30(1.49.3.54)", "0.000", "1.80 (1.18, 2.77)", "0.006", "1.43 (0.94, 2.18)", "0.095", "0.85 (0.56, 1.29)", "0.440"], ["pN stage (N1+N2+N3 vs. N0)", "362", "2.23 (1.43, 3.50)", "0.000", "1.62 (1.05, 2.52)", "0.029", "1.19 (0.77, 1.84)", "0.431", "1.98 (1.28, 3.09)", "0.002", "0.76 (0.49, 1.18)", "0.222"], ["pM stage (M1 vs. M0)", "204", "1.23 (0.34, 4.22)", "0.741", "2.02 (0.59, 7.22)", "0.261", "2.64 (0.77, 10.35)", "0.132", "1.56(0.45, 5.57)", "0.477", "0.74 (0.19, 2.54)", "0.642"], ["Age (>60 vs. ≤ 60)", "403", "2.06(1.31, 3.27)", "0.002", "1.28 (0.82, 2.01)", "0.271", "1.58 (1.01, 2.48)", "0.046", "1.16 (0.74, 1.81)", "0.516", "0.86 (0.55, 1.34)", "0.498"], ["Gender (male vs. female)", "403", "0.87 (0.56, 1.36)", "0.551", "0.87(0.56, 1.36)", "0.551", "0.87 (0.56, 1.36)", "0.551", "1.07 (0.69, 1.68)", "0.756", "0.68 (0.43, 1.06)", "0.091"]], "row_count": 30, "column_count": 17, "numeric_cells": 263, "header_rows": 1, "locator": "section[17]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:32292720:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b89daeee4f84af205ceae7f8b07ca2ba2942b47860f69b9f6d8deff980d41240", "bytes": 1075, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#T3", "version": null, "note": "Univariate and multivariate Cox analyses between expression levels of the five DEGs and patient survival based on TCGA.", "structure": {"pmcid": "PMC7118735", "section_index": 17, "section_title": "Correlations Between Expression Levels of the 5 Hub Genes and Clinical Outcomes in TCGA BLCA Dataset", "row_count": 13, "column_count": 5}, "table": {"label": "Table 3", "caption": "Univariate and multivariate Cox analyses between expression levels of the five DEGs and patient survival based on TCGA.", "rows": [["Items", "Univariate Cox", "P-value", "Multivariate Cox", "P-value"], ["Histological grade", "-", "0.996", "-", "-"], ["UICC stage", "1.51 (1.06, 2.15)", "0.024", "1.27 (0.85, 1.9)", "0.245"], ["pT stage", "-", "0.997", "-", "-"], ["pM stage", "2.09 (0.75, 5.80)", "0.158", "1.29 (0.44, 3.8)", "0.641"], ["pN stage", "2.18 (1.30, 3.66)", "0.003", "1.97 (1.08, 3.58)", "0.026"], ["Age", "2.30 (1.09, 4.85)", "0.029", "2.58 (1.18, 5.64)", "0.018"], ["Gender", "0.59 (0.34, 1.03)", "0.062", "0.61 (0.34, 1.09)", "0.095"], ["CRYAB", "1.26 (1.03, 1.55)", "0.026", "1.12 (0.83, 1.52)", "0.443"], ["ECM1", "1.42 (1.18, 1.71)", "<0.001", "1.44 (1.17, 1.78)", "0.001"], ["CGNL1", "1.19 (0.71, 1.98)", "0.511", "0.98 (0.52, 1.85)", "0.957"], ["CRNN", "1.16 (0.86, 1.57)", "0.339", "0.94 (0.68, 1.3)", "0.700"], ["GPX3", "0.97 (0.82, 1.15)", "0.716", "0.81 (0.65, 0.99)", "0.043"]], "row_count": 13, "column_count": 5, "numeric_cells": 42, "header_rows": 1, "locator": "section[17]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:32292720:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:78b76d14f8b3dbed0a4750a7b6e0f00e139bfd31c40c452de46ef8334c1d3e69", "bytes": 4029, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#T4", "version": null, "note": "GO functional and KEGG pathway enrichments of PPI networks based on the four gene modules.", "structure": {"pmcid": "PMC7118735", "section_index": 19, "section_title": "PPI Network Analyses and Module Functional Enrichment", "row_count": 26, "column_count": 12}, "table": {"label": "Table 4", "caption": "GO functional and KEGG pathway enrichments of PPI networks based on the four gene modules.", "rows": [["CGNL1", "GPX3", "ECM1", "CRYAB"], ["GOterm/pathway", "Description", "FDR", "GOterm/pathway", "Description", "FDR", "GOterm/pathway", "Description", "FDR", "GOterm/pathway", "Description", "FDR"], ["BP (GO)"], ["GO:0051694", "Pointed-end actin filament capping", "0.0067", "GO:1990748", "Cellular detoxification", "3.60E-14", "GO:0002576", "Platelet degranulation", "6.94E-22", "GO:0007601", "Visual perception", "5.15E-07"], ["GO:0031032", "Actomyosin structure organization", "0.0067", "GO:0098869", "Cellular oxidant detoxification", "3.53E-12", "GO:0010466", "Negative regulation of peptidase activity", "7.33E-06", "GO:0051260", "Protein homooligomerization", "0.00011"], ["GO:0030036", "Actin cytoskeleton organization", "0.0135", "GO:0006749", "Glutathione metabolic process", "9.98E-09", "GO:0030162", "Regulation of proteolysis", "4.12E-05", "GO:0003008", "System process", "0.00013"], ["GO:0016338", "Calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules", "0.0135", "GO:0006979", "Response To Oxidative Stress", "3.25E-08", "GO:0010951", "Negative regulation of endopeptidase activity", "0.00021", "GO:0050877", "Nervous system process", "0.00018"], ["GO:0007015", "Actin filament organization", "0.0172", "GO:0034599", "Cellular response to oxidative stress", "9.65E-08", "GO:0051336", "Regulation of hydrolase activity", "0.00059", "GO:0032387", "Negative regulation of intracellular transport", "0.00051"], ["MF (GO)"], ["GO:0005523", "Tropomyosin binding", "0.0027", "GO:0016209", "Antioxidant activity", "7.12E-13", "GO:0004866", "Endopeptidase inhibitor activity", "8.89E-05", "GO:0005212", "Structural constituent of eye lens", "1.02E-19"], ["GO:0008092", "Cytoskeletal protein binding", "0.0426", "GO:0016491", "Oxidoreductase activity", "2.24E-08", "GO:0030234", "Enzyme regulator activity", "0.0011", "GO:0051082", "Unfolded protein binding", "0.00069"], ["GO:0005515", "Protein binding", "0.0426", "GO:0004784", "Superoxide dismutase activity", "2.19E-07", "GO:0004867", "Serine-type endopeptidase inhibitor activity", "0.0087", "GO:0042802", "Identical protein binding", "0.0031"], ["—", "—", "—", "GO:0003824", "Catalytic Activity", "1.87E-05", "GO:0002020", "Protease binding", "0.0137", "GO:0001540", "Amyloid-beta binding", "0.0074"], ["—", "—", "—", "GO:0043295", "Glutathione binding", "0.00033", "GO:0008201", "Heparin binding", "0.0173", "—", "—", "—"], ["CC (GO)"], ["GO:0043296", "Apical junction complex", "0.00015", "GO:0031970", "Organelle envelope lumen", "0.0016", "GO:0031089", "Platelet dense granule lumen", "6.28E-32", "—", "—", "—"], ["GO:0005911", "Cell-cell junction", "0.00015", "GO:1904813", "Ficolin-1-rich granule Lumen", "0.0472", "GO:0005576", "Extracellular region", "7.36E-10", "—", "—", "—"], ["GO:0005923", "Bicellular tight junction", "0.0023", "GO:0044444", "Cytoplasmic part", "0.0472", "GO:0044421", "Extracellular region part", "7.40E-06", "—", "—", "—"], ["GO:0044430", "Cytoskeletal part", "0.0024", "GO:0044429", "Mitochondrial part", "0.0472", "GO:0005615", "Extracellular space", "4.37E-05", "—", "—", "—"], ["GO:0019897", "Extrinsic component of plasma membrane", "0.0024", "GO:0044421", "Extracellular region part", "0.0472", "GO:0031012", "Extracellular matrix", "0.0012", "—", "—", "—"], ["KEGG"], ["hsa04530", "Tight junction", "0.0018", "hsa00480", "Glutathione metabolism", "1.92E-09", "—", "—", "—", "hsa04141", "Protein processing in endoplasmic reticulum", "0.0216"], ["hsa05152", "Tuberculosis", "0.0265", "hsa04213", "Longevity regulating pathway-multiple species", "7.82E-05", "—", "—", "—", "—", "—", "—"], ["hsa04145", "Phagosome", "0.0265", "hsa04146", "Peroxisome", "0.00012", "—", "—", "—", "—", "—", "—"], ["—", "—", "—", "hsa05418", "Fluid shear stress and atherosclerosis", "0.00038", "—", "—", "—", "—", "—", "—"], ["—", "—", "—", "hsa05014", "Amyotrophic lateral sclerosis", "0.0022", "—", "—", "—", "—", "—", "—"]], "row_count": 26, "column_count": 12, "numeric_cells": 123, "header_rows": 2, "locator": "section[19]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:32292720:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:66d9922e67f97994348e7bed128832476525112b36424043d337b4c8f2b5790b", "bytes": 969, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#T5", "version": null, "note": "Comparison of immunohistochemistry expression level between normal bladder and HGBC by Fisher's Exact test from The Human Protein Atlas.", "structure": {"pmcid": "PMC7118735", "section_index": 21, "section_title": "Immunohistochemistry From the Human Protein Atlas", "row_count": 12, "column_count": 8}, "table": {"label": "Table 5", "caption": "Comparison of immunohistochemistry expression level between normal bladder and HGBC by Fisher's Exact test from The Human Protein Atlas.", "rows": [["Gene name", "", "N", "Immunohistochemistry expression level", "P-value"], ["", "", "", "Negative (–)", "Weakly positive (+)", "Positive (++)", "Strongly positive (+++)", ""], ["GPX3", "Normal bladder tissue", "2", "0", "2", "0", "0", "0.016"], ["", "HGBC tissue", "8", "7", "1", "0", "0", ""], ["ECM1", "Normal bladder tissue", "2", "0", "2", "0", "0", "0.001"], ["", "HGBC tissue", "9", "9", "0", "0", "0", ""], ["CRYAB", "Normal bladder tissue", "5", "5", "0", "0", "0", "0.439"], ["", "HGBC tissue", "9", "8", "0", "0", "1", ""], ["CGNL1", "Normal bladder tissue", "3", "3", "0", "0", "0", "0.569"], ["", "HGBC tissue", "10", "9", "1", "0", "0", ""], ["CRNN", "Normal bladder tissue", "4", "2", "2", "0", "0", "0.477"], ["", "HGBC tissue", "7", "5", "2", "0", "0", ""]], "row_count": 12, "column_count": 8, "numeric_cells": 55, "header_rows": 2, "locator": "section[21]/table-wrap[1]#T5"}}, {"id": "asset:table:pmid:32292720:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e668cbfde5e5b30b786f3c1a12a13135e8a8245fd1d4951a13664228f40d3bda", "bytes": 766, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#T6", "version": null, "note": "Characteristics of enrolled participants from Tianjin validation cohort.", "structure": {"pmcid": "PMC7118735", "section_index": 22, "section_title": "Expression of GPX3, ECM1, CRYAB, CGNL1, and CRNN in Tianjin Validation Cohort", "row_count": 15, "column_count": 5}, "table": {"label": "Table 6", "caption": "Characteristics of enrolled participants from Tianjin validation cohort.", "rows": [["", "BC patients (n = 30)", "Controls (n = 30)", "chi-square", "P-value"], ["Age (years)"], ["≤60", "14 (46.67%)", "12 (40.00%)", "0.271", "0.602"], [">60", "16 (53.33%)", "18 (60.00%)", "", ""], ["Gender"], ["Male", "13 (43.33%)", "16 (53.33%)", "0.601", "0.438"], ["Female", "17 (56.67%)", "14 (46.67%)", "", ""], ["UICC stage"], ["Stage I", "7 (23.33%)", "", "", ""], ["Stage II", "8 (26.67%)", "", "", ""], ["Stage III", "9 (30.00%)", "", "", ""], ["Stage IV", "6 (20.00%)", "", "", ""], ["Histological grade"], ["Low grade", "13 (43.33%)", "", "", ""], ["High grade", "17 (56.67%)", "", "", ""]], "row_count": 15, "column_count": 5, "numeric_cells": 22, "header_rows": 1, "locator": "section[22]/table-wrap[1]#T6"}}], "gaps": ["asset:data:geo:GSE68020 not downloaded", "asset:data:geo:GSE68020 licence not read"]}, "analysis": {"state": "partial", "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": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To identify DEGs in GSE68020 and TCGA BLCA datasets between BC patients and non-tumor healthy controls, we utilized limma R package (12)."}}, {"id": "method-2", "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-3", "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": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-4", "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"}}, {"id": "method-5", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.7, "band": "medium", "quote": "logistic regression"}}, {"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": "protein-protein interaction"}}, {"id": "method-7", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.7, "band": "medium", "quote": "Chi-square"}}], "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: 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": ["GSE68020"], "resolved_accessions": ["GSE68020"], "statements": ["Publicly available datasets were analyzed in this study. The data can be found in Gene Expression Omnibus (GEO: http://www.ncbi.nlm.nih.gov/geo/), The Cancer Genome Atlas (TCGA: http://tcga-data.nci.nih.gov/tcga/), and The Human Protein Atlas (THPA: http://www.proteinatlas.org/). GSE68020 dataset was from GEO; BLCA (Bladder Urothelial Carcinoma) dataset was from TCGA; and immunohistochemistry was from THPA. All the data are open access. Summarized detailed characteristics of immunohistochemistry data from THPA are in Supplementary Table 1."], "basis": "The paper names GSE68020 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:32292720", "data:geo:GSE68020", "asset:table:pmid:32292720:1", "asset:table:pmid:32292720:2", "asset:table:pmid:32292720:3", "asset:table:pmid:32292720:4", "asset:table:pmid:32292720:5", "asset:table:pmid:32292720:6", "asset:table:pmid:32292720:7"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE68020"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 41116, "completion_tokens": 1686, "cached_tokens": 13832}}, "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:32292720", "type": "paper", "label": "pmid:32292720"}, {"id": "source:pmid:32292720", "type": "manuscript", "label": "PMID 32292720 full text"}, {"id": "data:geo:GSE68020", "type": "dataset", "label": "GEO GSE68020"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32292720", "type": "paper", "label": "pmid:32292720"}, {"id": "source:pmid:32292720", "type": "manuscript", "label": "PMID 32292720 full text"}, {"id": "data:geo:GSE68020", "type": "dataset", "label": "GEO GSE68020"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32292720", "type": "extraction", "used": ["source:pmid:32292720"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE68020", "type": "accession_resolution", "used": ["data:geo:GSE68020"], "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:32292720", "parent_hash": "sha256:16d6cc1469a21251e617e66d9bfcce8bb7b6bd320ed4636f9282e865d52c6e38", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE68020 licence not read", "asset:data:geo:GSE68020 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": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["and GPX3 are involved in tumor progression. Immunohistochemistry based on The Human Protein Atlas and quantit"], "order_basis": "paper_text_order:1284", "id": "assay:1"}, {"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": ["To identify DEGs in GSE68020 and TCGA BLCA datasets between BC patients and non-tumor healthy controls, we utilized limma R package (12)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T01:25:07+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}}}