{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33282565", "kind": "science-record", "revision": 7, "content_hash": "sha256:d880d683d7a31e38a3a043b56944866a8cbf36f608558506b85d45a92cf8fc29", "created_at": "2026-11-01T15:41:18Z", "updated_at": "2026-11-01T22:02:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying MMP14 and COL12A1 as a potential combination of prognostic biomarkers in pancreatic ductal adenocarcinoma using integrated bioinformatics analysis.", "doi": "10.7717/peerj.10419", "pmid": "33282565", "authors": ["Jingyi Ding", "Yanxi Liu", "Yu Lai"], "journal": "PeerJ", "year": 2020, "abstract": "BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a fatal malignant neoplasm. It is necessary to improve the understanding of the underlying molecular mechanisms and identify the key genes and signaling pathways involved in PDAC.\nMETHODS: The microarray datasets GSE28735, GSE62165, and GSE91035 were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified by integrated bioinformatics analysis, including protein-protein interaction (PPI) network, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The PPI network was established using the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. GO functional annotation and KEGG pathway analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. Hub genes were validated via the Gene Expression Profiling Interactive Analysis tool (GEPIA) and the Human Protein Atlas (HPA) website.\nRESULTS: A total of 263 DEGs (167 upregulated and 96 downregulated) were common to the three datasets. We used STRING and Cytoscape software to establish the PPI network and then identified key modules. From the PPI network, 225 nodes and 803 edges were selected. The most significant module, which comprised 11 DEGs, was identified using the Molecular Complex Detection plugin. The top 20 hub genes, which were filtered by the CytoHubba plugin, comprised FN1, COL1A1, COL3A1, BGN, POSTN, FBN1, COL5A2, COL12A1, THBS2, COL6A3, VCAN, CDH11, MMP14, LTBP1, IGFBP5, ALB, CXCL12, FAP, MATN3, and COL8A1. These genes were validated using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, and the encoded proteins were subsequently validated using the HPA website. The GO analysis results showed that the most significantly enriched biological process, cellular component, and molecular function terms among the 20 hub genes were cell adhesion, proteinaceous extracellular matrix, and calcium ion binding, respectively. The KEGG pathway analysis showed that the 20 hub genes were mainly enriched in ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway, and protein digestion and absorption. These findings indicated that FBN1 and COL8A1 appear to be involved in the progression of PDAC. Moreover, patient survival analysis performed via the GEPIA using TCGA and GTEx databases demonstrated that the expression levels of COL12A1 and MMP14 were correlated with a poor prognosis in PDAC patients (p < 0.05).\nCONCLUSIONS: The results demonstrated that upregulation of MMP14 and COL12A1 is associated with poor overall survival, and these might be a combination of prognostic biomarkers in PDAC.", "claims": [{"id": "claim-method", "statement": "Patient survival analysis performed via the GEPIA using TCGA and GTEx databases demonstrated that the high expression levels of COL12A1 and MMP14 were correlated with an unfavorable prognosis in PDAC patients (p < 0.05) (Fig. 5).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33282565", "locator": "sections[13] \"Overall survival analysis of the top 20 hub genes\" paragraph 2", "quote": "Patient survival analysis performed via the GEPIA using TCGA and GTEx databases demonstrated that the high expression levels of COL12A1 and MMP14 were correlated with an unfavorable prognosis in PDAC patients (p < 0.05) (Fig. 5)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThree microarray datasets are available at NCBI GEO: GSE28735, GSE62165, GSE91035. All the original figures and tables are available as Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33282565", "locator": "sections[28] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nThree microarray datasets are available at NCBI GEO: GSE28735, GSE62165, GSE91035. All the original figures and tables are available as Supplemental Files."}], "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:33282565"], "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:GSE28735"], "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:GSE28735"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33282565", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.10419", "sha256": "sha256:f8a17c9bdb4ca94790b2a9d0f5070f50fc06763bf8f286db22e5b4007edc18fa", "bytes": 63405, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.10419", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7690310", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28735", "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=GSE28735", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28735", "version": null, "note": "The following information was supplied regarding data availability:\nThree microarray datasets are available at NCBI GEO: GSE28735, GSE62165, GSE91035. All the original figures and tables are available as Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThree microarray datasets are available at NCBI GEO: GSE28735, GSE62165, GSE91035. 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All the original figures and tables are available as Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThree microarray datasets are available at NCBI GEO: GSE28735, GSE62165, GSE91035. All the original figures and tables are available as Supplemental Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1520738", "GSM1520739", "GSM1520740", "GSM1520741", "GSM1520742", "GSM1520743", "GSM1520744", "GSM1520745", "GSM1520746", "GSM1520747", "GSM1520748", "GSM1520749", "GSM1520750", "GSM1520751", "GSM1520752", "GSM1520753", "GSM1520754", "GSM1520755", "GSM1520756", "GSM1520757", "GSM1520758", "GSM1520759", "GSM1520760", "GSM1520761", "GSM1520762", "GSM1520763", "GSM1520764", "GSM1520765", "GSM1520766", "GSM1520767", "GSM1520768", "GSM1520769", "GSM1520770", "GSM1520771", "GSM1520772", "GSM1520773", "GSM1520774", "GSM1520775", "GSM1520776", "GSM1520777", "GSM1520778", "GSM1520779", "GSM1520780", "GSM1520781", "GSM1520782", "GSM1520783", "GSM1520784", "GSM1520785", "GSM1520786", "GSM1520787", "GSM1520788", "GSM1520789", "GSM1520790", "GSM1520791", "GSM1520792", "GSM1520793", "GSM1520794", "GSM1520795", "GSM1520796", "GSM1520797", "GSM1520798", "GSM1520799", "GSM1520800", "GSM1520801", "GSM1520802", "GSM1520803", "GSM1520804", "GSM1520805", "GSM1520806", "GSM1520807", "GSM1520808", "GSM1520809", "GSM1520810", "GSM1520811", "GSM1520812", "GSM1520813", "GSM1520814", "GSM1520815", "GSM1520816", "GSM1520817", "GSM1520818", "GSM1520819", "GSM1520820", "GSM1520821", "GSM1520822", "GSM1520823", "GSM1520824", "GSM1520825", "GSM1520826", "GSM1520827", "GSM1520828", "GSM1520829", "GSM1520830", "GSM1520831", "GSM1520832", "GSM1520833", "GSM1520834", "GSM1520835", "GSM1520836", "GSM1520837", "GSM1520838", "GSM1520839", "GSM1520840", "GSM1520841", "GSM1520842", "GSM1520843", "GSM1520844", "GSM1520845", "GSM1520846", "GSM1520847", "GSM1520848", "GSM1520849", "GSM1520850", "GSM1520851", "GSM1520852", "GSM1520853", "GSM1520854", "GSM1520855", "GSM1520856", "GSM1520857", "GSM1520858", "GSM1520859", "GSM1520860", "GSM1520861", "GSM1520862", "GSM1520863", "GSM1520864", "GSM1520865", "GSM1520866", "GSM1520867", "GSM1520868"], "sample_count": 131, "group_sizes": null, "group_sizes_basis": null, "platform": "13667", "taxon": "Homo sapiens", "title": "Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE91035", "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=GSE91035", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE91035", "version": null, "note": "The following information was supplied regarding data availability:\nThree microarray datasets are available at NCBI GEO: GSE28735, GSE62165, GSE91035. All the original figures and tables are available as Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThree microarray datasets are available at NCBI GEO: GSE28735, GSE62165, GSE91035. All the original figures and tables are available as Supplemental Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2419974", "GSM2419975", "GSM2419976", "GSM2419977", "GSM2419978", "GSM2419979", "GSM2419980", "GSM2419981", "GSM2419982", "GSM2419983", "GSM2419984", "GSM2419985", "GSM2419986", "GSM2419987", "GSM2419988", "GSM2419989", "GSM2419990", "GSM2419991", "GSM2419992", "GSM2419993", "GSM2419994", "GSM2419995", "GSM2419996", "GSM2419997", "GSM2419998", "GSM2419999", "GSM2420000", "GSM2420001", "GSM2420002", "GSM2420003", "GSM2420004", "GSM2420005", "GSM2420006", "GSM2420007", "GSM2420008", "GSM2420009", "GSM2420010", "GSM2420011", "GSM2420012", "GSM2420013", "GSM2420014", "GSM2420015", "GSM2420016", "GSM2420017", "GSM2420018", "GSM2420019", "GSM2420020", "GSM2420021", "GSM2420022", "GSM2420023"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "22763", "taxon": "Homo sapiens", "title": "The gene expression signatures of human normal, benign and PDAC pancreatic tisssues.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33282565:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:936f826d508e32db4c6166f57d070399663a14688498e6126e13a124fb343089", "bytes": 2324, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#table-1", "version": null, "note": "A total of 263 DEGs were identified from the three microarray datasets, which consisted of 167 upregulated genes and 96 downregulated genes present in pancreatic ductal adenocarcinoma (PDAC) tissues in comparison with non-tumor tissues.", "structure": {"pmcid": "PMC7690310", "section_index": 10, "section_title": "Identification of DEGs", "row_count": 3, "column_count": 2}, "table": {"label": "Table 1", "caption": "A total of 263 DEGs were identified from the three microarray datasets, which consisted of 167 upregulated genes and 96 downregulated genes present in pancreatic ductal adenocarcinoma (PDAC) tissues in comparison with non-tumor tissues.", "rows": [["DEGs", "Gene names"], ["Upregulated", "XDH, RTKN2, PTPRR, ADAM12, STYK1, TPX2, PADI1, HEPH, CEACAM6, ITGA3, COL1A1, ANLN, FNDC1, PCDH7, SLC6A6, TRIM29, PXDN, EDNRA, LTBP1, MFAP5, PLA2R1, FN1, KRT17, PGM2L1, IFI27, ASAP2, LAMB3, TNFAIP6, HOXB5, OAS1, NTM, COL5A2, OSBPL3, TMPRSS4, ANTXR1, SDR16C5, OLR1, NT5E, CTSK, SULF2, MXRA5, APOL1, CDH11, AREG, MALL, S100A16, BGN, LAMA3, COL8A1, IGFBP5, MMP12, ADAMTS6, SLC2A1, CD109, ECT2, KIF23, MMP11, CDH3, LMO7, CCL18, ATP2C2, POSTN, MMP14, ADAM28, SRPX2, CEACAM5, TMC5, OAS2, MUC17, GABRP, COMP, SYTL2, GPX8, RUNX2, DLGAP5, KRT19, VCAN, MKI67, SULF1, LAMC2, GCNT3, NMU, MUC13, CEACAM1, ETV1, COL12A1, AGR2, ST6GALNAC1, SLC44A4, PLAU, S100P, SERPINB5, FOXQ1, TGM2, ITGB4, DCBLD2, TRIM31, RAI14, NRP2, SGIP1, CST1, ARNTL2, LEF1, MYOF, ANO1, S100A14, DDX60, KYNU, CAPG, CCL20, MATN3, NPR3, GPRC5A, NOX4, IL1RAP, ACSL5, HPGD, GREM1, SCEL, FBN1, IGFL2, SLC6A14, KRT6A, DHRS9, ANGPT2, MST1R, COL3A1, TMEM45B, EDIL3, ASPM, FAP, INPP4B, LOXL2, NQO1, CYP2C18, IFI44L, HK2, EFNB2, AEBP1, SLC16A3, CORIN, THBS2, BCAS1, DSG3, DKK1, RHBDL2, COL17A1, TSPAN1, FERMT1, CXCL5, COL6A3, COL10A1, ACTA2, PLAC8, AHNAK2, MLPH, FBXO32, TGFBI, KCNN4, CLDN18, FGD6, MTMR11, FXYD3, MBOAT2, SEMA3C, DPYSL3, CENPF"], ["Downregulated", "EPB41L4B, GSTA2, KIAA1324, CELA3A, ACADL, CEL, SLC39A5, LONRF2, SLC3A1, NRG4, MT1G, PROX1, G6PC2, C5, EGF, FAM3B, AQP8, CLPS, SLC17A4, CPB1, GP2, PDK4, RBPJL, PDIA2, PM20D1, CTRC, IAPP, PLA2G1B, ERP27, CELA2B, GRPR, REG1A, KIF1A, GUCA1C, CTRL, SYCN, CHRM3, TMED6, ALB, KCNJ16, REG3A, SLC4A4, AOX1, SERPINA5, CELA2A, SPINK1, FAM129A, FAM150B, SLC16A12, F11, CPA2, SV2B, BNIP3, C2CD4B, SLC1A2, REG1B, SCGN, PAK3, PRSS3, GRB14, REG3G, DCDC2, F8, GPHA2, EPHX2, PNLIPRP2, SLC7A2, CPA1, PRKAR2B, ONECUT1, BACE1, NUCB2, HOMER2, CXCL12, SLC43A1, GNMT, NR5A2, ALDH1A1, IL22RA1, BEX1, ANPEP, CFTR, FLRT2, LMO3, FGL1, NRCAM, FABP4, PNLIPRP1, KLK1, SERPINI2, GATM, DPP10, C6, SLC16A10, PRSS1, PAH"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[10]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:33282565:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:49c6cbaff8badbf88be2595d7674fcc54788f9644ca192190d97577041d38026", "bytes": 1559, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#table-2", "version": null, "note": "Results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the most significant module.", "structure": {"pmcid": "PMC7690310", "section_index": 12, "section_title": "GO and KEGG pathway analysis of DEGs", "row_count": 13, "column_count": 6}, "table": {"label": "Table 2", "caption": "Results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the most significant module.", "rows": [["Pathway ID", "Pathway description", "Count in gene set", "p-value", "FDR", "DEGs"], ["GO:0007155", "Cell adhesion", "5", "1.37E−06", "0.001121514", "COL6A3, COL12A1, VCAN, POSTN, THBS2"], ["GO:0001501", "Skeletal system development", "3", "3.80E−04", "0.310820683", "FBN1, VCAN, COL5A2"], ["GO:0030199", "Collagen fibril organization", "2", "0.017003019", "13.1195401", "COL5A2, CDH11"], ["GO:0005201", "Extracellular matrix structural constituent", "4", "2.39E−06", "0.001487027", "COL3A1, FBN1, VCAN, COL5A2"], ["GO:0005509", "Calcium ion binding", "4", "0.003312243", "2.045566581", "FBN1, VCAN, THBS2, CDH11"], ["GO:0005578", "Proteinaceous extracellular matrix", "6", "1.81E−08", "1.29E−05", "COL3A1, COL6A3, FBN1, COL12A1, VCAN, POSTN"], ["GO:0005581", "Collagen trimer", "3", "3.07E−04", "0.217600344", "COL3A1, COL6A3, COL12A1"], ["GO:0031012", "Extracellular matrix", "3", "0.001912518", "1.350246354", "FBN1, COL12A1, THBS2"], ["GO:0005615", "Extracellular space", "4", "0.008881226", "6.138544445", "COL6A3, FBN1, COL12A1, POSTN"], ["GO:0005604", "Basement membrane", "2", "0.032936583", "21.16653102", "FBN1, THBS2"], ["gga04512", "ECM–receptor interaction", "4", "4.51E−05", "0.019602271", "COL3A1, COL6A3, THBS2, COL5A2"], ["gga04510", "Focal adhesion", "4", "7.12E−04", "0.309146908", "COL3A1, COL6A3, THBS2, COL5A2"]], "row_count": 13, "column_count": 6, "numeric_cells": 55, "header_rows": 1, "locator": "section[12]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:33282565:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b95bb7176239915d59f07ed7eb449602383c84fcd3bf131060e6e77c4e845286", "bytes": 2602, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#table-3", "version": null, "note": "Results of GO and KEGG pathway analyses of 20 hub genes.", "structure": {"pmcid": "PMC7690310", "section_index": 12, "section_title": "GO and KEGG pathway analysis of DEGs", "row_count": 24, "column_count": 6}, "table": {"label": "Table 3", "caption": "Results of GO and KEGG pathway analyses of 20 hub genes.", "rows": [["Pathway ID", "Pathway description", "Count in gene set", "p-value", "FDR", "DEGs"], ["GO:0007155", "Cell adhesion", "6", "3.07E−07", "3.44E−04", "COL12A1, POSTN, VCAN, COL8A1, THBS2, FN1"], ["GO:0035987", "Endodermal cell differentiation", "4", "6.17E−06", "0.006927836", "COL12A1, MMP14, COL8A1, FN1"], ["GO:0018149", "Peptide cross-linking", "2", "0.02230059", "22.35847168", "COL3A1, FN1"], ["GO:0043588", "Skin development", "2", "0.035457234", "33.30840338", "COL3A1, COL5A2"], ["GO:0030199", "Collagen fibril organization", "2", "0.035457234", "33.30840338", "COL3A1, COL5A2"], ["GO:0042060", "Wound healing", "2", "0.039805932", "36.60570116", "COL3A1, FN1"], ["GO:0001501", "Skeletal system development", "2", "0.048448486", "42.72191792", "FBN1, COL5A2"], ["GO:0005578", "Proteinaceous extracellular matrix", "7", "1.25E−08", "1.13E−05", "MATN3, BGN, FBN1, COL12A1, POSTN, COL1A1, FN1"], ["GO:0031012", "Extracellular matrix", "4", "1.37E−04", "0.123843274", "COL12A1, VCAN, MMP14, COL8A1"], ["GO:0005581", "Collagen trimer", "3", "7.87E−04", "0.70897958", "COL12A1, COL1A1, COL8A1"], ["GO:0005615", "Extracellular space", "6", "0.001248571", "1.122732142", "ALB, FAP, COL3A1, FBN1, COL12A1, VCAN"], ["GO:0005604", "Basement membrane", "3", "0.001310663", "1.178271997", "FBN1, COL8A1, THBS2"], ["GO:0001527", "Microfibril", "2", "0.008113224", "7.097635089", "LTBP1, FBN1"], ["GO:0070062", "Extracellular exosome", "7", "0.033863185", "26.75315613", "BGN, ALB, FBN1, COL12A1, COL8A1, FN1, CDH11"], ["GO:0005509", "Calcium ion binding", "7", "9.57E−06", "0.007173793", "MMP14, MATN3, LTBP1, FBN1, VCAN, THBS2, CDH11"], ["GO:0005201", "Extracellular matrix structural constituent", "3", "4.84E−04", "0.362368483", "COL3A1, FBN1, COL5A2"], ["GO:0008201", "Heparin binding", "3", "0.003684116", "2.728227814", "POSTN, THBS2, FN1"], ["ocu04512", "ECM–receptor interaction", "6", "5.00E−08", "4.15E−05", "COL3A1, COL6A3, COL1A1, COL5A2, THBS2, FN1"], ["ocu04510", "Focal adhesion", "6", "3.64E−06", "0.003011517", "COL3A1, COL6A3, COL1A1, COL5A2, THBS2, FN1"], ["ocu04974", "Protein digestion and absorption", "5", "8.69E−06", "0.007197854", "COL3A1, COL6A3, COL12A1, COL1A1, COL5A2"], ["ocu04151", "PI3K-Akt signaling pathway", "6", "3.26E−05", "0.026969277", "COL3A1, COL6A3, COL1A1, COL5A2, THBS2, FN1"], ["ocu05146", "Amoebiasis", "4", "3.54E−04", "0.292970736", "COL3A1, COL1A1, COL5A2, FN1"], ["ocu04611", "Platelet activation", "3", "0.012199259", "9.669074187", "COL3A1, COL1A1, COL5A2"]], "row_count": 24, "column_count": 6, "numeric_cells": 101, "header_rows": 1, "locator": "section[12]/table-wrap[2]#table-3"}}], "gaps": ["asset:data:geo:GSE28735 not downloaded", "asset:data:geo:GSE28735 licence not read", "asset:data:geo:GSE62165 not downloaded", "asset:data:geo:GSE62165 licence not read", "asset:data:geo:GSE91035 not downloaded", "asset:data:geo:GSE91035 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "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": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Overall survival analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Patient survival analysis performed via the GEPIA using TCGA and GTEx databases demonstrated that the high expression levels of COL12A1 and MMP14 were correlated with an unfavorable prognosis in PDAC patients (p < 0.05) (Fig. 5)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE28735", "GSE62165", "GSE91035"], "resolved_accessions": ["GSE28735", "GSE62165", "GSE91035"], "statements": ["The following information was supplied regarding data availability:\nThree microarray datasets are available at NCBI GEO: GSE28735, GSE62165, GSE91035. All the original figures and tables are available as Supplemental Files."], "basis": "The paper names GSE28735, GSE62165, GSE91035 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:33282565", "data:geo:GSE28735", "asset:table:pmid:33282565:1", "asset:table:pmid:33282565:2", "asset:table:pmid:33282565:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE28735"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:56Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 52971, "completion_tokens": 1896, "cached_tokens": 776}}, "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:33282565", "type": "paper", "label": "pmid:33282565"}, {"id": "source:pmid:33282565", "type": "manuscript", "label": "PMID 33282565 full text"}, {"id": "data:geo:GSE28735", "type": "dataset", "label": "GEO GSE28735"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33282565", "type": "paper", "label": "pmid:33282565"}, {"id": "source:pmid:33282565", "type": "manuscript", "label": "PMID 33282565 full text"}, {"id": "data:geo:GSE28735", "type": "dataset", "label": "GEO GSE28735"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33282565", "type": "extraction", "used": ["source:pmid:33282565"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE28735", "type": "accession_resolution", "used": ["data:geo:GSE28735"], "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:33282565", "parent_hash": "sha256:54fffd7d5fffdf6bdd27ba2f73fc6e1d50b86bc486c1151182dbce125ef53b03", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE28735 licence not read", "asset:data:geo:GSE28735 not downloaded", "asset:data:geo:GSE62165 licence not read", "asset:data:geo:GSE62165 not downloaded", "asset:data:geo:GSE91035 licence not read", "asset:data:geo:GSE91035 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ling pathways involved in PDAC. METHODS: The microarray datasets GSE28735, GSE62165, and GSE91035 we", "ds ratio. Supplementary Materials File S1The microarray datasets GSE28735 , GSE62165, and GSE9103510", "nal data file. Supplemental Information 3The microarray datasets GSE28735 , GSE62165, and GSE9103510"], "order_basis": "paper_text_order:363", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T04:24:38+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}}}