{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29286311", "kind": "science-record", "revision": 8, "content_hash": "sha256:ea5d6158fec3495be96785d653dcb44002e230222db32c04c79f7c3fb19e2592", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T22:43:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative Proteomics Analysis of Urine Reveals Down-Regulation of Acute Phase Response Signaling and LXR/RXR Activation Pathways in Prostate Cancer.", "doi": "10.3390/proteomes6010001", "pmid": "29286311", "authors": ["Katarina Davalieva", "Sanja Kiprijanovska", "Ivana Maleva Kostovska", "Sotir Stavridis", "Oliver Stankov", "Selim Komina", "Gordana Petrusevska", "Momir Polenakovic"], "journal": "Proteomes", "year": 2017, "abstract": "Detecting prostate cancer (PCa) using non-invasive diagnostic markers still remains a challenge. The aim of this study was the identification of urine proteins that are sufficiently sensitive and specific to detect PCa in the early stages. Comparative proteomics profiling of urine from patients with PCa, benign prostate hyperplasia, bladder cancer, and renal cancer, coupled with bioinformatics analysis, were performed. Statistically significant difference in abundance showed 20 and 85 proteins in the 2-D DIGE/MS and label-free LC-MS/MS experiments, respectively. In silico analysis indicated activation, binding, and cell movement of subset of immune cells as the top affected cellular functions in PCa, together with the down-regulation of Acute Phase Response Signaling and Liver X Receptor/ Retinoid X Receptor (LXR/RXR) activation pathways. The most promising biomarkers were 35, altered in PCa when compared to more than one group. Half of these have confirmed localization in normal or PCa tissues. Twenty proteins (CD14, AHSG, ENO1, ANXA1, CLU, COL6A1, C3, FGA, FGG, HPX, PTGDS, S100A9, LMAN2, ITIH4, ACTA2, GRN, HBB, PEBP1, CTSB, SPP1) are oncogenes, tumor suppressors, and multifunctional proteins with highly confirmed involvement in PCa, while 9 (AZU1, IGHG1, RNASE2, PZP, REG1A, AMY1A, AMY2A, ACTG2, COL18A1) have been associated with different cancers, but not with PCa so far, and may represent novel findings. LC-MS/MS data are available via ProteomeXchange with identifier PXD008407.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29286311", "locator": "sections[6] \"2.4. 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Analysis of the Proteomics Data\" paragraph 2", "quote": "Proteins with differential abundance among the four groups were considered with fold change ≥ 1.5 and Anova ≤ 0.05. p-values between groups were calculated using t-test (independent, 2-tailed, unequal variance) and subsequently false discovery rate (FDR) correction for multiple testing [21] was applied."}, {"asset": "source:pmid:29286311", "locator": "sections[6] \"2.4. 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"6.81", "70", "1.8 × 10−3", "99", "8/11", "13"], ["7", "2.3 × 10−2", "3.5", "", "", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "94", "7.9 × 10−6", "88", "9/13", "18"], ["8", "4.3 × 10−2", "2.6", "6.2 × 10−5", "3.0", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "156", "5.1 × 10−12", "43", "17/24", "24"], ["9", "", "", "2.2 × 10−2", "2.4", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "139", "2.5 × 10−10", "56", "14/20", "24"], ["10", "", "", "3.4 × 10−2", "2.6", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "131", "1.6 × 10−9", "101", "11/12", "18"], ["11", "4.5 × 10−2", "2.5", "6.9 × 10−3", "4.4", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "111", "1.6 × 10−7", "35", "10/14", "19"], ["12", "", "", "5.5 × 10−3", "3.1", "", "", "Kininogen-1", "KNG1", "73.0", "6.34", "90", "5.6 × 10−6", "58", "9/14", "18"], ["13", "1.3 × 10−2", "−2.8", "3.7 × 10−2", "−2.6", "", "", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "65/81", "2.4 × 10−3/ 1.1 × 10−4", "48/45", "6/6/8", "14/20"], ["14", "3.9 × 10−2", "−2.4", "1.9 × 10−2", "−2.7", "", "", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "59/82", "2.4 × 10−2/ 1.3 × 10−4", "48/45", "5/6/8", "13/20"], ["15", "2.2 × 10−2", "−2.9", "1.3 × 10−2", "−2.5", "", "", "Ig alpha-1 chain C region", "IGHA1", "38.5", "6.08", "84", "8.8 × 10−5", "13", "7/13", "31"], ["16", "", "", "8.3 × 10−3", "−2.1", "", "", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "111/84", "1.6 × 10−7/ 7.7 × 10−5", "59/63", "10/8/19", "38/27"], ["17", "2.1 × 10−2", "−2.7", "3.5 × 10−2", "−2.5", "", "", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "102/84", "1.3 × 10−6/ 7.7 × 10−5", "89/93", "9/8/19", "33/27"], ["18", "3.1 × 10−2", "−2.2", "1.2 × 10−2", "−2.1", "5.1 × 10−3", "−1.6", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1", "38.5/ 37.3", "6.08/ 5.71", "92/56", "1.2 × 10−5/ 5.0 × 10−2", "23/28", "7/6/20", "28/26"], ["19", "1.4 × 10−2", "−2.4", "", "", "5.6 × 10−2", "−1.6", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "97/69", "3.8 × 10−6/ 2.4 × 10−3", "37/37", "10/8/38", "38/27"], ["20", "2.9 × 10−2", "−2.0", "6.4 × 10−3", "−2.0", "6.7 × 10−2", "−1.7", "mix (Ig alpha-1 chain C region/Ig alpha-2 chain C region)", "IGHA1/ IGHA2", "38.5/ 37.3", "6.08/ 5.71", "122/82", "1.3 × 10−8/ 1.4 × 10−4", "11/12", "9/8/12", "26/21"], ["21 a", "", "", "2.0 × 10−2", "−3.2", "", "", "Arginyl-tRNA-protein transferase 1", "ATE1", "60.0", "8.17", "98", "3.6 × 10−6", "67", "9/16", "28"], ["22", "", "", "1.8 × 10−2", "−2.0", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "121", "1.6 × 10−8", "43", "12/23", "38"], ["23", "", "", "2.1 × 10−2", "−5.3", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "174", "8.0 × 10−14", "39", "14/18", "42"], ["24", "", "", "3.4 × 10−2", "−5.7", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "117", "4.0 × 10−8", "83", "12/19", "31"], ["25", "", "", "3.5 × 10−2", "−7.1", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "107", "4.0 × 10−7", "35", "12/26", "32"], ["26", "", "", "4.1 × 10−2", "−5.8", "", "", "Fibrinogen gamma chain", "FGG", "52.1", "5.37", "139", "2.5 × 10−10", "39", "13/25", "37"], ["27", "", "", "2.0 × 10−3", "2.1", "", "", "Zinc-alpha-2-glycoprotein", "AZGP1", "34.5", "5.71", "102", "1.3 × 10−6", "45", "13/27", "30"], ["28", "", "", "2.0 × 10−2", "−4.7", "", "", "Haptoglobin", "HP", "45.9", "6.13", "87", "3.8 × 10−5", "104", "8/17", "18"], ["29", "", "", "1.9 × 10−2", "−6.7", "", "", "Haptoglobin", "HP", "45.9", "6.13", "108", "3.2 × 10−7", "11", "13/25", "27"], ["30", "", "", "2.2 × 10−2", "−6.3", "", "", "Haptoglobin", "HP", "45.9", "6.13", "107", "4.0 × 10−7", "53", "16/37", "28"], ["31", "", "", "2.6 × 10−2", "−7.5", "", "", 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× 10−2", "4.8", "", "", "Protein AMBP", "AMBP", "39.9", "5.95", "94", "8.0 × 10−6", "66", "11/30", "24"], ["39", "", "", "1.5 × 10−2", "5.0", "", "", "Protein AMBP", "AMBP", "39.9", "5.95", "135", "6.4 × 10−10", "37", "13/18", "32"], ["40", "", "", "1.4 × 10−2", "5.2", "", "", "Protein AMBP", "AMBP", "39.9", "5.95", "108", "3.2 × 10−7", "91", "10/19", "18"], ["41", "5.3 × 10−3", "2.0", "", "", "", "", "Protein AMBP", "AMBP", "39.9", "5.95", "74", "7.3 × 10−4", "12", "9/17", "26"], ["42", "", "", "3.3 × 10−3", "4.0", "", "", "Prostaglandin-H2 D-isomerase", "PTGDS", "21.2", "7.66", "64", "7.3 × 10−3", "63", "7/15", "33"], ["43", "", "", "6.2 × 10−3", "4.0", "", "", "Prostaglandin-H2 D-isomerase", "PTGDS", "21.2", "7.66", "70", "2.3 × 10−3", "72", "8/25", "27"], ["44", "", "", "8.9 × 10−3", "3.3", "", "", "Prostaglandin-H2 D-isomerase", "PTGDS", "21.2", "7.66", "60", "1.9 × 10−2", "93", "7/26", "26"], ["45 a", "", "", "4.6 × 10−2", "1.9", "", "", "Ig kappa chain C region", "IGKC", "11.8", 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identified proteins with differential abundance in PCa when compared to the three groups (BPH, BC, and RC) by LC-MS/MS.", "structure": {"pmcid": "PMC5874760", "section_index": 10, "section_title": "3.2. LC-MS/MS Analysis", "row_count": 122, "column_count": 13}, "table": {"label": "Table 2", "caption": "List of identified proteins with differential abundance in PCa when compared to the three groups (BPH, BC, and RC) by LC-MS/MS.", "rows": [["Uniprot Accession No.", "Protein Name", "Gene Name", "Peptide Count", "Unique Peptides", "Confidence Score", "ANOVA", "Max Fold Change", "Highest Mean Condition", "Lowest Mean Condition", "Group Comparison", "p-Value a", "Ratio"], ["P08571", "Monocyte differentiation antigen", "CD14", "8", "7", "75.64", "8.87 × 10−10", "2.70", "PCa", "Bc", "PCa vs. BC", "2.71 × 10−4", "2.7"], ["", "CD14", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.67 × 10−3", "1.8"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. RC", "2.61 × 10−2", "1.6"], ["P62736", "Actin_ aortic smooth muscle", "ACTA2", "3", "3", "24.21", "1.75 × 10−9", "5.89", "Bc", "PCa", "PCa vs. BC", "3.40 × 10−4", "0.2"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.75 × 10−2", "0.4"], ["P02765", "Alpha-2-HS-glycoprotein", "AHSG", "9", "9", "94.63", "5.73 × 10−4", "2.70", "PCa", "Bc", "PCa vs. BC", "9.03 × 10−3", "2.7"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.14 × 10−2", "2.1"], ["P04745", "Alpha-amylase 1", "AMY1A", "9", "5", "101.49", "1.42 × 10−7", "3.46", "PCa", "Bc", "PCa vs. BC", "3.40 × 10−4", "3.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.14 × 10−2", "1.7"], ["P19961", "Alpha-amylase 2B", "AMY2B", "3", "1", "21.24", "3.52 × 10−6", "12.86", "Rc", "Bc", "PCa vs. BC", "1.25 × 10−2", "11.9"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.32 × 10−2", "4.1"], ["P06733", "Alpha-enolase", "ENO1", "2", "2", "14.73", "3.64 × 10−5", "1.78", "BPH", "PCa", "PCa vs. BC", "1.54 × 10−2", "0.7"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "7.97 × 10−3", "0.6"], ["P04083", "Annexin A1", "ANXA1", "5", "5", "41.02", "5.95 × 10−12", "5.45", "Rc", "Bc", "PCa vs. BC", "1.08 × 10−3", "3.8"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.20 × 10−2", "2.2"], ["P20160", "Azurocidin", "AZU1", "2", "2", "13.76", "7.34 × 10−5", "2.80", "BPH", "PCa", "PCa vs. BC", "3.35 × 10−2", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "8.89 × 10−3", "0.4"], ["P10909", "Clusterin", "CLU", "10", "10", "99.24", "6.33 × 10−6", "2.26", "BPH", "PCa", "PCa vs. BC", "5.24 × 10−3", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.55 × 10−2", "0.4"], ["P12109", "Collagen alpha-1(VI)", "COL6A1", "6", "4", "46.91", "2.05 × 10−7", "3.44", "BPH", "PCa", "PCa vs. BC", "7.15 × 10−4", "0.4"], ["", "chain", "", "", "", "", "", "", "", "", "PCa vs. BPH", "8.66 × 10−3", "0.3"], ["P39060", "Collagen alpha-1(XVIII)", "COL18A1", "2", "2", "14.39", "2.92 × 10−9", "14.26", "Rc", "Bc", "PCa vs. BC", "6.21 × 10−3", "7.1"], ["", "chain", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.30 × 10−2", "4.2"], ["P01024", "Complement C3", "C3", "57", "57", "545.51", "2.30 × 10−7", "3.43", "Rc", "Bc", "PCa vs. BC", "6.30 × 10−3", "2.9"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.77 × 10−2", "2.2"], ["P24855", "Deoxyribonuclease-1", "DNASE1", "3", "3", "23.62", "1.84 × 10−10", "4.85", "Rc", "Bc", "PCa vs. BC", "6.30 × 10−3", "3.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "3.55 × 10−2", "2.3"], ["O94919", "Endonuclease domain-containing 1", "ENDOD1", "3", "3", "24.51", "1.64 × 10−7", "2.97", "PCa", "Bc", "PCa vs. BC", "1.01 × 10−3", "3.0"], ["", "protein", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.67 × 10−3", "2.8"], ["P02671", "Fibrinogen alpha chain", "FGA", "24", "24", "293.54", "7.67 × 10−6", "2.72", "BPH", "Rc", "PCa vs. BC", "2.94 × 10−3", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "3.15 × 10−2", "0.4"], ["P02679", "Fibrinogen gamma chain", "FGG", "20", "20", "251.65", "1.07 × 10−4", "2.32", "BPH", "Rc", "PCa vs. BC", "2.48 × 10−2", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.25 × 10−2", "0.5"], ["P28799", "Granulins", "GRN", "2", "2", "18.13", "2.87 × 10−8", "3.92", "BPH", "PCa", "PCa vs. BC", "2.32 × 10−3", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "8.89 × 10−3", "0.3"], ["P68871", "Hemoglobin subunit beta", "HBB", "10", "10", "138.23", "1.54 × 10−5", "4.62", "Bc", "PCa", "PCa vs. BC", "2.96 × 10−2", "0.2"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.75 × 10−2", "0.3"], ["P02790", "Hemopexin", "HPX", "16", "16", "164.63", "4.66 × 10−6", "2.44", "BPH", "PCa", "PCa vs. BC", "6.60 × 10−3", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.30 × 10−2", "0.4"], ["P01857", "Ig gamma-1 chain C region", "IGHG1", "6", "6", "76.08", "6.40 × 10−4", "3.29", "BPH", "PCa", "PCa vs. BC", "6.71 × 10−3", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.14 × 10−2", "0.3"], ["P05451", "Lithostathine-1-alpha", "REG1A", "5", "4", "35.95", "3.83 × 10−4", "3.96", "PCa", "BPH", "PCa vs. BC", "6.30 × 10−3", "3.8"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.50 × 10−2", "4.0"], ["P11117", "Lysosomal acid", "ACP2", "5", "4", "45.84", "5.59 × 10−6", "2.11", "BPH", "PCa", "PCa vs. BC", "7.15 × 10−4", "0.6"], ["", "phosphatase", "", "", "", "", "", "", "", "", "PCa vs. BPH", "6.07 × 10−3", "0.5"], ["P08246", "Neutrophil elastase", "ELANE", "3", "3", "39.04", "6.45 × 10−3", "3.25", "BPH", "PCa", "PCa vs. BC", "2.74 × 10−2", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.99 × 10−2", "0.3"], ["P10153", "Non-secretory", "RNASE2", "4", "3", "51.80", "3.38 × 10−8", "5.21", "PCa", "Bc", "PCa vs. BC", "8.08 × 10−3", "5.2"], ["", "ribonuclease", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.55 × 10−2", "3.9"], ["P10451", "Osteopontin", "SPP1", "12", "11", "164.02", "1.10 × 10−11", "15.72", "Rc", "Bc", "PCa vs. BC", "2.32 × 10−3", "8.4"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.55 × 10−2", "2.6"], ["P04746", "Pancreatic alpha-amylase", "AMY2A", "3", "1", "27.44", "3.66 × 10−6", "5.06", "PCa", "Bc", "PCa vs. BC", "4.27 × 10−3", "5.1"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.32 × 10−2", "2.3"], ["P30086", "Phosphatidylethanolamine-", "PEBP1", "3", "3", "27.16", "2.93 × 10−5", "3.38", "BPH", "PCa", "PCa vs. BC", "7.15 × 10−4", "0.5"], ["", "binding protein 1", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.75 × 10−2", "0.3"], ["P20742", "Pregnancy zone protein", "PZP", "7", "7", "82.62", "4.09 × 10−8", "2.27", "Bc", "Rc", "PCa vs. BC", "2.32 × 10−3", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.76 × 10−2", "0.7"], ["P41222", "Prostaglandin-H2", "PTGDS", "9", "7", "140.59", "4.51 × 10−11", "5.56", "PCa", "Bc", "PCa vs. BC", "3.40 × 10−4", "5.6"], ["", "D-isomerase", "", "", "", "", "", "", "", "", "PCa vs. BPH", "1.75 × 10−2", "1.8"], ["P06702", "Protein S100-A9", "S100A9", "3", "3", "26.61", "1.49 × 10−6", "6.46", "BPH", "PCa", "PCa vs. BC", "1.22 × 10−3", "0.5"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "5.03 × 10−2", "0.2"], ["Q8WZ75", "Roundabout homolog 4", "ROBO4", "7", "7", "55.71", "3.32 × 10−3", "2.27", "BPH", "PCa", "PCa vs. BC", "1.47 × 10−2", "0.6"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.96 × 10−2", "0.4"], ["Q12907", "Vesicular integral-membrane", "LMAN2", "9", "8", "94.66", "1.64 × 10−6", "2.48", "Rc", "Bc", "PCa vs. BC", "2.32 × 10−3", "2.4"], ["", "protein VIP36", "", "", "", "", "", "", "", "", "PCa vs. BPH", "2.55 × 10−2", "1.7"], ["Q14624", "Inter-alpha-trypsin inhibitor heavy", "ITIH4", "9", "9", "94.01", "3.21 × 10−13", "5.55", "Rc", "Bc", "PCa vs. BC", "5.07 × 10−5", "3.5"], ["", "chain H4", "", "", "", "", "", "", "", "", "PCa vs. BPH", "4.67 × 10−3", "1.6"], ["P63267", "Actin_ gamma-enteric", "ACTG2", "3", "3", "19.63", "4.29 × 10−2", "1.79", "PCa", "Rc", "PCa vs. BC", "1.08 × 10−3", "1.7"], ["", "smooth muscle", "", "", "", "", "", "", "", "", "PCa vs. RC", "2.56 × 10−3", "1.8"], ["P07858", "Cathepsin B", "CTSB", "3", "2", "19.04", "5.87 × 10−3", "3.16", "Bc", "PCa", "PCa vs. BC", "3.10 × 10−2", "0.3"], ["", "", "", "", "", "", "", "", "", "", "PCa vs. RC", "3.14 × 10−2", "0.4"], ["P01023", "Alpha-2-macroglobulin", "A2M", "38", "38", "491.82", "1.42 × 10−4", "2.29", "BPH", "PCa", "PCa vs. BPH", "6.07 × 10−3", "0.4"], ["P15144", "Aminopeptidase N", "ANPEP", "2", "2", "14.55", "3.31 × 10−4", "1.70", "BPH", "PCa", "PCa vs. BPH", "4.20 × 10−2", "0.6"], ["P07355", "Annexin A2", "ANXA2", "2", "2", "16.06", "9.99 × 10−5", "4.27", "Rc", "BPH", "PCa vs. BPH", "4.76 × 10−2", "4.1"], ["P06727", "Apolipoprotein A-IV", "APOA4", "3", "3", "31.32", "3.77 × 10−3", "2.28", "BPH", "PCa", "PCa vs. BPH", "5.03 × 10−2", "0.4"], ["Q8NFZ8", "Cell adhesion molecule 4", "CADM4", "8", "7", "60.30", "1.09 × 10−3", "2.26", "BPH", "PCa", "PCa vs. BPH", "3.15 × 10−2", "0.4"], ["P17900", "Ganglioside GM2 activator", "GM2A", "4", "3", "40.41", "4.80 × 10−2", "1.81", "BPH", "PCa", "PCa vs. BPH", "4.97 × 10−2", "0.6"], ["P69905", "Hemoglobin subunit alpha", "HBA1", "5", "5", "56.91", "9.41 × 10−3", "4.36", "Bc", "PCa", "PCa vs. BPH", "4.67 × 10−3", "0.6"], ["P02042", "Hemoglobin subunit delta", "HBD", "3", "3", "29.39", "1.38 × 10−5", "13.11", "Bc", "Rc", "PCa vs. BPH", "4.20 × 10−2", "0.5"], ["P01859", "Ig gamma-2 chain C region", "IGHG2", "7", "7", "67.03", "6.75 × 10−5", "2.18", "BPH", "Bc", "PCa vs. BPH", "6.07 × 10−3", "0.5"], ["P01861", "Ig gamma-4 chain C region", "IGHG4", "6", "6", "72.40", "9.74 × 10−4", "2.05", "BPH", "Rc", "PCa vs. BPH", "4.32 × 10−2", "0.6"], ["P01772", "Ig heavy chain V-III region KOL", "IGHV3-33", "2", "1", "12.43", "4.33 × 10−3", "1.57", "BPH", "PCa", "PCa vs. BPH", "4.89 × 10−2", "0.6"], ["P0CF74", "Ig lambda-6 chain C region", "IGLC6", "3", "3", "28.38", "7.00 × 10−4", "1.97", "BPH", "Bc", "PCa vs. BPH", "2.30 × 10−2", "0.5"], ["P02788", "Lactotransferrin", "LTF", "43", "41", "601.64", "8.73 × 10−5", "2.61", "BPH", "Rc", "PCa vs. BPH", "4.20 × 10−2", "0.5"], ["P10253", "Lysosomal alpha-glucosidase", "GAA", "8", "8", "80.33", "9.63 × 10−5", "1.77", "BPH", "PCa", "PCa vs. BPH", "4.14 × 10−2", "0.6"], ["P05164", "Myeloperoxidase", "MPO", "16", "15", "159.24", "4.69 × 10−5", "1.76", "BPH", "PCa", "PCa vs. BPH", "4.67 × 10−3", "0.6"], ["P32119", "Peroxiredoxin-2", "PRDX2", "3", "1", "23.32", "2.58 × 10−2", "13.40", "Bc", "PCa", "PCa vs. BPH", "5.03 × 10−2", "0.2"], ["P05155", "Plasma protease C1 inhibitor", "SERPING1", "4", "4", "35.56", "4.75 × 10−3", "1.71", "BPH", "PCa", "PCa vs. BPH", "4.99 × 10−2", "0.6"], ["Q6S8J3", "POTE ankyrin domain family member E", "POTEE", "11", "8", "93.51", "3.30 × 10−4", "2.04", "BPH", "Rc", "PCa vs. BPH", "4.76 × 10−2", "0.5"], ["P43652", "Afamin", "AFM", "6", "5", "48.31", "8.56 × 10−4", "1.65", "PCa", "Bc", "PCa vs. BC", "5.76 × 10−3", "1.6"], ["P02647", "Apolipoprotein A-I", "APOA1", "12", "12", "145.00", "4.72 × 10−4", "1.86", "BPH", "Rc", "PCa vs. BC", "3.02 × 10−2", "0.7"], ["P05090", "Apolipoprotein D", "APOD", "6", "6", "69.92", "4.00 × 10−7", "2.12", "PCa", "Bc", "PCa vs. BC", "1.19 × 10−3", "2.1"], ["P02749", "Beta-2-glycoprotein 1", "APOH", "11", "10", "112.68", "1.13 × 10−4", "3.66", "Bc", "Rc", "PCa vs. BC", "7.15 × 10−4", "0.3"], ["P19835", "Bile salt-activated lipase", "CEL", "3", "3", "20.03", "1.76 × 10−6", "2.04", "Rc", "Bc", "PCa vs. BC", "7.58 × 10−3", "1.6"], ["P07339", "Cathepsin D", "CTSD", "6", "6", "54.69", "1.61 × 10−3", "1.85", "PCa", "Bc", "PCa vs. BC", "1.38 × 10−2", "1.9"], ["P13987", "CD59 glycoprotein", "CD59", "5", "5", "85.01", "1.42 × 10−6", "4.38", "Rc", "Bc", "PCa vs. BC", "2.94 × 10−3", "4.3"], ["P0C0L4", "Complement C4-A", "C4A", "3", "3", "21.19", "1.16 × 10−2", "1.85", "Bc", "PCa", "PCa vs. BC", "6.21 × 10−3", "0.5"], ["P08174", "Complement decay-accelerating factor", "CD55", "5", "5", "40.67", "2.66 × 10−5", "2.37", "Rc", "Bc", "PCa vs. BC", "1.02 × 10−2", "2.2"], ["Q02487", "Desmocollin-2", "DSC2", "4", "3", "24.44", "4.00 × 10−6", "2.62", "Bc", "BPH", "PCa vs. BC", "1.78 × 10−3", "0.6"], ["Q9UHL4", "Dipeptidyl peptidase 2", "DPP7", "2", "2", "12.10", "4.08 × 10−2", "4.13", "BPH", "PCa", "PCa vs. BC", "2.84 × 10−2", "0.6"], ["Q9HCU0", "Endosialin", "CD248", "6", "6", "43.09", "2.31 × 10−6", "2.20", "PCa", "Bc", "PCa vs. BC", "1.14 × 10−2", "2.2"], ["P01834", "Ig kappa chain C region", "IGKC", "9", "9", "154.85", "3.59 × 10−3", "2.04", "PCa", "Bc", "PCa vs. BC", "1.11 × 10−3", "2.0"], ["P01617", "Ig kappa chain V-II region TEW", "IGKV2D-28", "5", "3", "60.57", "1.37 × 10−2", "2.22", "Rc", "Bc", "PCa vs. BC", "7.15 × 10−4", "1.6"], ["P01625", "Ig kappa chain V-IV region Len", "IGKV4-1", "2", "1", "17.70", "1.49 × 10−3", "1.62", "Rc", "Bc", "PCa vs. BC", "7.58 × 10−3", "1.6"], ["P80748", "Ig lambda chain V-III region LOI", "IGLV3-21", "3", "3", "29.50", "1.01 × 10−3", "2.13", "PCa", "Bc", "PCa vs. BC", "1.00 × 10−4", "2.1"], ["P0CG04", "Ig lambda-1 chain C regions", "IGLC1", "6", "6", "112.58", "6.98 × 10−3", "2.14", "BPH", "Bc", "PCa vs. BC", "2.40 × 10−3", "1.8"], ["P0CG05", "Ig lambda-2 chain C regions", "IGLC2", "3", "3", "57.93", "1.94 × 10−2", "1.73", "BPH", "Bc", "PCa vs. BC", "3.90 × 10−3", "1.7"], ["P01042", "Kininogen-1", "KNG1", "27", "27", "362.50", "8.88 × 10−7", "2.71", "Rc", "Bc", "PCa vs. BC", "8.22 × 10−3", "1.7"], ["P14543", "Nidogen-1", "NID1", "9", "8", "84.01", "5.13 × 10−5", "3.95", "BPH", "Bc", "PCa vs. BC", "2.23 × 10−3", "2.0"], ["O75594", "Peptidoglycan recognition protein 1", "PGLYRP1", "5", "5", "50.82", "6.11 × 10−5", "2.30", "BPH", "Bc", "PCa vs. BC", "3.28 × 10−3", "1.9"], ["P01833", "Polymeric immunoglobulin receptor", "PIGR", "25", "24", "263.55", "5.20 × 10−5", "2.50", "Rc", "Bc", "PCa vs. BC", "6.21 × 10−3", "1.6"], ["P02760", "Protein AMBP", "AMBP", "25", "24", "366.65", "4.27 × 10−3", "2.49", "Rc", "Bc", "PCa vs. BC", "1.02 × 10−2", "1.9"], ["P00734", "Prothrombin", "F2", "16", "14", "176.60", "3.60 × 10−5", "5.38", "Rc", "Bc", "PCa vs. BC", "7.15 × 10−4", "2.7"], ["P07998", "Ribonuclease pancreatic", "RNASE1", "4", "4", "39.91", "7.99 × 10−15", "4.42", "Rc", "Bc", "PCa vs. BC", "7.63 × 10−4", "3.5"], ["Q9UBC9", "Small proline-rich protein 3", "SPRR3", "2", "2", "22.69", "7.14 × 10−3", "2.10", "PCa", "Bc", "PCa vs. BC", "1.25 × 10−2", "2.1"], ["Q9UGT4", "Sushi domain-containing protein 2", "SUSD2", "2", "2", "13.45", "5.40 × 10−5", "32.32", "PCa", "Bc", "PCa vs. BC", "4.99 × 10−2", "32.3"], ["P07911", "Uromodulin", "UMOD", "27", "27", "399.14", "6.23 × 10−6", "2.98", "Rc", "Bc", "PCa vs. BC", "4.00 × 10−2", "1.7"], ["P22891", "Vitamin K-dependent protein Z", "PROZ", "4", "3", "42.25", "1.29 × 10−2", "2.21", "PCa", "Bc", "PCa vs. BC", "2.92 × 10−2", "2.2"], ["P25311", "Zinc-alpha-2-glycoprotein", "AZGP1", "17", "15", "230.16", "1.61 × 10−2", "2.47", "PCa", "Bc", "PCa vs. BC", "1.25 × 10−2", "2.5"], ["P06870", "Kallikrein-1", "KLK1", "6", "6", "64.59", "4.90 × 10−4", "2.36", "BPH", "Bc", "PCa vs. RC", "2.61 × 10−2", "0.6"], ["Q96PD5", "N-acetylmuramoyl-L-alanine amidase", "PGLYRP2", "5", "5", "56.28", "7.41 × 10−3", "2.14", "PCa", "Rc", "PCa vs. RC", "2.56 × 10−3", "2.1"]], "row_count": 122, "column_count": 13, "numeric_cells": 788, "header_rows": 1, "locator": "section[10]/table-wrap[1]#proteomes-06-00001-t002"}}], "gaps": ["asset:data:geo:PXD008407 not downloaded", "asset:data:geo:PXD008407 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "reordered", "quote": "“Proteins with differential abundance among the four groups were considered with fold change ≥ 1.5 and Anova ≤ 0.05. p-values between groups were calculated using t-test (independent, 2-tailed, unequal variance) and subsequently false discovery rate (FDR) correction for multiple testing [21] was applied.” “The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.”"}}], "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD008407"], "resolved_accessions": ["PXD008407"], "statements": ["The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407."], "basis": "The paper names PXD008407 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:29286311", "data:geo:PXD008407", "asset:table:pmid:29286311:1", "asset:table:pmid:29286311:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD008407"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:19Z", "independence": "same_provider"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 129568, "completion_tokens": 4647, "cached_tokens": 2088}}, "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:29286311", "type": "paper", "label": "pmid:29286311"}, {"id": "source:pmid:29286311", "type": "manuscript", "label": "PMID 29286311 full text"}, {"id": "data:geo:PXD008407", "type": "dataset", "label": "GEO PXD008407"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29286311", "type": "paper", "label": "pmid:29286311"}, {"id": "source:pmid:29286311", "type": "manuscript", "label": "PMID 29286311 full text"}, {"id": "data:geo:PXD008407", "type": "dataset", "label": "GEO PXD008407"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29286311", "type": "extraction", "used": ["source:pmid:29286311"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD008407", "type": "accession_resolution", "used": ["data:geo:PXD008407"], "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:29286311", "parent_hash": "sha256:595fb876549167132f97b1aa0c28d12281575c997a41347cac6ef88aed8eeaa7", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD008407 licence not read", "asset:data:geo:PXD008407 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Comparative Proteomics Analysis of Urine Reveals Down-Regulation of", "detect PCa in the early stages. Comparative proteomics profiling of urine from patients with PCa, b", "a, Buchs, Switzerland). 2.5. Analysis of the Proteomics Data Proteins with differential abundance am", "5 proteins in the 2-D DIGE/MS and label-free LC-MS/MS experiments, respectively. In silico analysi"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"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": ["on is determined based on antibody staining (immunohistochemistry, Western blot) and protein arrays. Supplemen"], "order_basis": "paper_text_order:7593", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["on antibody staining (immunohistochemistry, Western blot) and protein arrays. Supplementary Materials"], "order_basis": "paper_text_order:7616", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["“Proteins with differential abundance among the four groups were considered with fold change ≥ 1.5 and Anova ≤ 0.05. p-values between groups were calculated using t-test (independent, 2-tailed, unequal variance) and subsequently false discovery rate (FDR) correction for multiple testing [21] was applied.” “The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [20] with data set identifier PXD008407 and 10.6019/PXD008407.”"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]},"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":"2026-11-04T00:33:22+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}}}