{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30678426", "kind": "science-record", "revision": 8, "content_hash": "sha256:92a0191a570d0031222f8dcde4fb44121125e153b1e6dee863e0a4b839607a72", "created_at": "2026-11-01T15:40:41Z", "updated_at": "2026-11-01T22:00:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Candidate Genes and Pathways for Relationship between Ovarian Cancer and Diabetes Mellitus Using Bioinformatical Analysis", "doi": "10.31557/APJCP.2019.20.1.145", "pmid": "30678426", "authors": ["Yi Sun", "Huang Xiaoyan", "Liu Yun", "Liu Chaoqun", "Wen Jialing", "Yang Liu", "Zhao Yingqi", "Yi Peipei", "Peng Junjun", "Lu Yuanming"], "journal": "Asian Pacific journal of cancer prevention : APJCP", "year": 2019, "abstract": "Ovarian cancer is one of the three major gynecologic cancers in the world. The aim of this study is to find the relationship between ovarian cancer and diabetes mellitus by using the genetic screening technique. By GEO database query and related online tools of analysis, we analyzed 185 cases of ovarian cancer and 10 control samples from GSE26712, and a total of 379 different genes were identified, including 104 up-regulated genes and 275 down-regulated genes. The up-regulated genes were mainly enriched in biological processes, including cell adhesion, transcription of nucleic acid and biosynthesis, and negative regulation of cell metabolism. The down-regulated genes were enriched in cell proliferation, migration, angiogenesis and macromolecular metabolism. Protein-protein interaction was analyzed by network diagram and module synthesis analysis. The top ten hub genes (CDC20, H2AFX, ENO1, ACTB, ISG15, KAT2B, HNRNPD, YWHAE, GJA1 and CAV1) were identified, which play important roles in critical signaling pathways that regulate the process of oxidation-reduction reaction and carboxylic acid metabolism. CTD analysis showed that the hub genes were involved in 1,128 distinct diseases (bonferroni-corrected P<0.05). Further analysis by drawing the Kaplan-Meier survival curve indicated that CDC20 and ISG15 were statistically significant (P<0.05). In conclusion, glycometabolism was related to ovarian cancer and genes and proteins in glycometabolism could serve as potential targets in ovarian cancer treatment.", "claims": [{"id": "claim-method", "statement": "The Kaplan-Meier survival curve showed that the survival time of CDC20, H2AFX, HNRNPD and ISG15 is significantly correlated with the survival time of OC (P < 0.05), as showed in Fig.4.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30678426", "locator": "sections[10] \"The clinical significance of ten abnormally expressed hub genes\" paragraph 2", "quote": "The Kaplan-Meier survival curve showed that the survival time of CDC20, H2AFX, HNRNPD and ISG15 is significantly correlated with the survival time of OC (P < 0.05), as showed in Fig.4."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE26712 gene expression profiles were downloaded from the GEO database. GSE26712 was submitted by Michael Birrer based on the agilent GPL96 platform ([hg-u133a] Affymetrix Human Genome U133A Array). The database consisted of 195 samples in total, including185 tissues from ovarian cancer patients and 10 from normal human. We downloaded the raw data in text form (agilent platform).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30678426", "locator": "sections[3] \"Microarray data information and DEGs identification\" paragraph 2", "quote": "GSE26712 gene expression profiles were downloaded from the GEO database. GSE26712 was submitted by Michael Birrer based on the agilent GPL96 platform ([hg-u133a] Affymetrix Human Genome U133A Array). The database consisted of 195 samples in total, including185 tissues from ovarian cancer patients and 10 from normal human. We downloaded the raw data in text form (agilent platform)."}], "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:30678426"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE26712"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE26712"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30678426", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.31557/APJCP.2019.20.1.145", "sha256": "sha256:6c1b25e677cbdfcc345e9e31a29bd589e0ae2774064de6475b9c76fa93333f03", "bytes": 26929, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.31557/APJCP.2019.20.1.145", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6485580", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE26712", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26712", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26712", "version": null, "note": "GSE26712 gene expression profiles were downloaded from the GEO database. GSE26712 was submitted by Michael Birrer based on the agilent GPL96 platform ([hg-u133a] Affymetrix Human Genome U133A Array). The database consisted of 195 samples in total, including185 tissues from ovarian cancer patients and 10 from normal human. We downloaded the raw data in text form (agilent platform).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE26712 gene expression profiles were downloaded from the GEO database. GSE26712 was submitted by Michael Birrer based on the agilent GPL96 platform ([hg-u133a] Affymetrix Human Genome U133A Array). The database consisted of 195 samples in total, including185 tissues from ovarian cancer patients and 10 from normal human. 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"identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30678426:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b709bb32c3cd7c6884ed9b1d63bb9965ef874f127f663e4517067e40c340da30", "bytes": 3022, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T1", "version": null, "note": "Identification of the Up-Regulated and Down-Regulated Differential Genes", "structure": {"pmcid": "PMC6485580", "section_index": 8, "section_title": "Identification of differential genes in ovarian cancer", "row_count": 21, "column_count": 2}, "table": {"label": "Table 1", "caption": "Identification of the Up-Regulated and Down-Regulated Differential Genes", "rows": [["DEGs", "Genes Name"], ["Up-regulated", "CD24 CD24 SNORA68 RPL18A CD24 CLDN3 IGFBP2 LOC101929219 LOC100505650 C1orf186 HIST2H2AA4 HIST2H2AA3 CALR WFDC2 SCGB2A1 FOLR1 CD24 PFN1 CRABP2"], ["PKM COL1A1 RPL37ASOX17 RPS7 CD24 PPDPF MUC1 MECOM C9orf16 NOTCH3 CLDN3 ACTB RHOB S100A13 ELF3 LCN2 SLC52A2 IGLC1 KLK6 S100A11 DEFB1"], ["INS-IGF2 IGF2 HMGA1 ISG15 FOLR1 GSTP1 TAGLN S100A2 H2BFS IGLC1 CALR COL1A1 CKS2 CP IGHA2 IGHA1 IGH ATP5H H2AFX YWHAE PEA15 ADGRG1 PRMT1"], ["S100A6 LSM4 SOX9 MMP11 SETSIP SETP4 SET CYAT1 IGLV1-44 IGLC1 PRKCSH MIR7113 MIR4691 NDUFS8 CL2L2-PABPN1 PABPN1 C9orf16 GRINA LOC100506248"], ["MIR1244-2 MIR1244-3 MIR1244-1 LOC728026 PTMA MMP7 ACTB NT5DC2 BCAM COL6A2 FXYD3 JUNB MUC1 PAX8 UBE2C CLDN4 LYPD1 UQCRQ HSPG2 MRPS12"], ["ZNF593 CDC20 IGLV1-44 C1orf106 IDH2 IFI6 ENO1 COX7B SLC39A4 IFI27 KLK8 KDELR1 MDK HIST1H1C UCP2 MIR1282 HYPK SERF2 TMED2 PRSS8 ATP2A2 BCAM"], ["CHMP5 PAXBP1 EZR MEF2C SCP2 RARRES1 PLIN2 HSD17B11 PRNP DCUN1D4 HAS1 DLG5 EPS15 PNRC2 PDZD2 ATF1 ADGRG6 CPE BAMBI PRKAR1A GJA1 NR2F2"], ["RSRP1 PLCB1 CHMP2B VPS13C TJP2 ADH5 NEFH CAV2 ANK3 SMARCA2 CHGB ZNF45 RARRES1 RHOT1 LIPA EFHC1 ATMIN PURA GLS WT1 SFRP1 C21orf62"], ["LOC101929500 CRIM1 KAT2B BICC1 SERPINB9 ADAMTS3 PRKAR2B GALNT12 PDPN HNRNPD GNG11 TOB1 SEL1L3 DCN GPR137B ISOC1 MAP3K8 TSPYL1 SNX7 UPK3B"], ["CIRBP PREPL PTPRC NT5C1B-RDH14 RDH14 CLK1 PODXL SNORD45C SNORD45A SNORD45B RABGGTB HPR HP CELF2 ANOS1 LGALS2 PCDH9 PKD2 ARAP2 CELF2"], ["CAV2 KLF4 PCOLCE2 PLCE1 LUC7L3 ARHGAP44 LAMB1 FZD7 SLC16A1 PRKAR1A ARHGAP6 GFPT2 DAPK1 FZD7 CLDN15 S100PBP ACSL1 ZDHHC17 DSC3 ADAM9"], ["FLRT3 SEMA5A ITGAM CFH PGRMC2 SOBP GABARAPL3 GABARAPL1 PSD3 TSPAN8 ATP10D ME1 ZBTB20 IGFBP6 RBM25 WSB1 RAP2C TCF21 PTGER3 GPRASP1"], ["CSGALNACT1 SLK GCOM1 POLR2M ATP8A1 GALC GCA TSPAN13 ATXN1 CFHR1 CFH DOCK4MIR22 MIR22HG OGN UFSP2 TLE4 RECK SARAF FEZ2 SMARCA2"], ["Down-regulated", "TPD52L1 PDGFC PDE8B GSAP GSAP HBA2 HBA1 FGF9 PHACTR2 PNISR CREBL2 CPVL SLC46A3 OLFML1 HBG2 HBG1 MTUS1 CLEC4M TRPC1 LXN CAST CLEC4M HBA2"], ["BA1 GHR CPE SEMA3C SULF1 HBA2 HBA1 DPYSL2 TACC1 SLC16A1 NSG1 METTL7A ECM2 QKI HBA2 HBA1 NKX3-1 CFI CLIC5 PTGIS LOC101926921 DAB2 RARRES1"], ["DMD HOXC6 WNT2B ZNF330 PTGER4 NR2F1 GREB1 SNCAIP MARCO GAS1 LAMA4 FRMD4B AQP9 IL6ST BTAF1 HP SCG5 ZFPM2 FGF13 FAM13B RSRP1 DIRAS3"], ["ALDH1A1 WNT5A TMX4 AMIGO2 ANXA3 CREBL2 ID4 N4BP2L2 GATA6 RGS4 CAV1 HBA2 HBA1 DDX17 LOC101926921 DAB2 TFPI2 PLPP1 RNASE4 RTN1 PRG4 HBB"], ["REEP1 PDGFD MEIS2 TFPI2 DSE FRY KDR HEG1 HBB PEG3 SFRP1 MAF SPOCK1 MET LGALS8 NAP1L3 PSD3 TMEM255A DFNA5 PROS1 LGALS8 PLSCR4 ANXA8L1"], ["ANXA8 ARMCX1 PROCR ADH1B HBA2 HBA1 CHRDL1 SLC39A8 ADH1B SLC4A4NPY1R NELL2 DPYD BNC1 LHX2 GPM6A EFEMP1 CALB2 REEP1 STK26 OC100506718"], ["FLRT2 TCEAL2 HB ABCA8 EFEMP1 AOX1 LOC101928635 ALDH1A2 BCHE MNDA LOC101930363 LOC101928349 LOC100507387 FAM153C FAM153A FAM153B"]], "row_count": 21, "column_count": 2, "numeric_cells": 20, "header_rows": 1, "locator": "section[8]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:30678426:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f6805ad5e9c5649cf85acd272269dafb2eb1de62fca9268b08e56a9d56abeb87", "bytes": 3255, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T2", "version": null, "note": "Gene Ontology Analysis of Differentially Expressed Genes Associated with Ovarian Cancer3.3 Signal Path Enrichment Analyses", "structure": {"pmcid": "PMC6485580", "section_index": 9, "section_title": "The ontology analysis of differential genes in ovarian cancer", "row_count": 33, "column_count": 5}, "table": {"label": "Table 2", "caption": "Gene Ontology Analysis of Differentially Expressed Genes Associated with Ovarian Cancer3.3 Signal Path Enrichment Analyses", "rows": [["Expression", "Category", "Term", "Count %", "P- Value"], ["Up-reulated"], ["GOTERM_BP_FAT", "GO:0007399~nervous system development", "25", "27.47252747", "5.33E-05"], ["GOTERM_BP_FAT", "GO:0007155~cell adhesion", "21", "23.07692308", "1.16E-04"], ["GOTERM_BP_FAT", "GO:0022610~biological adhesion", "21", "23.07692308", "1.22E-04"], ["GOTERM_BP_FAT", "GO:1901700~response to oxygen-containing compound", "19", "20.87912088", "1.64E-04"], ["GOTERM_BP_FAT", "GO:0033993~response to lipid", "14", "15.38461538", "2.15E-04"], ["GOTERM_BP_FAT", "GO:0045892~negative regulation of transcription, DNA-templated", "16", "17.58241758", "2.77E-04"], ["GOTERM_BP_FAT", "GO:0010558~negative regulation of macromolecule biosynthetic process", "18", "19.78021978", "3.42E-04"], ["GOTERM_BP_FAT", "GO:1903507~negative regulation of nucleic acid-templated transcription", "16", "17.58241758", "4.28E-04"], ["GOTERM_BP_FAT", "GO:0010605~negative regulation of macromolecule metabolic process", "24", "26.37362637", "4.34E-04"], ["GOTERM_BP_FAT", "GO:0031324~negative regulation of cellular metabolic process", "24", "26.37362637", "4.88E-04"], ["GOTERM_BP_FAT", "GO:0009890~negative regulation of biosynthetic process", "18", "19.78021978", "6.74E-04"], ["GOTERM_BP_FAT", "GO:0010033~response to organic substance", "26", "28.57142857", "0.0011882"], ["GOTERM_BP_FAT", "GO:0009892~negative regulation of metabolic process", "24", "26.37362637", "0.001356973"], ["GOTERM_BP_FAT", "GO:0023051~regulation of signaling", "27", "29.67032967", "0.00178692"], ["GOTERM_BP_FAT", "GO:0010604~positive regulation of macromolecule metabolic process", "25", "27.47252747", "0.003192651"], ["Down-regulated"], ["GOTERM_BP_FAT", "GO:0040011~locomotion", "48", "21.33333333", "5.62E-09"], ["GOTERM_BP_FAT", "GO:0008283~cell proliferation", "53", "23.55555556", "1.77E-08"], ["GOTERM_BP_FAT", "GO:0006928~movement of cell or subcellular component", "51", "22.66666667", "4.02E-08"], ["GOTERM_BP_FAT", "GO:0016477~cell migration", "38", "16.88888889", "2.14E-07"], ["GOTERM_BP_FAT", "GO:0032268~regulation of cellular protein metabolic process", "56", "24.88888889", "2.11E-06"], ["GOTERM_BP_FAT", "GO:0007399~nervous system development", "52", "23.11111111", "5.25E-06"], ["GOTERM_BP_FAT", "GO:0010604~positive regulation of macromolecule metabolic process", "62", "27.55555556", "1.04E-05"], ["GOTERM_BP_FAT", "GO:0010605~negative regulation of macromolecule metabolic process", "53", "23.55555556", "1.72E-05"], ["GOTERM_BP_FAT", "GO:0009605~response to external stimulus", "48", "21.33333333", "3.47E-05"], ["GOTERM_BP_FAT", "GO:0050790~regulation of catalytic activity", "52", "23.11111111", "5.13E-05"], ["GOTERM_BP_FAT", "GO:0048514~blood vessel morphogenesis", "19", "8.444444444", "4.92E-05"], ["GOTERM_BP_FAT", "GO:0072358~cardiovascular system development", "33", "14.66666667", "2.77E-07"], ["GOTERM_BP_FAT", "GO:0008285~negative regulation of cell proliferation", "25", "11.11111111", "2.34E-06"], ["GOTERM_BP_FAT", "GO:0060537~muscle tissue development", "18", "8", "4.03E-06"], ["GOTERM_BP_FAT", "GO:0007155~cell adhesion", "43", "19.11111111", "1.33E-05"]], "row_count": 33, "column_count": 5, "numeric_cells": 120, "header_rows": 1, "locator": "section[9]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:30678426:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7142374b328c5bf02895016428dd3726e0679a05fd6ccb4425df8f0e992358aa", "bytes": 466, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#T3", "version": null, "note": "Significantly Enriched Pathway Terms of DEGs in Ovarian Cancer", "structure": {"pmcid": "PMC6485580", "section_index": 9, "section_title": "The ontology analysis of differential genes in ovarian cancer", "row_count": 5, "column_count": 2}, "table": {"label": "Table 3", "caption": "Significantly Enriched Pathway Terms of DEGs in Ovarian Cancer", "rows": [["Significant Enriched Pathway terms", "P-Value"], ["PI3K-Akt signaling pathway |HAS-04151", "0.037083032"], ["Wnt signaling pathway |HAS-04310", "0.035010312"], ["Ras signaling pathway |HAS-04014", "0.02893891"], ["Rap1 signaling pathway |HAS-04015", "0.001684852"]], "row_count": 5, "column_count": 2, "numeric_cells": 8, "header_rows": 1, "locator": "section[9]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:30678426:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e5de69610e246609a2def6f0806807374e4df33faf36030c8bee52ae2b988af2", "bytes": 1065, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[3]#T4", "version": null, "note": "KEGG Pathway Analysis of Differentially Expressed Genes Associated with Ovarian Cancer", "structure": {"pmcid": "PMC6485580", "section_index": 9, "section_title": "The ontology analysis of differential genes in ovarian cancer", "row_count": 9, "column_count": 6}, "table": {"label": "Table 4", "caption": "KEGG Pathway Analysis of Differentially Expressed Genes Associated with Ovarian Cancer", "rows": [["Pathway", "Name", "Gene", "%", "P Value", "Genes ID"], ["Up-reulated", "DEGs", "", "", "", ""], ["hsa01230:Biosynthesis of amino acid", "3", "3.296703297", "0.074028877", "IDH2, ENO1, PKM"], ["hsa05010:Alzheimer’s disease", "4", "4.395604396", "", "ATP2A2, ATP5H , UQCRQ , COX7B"], ["hsa04512:ECM-receptor interaction", "3", "3.296703297", "0.097658172", "COL1A1, COL1A1, HSPG2, COL6A2"], ["Down-reulated", "DEGS", "", "", "", ""], ["hsa05205:Proteoglycans in cancer", "11", "4.888888889", "2.75E-04", "WNT5A, CAV2, CAV1, PLCE1, EZR, ANK3, MET, DCN, FZD7, KDR, WNT2B"], ["hsa04015:Rap1 signaling pathway", "10", "4.444444444", "0.001684852", "PLCE1, FGF9, MET, FGF13, PDGFC, PDGFD, PLCB1, ITGAM, KDR, DOCK4"], ["hsa05200:Pathways in cancer", "14", "6.222222222", "0.001775521", "WNT5A, PTGER3, PTGER4, FGF9, MET, GNG11, FGF13, FZD7, DAPK1, WNT2B,LAMA4, KX3-1, LAMB1, PLCB1"]], "row_count": 9, "column_count": 6, "numeric_cells": 25, "header_rows": 1, "locator": "section[9]/table-wrap[3]#T4"}}, {"id": "asset:table:pmid:30678426:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8c94f03da9d68ece9152aeeb4423cea9b7d05c0be60df6085624d9545f3bab14", "bytes": 710, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[4]#T5", "version": null, "note": "Pathway Enrichment Analysis of Module Agenes Function", "structure": {"pmcid": "PMC6485580", "section_index": 9, "section_title": "The ontology analysis of differential genes in ovarian cancer", "row_count": 8, "column_count": 3}, "table": {"label": "Table 5", "caption": "Pathway Enrichment Analysis of Module Agenes Function", "rows": [["Gene Set", "FDR", "Node"], ["positive regulation of biological process", "0.00364", "ACTB,ALDH1A1,BUB1,CALR,CCNB1,CDC16,CDC23,CDC27,CDK1,DD"], ["X17,H2AFX,HNRNPD,ISG15,KAT2B,MAD2L1,PFN1,YWHAE"], ["ALDH1A1,BUB1,BUB1B,CALR,CDC16,CDC20,CDC23,CDC27,CDK1,D"], ["regulation of metabolic process", "0.016", "DX17,ENO1,EZR,GJA1,H2AFX,ISG15,KAT2B,MAD2L1,YWHAE"], ["ACTB,ALDH1A1,BUB1,CALR,CDC16,CDC20,CDC23,CDC27,CDK1,DD"], ["cellular metabolic process", "0.0487", "X17,DPYD,ENO1,EZR,H2AFX,HAS1,HNRNPD,IDH2,KAT2B,MAD2L1,"], ["YWHAE"]], "row_count": 8, "column_count": 3, "numeric_cells": 9, "header_rows": 1, "locator": "section[9]/table-wrap[4]#T5"}}, {"id": "asset:table:pmid:30678426:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2a4bb6b1248db8244361c3ca66fa251d69763cd727af601e44590efc1512ea90", "bytes": 531, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[5]#T6", "version": null, "note": "Pathway Enrichment Analysis of Module B Genes Function", "structure": {"pmcid": "PMC6485580", "section_index": 9, "section_title": "The ontology analysis of differential genes in ovarian cancer", "row_count": 4, "column_count": 3}, "table": {"label": "Table 6", "caption": "Pathway Enrichment Analysis of Module B Genes Function", "rows": [["Gene Set", "FDR", "Node"], ["oxidation-reduction process", "5.82E-10", "ALDH1A1,DPYD,ENO1,ENO2,ENO3,GAPDH,IDH2,PGK1,PKLR,PKM,TPI1"], ["Carboxylic acid metabolic process", "2.87E-09", "CAD,DPYD,DPYS,ENO1,ENO2,ENO3,GAPDH,IDH2,PGK1,TPI1"], ["single-organism catabolic process", "7.08E-09", "DPYD,DPYS,ENO1,ENO2,ENO3,GAPDH,PGK1,PKLR,PKM,TPI1"]], "row_count": 4, "column_count": 3, "numeric_cells": 3, "header_rows": 1, "locator": "section[9]/table-wrap[5]#T6"}}, {"id": "asset:table:pmid:30678426:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:647506ed3145d02503b804188c2f1459f85236e0d84d827b99e9a72d1418bb29", "bytes": 525, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[6]#T7", "version": null, "note": "Pathway Enrichment Analysis of Module C Genes Function", "structure": {"pmcid": "PMC6485580", "section_index": 9, "section_title": "The ontology analysis of differential genes in ovarian cancer", "row_count": 4, "column_count": 3}, "table": {"label": "Table 7", "caption": "Pathway Enrichment Analysis of Module C Genes Function", "rows": [["Gene Set", "FDR", "Node"], ["oxidation-reduction process", "7.86E-12", "ALDH1A1,DPYD,ENO1,ENO2,ENO3,GAPDH,IDH2,PGK1,PKLR,PKM,TPI1"], ["generation of precursor metabolites and energy", "2.45E-11", "ENO1,ENO2,ENO3,GAPDH,IDH2,PGK1,PKLR,PKM,TPI1"], ["nucleoside metabolic process", "2.75E-10", "DPYD,ENO1,ENO2,ENO3,GAPDH,PGK1,TPI1,UMPS"]], "row_count": 4, "column_count": 3, "numeric_cells": 3, "header_rows": 1, "locator": "section[9]/table-wrap[6]#T7"}}, {"id": "asset:table:pmid:30678426:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:35f1eb85d40be2bacb3cb7adf5e7e4934dd6a8394aa3a41688b6befcfd3ca8c9", "bytes": 938, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[7]#T8", "version": null, "note": "The Relationship between Hub Gene with Ovarian Cancer or Metabolic Disease of the Comparative Toxicogenomics Database Prediction", "structure": {"pmcid": "PMC6485580", "section_index": 9, "section_title": "The ontology analysis of differential genes in ovarian cancer", "row_count": 12, "column_count": 5}, "table": {"label": "Table 8", "caption": "The Relationship between Hub Gene with Ovarian Cancer or Metabolic Disease of the Comparative Toxicogenomics Database Prediction", "rows": [["Hube Gene", "Disease cantegories (p-value)"], ["OC", "Diabetes Mellitus, Type 1", "Diabetes Mellitus, Type 2", "Hypertriglyceridemia"], ["CDC20", "2.22E-09", "1.56E-38", "3.37E-98", "5.93E-11"], ["H2AFX", "2.14E-09", "1.32E-38", "2.17E-98", "5.67E-11"], ["ENO1", "2.24E-09", "1.62E-38", "3.69E-98", "5.98E-11"], ["ACTB", "-", "4.35E-35", "1.21E-92", "5.07E-11"], ["ISG15", "2.20E-09", "1.49E-38", "2.97E-98", "5.85E-11"], ["KAT2B", "2.12E-09", "1.27E-38", "1.95E-98", "5.60E-11"], ["HNRNPD", "2.15E-09", "1.35E-38", "2.30E-98", "5.70E-11"], ["YWHAE", "1.88E-09", "7.51E-39", "4.88E-99", "3.35E-09"], ["GJA1", "2.10E-09", "1.23E-38", "1.78E-98", "5.55E-11"], ["CAV1", "2.12E-09", "1.27E-38", "1.95E-98", "5.60E-11"]], "row_count": 12, "column_count": 5, "numeric_cells": 43, "header_rows": 2, "locator": "section[9]/table-wrap[7]#T8"}}], "gaps": ["asset:data:geo:GSE26712 not downloaded", "asset:data:geo:GSE26712 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Kaplan-Meier survival curve showed that the survival time of CDC20, H2AFX, HNRNPD and ISG15 is significantly correlated with the survival time of OC (P < 0.05), as showed in Fig.4."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE26712"], "resolved_accessions": ["GSE26712"], "statements": ["GSE26712 gene expression profiles were downloaded from the GEO database. GSE26712 was submitted by Michael Birrer based on the agilent GPL96 platform ([hg-u133a] Affymetrix Human Genome U133A Array). The database consisted of 195 samples in total, including185 tissues from ovarian cancer patients and 10 from normal human. We downloaded the raw data in text form (agilent platform)."], "basis": "The paper names GSE26712 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:30678426", "data:geo:GSE26712", "asset:table:pmid:30678426:1", "asset:table:pmid:30678426:2", "asset:table:pmid:30678426:3", "asset:table:pmid:30678426:4", "asset:table:pmid:30678426:5", "asset:table:pmid:30678426:6", "asset:table:pmid:30678426:7", "asset:table:pmid:30678426:8"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE26712"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:38Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 19321, "completion_tokens": 1211, "cached_tokens": 788}}, "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:30678426", "type": "paper", "label": "pmid:30678426"}, {"id": "source:pmid:30678426", "type": "manuscript", "label": "PMID 30678426 full text"}, {"id": "data:geo:GSE26712", "type": "dataset", "label": "GEO GSE26712"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30678426", "type": "paper", "label": "pmid:30678426"}, {"id": "source:pmid:30678426", "type": "manuscript", "label": "PMID 30678426 full text"}, {"id": "data:geo:GSE26712", "type": "dataset", "label": "GEO GSE26712"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30678426", "type": "extraction", "used": ["source:pmid:30678426"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE26712", "type": "accession_resolution", "used": ["data:geo:GSE26712"], "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:30678426", "parent_hash": "sha256:0cf5cd65ae5a255b5f34a9fe07113e743423e8f5edbaee87942c3b6cdcd71dd2", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE26712 licence not read", "asset:data:geo:GSE26712 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Kaplan-Meier survival curve showed that the survival time of CDC20, H2AFX, HNRNPD and ISG15 is significantly correlated with the survival time of OC (P < 0.05), as showed in Fig.4."], "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":"2026-11-04T03:37:04+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}}}