{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32575983", "kind": "science-record", "revision": 6, "content_hash": "sha256:438dbf556eb58ddad2607e20bf1822920fc94ae44ed4a6f4471de0cf13db0956", "created_at": "2026-11-01T15:41:04Z", "updated_at": "2026-11-01T21:23:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Top-Down Proteomics of Human Saliva Discloses Significant Variations of the Protein Profile in Patients with Mastocytosis.", "doi": "10.1021/acs.jproteome.0c00207", "pmid": "32575983", "authors": ["Simone Serrao", "Davide Firinu", "Alessandra Olianas", "Margherita Deidda", "Cristina Contini", "Federica Iavarone", "M Teresa Sanna", "Mozhgan Boroumand", "Francisco Amado", "Massimo Castagnola", "Irene Messana", "Stefano Del Giacco", "Barbara Manconi", "Tiziana Cabras"], "journal": "Journal of proteome research", "year": 2020, "abstract": "Mastocytosis is a myeloproliferative neoplasm causing abnormal clonal mast cell accumulation in different tissues, such as skin and bone marrow. A cutaneous subtype (CM) is distinguished from a systemic one (SM); SM patients can be grouped into SM with (SM+C) or without (SM-C) additional cutaneous lesions, and their classification is often challenging. This study was purposed to highlight variations in the salivary proteome of patients with different mastocytosis subtypes and compared to healthy controls. A top-down proteomics approach coupled to a label-free quantitation revealed salivary profiles in patients different from those of controls and a down-regulation of peptides/proteins involved in the mouth homeostasis and defense, such as statherin, histatins, and acidic proline-rich proteins (aPRPs), and in innate immunity and inflammation, such as the cathepsin inhibitors, suggesting a systemic condition associated with an exacerbated inflammatory state. The up-regulation of antileukoproteinase and S100A8 suggested a protective role against the disease status. The two SM forms were distinguished by the lower levels of truncated forms of aPRPs, statherin, P-B peptide, and cystatin D and the higher levels of thymosin β4 and α-defensins 1 and 4 in SM-C patients with respect to SM+C. Data are available via ProteomeXchange with identifier PXD017759.", "claims": [{"id": "claim-method", "statement": "The comparisons between the three groups of patients and that of the controls and between the three groups of patients have been performed with Mann–Whitney and Welch-corrected t tests, depending on the distribution (skewed or normal) and the variance (unequal or homogeneous). Correlation analyses, between the XIC peak area of the proteins/peptides under analysis and the tryptase levels of each patient, were performed with the Spearman test and considered significant when the p value was <0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32575983", "locator": "sections[7] \"Statistical Analysis\" paragraph 2", "quote": "The comparisons between the three groups of patients and that of the controls and between the three groups of patients have been performed with Mann–Whitney and Welch-corrected t tests, depending on the distribution (skewed or normal) and the variance (unequal or homogeneous)."}, {"asset": "source:pmid:32575983", "locator": "sections[7] \"Statistical Analysis\" paragraph 2", "quote": "Correlation analyses, between the XIC peak area of the proteins/peptides under analysis and the tryptase levels of each patient, were performed with the Spearman test and considered significant when the p value was <0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD017759.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32575983", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD017759."}], "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:32575983"], "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. 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Absence (N) of Aphtosis and/or Gastrointestinal (GI) Symptoms, Tryptase Serum Level, and Eventual Mutation of c-Kit Genes of each Patient at the Time of the Study", "structure": {"pmcid": "PMC8008451", "section_index": 4, "section_title": "Study Subjects and Controls and Clinical Data", "row_count": 42, "column_count": 8}, "table": {"label": "Table 1", "caption": "Age/Gender, Diagnosis, Presence (Y) or Absence (N) of Aphtosis and/or Gastrointestinal (GI) Symptoms, Tryptase Serum Level, and Eventual Mutation of c-Kit Genes of each Patient at the Time of the Study", "rows": [["patient", "age/gender", "diagnosis", "secondary cutaneous symptoms", "aphtosis", "GI", "tryptase (μg/L)", "mutation(s)"], ["#2", "59/F", "SM", "", "N", "Y", "17.5", ""], ["#5", "54/F", "SM", "", "N", "Y", "16.5", ""], ["#6", "72/F", "SM", "", "N", "Y", "41.0", ""], ["#9", "45/M", "SM", "Y", "N", "Y", "33.6", "M541L"], ["#10", "44/F", "SM", "Y", "Y", "Y", "16.2", ""], ["#11", "58/F", "SM", "Y", "Y", "Y", "20.2", "D816V"], ["#12", "53/M", "SM", "Y", "N", "Y", "5.5", "D816V/M541L"], ["#13", "35/F", "SM", "Y", "Y", "Y", "44.7", ""], ["#14", "22/F", "CM", "", "N", "N", "5.0", ""], ["#15", "38/F", "SM", "Y", "Y", "Y", "7.7", "D816V"], ["#16", "52/M", "SM", "Y", "N", "Y", "37.5", "D816V"], ["#17", "46/F", "CM", "", "Y", "Y", "4.5", ""], ["#18", "55/M", "SM", "", "Y", "Y", "27.1", "D816V"], ["#19", "48/M", "SM", "Y", "N", "Y", "16.2", ""], ["#20", "32/M", "SM", "Y", "N", "Y", "53.5", "D816V"], ["#21", "44/F", "SM", "", "N", "N", "16.0", ""], ["#22", "60/F", "SM", "Y", "N", "Y", "23.6", ""], ["#23", "62/F", "SM", "", "N", "N", "80.4", "D816V"], ["#24", "49/M", "SM", "Y", "N", "Y", "29.1", "D816V"], ["#25", "49/F", "SM", "Y", "N", "Y", "37.4", ""], ["#26", "35/F", "SM", "Y", "Y", "Y", "16.5", ""], ["#27", "67/F", "CM", "", "N", "N", "7.2", ""], ["#28", "38/F", "SM", "Y", "Y", "Y", "26.2", "D816V"], ["#29", "57/M", "SM", "Y", "Y", "Y", "77.4", "D816V"], ["#30", "32/M", "SM", "Y", "Y", "Y", "40.8", "D816V"], ["#31", "39/M", "CM", "", "Y", "Y", "8.8", ""], ["#35", "34/M", "SM", "Y", "Y", "Y", "28.7", ""], ["#36", "52/F", "SM", "Y", "N", "Y", "16.1", "D816V"], ["#37", "28/F", "CM", "", "N", "N", "7.7", ""], ["#43", "71/F", "SM", "", "N", "N", "9.7", ""], ["#45", "23/M", "CM", "", "N", "N", "4.3", ""], ["#46", "75/F", "SM", "", "N", "N", "18.2", ""], ["#47", "46/F", "SM", "Y", "Y", "Y", "7.3", ""], ["#51", "29/M", "SM", "Y", "N", "Y", "64.5", ""], ["#52", "44/M", "SM", "Y", "N", "Y", "7.41", "D816V"], ["#58", "38/M", "SM", "Y", "N", "Y", "26.3", ""], ["#59", "67/F", "SM", "Y", "Y", "Y", "30.6", ""], ["#60", "49/F", "SM", "Y", "N", "Y", "15.8", "D816V"], ["#63", "56/M", "SM", "Y", "N", "Y", "60.8", "D816V"], ["#64", "24/M", "SM", "Y", "Y", "Y", "11.4", "D816V"], ["#66", "36/F", "SM", "Y", "N", "Y", "6.6", "D816V"]], "row_count": 42, "column_count": 8, "numeric_cells": 141, "header_rows": 1, "locator": "section[4]/table-wrap[1]#tbl1"}}, {"id": "asset:table:pmid:32575983:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7cf7cebad78ccb7a0832cb07abdd0ce9f2eae73cad59748719bad2c60bd423e8", "bytes": 11835, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#tbl2", "version": null, "note": "UniProt-KB Code, Experimental and Theoretical Average Mass Values ± Standard Deviations (SD), Average (Mav) and Monoisotopic ([M + H]+), Elution Times of Proteins and Peptides Analyzed, and Their PTMsb", "structure": {"pmcid": "PMC8008451", "section_index": 6, "section_title": "RP-HPLC-Low-Resolution ESI-MS Analysis", "row_count": 64, "column_count": 7}, "table": {"label": "Table 2", "caption": "UniProt-KB Code, Experimental and Theoretical Average Mass Values ± Standard Deviations (SD), Average (Mav) and Monoisotopic ([M + H]+), Elution Times of Proteins and Peptides Analyzed, and Their PTMsb", "rows": [["proteins/peptides", "el. time (min ± 0.5)", "Mav ± SD exper. (theor)", "m/z (charge) for XIC search", "[M + H]+ ± SD exper. (theor)", "PTMs", "m/z (charge) for MS/MS"], ["Acid proline-rich proteins (PRP-1 and PRP-3 types)a"], ["PRP-1 (P02810)", "22.2", "15515 ± 2 (15514–15,515)", "1293.9(+12), 1194.4(+13), 1035.3(+15), 970.7(+16), 913.6(+17)", "15506.1 ± 0.1 (15506.24–15507.22)", "Q1 pyroglutamination, S8 and S22 phosphorylation", "1293.68(+12); 1194(+13); 1035.28 (+15); 970.58 (+16); 862.85(+18)"], ["PRP-1 1P", "22.9", "15435 ± 2 (15434–15,435)", "1287.2(+12), 1188.3(+13), 1030.0(+15), 965.7(+16), 908.9(+17)", "15426.1 ± 0.1 (15426.27–15427.26)", "Q1 pyroglutamination, S8 or S22 phosphorylation", "1287.01(+12); 1188.3(+13); 1030.0 (+15)"], ["PRP-1 0P", "23.2", "15355 ± 2 (15354–15,355)", "1280.5(+12), 1182.1(+13), 1024.6(+15), 960.7(+16), 904.2(+17)", "15346.1 ± 0.1 (15346.31–15347.29)", "Q1 pyroglutamination", "1534.42 (+10); 904.08 (+17)"], ["PRP-1 3P", "21.6", "15595 ± 2 (15594–15,595)", "1418.7(+11), 1300.5(+12), 1200.6(+13), 1040.6(+15), 975.7(+16)", "15585.8 ± 0.1 (15586.21–15587.19)", "Q1 pyroglutamination, S8, S17, and S22 phosphorylation", "1733.70 (+9); 1560.08 (+10); 1114.61 (+14); 975.56 (+16)"], ["PRP-3 (P02810)", "22.8", "11161 ± 1 (11161–11,162)", "1595.5(+7), 1396.2(+8), 1015.7(+11), 931.1(+12), 859.6(+13)", "11155.01 ± 0.07 (11156.08–11157.06)", "Q1 pyroglutamination, S8 and S22 phosphorylation", "931.09(+12); 798.07(+14); 745.00(+15)"], ["PRP-3 1P", "23.4", "11081 ± 1 (11081–11,082)", "1584.1(+7), 1386.2(+8), 1008.4(+11), 924.5(+12), 853.4(+13)", "11075.98 ± 0.07 (11076.11–11077.09)", "Q1 pyroglutamination, S8 or S22 monophosphorylation", "1386.13(+8); 1008.28(+11); 853.31(+13)"], ["PRP-3 0P", "23.8", "11001 ± 1 (11001–11,002)", "1376.2(+8), 1101.2(+10), 917.8(+12) 786.8(+14)", "10996.01 ± 0.07 (10996.14–10997.13)", "Q1 pyroglutamination", "1001.10(+11); 786.72(+14)"], ["PRP-3 desR6", "22.8", "11004 ± 1 (11005–11,006)", "1573.2(+7), 1223.8(+9), 1001.5(+11), 847.6(+13)", "10999.85 ± 0.07 (10999.97–11000.96)", "C-term. R106 removal from PRP-3", "1001.45(+11); 918.08(+12)"], ["P-C peptide (P02810)", "15.0", "4370.9 ± 0.4 (4370.8)", "1457.9(+3), 1093.7(+4)", "4369.19 ± 0.03 (4369.20)", "", "1457.07(+3); 1093.05(+4); 874.64(+5); 729.04(+6)"], ["Statherin"], ["statherin (P02808)", "29.2", "5380.0 ± 0.5 (5379.7)", "1794.2(+3), 1345.9(+4), 1076.9(+5)", "5377.46 ± 0.03 (5377.45)", "S2 and S3 phosphorylation", "1793.17(+3); 1345.12(+4); 1076.30(+5)"], ["statherin 1P", "28.9", "5299.9 ± 0.5 (5299.7)", "1767.6(+3), 1325.9(+4), 1060.9(+5)", "5297.46 ± 0.03 (5297.48)", "S2 or S3 phosphorylation", "1325.12(+4); 1060.30(+5)"], ["statherin des-F43", "27.8", "5232.4 ± 0.5 (5232.5)", "1745.1(+3), 1309.1(+4), 1047.5(+5)", "5230.39 ± 0.03 (5230.38)", "C-term. F43 removal from statherin", "1744.13(+3); 1308.35(+4); 1046.88(+5)"], ["statherin desT42-F43", "27.9", "5131.2 ± 0.5 (5131.4)", "1711.4(+3), 1283.8(+4), 1027.2(+5)", "5129.34 ± 0.03 (5129.33)", "C-term. T42 and F43 removal from statherin", "1710.45(+3); 1283.09(+4); 1026.67(+5)"], ["statherin desD1", "28.7", "5264.7 ± 0.5 (5264.6)", "1755.9(+3), 1317.2(+4), 1053.9(+5)", "5262.43 ± 0.03 (5262.42)", "N-term D1 removal from statherin", "1754.81(+3); 1316.36(+4); 1053.29(+5)"], ["statherin des1-9", "28.5", "4127.9 ± 0.4 (4127.6)", "1376.9(+3), 1032.9(+4)", "4126.00 ± 0.02 (4125.99)", "removal of D1SSEEKFLR9 from statherin", "1376.00(+3); 1032.25(+4)"], ["statherin des1-10", "28.0", "3971.3 ± 0.4 (3971.4)", "1986.7(+2), 1324.8(+3)", "3969.88 ± 0.02 (3969.89)", "Removal of D1SSEEKFLRR10 from statherin", "1323.96(+3); 993.22(+4)"], ["statherin des1-13", "27.5", "3645.2 ± 0.4 (3645.0)", "1823.6(+2), 1216.1(+3)", "3643.69 ± 0.02 (3643.68)", "Removal of D1SSEEKFLRRIGR13 from statherin", "1215.23(+3); 911.68(+4)"], ["P-B peptide"], ["P-B peptide (P02814)", "30.0", "5792.9 ± 0.5 (5792.7)", "1932.0(+3), 1449.2(+4), 1159.6(+5)", "5790.05 ± 0.04 (5790.04)", "", "1930.68(+3); 1448.27(+4); 1158.82(+5)"], ["P-B des1-4", "30.0", "5371.0 ± 0.5 (5371.3)", "1791.4(+3), 1343.8(+4), 1075.3(+5)", "5368.83 ± 0.03 (5368.82)", "removal of Q1RGP4 from P-B", "1790.25(+3); 1342.96(+4); 1074.57(+5)"], ["P-B des1-5", "30.3", "5215.0 ± 0.5 (5215.1)", "1739.4(+3), 1304.8(+4), 1044.0(+5)", "5212.74 ± 0.03 (5212.73)", "removal of Q1RGPR5 from P-B", "1303.93(+4); 1043.35(+5)"], ["P-B des1-7", "30.1", "5060.1 ± 0.5 (5060.9)", "1688.0(+3), 1266.2(+4), 1013.2(+5)", "5058.66 ± 0.03 (5058.65)", "removal of Q1RGPRGP7 from P-B", "1686.88(+3); 1265.42(+4); 1012.54(+5)"], ["P-B des1-12", "27.5", "4549.0 ± 0.5 (4549.3)", "1517.5(+3), 1138.3(+4)", "4547.41 ± 0.02 (4547.41)", "removal of Q1RGPRGPYPPGP12 from P-B", "1137.61(+4)"], ["Histatins"], ["Hst-1 (P15515)", "21.9", "4928.2 ± 0.5 (4928.2)", "1644.1(+3), 1233.5(+4)", "4926.19 ± 0.03 (4926.20)", "S2 phosphorylation", "986.05(+5); 821.87(+6); 704.61(+7)"], ["Hst-1 0P", "22.0", "4848.2 ± 0.5 (4848.2)", "1617.4(+3), 1213.5(+4)", "4846.24 ± 0.03 (4846.23)", "", "970.05(+5)"], ["Hst-3 (P15516)", "17.7", "4062.2 ± 0.4 (4062.4)", "1355.1(+3), 1016.6(+4)", "4060.97 ± 0.02 (4060.98)", "", "1015.99(+4); 813.00(+5); 677.67(+6)"], ["Hst-3 1/25", "14.3", "3192.4 ± 0.3 (3192.5)", "1065.1(+3), 799.1(+4)", "3191.63 ± 0.02 (3191.62)", "removal of S26NYLYDN32 from Hst-3", "400.09(+8); 456.95(+9)"], ["Hst-3 1/24", "14.6", "3036.5 ± 0.3 (3036.3)", "1013.2(+3), 760.1(+4)", "3035.53 ± 0.02 (3035.52)", "removal of S26NYLYD31 from Hst-3", "608.11(+5); 506.93(+6); 434.65(+7)"], ["Cystatins"], ["cystatin A (P01040)", "31.8", "11005 ± 2 (11006.5)", "1001.59(+11), 1101.59(+10), 1223.94(+9), 1376.81(+8), 1573.36(+7), 1835.42(+6)", "11000.65 ± 0.07 (11000.67)", "", "1376.83(+8); 847.74(+13); 787.19(+14); 734.85(+15);"], ["cystatin A Nα-Ac", "33", "11047 ± 2 (11048.5)", "1005.41(+11), 1105.85(+10), 1228.61(+9), 1382.06(+8), 1579.36(+7), 1842.42(+6)", "11042.55 ± 0.07 (11042.68)", "N-terminal acetylation", "1381.79(+8); 789.98(+14)"], ["cystatin B-SSG (P04080)", "32.8", "11486 ± 2 (11486.9)", "1915.5(+6), 1642.0(+7), 1436.9(+8), 1277.3(+9), 1149.7(+10), 1045.3(+11)", "11480.61 ± 0.07 (11480.68)", "N-terminal acetylation, C3 glutathionylation", "1436.72(+8); 1277.31(+9); 766.91(+15), 718.79(+16)"], ["cystatin C (P01034)", "35.1", "13342 ± 2 (13343.1)", "1483.57(+9), 1335.32(+10), 1214.02(+11), 1112.93(+12), 1027.40(+13)", "13335.31 ± 0.08 (13335.58)", "2 disulfide bridges", "1112.81(+12); 890.50(+15)"], ["cystatin C Mox", "35.3", "13358 ± 1 (13358.4)", "1485.28(+9), 1336.85(+10), 1215.41(+11), 1114.21(+12), 1028.58(+13)", "13351.60 ± 0.08 (13351.57)", "M14 oxidation of cystatin C", "1114.23(+12); 954.20(+14)"], ["cystatin D-R26 des1-8 (P28325)", "38.0", "13163 ± 2 (13163.0)", "1646.40 (+8), 1463.60 (+9), 1317.30 (+10), 1197.60 (+11), 1097.90 (+12), 1013.50 (+13)", "13155.25 ± 0.08 (13155.48)", "removal of G1SASAQSR8, 2 disulfide bridges", "941.09(+14); 823.71(+16)"], ["cystatin D-R26 des1-5", "37.7", "13517 ± 2 (13517.3)", "1690.70(+8), 1502.90(+9), 1352.70 (+10), 1229.80 (+11), 1127.4 (+12), 1040.40 (+13)", "13509.41 ± 0.08 (13509.65)", "Q1 pyroglutamination after removal of G1SASA5, 2 disulfide bridges", "1502.63(+9), 1040.87(+13) 966.48(+14); 845.72(+16)"], ["cystatin S (P01036)", "35.3", "14186 ± 2 (14185)", "1774.3(+8), 1577.2(+9), 1419.6(+10), 1290.6(+11), 1183.2(+12), 1092.2(+13), 1014.3(+14)", "14176.61 ± 0.08 (14176.81)", "2 disulfide bridges", "946.58(+15); 835.22(+17)"], ["cystatin S1", "35.3", "14266 ± 2 (14265)", "1784.3(+8), 1586.1(+9), 1427.6(+10), 1297.9(+11), 1189.8(+12), 1098.4(+13), 1020.0(+14)", "14256.66 ± 0.09 (14256.77)", "S3 phosphorylation of cystatin S, 2 disulfide bridges", "1098.37(+13); 1019.69(+14); 951.91(+15)"], ["cystatin S1ox", "35.3", "14281 ± 2 (14280.7)", "1786.40(+8), 1589.70 (+9), 1429.30 (+10), 1299.50 (+11), 1191.30 (+12), 1099.70 (+13)", "14272.66 ± 0.09 (14272.77)", "W23 oxidation of cystatin S1", "1299.08(+11); 1099.36(+13); 894.67(+16)"], ["cystatin S2", "35.3", "14346 ± 2 (14345)", "1794.3(+8), 1595.0(+9), 1435.6(+10), 1305.2(+11), 1196.5(+12), 1104.5(+13), 1025.7(+14)", "14336.58 ± 0.09 (14336.74)", "S1 and S3 phosphorylation of cystatin S, 2 disulfide bridges", "957.31(+15); 897.55(+16)"], ["cystatin SN (P01037)", "34.6", "14312 ± 2 (14313)", "1790.0(+8), 1591.2(+9), 1432.2(+10), 1302.1(+11), 1193.7(+12), 1101.9(+13), 1023.3(+14)", "14304.03 ± 0.09 (14304.09)", "2 disulfide bridges", "1023.29(+14); 796.01(+18); 716.50(+20)"], ["cystatin SNox", "34.6", "14328 ± 2 (14328)", "1792.30(+8), 1593.20 (+9), 1434.00 (+10), 1303.30 (+11), 1195.20 (+12), 1103.30 (+13)", "14320.09 ± 0.09 (14319.84)", "2 disulfide bridges, W23 oxidation", "843.64(+17); 754.26(+19); 717.35(+20); 682.52(+21)"], ["cystatin SA (P09228)", "36.8", "14347 ± 2 (14346)", "1794.4(+8), 1595.1(+9), 1435.7(+10), 1305.3(+11), 1196.6(+12), 1104.6(+13), 1025.8(+14)", "14337.87 ± 0.09 (14338.01)", "1 disulfide bridge", "897.50(+16); 844.88(+17); 798.78(+18);"], ["Antileukoproteinase"], ["SLPI (P03973)", "26.2", "11709 ± 1 (11710)", "1952.64(+6), 1673.84(+7), 1464.73(+8), 1302.10(+9)", "11702.41 ± 0.07 (11702.36)", "8 disulfide bridges", "1171.82(+10); 1065.47(+11); 976.69(+12); 837.45(+14)"], ["α-Defensins"], ["α-defensin 1 (P59665)", "23.5", "3442.5 ± 0.3 (3442.1)", "1772.03(+2), 1148.36(+3), 861.52(+4)", "3440.45 ± 0.02 (3440.519)", "3 disulfide bridges", "861.14(+4); 689.11(+5)"], ["α-defensin 2 (P59665/6)", "23.5", "3370.7 ± 0.3 (3370.9)", "1686.49(+2), 1124.66(+3), 843.75(+4)", "3370.41 ± 0.02 (3370.484)", "3 disulfide bridges", "843.61(+4); 675.10(+5)"], ["α-defensin 3 (P59666)", "23.5", "3485.8 ± 0.3 (3486.1)", "1744.03(+2), 1163.03(+3), 872.52(+4)", "3484.53 ± 0.02 (3484.509)", "3 disulfide bridges", "872.11(+4); 698.09(+5)"], ["α-defensin 4 (P12838)", "27.2", "3709.1 ± 0.3 (3709.4)", "1855.71(+2), 1237.48(+3), 928.36(+4)", "3707.68 ± 0.02 (3707.767)", "3 disulfide bridges", "928.18(+4); 742.74(+5);"], ["Thymosin β4"], ["Tβ4 (P62328)", "18.5", "4963.7 ± 0.5 (4963.5)", "1655.51(+3), 1241.88(+4), 993.71(+5)", "4961.47 ± 0.03 (4961.494)", "N-terminal acetylation", "710.08(+7), 621.32(+8)"], ["S100A proteins"], ["S100A8 (P05109)", "40.4", "10834 ± 2 (10834.6)", "1355.3(+8), 1204.8(+9), 1084.5(+10), 985.9(+11)", "10827.41 ± 0.07 (10828.66)", "", "903.62(+12); 834.11(+13); 774.75(+14)"], ["S100A8 SNO", "40.8", "10863 ± 2 (10863.5)", "1358.9(+8), 1208.1(+9), 1087.3(+10), 988.6(+11)", "10857.37 ± 0.07 (10857.65)", "C42 nitrosylation", "1087.49(+10); 680.03(+16); 640.03(+17)"], ["S100A8 hyperoxidized", "39.3", "10915 ± 2 (10914.6)", "1365.3(+8), 1213.7(+9), 1092.5(+10), 993.2(+11)", "10908.40 ± 0.07 (10908.63)", "C42-SO3H, W54 dioxidation or C42-SO3H, W54, and M78 oxidation", "993.20(+11); 910.37(+12); 683.16(+16); 642.85(+17)"], ["S100A9(S) (P06702)", "42.2", "12690 ± 2 (12689.3)", "1410.9(+9), 1269.9(+10), 1154.6(+11), 1058.4(+12), 977.1(+13)", "12682.21 ± 0.08 (12682.29)", "N-term. Acetylation after M1TCKM5 removal", "1410.67(+9); 1269.93(+10); 977.22(+13); 793.95(+16); 747.48(+17); 705.85(+18);"], ["S100A9(S) 1P", "42.2", "12770 ± 2 (12769.3)", "1419.8(+9), 1277.9(+10), 1161.8(+11), 1065.1(+12), 983.3(+13)", "12762.05 ± 0.08 (12762.26)", "T108 phosphorylation of S100A9(S)", "1161.66(+11); 798.96(+16); 710.29(+18)"], ["S100A9(S)ox", "41.3", "12706 ± 2 (12705.3)", "1412.7(+9), 1271.5(+10), 1156.0(+11), 1059.8(+12), 978.3(+13)", "12698.14 ± 0.08 (12698.29)", "M89, or 78 or 76 or 58 oxidation of S100A9(S)", "1271.41(+10); 1155.92(+11); 908.51(+14)"], ["S100A9(S)ox 1P", "41.3", "12786 ± 2 (12785.3)", "1421.9(+9), 1279.5(+10), 1163.3(+11), 1066.4(+12), 984.5(+13)", "12778.21 ± 0.08 (12778.25)", "T108 phosphorylation of S100A9(S)ox", "1419.82(+9); 983.26(+13); 913.10(+14)"]], "row_count": 64, "column_count": 7, "numeric_cells": 355, "header_rows": 1, "locator": "section[6]/table-wrap[1]#tbl2"}}, {"id": "asset:table:pmid:32575983:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:abf58967b1d8178cc9fd9ab79bd07f8993cdb2d176bd48ae907ef9ecef227df1", "bytes": 5282, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#tbl3", "version": null, "note": "XIC Peak Areas Values (Mean ± SD), Frequencies, and p Values Obtained by Statistical Analysis by Comparing the Three Patients’ Groups with Respect to the Controls and Each Othera", "structure": {"pmcid": "PMC8008451", "section_index": 10, "section_title": "Quantitative Comparison between Controls and Patients", "row_count": 49, "column_count": 7}, "table": {"label": "Table 3", "caption": "XIC Peak Areas Values (Mean ± SD), Frequencies, and p Values Obtained by Statistical Analysis by Comparing the Three Patients’ Groups with Respect to the Controls and Each Othera", "rows": [["", "", "XIC peak area ×108 (mean ± SD) and frequency", "p values"], ["no.", "protein/peptide", "CM", "SM", "Ctrls", "CM vs Ctrls", "SM vs Ctrls"], ["#1", "PRP-1", "17.8 ± 10.1 (6/6)", "27.4 ± 27.2 (35/35)", "99.9 ± 70.9 (48/48)", "<0.0001 ↓CM", "< 0.0001 ↓SM"], ["#2", "PRP-1 1P", "2.5 ± 3.1 (5/6)", "3.7 ± 5.2 (29/35)", "12.8 ± 12.9 (47/48)", "0.002 ↓CM", "< 0.0001 ↓SM"], ["#3", "PRP-1 0P", "(0/6)", "0.09 ± 0.3 (6/35)", "0.5 ± 0.9 (22/48)", "NA", "0.003 ↓SM"], ["#4", "PRP-1 3P", "0.2 ± 0.2 (4/6)", "0.4 ± 0.6 (22/35)", "2.0 ± 1.9 (44/48)", "0.002 ↓CM", "< 0.0001 ↓SM"], ["#5", "PRP-3", "5.9 ± 4.4 (6/6)", "9.5 ± 11.3 (33/35)", "35.1 ± 29.3 (48/48)", "0.0002 ↓CM", "< 0.0001 ↓SM"], ["#6", "PRP-3 1P", "1.1 ± 1.0 (6/6)", "1.5 ± 1.8 (29/35)", "4.9 ± 4.1 (47/48)", "0.002 ↓CM", "< 0.0001 ↓SM"], ["#7", "PRP-3 0P", "(0/10)", "0.004 ± 0.02 (2/35)", "0.4 ± 1.1 (18/48)", "NA", "0.0003 ↓SM"], ["#8", "PRP-3 desR106", "3.1 ± 2.7 (6/6)", "2.8 ± 5.9 (26/35)", "3.8 ± 6.2 (40/48)", "•", "•"], ["#9", "P-C peptide", "4.1 ± 4.4 (6/6)", "7.0 ± 10.0 (33/35)", "20.4 ± 16.2 (48/48)", "0.001 ↓CM", "< 0.0001 ↓SM"], ["#10", "statherin", "5.4 ± 6.6 (5/6)", "6.0 ± 6.6 (34/35)", "13.4 ± 10.1 (47/47)", "0.02 ↓CM", "0.0001 ↓SM"], ["#11", "Stath. 1P", "0.2 ± 0.2 (3/6)", "0.1 ± 0.2 (17/35)", "0.3 ± 0.4 (32/47)", "•", "0.03 ↓SM"], ["#12", "Stath. des-F43", "1.1 ± 1.0 (6/6)", "1.0 ± 0.9 (34/35)", "1.9 ± 1.8 (46/47)", "•", "0.006 ↓SM"], ["#13", "Stath. desT42-F43", "0.7 ± 0.4 (6/6)", "0.4 ± 0.4 (25/35)", "0.7 ± 0.7 (46/47)", "•", "•"], ["#14", "Stath. desD1", "0.7 ± 0.9 (5/6)", "0.5 ± 0.5 (31/35)", "0.8 ± 0.8 (46/47)", "•", "0.02 ↓SM"], ["#15", "Stath. des1-9", "0.1 ± 0.2 (5/6)", "0.2 ± 0.4 (18/35)", "0.7 ± 0.7 (40/47)", "•", "< 0.0001 ↓SM"], ["#16", "Stath. des1-10", "0.2 ± 0.2 (5/6)", "0.3 ± 0.4 (24/35)", "0.5 ± 0.5 (44/47)", "•", "0.001 ↓SM"], ["#17", "Stath. des1-13", "0.1 ± 0.1 (4/6)", "0.1 ± 0.2 (22/35)", "0.3 ± 0.2 (45/47)", "0.04 ↓CM", "< 0.0001 ↓SM"], ["#18", "P-B peptide", "7.6 ± 7.9 (6/6)", "9.2 ± 7.8 (34/35)", "21.9 ± 14.3 (47/47)", "0.004 ↓CM", "< 0.0001 ↓SM"], ["#19", "P-B des1-4", "0.9 ± 0.6 (6/6)", "1.0 ± 0.8 (31/35)", "1.5 ± 1.7 (39/48)", "•", "•"], ["#20", "P-B des1-5", "3.0 ± 3.6 (6/6)", "1.8 ± 2.4 (30/35)", "2.3 ± 2.8 (42/48)", "•", "•"], ["#21", "P-B des1-7", "1.7 ± 0.9 (6/6)", "1.7 ± 1.5 (32/35)", "4.4 ± 2.8 (47/48)", "0.007 ↓CM", "< 0.0001 ↓SM"], ["#22", "P-B des1-12", "0.8 ± 0.4 (6/6)", "0.6 ± 0.6 (31/35)", "1.0 ± 1.4 (46/48)", "•", "•"], ["#23", "Hst-1", "1.1 ± 1.6 (4/6)", "1.1 ± 1.5 (24/35)", "2.9 ± 2.9 (34/48)", "•", "0.02 ↓SM"], ["#24", "Hst-1 0P", "(0/6)", "0.2 ± 0.3 (15/35)", "0.4 ± 0.7 (23/48)", "NA", "•"], ["#25", "Hst-3", "0.01 ± 0.03 (1/6)", "0.3 ± 0.6 (12/35)", "1.2 ± 1.7 (26/48)", "NA", "0.008 ↓SM"], ["#26", "Hst-3 1/25", "(0/6)", "0.04 ± 0.1 (6/35)", "0.9 ± 1.2 (25/48)", "NA", "0.0001 ↓SM"], ["#27", "Hst-3 1/24", "(0/6)", "0.8 ± 1.7 (15/27)", "3.0 ± 3.4 (40/48)", "NA", "< 0.0001 ↓SM"], ["#28", "Cyst. A", "2.0 ± 1.4 (6/6)", "1.2 ± 1.2 (35/35)", "2.2 ± 1.9 (47/48)", "•", "0.001 ↓SM"], ["#29", "Cyst B (all proteoforms)", "1.3 ± 1.1 (6/6)", "1.2 ± 1.2 (34/35)", "1.4 ± 1.3 (43/48)", "•", "•"], ["#30", "Cyst. C (all proteoforms)", "0.03 ± 0.07 (1/6)", "0.05 ± 0.2 (3/35)", "0.6 ± 0.7 (32/48)", "NA", "< 0.0001 ↓SM"], ["#31", "Cyst. D-R26 des1-5", "0.4 ± 0.9 (1/6)", "0.5 ± 0.8 (19/35)", "0.8 ± 1.1 (28/48)", "NA", "•"], ["#32", "Cyst. D-R26 des1-8", "(0/6)", "0.06 ± 0.1 (11/35)", "0.1 ± 0.2 (15/48)", "NA", "•"], ["#33", "Cyst. S", "(0/6)", "0.3 ± 0.7 (11/35)", "2.5 ± 0.5 (29/48)", "NA", "0.0007 ↓SM"], ["#34", "Cyst. S1 (all proteoforms)", "11.3 ± 12.7 (6/6)", "4.5 ± 3.8 (33/35)", "10.3 ± 10.6 (45/48)", "•", "0.002 ↓SM"], ["#35", "Cyst. S2", "1.9 ± 3.0 (2/6)", "2.2 ± 3.6 (22/35)", "3.8 ± 3.9 (45/48)", "•", "0.002 ↓SM"], ["#36", "Cyst. SN (all proteoforms)", "10.2 ± 13.8 (4/6)", "9.2 ± 11.1 (31/35)", "20.7 ± 17.1 (47/48)", "•", "0.0005 ↓SM"], ["#37", "Cyst. SA", "0.9 ± 1.9 (2/6)", "0.8 ± 2.1 (9/35)", "2.9 ± 3.8 (35/48)", "•", "<0.0001 ↓SM"], ["#38", "Tβ4", "0.4 ± 0.3 (5/6)", "0.4 ± 0.5 (24/35)", "0.8 ± 1.0 (30/48)", "•", "•"], ["#39", "α-defensin 1", "1.1 ± 0.7 (6/6)", "1.4 ± 1.9 (33/35)", "1.9 ± 2.9 (41/48)", "•", "•"], ["#40", "α-defensin 2", "0.8 ± 0.6 (6/6)", "0.7 ± 0.9 (31/35)", "1.3 ± 1.7 (37/48)", "•", "•"], ["#41", "α-defensin 3", "0.6 ± 0.7 (5/6)", "0.3 ± 0.4 (21/35)", "0.8 ± 1.3 (30/48)", "•", "•"], ["#42", "α-defensin 4", "0.2 ± 0.1 (3/6)", "0.1 ± 0.2 (15/35)", "0.3 ± 0.4 (23/48)", "•", "•"], ["#43", "S100A9(S) + (S)ox", "1.3 ± 1.5 (4/6)", "1.5 ± 1.9 (24/35)", "2.3 ± 2.7 (39/48)", "•", "•"], ["#44", "S100A9(S) 1P + (S)ox 1P", "0.4 ± 0.5 (3/6)", "0.6 ± 1.0 (16/35)", "0.5 ± 1.0 (17/48)", "•", "•"], ["#45", "SLPI", "0.2 ± 0.3 (3/6)", "0.2 ± 0.8 (18/35)", "0.1 ± 0.20 (10/48)", "•", "0.005 ↑SM"], ["#46", "S100A8 (all proteoforms)", "0.5 ± 1.1 (1/6)", "0.6 ± 1.1 (14/35)", "0.2 ± 0.6 (9/48)", "NA", "0.02 ↑SM"], ["#47", "S100A8-SNO", "0.5 ± 1.1 (1/6)", "0.3 ± 0.7 (8/35)", "0.1 ± 0.5 (6/48)", "NA", "•"]], "row_count": 49, "column_count": 7, "numeric_cells": 263, "header_rows": 2, "locator": "section[10]/table-wrap[1]#tbl3"}}, {"id": "asset:table:pmid:32575983:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a1905f171d1bc6d3b40026923a10bf24cb17ef2c110aed3852a417f46b60af36", "bytes": 1053, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tbl4", "version": null, "note": "Results of Correlation Analysis between Salivary Proteins/Peptides and Tryptase Levels in SM Patients and in the Subgroup SM-Ca", "structure": {"pmcid": "PMC8008451", "section_index": 12, "section_title": "Correlation Analysis with Tryptase and with Oral Aphtosis and GI Symptoms", "row_count": 14, "column_count": 6}, "table": {"label": "Table 4", "caption": "Results of Correlation Analysis between Salivary Proteins/Peptides and Tryptase Levels in SM Patients and in the Subgroup SM-Ca", "rows": [["", "SM (n = 35)", "SM-C (n = 8)", ""], ["protein/peptide", "p value", "R", "p value", "R", "distinctive between SM-C and SM+C"], ["PRP-1 1P", "", "", "0.04 (+)", "0.77", ""], ["PRP-3 1P", "", "", "0.03 (+)", "0.77", ""], ["PRP-3 desR106", "", "", "0.007 (+)", "0.88", "Y (↑ in SM-C)"], ["Statherin desD1", "", "", "0.01 (+)", "0.86", ""], ["Statherin des1-10", "0.03 (+)", "0.40", "0.02 (+)", "0.79", ""], ["Statherin des1-13", "0.02 (+)", "0.40", "0.02 (+)", "0.79", ""], ["P-B des1-4", "0.02 (+)", "0.38", "0.002 (+)", "0.93", ""], ["P-B des1-5", "", "", "0.02 (+)", "0.81", "Y (↑ in SM-C)"], ["P-B des1-7", "", "", "0.01 (+)", "0.86", ""], ["P-B des1-12", "", "", "0.006 (+)", "0.89", ""], ["Cystatin D-R26 des1-5", "0.02 (+)", "0.40", "0.005 (+)", "0.90", "Y (↑ in SM-C)"], ["Thymosin β4", "", "", "0.005 (−)", "–0.84", "Y (↓ in SM-C)"]], "row_count": 14, "column_count": 6, "numeric_cells": 45, "header_rows": 2, "locator": "section[12]/table-wrap[1]#tbl4"}}], "gaps": ["asset:data:geo:PXD017759 not downloaded", "asset:data:geo:PXD017759 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "welch_t_test", "label": "Group comparison", "dsl_operations": ["welch_t"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The comparisons between the three groups of patients and that of the controls and between the three groups of patients have been performed with Mann–Whitney and Welch-corrected t tests, depending on the distribution (skewed or normal) and the variance (unequal or homogeneous). Correlation analyses, between the XIC peak area of the proteins/peptides under analysis and the tryptase levels of each patient, were performed with the Spearman test and considered significant when the p value was <0.05."}}], "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": ["welch_t"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: welch_t_test."}, "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": ["PXD017759"], "resolved_accessions": ["PXD017759"], "statements": ["Data are available via ProteomeXchange with identifier PXD017759."], "basis": "The paper names PXD017759 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": ["welch_t"], "assets": ["source:pmid:32575983", "data:geo:PXD017759", "asset:table:pmid:32575983:1", "asset:table:pmid:32575983:2", "asset:table:pmid:32575983:3", "asset:table:pmid:32575983:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD017759"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:34Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 44102, "completion_tokens": 1156, "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:32575983", "type": "paper", "label": "pmid:32575983"}, {"id": "source:pmid:32575983", "type": "manuscript", "label": "PMID 32575983 full text"}, {"id": "data:geo:PXD017759", "type": "dataset", "label": "GEO PXD017759"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32575983", "type": "paper", "label": "pmid:32575983"}, {"id": "source:pmid:32575983", "type": "manuscript", "label": "PMID 32575983 full text"}, {"id": "data:geo:PXD017759", "type": "dataset", "label": "GEO PXD017759"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32575983", "type": "extraction", "used": ["source:pmid:32575983"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD017759", "type": "accession_resolution", "used": ["data:geo:PXD017759"], "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:32575983", "parent_hash": "sha256:a7019602b245c7fa0a5763f9973d9d96a4ac082d1a5a9398e9a5df412a9ca938", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD017759 licence not read", "asset:data:geo:PXD017759 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["welch_t"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The comparisons between the three groups of patients and that of the controls and between the three groups of patients have been performed with Mann–Whitney and Welch-corrected t tests, depending on the distribution (skewed or normal) and the variance (unequal or homogeneous). Correlation analyses, between the XIC peak area of the proteins/peptides under analysis and the tryptase levels of each patient, were performed with the Spearman test and considered significant when the p value was <0.05."], "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":"2026-11-04T02:39:28+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}}}