{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40524029", "kind": "science-record", "revision": 2, "content_hash": "sha256:a90f32ecd4d974479335b998f7d5234506a4746b0820f70efd6c5b0f37ef10ed", "created_at": "2026-11-01T10:25:51Z", "updated_at": "2026-11-01T14:01:42Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "To reveal the key mechanism of Citri Reticulatae Pericarpium-Reynoutria japonica Houtt in the treatment of liver cancer and its correlation with lipid metabolism: synergetic effect with network pharmacology, molecular docking and bioinformatics.", "doi": "10.1007/s12672-025-02708-8", "pmid": "40524029", "authors": null, "journal": "Discover oncology", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40524029"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:40524029", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40524029' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40524029", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-025-02708-8", "sha256": "sha256:713cbdf8624639ae2e73a6d4cdaaee9049527d3d1daf137aff4500511bf29b67", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-025-02708-8", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40524029:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dc84ad32811b7ffff4ea46866d3a8e152e71f70b6ad2be4ba101e7632708c4c6", "bytes": 926, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab1", "version": null, "note": "Grid box centers and sizes for molecular docking of target genes", "structure": {"pmcid": "PMC12170481", "section_index": 13, "section_title": "Molecular docking validation and ADMET analysis", "row_count": 9, "column_count": 3}, "table": {"label": "Table 1", "caption": "Grid box centers and sizes for molecular docking of target genes", "rows": [["Gene name", "Grid box center", "Grid box size"], ["TP53", "x = 122.593, y = 97.379, z = −41.654", "x = 24 Å, y = 26 Å, z = 28 Å"], ["ESR1", "x = 26.6, y = −12.807, z = 16.742", "x = 32 Å, y = 26 Å, z = 34 Å"], ["BCL2", "x = −0.141, y = −5.997, z = 5.575", "x = 28 Å, y = 22 Å, z = 20 Å"], ["JUN", "x = 23.99, y = −20.976, z = −4.06", "x = 30 Å, y = 24 Å, z = 26 Å"], ["TNF", "x = 16.05, y = 15.494, z = 114.301", "x = 30 Å, y = 28 Å, z = 34 Å"], ["HSP90 AA1", "x = −43.634, y = 15.277, z = −18.917", "x = 18 Å, y = 24 Å, z = 36 Å"], ["AKT1", "x = 19.901, y = 18.534, z = 15.857", "x = 24 Å, y = 18 Å, z = 26 Å"], ["IL-6", "x = 8.185, y = −25.073, z = −0.568", "x = 28 Å, y = 26 Å, z = 16 Å"]], "row_count": 9, "column_count": 3, "numeric_cells": 19, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:40524029:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3c5346064fb94cfbb6275d5a04fd7ab61743c174e72046e36723b51e4414df7d", "bytes": 2052, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab2", "version": null, "note": "The 123 common targets between active compound targets of CR and liver cancer disease targets", "structure": {"pmcid": "PMC12170481", "section_index": 17, "section_title": "Active components of CR and Potential targets in LC", "row_count": 21, "column_count": 14}, "table": {"label": "Table 2", "caption": "The 123 common targets between active compound targets of CR and liver cancer disease targets", "rows": [["No.", "Target", "No.", "Target", "No.", "Target", "No.", "Target", "No.", "Target", "No.", "Target", "No.", "Target"], ["1", "AKT1", "21", "CDK4", "41", "RXRA", "61", "ADIPOQ", "81", "INSR", "101", "CYP1B1", "121", "GJA1"], ["2", "APOB", "22", "MYC", "42", "IL10", "62", "CYP19A1", "82", "ESR2", "102", "HSPB1", "122", "CAT"], ["3", "CASP8", "23", "MAPK1", "43", "GSTM1", "63", "PPARA", "83", "SPP1", "103", "CCNA2", "123", "ODC1"], ["4", "CCND1", "24", "NFE2L2", "44", "CDK2", "64", "STAT1", "84", "E2 F1", "104", "F3", "", ""], ["5", "CDKN2A", "25", "IL6", "45", "EGF", "65", "MAPK8", "85", "RASSF1", "105", "CCNB1", "", ""], ["6", "EGFR", "26", "TNF", "46", "PIK3CG", "66", "IGFBP3", "86", "NOS2", "106", "PRKCA", "", ""], ["7", "EPHB2", "27", "PPARG", "47", "CDKN1A", "67", "CCL2", "87", "HMOX1", "107", "CREB1", "", ""], ["8", "ERBB2", "28", "TGFB1", "48", "GSTP1", "68", "PGR", "88", "MAPK3", "108", "CTSD", "", ""], ["9", "ESR1", "29", "ERBB3", "49", "ICAM1", "69", "FASN", "89", "CASP9", "109", "NOS3", "", ""], ["10", "IL1B", "30", "VEGFA", "50", "CXCL8", "70", "CAV1", "90", "IL4", "110", "HMGCR", "", ""], ["11", "IRF1", "31", "JUN", "51", "PTGS2", "71", "ABCC1", "91", "NFKBIA", "111", "SOD1", "", ""], ["12", "MPO", "32", "BAX", "52", "CYP1A1", "72", "PARP1", "92", "IL1A", "112", "CD40LG", "", ""], ["13", "NQO1", "33", "IGF2", "53", "IFNG", "73", "CRP", "93", "RELA", "113", "CHUK", "", ""], ["14", "PTEN", "34", "MDM2", "54", "MMP9", "74", "SERPINE1", "94", "GSK3B", "114", "TOP1", "", ""], ["15", "RB1", "35", "IL2", "55", "UGT1A1", "75", "MMP1", "95", "MAPK14", "115", "MMP3", "", ""], ["16", "TP53", "36", "HIF1A", "56", "MMP2", "76", "TIMP1", "96", "NR1I2", "116", "DPP4", "", ""], ["17", "TOP2A", "37", "RAF1", "57", "CASP3", "77", "BCL2L1", "97", "MCL1", "117", "ACACA", "", ""], ["18", "CHEK2", "38", "CYP3A4", "58", "CYP1A2", "78", "PLAU", "98", "CHEK1", "118", "VCAM1", "", ""], ["19", "MET", "39", "BCL2", "59", "BIRC5", "79", "PCNA", "99", "SREBF1", "119", "AHR", "", ""], ["20", "AR", "40", "HSP90AA1", "60", "ABCG2", "80", "FOS", "100", "HSPA5", "120", "BAD", "", ""]], "row_count": 21, "column_count": 14, "numeric_cells": 129, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:40524029:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:03b3bb347fa6b9ec5613593dfb2aacd94e0b7b24ca22104e8308b457596eecbf", "bytes": 664, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#Tab3", "version": null, "note": "Top 28 targets, ranked by degree in the compound–target–pathway network of liver cancer", "structure": {"pmcid": "PMC12170481", "section_index": 18, "section_title": "PPI network construction and analysis", "row_count": 15, "column_count": 4}, "table": {"label": "Table 3", "caption": "Top 28 targets, ranked by degree in the compound–target–pathway network of liver cancer", "rows": [["Gene name", "Degree", "Gene name", "Degree"], ["TP53", "96", "RELA", "32"], ["AKT1", "64", "CASP3", "32"], ["JUN", "56", "MDM2", "32"], ["IL6", "50", "FOS", "28"], ["TNF", "48", "MAPK8", "28"], ["HSP90AA1", "46", "CDKN1A", "28"], ["ESR1", "46", "CXCL8", "26"], ["BCL2", "42", "IFNG", "26"], ["MAPK3", "40", "CCL2", "26"], ["CCND1", "40", "HIF1A", "26"], ["MAPK1", "40", "CDKN2A", "24"], ["MYC", "38", "CDK4", "24"], ["EGFR", "34", "BCL2L1", "24"], ["IL1B", "34", "MAPK14", "24"]], "row_count": 15, "column_count": 4, "numeric_cells": 31, "header_rows": 1, "locator": "section[18]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:40524029:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:68583bcdc03805f201d73f318d0b33665d68c70012f0e6968c429791dfcbe47a", "bytes": 489, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#Tab4", "version": null, "note": "Top 16 targets, ranked by degree in the compound–target–pathway network of liver cancer", "structure": {"pmcid": "PMC12170481", "section_index": 20, "section_title": "Analysis of compound–target–pathway interactions and core target identification in liver cancer", "row_count": 9, "column_count": 4}, "table": {"label": "Table 4", "caption": "Top 16 targets, ranked by degree in the compound–target–pathway network of liver cancer", "rows": [["Gene name", "Degree", "Gene name", "Degree"], ["RB1", "18", "AR", "5"], ["PTGS2", "11", "GSTP1", "4"], ["HSP90AA1", "11", "IL10", "4"], ["TOP2A", "9", "DPP4", "4"], ["GSK3B", "8", "ESR1", "4"], ["JUN", "7", "BCL2", "4"], ["PIK3CG", "7", "CASP9", "4"], ["PPARG", "6", "CASP3", "4"]], "row_count": 9, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[20]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:40524029:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:aaa5212de3ca038e686980458f8e2ff2a6679896726baaf0473f12c028ad5acb", "bytes": 1040, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[2]#Tab5", "version": null, "note": "Details of the top 10 compounds in the compound–target–pathway network of liver cancer", "structure": {"pmcid": "PMC12170481", "section_index": 20, "section_title": "Analysis of compound–target–pathway interactions and core target identification in liver cancer", "row_count": 11, "column_count": 8}, "table": {"label": "Table 5", "caption": "Details of the top 10 compounds in the compound–target–pathway network of liver cancer", "rows": [["Rank", "Component ID", "Component name", "Structure", "CAS", "Degree", "OB(%)", "DL"], ["1", "MOL000098", "Quercetin", "", "117-39-5", "97", "46.43", "0.28"], ["2", "MOL000006", "Luteolin", "", "491-70-3", "45", "36.16", "0.25"], ["3", "MOL004328", "Naringenin", "", "67604-48-2", "25", "59.29", "0.21"], ["4", "MOL005828", "Nobiletin", "", "478-01-3", "23", "61.67", "0.52"], ["5", "MOL000358", "Beta-sitosterol", "", "83-46-5", "13", "36.91", "0.75"], ["6", "MOL013287", "Physovenine", "", "6091-05-0", "12", "106.21", "0.19"], ["7", "MOL013281", "6,8-Dihydroxy-7-methoxyxanthone", "", "87339-74-0", "9", "35.83", "0.21"], ["8", "MOL000492", "(+)-catechin", "", "154-23-4", "6", "54.83", "0.24"], ["9", "MOL005100", "5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chroman-4-one", "", "520-33-2", "5", "47.74", "0.27"], ["10", "MOL002268", "Rhein", "", "478-43-3", "5", "47.07", "0.28"]], "row_count": 11, "column_count": 8, "numeric_cells": 62, "header_rows": 1, "locator": "section[20]/table-wrap[2]#Tab5"}}, {"id": "asset:table:pmid:40524029:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:160ed912667ec177723cb3a6f72ef33a7d30d929c2a0a5e96e7615167b89c810", "bytes": 557, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#Tab6", "version": null, "note": "Top 21 targets in the compound–target–pathway network of NAFLD-LMDs, ranked by degree", "structure": {"pmcid": "PMC12170481", "section_index": 22, "section_title": "Analysis of shared pathways and core targets in NAFLD and DLM-related LC", "row_count": 12, "column_count": 4}, "table": {"label": "Table 6", "caption": "Top 21 targets in the compound–target–pathway network of NAFLD-LMDs, ranked by degree", "rows": [["Gene name", "Degree", "Gene name", "Degree"], ["RB1", "15", "BCL2", "4"], ["PTGS2", "11", "CDKN1A", "3"], ["HSP90AA1", "11", "NOS3", "3"], ["JUN", "9", "RXRA", "3"], ["GSK3B", "7", "BAX", "3"], ["IL10", "7", "AKT1", "3"], ["PIK3CG", "7", "MMP9", "3"], ["PPARG", "6", "MAPK1", "3"], ["ADRB2", "4", "TP53", "3"], ["DPP4", "4", "GSTP1", "3"], ["ESR1", "4", "", ""]], "row_count": 12, "column_count": 4, "numeric_cells": 24, "header_rows": 1, "locator": "section[22]/table-wrap[1]#Tab6"}}, {"id": "asset:table:pmid:40524029:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5e1a227a403c5af25991dac5645aa8439222c2c0338fb25f3d2364047a986003", "bytes": 1456, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[1]#Tab7", "version": null, "note": "Molecular docking binding affinities (kcal/mol) between active compounds and target proteins", "structure": {"pmcid": "PMC12170481", "section_index": 24, "section_title": "Molecular docking", "row_count": 11, "column_count": 10}, "table": {"label": "Table 7", "caption": "Molecular docking binding affinities (kcal/mol) between active compounds and target proteins", "rows": [["ID", "Compounds", "AKT1(kcal/mol)", "JUN(kcal/mol)", "TP53(kcal/mol)", "TNF(kcal/mol)", "HSP90AA1(kcal/mol)", "ESR1(kcal/mol)", "BCL2(kcal/mol)", "IL6(kcal/mol)"], ["MOL000358", "Beta-sitosterol", "−7.0", "−5.9", "−6.1", "−7.6", "−7.9", "−6.7", "−7.7", "−6.3"], ["MOL013281", "6,8-Dihydroxy-7-methoxyxanthone", "−6.0", "−6.1", "−7.2", "−7.1", "−8.9", "−7.4", "−6.4", "−6.0"], ["MOL000492", "(+)-catechin", "−6.4", "−5.9", "−7.8", "−8.9", "−8.7", "−7.3", "−6.7", "−6.4"], ["MOL005100", "5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chroman-4-one", "−6.1", "−6.4", "−8.2", "−8.8", "−9.0", "−7.5", "−7.1", "−6.8"], ["MOL002268", "rhein", "−6.7", "−6.7", "−8.3", "−8.9", "−9.6", "−8.6", "−7.5", "−6.9"], ["MOL000006", "luteolin", "−6.1", "−6.5", "−8.0", "−8.8", "−9.3", "−8.0", "−6.9", "−7.2"], ["MOL004328", "naringenin", "−6.2", "−6.2", "−7.8", "−8.4", "−9.1", "−8.6", "−6.7", "−6.6"], ["MOL000098", "quercetin", "−6.0", "−6.4", "−7.9", "−9.0", "−9.1", "−7.3", "−6.9", "−7.1"], ["MOL005828", "nobiletin", "−5.7", "−5.8", "−6.9", "−7.3", "−8.3", "−6.9", "−6.2", "−6.0"], ["MOL013287", "Physovenine", "−6.0", "−6.4", "−6.8", "−6.2", "−7.5", "−7.5", "−6.8", "−5.5"]], "row_count": 11, "column_count": 10, "numeric_cells": 94, "header_rows": 1, "locator": "section[24]/table-wrap[1]#Tab7"}}, {"id": "asset:table:pmid:40524029:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f7c255d5bc2acba3519bf9a9259b13ba4a75bc661612802cba716820e43bfbab", "bytes": 1703, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[1]#Tab8", "version": null, "note": "ADMET profiling of compounds", "structure": {"pmcid": "PMC12170481", "section_index": 25, "section_title": "ADMET analysis", "row_count": 15, "column_count": 10}, "table": {"label": "Table 8", "caption": "ADMET profiling of compounds", "rows": [["Compounds", "Quercetin", "Luteolin", "Naringenin", "Nobiletin", "Physovenine", "6,8-Dihydroxy-7-methoxyxanthone", "(+)-catechin", "5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)chroman-4-one", "Rhein"], ["GIabsorption", "High", "High", "High", "High", "High", "High", "High", "High", "High"], ["BBBpermeant", "No", "No", "No", "No", "Yes", "No", "No", "No", "No"], ["Pgpsubstrate", "No", "No", "Yes", "No", "Yes", "No", "Yes", "Yes", "No"], ["CYP1A2 inhibitor", "Yes", "Yes", "Yes", "No", "No", "Yes", "No", "Yes", "No"], ["CYP2C19 inhibitor", "No", "No", "No", "No", "No", "No", "No", "No", "No"], ["CYP2C9 inhibitor", "No", "No", "No", "Yes", "No", "No", "No", "No", "No"], ["CYP2D6 inhibitor", "Yes", "Yes", "No", "No", "Yes", "Yes", "No", "No", "No"], ["CYP3A4 inhibitor", "Yes", "Yes", "Yes", "Yes", "No", "Yes", "No", "Yes", "No"], ["PredictedLD50", "159 mg/kg", "3919 mg/kg", "2000 mg/kg", "5000 mg/kg", "2 mg/kg", "3800 mg/kg", "10,000 mg/kg", "2000 mg/kg", "5000 mg/kg"], ["ToxicityReversemutationAmestest", "Non-Toxic", "Non-Toxic", "Non-Toxic", "Non-Toxic", "Non-Toxic", "Non-Toxic", "Non-Toxic", "Non-Toxic", "Non-Toxic"], ["Hepatotoxicity", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive"], ["Carcinogenicity", "Active (0.68)", "Active (0.68)", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive"], ["Mutagenicity", "Active (0.51)", "Active (0.51)", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive", "Active (0.76)"], ["Cytotoxicity", "Inactive", "Inactive", "Active (0.59)", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive", "Inactive"]], "row_count": 15, "column_count": 10, "numeric_cells": 19, "header_rows": 1, "locator": "section[25]/table-wrap[1]#Tab8"}}, {"id": "asset:table:pmid:40524029:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:780323f332689b4e2c1e2a4ad71b057acef6e810429dd9973506db572e1c4a0b", "bytes": 5241, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[36]/table-wrap[1]#Tab9", "version": null, "note": "Overview of data sets/tools/figures/tables", "structure": {"pmcid": "PMC12170481", "section_index": 36, "section_title": "Molecular docking and pharmacokinetic properties", "row_count": 42, "column_count": 4}, "table": {"label": "Table 9", "caption": "Overview of data sets/tools/figures/tables", "rows": [["Label", "Name of data file/data set", "File types(file extension)", "Data repository and identifier (DOI or accession number)"], ["Data set 1", "TCMSP database", "Database", "https://old.tcmsp-e.com/tcmsp.php"], ["Data set 2", "SwissTargetPrediction database", "Database", "http://www.swisstargetprediction.ch/"], ["Data set 3", "PharmMapper database", "Database", "https://www.lilab-ecust.cn/pharmmapper/index.html"], ["Data set 4", "The UniProt database", "Database", "https://www.uniprot.org/"], ["Data set 5", "GeneCards database", "Database", "http://www.genecards.org/"], ["Data set 6", "Therapeutic Target Database(TTD)", "Database", "http://db.idrblab.net/ttd"], ["Data set 7", "the Online Mendelian Inheritance in Man (OMIM) database", "Database", "https://omim.org/"], ["Data set 8", "The STRING v3.11.1 database", "Database", "https://string-db.org"], ["Data set 9", "The Gene Expression Omnibus (GEO) database", "Database", "https://www.ncbi.nlm.nih.gov/geo"], ["Data set 10", "DAVID database", "Database", "https://david.ncifcrf.gov/"], ["Data set 11", "BioGPS database", "Database", "https://biogps.org"], ["Data set 12", "The PubChem database", "Database", "https://pubchem.ncbi.nlm.nih.gov"], ["Tool 1", "VENNY 2.1.0", "Web-based tool", "https://bioinfogp.cnb.csic.es/tools/venny/index.html"], ["Tool 2", "The Bioinformatics platform", "Web-based tool", "https://bioinformatics.com.cn"], ["Tool 3", "PyMOL version 2.5.0", "Web-based tool", "https://pymol.org/2/"], ["Tool 4", "The RCSB Protein Data Bank", "Web-based tool", "https://www.pdb.org/"], ["Tool 5", "The AutoDock Tools 1.5.7", "Web-based tool", "https://ccsb.scripps.edu/mgltools/downloads/"], ["Tool 6", "AutoDock Vina Version 1.1.2", "Web-based tool", "https://vina.scripps.edu"], ["Tool 7", "SwissADME online server", "Web-based tool", "http://www.swissadme.ch/"], ["Tool 8", "ProToxII", "Web-based tool", "https://tox.charite.de/protox3/"], ["Tool 9", "GEPIA2", "Web-based tool", "http://gepia2.cancer-pku.cn/"], ["Figure 1", "A detailed workflow of the network pharmacological investigation strategy for CR in the treatment of LC", "Image (.png)", "Uploaded via journal submission system"], ["Figure 2", "A LC and CR target Venn diagram. B Herb–compound–target network", "Image (.png)", "Uploaded via journal submission system"], ["Figure 3", "A PPI analysis. B top 28 core targets. C Bar chart. D PPI network based on cluster analysis", "Image (.png)", "Uploaded via journal submission system"], ["Figure 4", "A KEGG enrichment analysis. B Sankey diagram of the KEGG pathway. C GO functional enrichment analysis. D GO enrichmentanalysis, exhibit BP, CC and MF respectively", "Image (.png)", "Uploaded via journal submission system"], ["Figure5", "A Compound-target-pathway network. B LC-PPI and Drug–Target–Path analysis Venn diagram. C Target-organ network", "Image (.png)", "Uploaded via journal submission system"], ["Figure6", "A PPI analysis. B Bar chart of the top 5 core targets. C Compound–target–pathway network.D NAFLD+DLM PPI and Drug-Target-Path analysis Venn diagram", "Image (.png)", "Uploaded via journal submission system"], ["Figure 7", "Heatmap of LC molecular docking scores", "Image (.png)", "Uploaded via journal submission system"], ["Figure 8", "Docking patterns of core targets and active compounds of Liver Cancer.", "Image (.png)", "Uploaded via journal submission system"], ["Figure 9", "Volcano and Heatmap plot. A GSE76427, B GSE87630, C GSE112790 datasets", "Image (.png)", "Uploaded via journal submission system"], ["Figure 10", "Pearson’s coefficient analysis A HSP90 AA1, B ESR1. Core targets’s Expression in LIHC. C HSP90 AA1, D ESR1E Survival map of Hazardous Ratio", "Image (.png)", "Uploaded via journal submission system"], ["Table 1", "Grid Box Centers and Sizes for Molecular Docking of Target Genes", "Table (.docx)", "Uploaded via journal submission system"], ["Table 2", "The 123 common targets between active compound targets of CR and Liver Cancer disease targets", "Table (.docx)", "Uploaded via journal submission system"], ["Table 3", "Top 28 targets, ranked by degree in the compound–target–pathway network of liver cancer", "Table (.docx)", "Uploaded via journal submission system"], ["Table 4", "Top 16 targets, ranked by degree in the compound–target–pathway network of Liver Cancer", "Table (.docx)", "Uploaded via journal submission system"], ["Table 5", "Details of the top 10 compounds in the compound–target–pathway network of Liver Cancer.", "Table (.docx)", "Uploaded via journal submission system"], ["Table 6", "Top 21 targets in the compound-target-pathway network of NAFLD-LMDs, ranked by degree", "Table (.docx)", "Uploaded via journal submission system"], ["Table 7", "ADMET profiling of compounds", "Table (.docx)", "Uploaded via journal submission system"], ["Table 8", "Molecular docking binding affinities (kcal/mol) between active compounds and target proteins.", "Table (.docx)", "Uploaded via journal submission system"], ["Table 9", "Overview of data sets/Tools/Figures/Tables", "Table (.docx)", "Uploaded via journal submission system"], ["Table 10", "Abbreviations", "Table (.docx)", "Uploaded via journal submission system"]], "row_count": 42, "column_count": 4, "numeric_cells": 54, "header_rows": 1, "locator": "section[36]/table-wrap[1]#Tab9"}}, {"id": "asset:table:pmid:40524029:10", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:329b71a5536e1125872648e18e251fb29d1c4395a81c0688e226da7b99108f74", "bytes": 1146, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[36]/table-wrap[2]#Tab10", "version": null, "note": "Abbreviations", "structure": {"pmcid": "PMC12170481", "section_index": 36, "section_title": "Molecular docking and pharmacokinetic properties", "row_count": 25, "column_count": 2}, "table": {"label": "Table10", "caption": "Abbreviations", "rows": [["Full name", "Abbreviations"], ["Absorption, distribution, metabolism, and excretion", "ADME"], ["betweenness centrality", "BC"], ["Citri Reticulatae Pericarpium", "CRP"], ["Citri Reticulatae Pericarpium-Reynoutria japonica", "CR"], ["Closeness centrality", "CC"], ["Degree centrality", "DC"], ["Drug likeness", "DL"], ["Gene Ontology", "GO"], ["Hepatocellular carcinoma", "HCC"], ["Kyoto Encyclopedia of Genes and Genomes", "KEGG"], ["Liver cancer", "LC"], ["Metabolic Lipid Disorders", "DLM"], ["Non-alcoholic fatty liver disease", "NAFLD"], ["Oral bioavailability", "OB"], ["Protein–protein interaction", "PPI"], ["Reynoutria japonica Houtt", "RJ"], ["The differentially expressed genes", "DEGs"], ["The Gene Expression Omnibus", "GEO"], ["The Molecular Complex Detection", "MCODE"], ["The Online Mendelian Inheritance in Man", "OMIM"], ["Therapeutic Target Database", "TTD"], ["Traditional Chinese Medicine", "TCM"], ["Traditional Chinese Medicine Systems Pharmacology", "TCMSP"], ["Tumour necrosis factor-alpha", "TNF-α"]], "row_count": 25, "column_count": 2, "numeric_cells": 0, "header_rows": 1, "locator": "section[36]/table-wrap[2]#Tab10"}}], "gaps": ["asset:source:pmid:40524029 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40524029", "asset:table:pmid:40524029:1", "asset:table:pmid:40524029:2", "asset:table:pmid:40524029:3", "asset:table:pmid:40524029:4", "asset:table:pmid:40524029:5", "asset:table:pmid:40524029:6", "asset:table:pmid:40524029:7", "asset:table:pmid:40524029:8", "asset:table:pmid:40524029:9", "asset:table:pmid:40524029:10"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40524029"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:cd40e1bc2e8f5f15c97edeb13eeeb362efd35198d3a42ed6f521cc575c24df0a", "type": "sep_package", "label": "SEP v1 package for pmid:40524029"}], "activities": [{"id": "activity:conversion:pmid:40524029", "type": "conversion", "used": ["package:cd40e1bc2e8f5f15c97edeb13eeeb362efd35198d3a42ed6f521cc575c24df0a"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40524029", "parent_hash": "sha256:6ea68431cf4c5e61761be4dfc238971ec479a763f11de2a44ec6a738b63063c7", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40524029 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40524029' does not resolve to a declared asset", "targets"]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:23:07+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}}}