{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30923657", "kind": "science-record", "revision": 8, "content_hash": "sha256:1b7ba9f11aef7680fdba5a1367857704fa610ac955135c78de28df067f51022c", "created_at": "2026-11-01T15:40:43Z", "updated_at": "2026-11-01T22:43:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis.", "doi": "10.7717/peerj.6645", "pmid": "30923657", "authors": ["Zhu Zhan", "Yuhe Chen", "Yuanqin Duan", "Lin Li", "Kenley Mew", "Peng Hu", "Hong Ren", "Mingli Peng"], "journal": "PeerJ", "year": 2019, "abstract": "BACKGROUND: Liver fibrosis is often a consequence of chronic liver injury, and has the potential to progress to cirrhosis and liver cancer. Despite being an important human disease, there are currently no approved anti-fibrotic drugs. In this study, we aim to identify the key genes and pathways governing the pathophysiological processes of liver fibrosis, and to screen therapeutic anti-fibrotic agents.\nMETHODS: Expression profiles were downloaded from the Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified by R packages (Affy and limma). Gene functional enrichments of each dataset were performed on the DAVID database. Protein-protein interaction (PPI) network was constructed by STRING database and visualized in Cytoscape software. The hub genes were explored by the CytoHubba plugin app and validated in another GEO dataset and in a liver fibrosis cell model by quantitative real-time PCR assay. The Connectivity Map L1000 platform was used to identify potential anti-fibrotic agents.\nRESULTS: We integrated three fibrosis datasets of different disease etiologies, incorporating a total of 70 severe (F3-F4) and 116 mild (F0-F1) fibrotic tissue samples. Gene functional enrichment analyses revealed that cell cycle was a pathway uniquely enriched in a dataset from those patients infected by hepatitis B virus (HBV), while the immune-inflammatory response was enriched in both the HBV and hepatitis C virus (HCV) datasets, but not in the nonalcoholic fatty liver disease (NAFLD) dataset. There was overlap between these three datasets; 185 total shared DEGs that were enriched for pathways associated with extracellular matrix constitution, platelet-derived growth-factor binding, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling. In the PPI network, 25 hub genes were extracted and deemed to be essential genes for fibrogenesis, and the expression trends were consistent with GSE14323 (an additional dataset) and liver fibrosis cell model, confirming the relevance of our findings. Among the 10 best matching anti-fibrotic agents, Zosuquidar and its corresponding gene target ABCB1 might be a novel anti-fibrotic agent or therapeutic target, but further work will be needed to verify its utility.\nCONCLUSIONS: Through this bioinformatics analysis, we identified that cell cycle is a pathway uniquely enriched in HBV related dataset and immune-inflammatory response is clearly enriched in the virus-related datasets. Zosuquidar and ABCB1 might be a novel anti-fibrotic agent or target.", "claims": [{"id": "claim-method", "statement": "Then, the Linear Models for Microarray Analysis R package (limma; version 3.30.11; Ritchie et al. (2015)) was applied for differential expression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30923657", "locator": "sections[4] \"Identification of differentially expressed genes\" paragraph 2", "quote": "Then, the Linear Models for Microarray Analysis R package (limma; version 3.30.11; Ritchie et al. (2015)) was applied for differential expression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw measurements are available in Data S1–S4.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30923657", "locator": "sections[21] \"Additional Information and Declarations\" paragraph 5", "quote": "The raw measurements are available in Data S1–S4."}], "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:30923657"], "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:GSE14323"], "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:GSE14323"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30923657", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.6645", "sha256": "sha256:ef549bbf6099412f1469bc8fbaeb8b2d75f42867954d8d94f657688428a784b0", "bytes": 30840, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.6645", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6432904", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14323", "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=GSE14323", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14323", "version": null, "note": "The raw measurements are available in Data S1–S4.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw measurements are available in Data S1–S4.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM358103", "GSM358104", "GSM358105", "GSM358106", "GSM358107", "GSM358108", "GSM358109", "GSM358110", "GSM358111", "GSM358112", "GSM358113", "GSM358114", "GSM358115", "GSM358116", "GSM358117", "GSM358118", "GSM358119", "GSM358120", "GSM358121", "GSM358122", "GSM358123", "GSM358124", "GSM358125", "GSM358126", "GSM358127", "GSM358128", "GSM358129", "GSM358130", "GSM358131", "GSM358132", "GSM358133", "GSM358134", "GSM358135", "GSM358136", "GSM358137", "GSM358138", "GSM358139", "GSM358140", "GSM358141", "GSM358142", "GSM358143", "GSM358144", "GSM358145", "GSM358146", "GSM358147", "GSM358148", "GSM358149", "GSM358151", "GSM358152", "GSM358153", "GSM358154", "GSM358155", "GSM358156", "GSM358157", "GSM358158", "GSM358159", "GSM358160", "GSM358161", "GSM358162", "GSM358163", "GSM358164", "GSM358165", "GSM358166", "GSM358167", "GSM358168", "GSM358169", "GSM358170", "GSM358171", "GSM358172", "GSM358173", "GSM358174", "GSM358175", "GSM358176", "GSM358177", "GSM358178", "GSM358179", "GSM358180", "GSM358181", "GSM358182", "GSM358183", "GSM358184", "GSM358185", "GSM358186", "GSM358187", "GSM358188", "GSM358189", "GSM358190", "GSM358191", "GSM358192", "GSM358193", "GSM358194", "GSM358195", "GSM358196", "GSM358197", "GSM358198", "GSM358199", "GSM358200", "GSM358201", "GSM358202", "GSM358203", "GSM358204", "GSM358205", "GSM358206", "GSM358207", "GSM358208", "GSM358209", "GSM358210", "GSM358211", "GSM358212", "GSM358213", "GSM358214", "GSM358215", "GSM358216", "GSM358217", "GSM358218", "GSM358219", "GSM358220", "GSM358221", "GSM358222", "GSM358223", "GSM358224", "GSM358225", "GSM358226", "GSM358227"], "sample_count": 124, "group_sizes": null, "group_sizes_basis": null, "platform": "571;96", "taxon": "Homo sapiens", "title": "RMA expression data for liver samples from subjects with HCV, HCV-HCC, or normal liver", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE49541", "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=GSE49541", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE49541", "version": null, "note": "The raw measurements are available in Data S1–S4.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw measurements are available in Data S1–S4.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM789110", "GSM789111", "GSM789112", "GSM789113", "GSM789114", "GSM789115", "GSM789116", "GSM789117", "GSM789118", "GSM789119", "GSM789120", "GSM789121", "GSM789122", "GSM789123", "GSM789124", "GSM789125", "GSM789126", "GSM789127", "GSM789128", "GSM789129", "GSM789130", "GSM789131", "GSM789132", "GSM789133", "GSM789134", "GSM789135", "GSM789136", "GSM789137", "GSM789138", "GSM789139", "GSM789140", "GSM789141", "GSM789142", "GSM789143", "GSM789144", "GSM789145", "GSM789146", "GSM789147", "GSM789148", "GSM789149", "GSM789150", "GSM789151", "GSM789152", "GSM789153", "GSM789154", "GSM789155", "GSM789156", "GSM789157", "GSM789158", "GSM789159", "GSM789160", "GSM789161", "GSM789162", "GSM789163", "GSM789164", "GSM789165", "GSM789166", "GSM789167", "GSM789168", "GSM789169", "GSM789170", "GSM789171", "GSM789172", "GSM789173", "GSM789174", "GSM789175", "GSM789176", "GSM789177", "GSM789178", "GSM789179", "GSM789180", "GSM789181"], "sample_count": 72, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data for Nonalcoholic fatty liver disease patients", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE6764", "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=GSE6764", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6764", "version": null, "note": "The raw measurements are available in Data S1–S4.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw measurements are available in Data S1–S4.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM155919", "GSM155920", "GSM155921", "GSM155922", "GSM155923", "GSM155924", "GSM155925", "GSM155926", "GSM155927", "GSM155928", "GSM155929", "GSM155930", "GSM155931", "GSM155932", "GSM155933", "GSM155934", "GSM155935", "GSM155936", "GSM155937", "GSM155938", "GSM155939", "GSM155940", "GSM155941", "GSM155942", "GSM155943", "GSM155944", "GSM155945", "GSM155946", "GSM155947", "GSM155948", "GSM155949", "GSM155950", "GSM155951", "GSM155952", "GSM155953", "GSM155954", "GSM155955", "GSM155956", "GSM155957", "GSM155958", "GSM155959", "GSM155960", "GSM155961", "GSM155962", "GSM155963", "GSM155964", "GSM155965", "GSM155966", "GSM155967", "GSM155968", "GSM155969", "GSM155970", "GSM155971", "GSM155972", "GSM155973", "GSM155974", "GSM155975", "GSM155976", "GSM155977", "GSM155978", "GSM155979", "GSM155980", "GSM155981", "GSM155982", "GSM155983", "GSM155984", "GSM155985", "GSM155986", "GSM155987", "GSM155988", "GSM155989", "GSM155990", "GSM155991", "GSM155992", "GSM155993"], "sample_count": 75, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma", "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:GSE84044", "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=GSE84044", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84044", "version": null, "note": "The raw measurements are available in Data S1–S4.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw measurements are available in Data S1–S4.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2226280", "GSM2226281", "GSM2226282", "GSM2226283", "GSM2226284", "GSM2226285", "GSM2226286", "GSM2226287", "GSM2226288", "GSM2226289", "GSM2226290", "GSM2226291", "GSM2226292", "GSM2226293", "GSM2226294", "GSM2226295", "GSM2226296", "GSM2226297", "GSM2226298", "GSM2226299", "GSM2226300", "GSM2226301", "GSM2226302", "GSM2226303", "GSM2226304", "GSM2226305", "GSM2226306", "GSM2226307", "GSM2226308", "GSM2226309", "GSM2226310", "GSM2226311", "GSM2226312", "GSM2226313", "GSM2226314", "GSM2226315", "GSM2226316", "GSM2226317", "GSM2226318", "GSM2226319", "GSM2226320", "GSM2226321", "GSM2226322", "GSM2226323", "GSM2226324", "GSM2226325", "GSM2226326", "GSM2226327", "GSM2226328", "GSM2226329", "GSM2226330", "GSM2226331", "GSM2226332", "GSM2226333", "GSM2226334", "GSM2226335", "GSM2226336", "GSM2226337", "GSM2226338", "GSM2226339", "GSM2226340", "GSM2226341", "GSM2226342", "GSM2226343", "GSM2226344", "GSM2226345", "GSM2226346", "GSM2226347", "GSM2226348", "GSM2226349", "GSM2226350", "GSM2226351", "GSM2226352", "GSM2226353", "GSM2226354", "GSM2226355", "GSM2226356", "GSM2226357", "GSM2226358", "GSM2226359", "GSM2226360", "GSM2226361", "GSM2226362", "GSM2226363", "GSM2226364", "GSM2226365", "GSM2226366", "GSM2226367", "GSM2226368", "GSM2226369", "GSM2226370", "GSM2226371", "GSM2226372", "GSM2226373", "GSM2226374", "GSM2226375", "GSM2226376", "GSM2226377", "GSM2226378", "GSM2226379", "GSM2226380", "GSM2226381", "GSM2226382", "GSM2226383", "GSM2226384", "GSM2226385", "GSM2226386", "GSM2226387", "GSM2226388", "GSM2226389", "GSM2226390", "GSM2226391", "GSM2226392", "GSM2226393", "GSM2226394", "GSM2226395", "GSM2226396", "GSM2226397", "GSM2226398", "GSM2226399", "GSM2226400", "GSM2226401", "GSM2226402", "GSM2226403"], "sample_count": 124, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Characterization of gene expression profile in HBV-related liver fibrosis patients", "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:30923657:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:323c9fba9f5b33601dba956f9e1f16b4a0c98423c851f533ce583e03d2839e8f", "bytes": 316, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#table-1", "version": null, "note": "Accession information for datasets downloaded from the GEO database. GSE6764, GSE49541 and GSE84044 was used for identifying DEGs; GSE14323 was used for validation.", "structure": {"pmcid": "PMC6432904", "section_index": 3, "section_title": "Microarray data", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Accession information for datasets downloaded from the GEO database. GSE6764, GSE49541 and GSE84044 was used for identifying DEGs; GSE14323 was used for validation.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[3]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:30923657:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9201b11ca5896b688ea9d310a8840fd3a17ef2039af86f1e670591690a6abf2b", "bytes": 292, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#table-2", "version": null, "note": "Top 10 GO_BP terms in each datasets ordered by FDR.Count: number of genes enriched in the corresponding pathway; FDR, false discovery rate.", "structure": {"pmcid": "PMC6432904", "section_index": 14, "section_title": "Functional enrichment analysis of DEGs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Top 10 GO_BP terms in each datasets ordered by FDR.Count: number of genes enriched in the corresponding pathway; FDR, false discovery rate.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:30923657:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eb309a461926baf91a57e551bc5e17c557957c57dea9a14263b1ba7aa6912def", "bytes": 205, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#table-3", "version": null, "note": "Top 10 KEGG pathways in each dataset ordered by FDR.", "structure": {"pmcid": "PMC6432904", "section_index": 14, "section_title": "Functional enrichment analysis of DEGs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "Top 10 KEGG pathways in each dataset ordered by FDR.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[2]#table-3"}}, {"id": "asset:table:pmid:30923657:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:38a5637f007f6a5aed555db279b2f003e12da0cf4f70297c62671231d51399ae", "bytes": 254, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#table-4", "version": null, "note": "Top 10 compounds predicted to have activity against liver fibrosis as predicted via connectivity map.", "structure": {"pmcid": "PMC6432904", "section_index": 18, "section_title": "Discussion", "row_count": 0, "column_count": 0}, "table": {"label": "Table 4", "caption": "Top 10 compounds predicted to have activity against liver fibrosis as predicted via connectivity map.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[18]/table-wrap[1]#table-4"}}, {"id": "asset:table:pmid:30923657:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2fa0b6113335dbeac3e2bf669ee67b5237ad10e21adce5cfcb879656f3e32b80", "bytes": 350, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[2]#table-5", "version": null, "note": "mRNA expression levels of selected genes in each datasets.logFC, log2 (Fold Change); Genes with an expression level of |logFC| > 0.585 and adj.P.Val < 0.05 were deemed to be the DEGs in this study.", "structure": {"pmcid": "PMC6432904", "section_index": 18, "section_title": "Discussion", "row_count": 0, "column_count": 0}, "table": {"label": "Table 5", "caption": "mRNA expression levels of selected genes in each datasets.logFC, log2 (Fold Change); Genes with an expression level of |logFC| > 0.585 and adj.P.Val < 0.05 were deemed to be the DEGs in this study.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[18]/table-wrap[2]#table-5"}}], "gaps": ["asset:data:geo:GSE14323 not downloaded", "asset:data:geo:GSE14323 licence not read", "asset:data:geo:GSE49541 not downloaded", "asset:data:geo:GSE49541 licence not read", "asset:data:geo:GSE6764 not downloaded", "asset:data:geo:GSE6764 licence not read", "asset:data:geo:GSE84044 not downloaded", "asset:data:geo:GSE84044 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Then, the Linear Models for Microarray Analysis R package (limma; version 3.30.11; Ritchie et al. (2015)) was applied for differential expression analysis."}}, {"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": "GO 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE6764", "GSE49541", "GSE84044", "GSE14323"], "resolved_accessions": ["GSE6764", "GSE49541", "GSE84044", "GSE14323"], "statements": ["The raw measurements are available in Data S1–S4."], "basis": "The paper names GSE6764, GSE49541, GSE84044, GSE14323 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:30923657", "data:geo:GSE14323", "asset:table:pmid:30923657:1", "asset:table:pmid:30923657:2", "asset:table:pmid:30923657:3", "asset:table:pmid:30923657:4", "asset:table:pmid:30923657:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14323"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:14:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22903, "completion_tokens": 1621, "cached_tokens": 7424}}, "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:30923657", "type": "paper", "label": "pmid:30923657"}, {"id": "source:pmid:30923657", "type": "manuscript", "label": "PMID 30923657 full text"}, {"id": "data:geo:GSE14323", "type": "dataset", "label": "GEO GSE14323"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30923657", "type": "paper", "label": "pmid:30923657"}, {"id": "source:pmid:30923657", "type": "manuscript", "label": "PMID 30923657 full text"}, {"id": "data:geo:GSE14323", "type": "dataset", "label": "GEO GSE14323"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30923657", "type": "extraction", "used": ["source:pmid:30923657"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14323", "type": "accession_resolution", "used": ["data:geo:GSE14323"], "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:30923657", "parent_hash": "sha256:18e008e3e301ddec057b728138e3bb4be33c3829266b438ecb78672c73125ec5", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE14323 licence not read", "asset:data:geo:GSE14323 not downloaded", "asset:data:geo:GSE49541 licence not read", "asset:data:geo:GSE49541 not downloaded", "asset:data:geo:GSE6764 licence not read", "asset:data:geo:GSE6764 not downloaded", "asset:data:geo:GSE84044 licence not read", "asset:data:geo:GSE84044 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["a liver fibrosis cell model by quantitative real-time PCR assay. The Connectivity Map L1000 platform w"], "order_basis": "paper_text_order:1013", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ll Life Science & Technology (Wuhan, China), cultured with Dulbecco Modified Eagle Medium (DMEM)-high g"], "order_basis": "paper_text_order:2781", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Then, the Linear Models for Microarray Analysis R package (limma; version 3.30.11; Ritchie et al. (2015)) was applied for differential expression analysis."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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":"2026-11-04T03:12:14+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}}}