{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28302149", "kind": "science-record", "revision": 7, "content_hash": "sha256:c9be403a1dabe772276a83182321e86b134b91c82a6177f4b24785f82286eee4", "created_at": "2026-11-01T15:40:24Z", "updated_at": "2026-11-01T21:59:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and interaction analysis of key genes and microRNAs in hepatocellular carcinoma by bioinformatics analysis.", "doi": "10.1186/s12957-017-1127-2", "pmid": "28302149", "authors": ["Tong Mou", "Di Zhu", "Xufu Wei", "Tingting Li", "Daofeng Zheng", "Junliang Pu", "Zhen Guo", "Zhongjun Wu"], "journal": "World journal of surgical oncology", "year": 2017, "abstract": "BACKGROUND: Hepatocellular carcinoma (HCC) is the most common liver malignancy worldwide. However, present studies of its multiple gene interaction and cellular pathways still could not explain the initiation and development of HCC perfectly. To find the key genes and miRNAs as well as their potential molecular mechanisms in HCC, microarray data GSE22058, GSE25097, and GSE57958 were analyzed.\nMETHODS: The microarray datasets GSE22058, GSE25097, and GSE57958, including mRNA and miRNA profiles, were downloaded from the GEO database and were analyzed using GEO2R. Functional and pathway enrichment analyses were performed using the DAVID database, and the protein-protein interaction (PPI) network was constructed using the Cytoscape software. Finally, miRDB was applied to predict the targets of the differentially expressed miRNAs (DEMs).\nRESULTS: A total of 115 differentially expressed genes (DEGs) were found in HCC, including 52 up-regulated genes and 63 down-regulated genes. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses from DAVID showed that up-regulated genes were significantly enriched in chromosome segregation and cell division, while the down-regulated genes were mainly involved in complement activation, protein activation cascades, carboxylic acid metabolic processes, oxoacid metabolic processes, and the immune response. From the PPI network, the 18 nodes with the highest degree were screened as hub genes. Among them, ESR1 was found to have close interactions with FOXO1, CXCL12, and GNAO1. In addition, a total of 64 DEMs were identified, which included 58 up-regulated miRNAs and 6 down-regulated miRNAs. ESR1 was potentially targeted by five miRNAs, including hsa-mir-18a and hsa-mir-221.\nCONCLUSIONS: The roles of DEMs like hsa-mir-221 in HCC through interactions with DEGs such as ESR1 and CXCL12 may provide new clues for the diagnosis and treatment of HCC patients.", "claims": [{"id": "claim-method", "statement": "The adjusted P values (adj. P) using Benjamini and Hochberg (BH) false discovery rate (FDR) method by default were applied to correct for the occurrence of false positive results. An adj. P < 0.05 and a |logFC| ≥ 1 were set as the cut-off criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28302149", "locator": "sections[5] \"Data processing\" paragraph 2", "quote": "The adjusted P values (adj. P) using Benjamini and Hochberg (BH) false discovery rate (FDR) method by default were applied to correct for the occurrence of false positive results. An adj. P < 0.05 and a |logFC| ≥ 1 were set as the cut-off criteria."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28302149", "locator": "sections[18] \"ack\" paragraph 1", "quote": "The datasets supporting the conclusions of this article are included within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study downloaded microarray datasets GSE22058, GSE25097, and GSE57958 from GEO and analyzed them with GEO2R using Benjamini–Hochberg-adjusted P values and a |logFC| ≥ 1 cutoff, identifying 115 DEGs and 64 DEMs in HCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28302149", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The microarray datasets GSE22058, GSE25097, and GSE57958, including mRNA and miRNA profiles, were downloaded from the GEO database and were analyzed using GEO2R."}, {"asset": "source:pmid:28302149", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 115 differentially expressed genes (DEGs) were found in HCC, including 52 up-regulated genes and 63 down-regulated genes."}, {"asset": "source:pmid:28302149", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In addition, a total of 64 DEMs were identified, which included 58 up-regulated miRNAs and 6 down-regulated miRNAs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study downloaded microarray datasets GSE22058, GSE25097, and GSE57958 from GEO and analyzed them with GEO2R using Benjamini–Hochberg-adjusted P values and a |logFC| ≥ 1 cutoff, identifying 115 DEGs and 64 DEMs in HCC.", "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:28302149"], "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:GSE22058"], "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:GSE22058"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28302149", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12957-017-1127-2", "sha256": "sha256:092d43423ffb7ed87f680688bb8fb903e00a692262279aeb4e135cb388b88d72", "bytes": 28558, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12957-017-1127-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5356276", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE22058", "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=GSE22058", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22058", "version": null, "note": "The datasets supporting the conclusions of this article are included within the article.", "structure": 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the genes in the module", "structure": {"pmcid": "PMC5356276", "section_index": 7, "section_title": "PPI network construction and analysis of modules", "row_count": 15, "column_count": 5}, "table": {"label": "Table 3", "caption": "Functional and pathway enrichment analysis of the genes in the module", "rows": [["Category", "Term", "Count", "%", "P Value"], ["GOTERM_BP_FAT", "GO:0000302 ~ response to reactive oxygen species", "4", "26.7", "8.25E-04"], ["GOTERM_BP_FAT", "GO:1901700 ~ response to oxygen-containing compound", "7", "46.7", "1.06E-03"], ["GOTERM_BP_FAT", "GO:0006979 ~ response to oxidative stress", "4", "26.7", "4.59E-03"], ["GOTERM_BP_FAT", "GO:0048545 ~ response to steroid hormone", "4", "26.7", "4.78E-03"], ["GOTERM_BP_FAT", "GO:1903047 ~ mitotic cell cycle process", "5", "33.3", "5.21E-03"], ["GOTERM_CC_FAT", "GO:0005654 ~ nucleoplasm", "9", "60.0", "1.54E-03"], ["GOTERM_CC_FAT", "GO:0005829 ~ cytosol", "8", "53.3", "1.94E-02"], ["GOTERM_CC_FAT", "GO:0005694 ~ chromosome", "4", "26.7", "4.75E-02"], ["GOTERM_MF_FAT", "GO:0044877 ~ macromolecular complex binding", "9", "60.0", "4.65E-06"], ["GOTERM_MF_FAT", "GO:0003682 ~ chromatin binding", "6", "40.0", "5.72E-05"], ["GOTERM_MF_FAT", "GO:0019899 ~ enzyme binding", "6", "40.0", "1.67E-02"], ["GOTERM_MF_FAT", "GO:0000982 ~ transcription factor activity, RNA polymer", "3", "20.0", "3.72E-02"], ["GOTERM_MF_FAT", "GO:0097367 ~ carbohydrate derivative binding", "6", "40.0", "4.13E-02"], ["KEGG_PATHWAY", "hsa04512:ECM-receptor interaction", "3", "20.0", "9.53E-03"]], "row_count": 15, "column_count": 5, "numeric_cells": 56, "header_rows": 1, "locator": "section[12]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:28302149:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:750de52125f3111231ee3af8d5d9c3ba96d95cdfab7808cc70ba5177ad1b25fe", "bytes": 2931, "access": "open", "state": "verified", "reader": "read_table", 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mitotic nuclear division", "8", "15.7", "1.44E-04"], ["GOTERM_CC_FAT", "GO:0000793 ~ condensed chromosome", "5", "9.8", "2.14E-03"], ["GOTERM_CC_FAT", "GO:0005829 ~ cytosol", "18", "35.3", "3.98E-03"], ["GOTERM_CC_FAT", "GO:0005578 ~ proteinaceous extracellular matrix", "5", "9.8", "1.51E-02"], ["GOTERM_CC_FAT", "GO:0098651 ~ basement membrane collagen trimer", "2", "3.9", "2.08E-02"], ["GOTERM_CC_FAT", "GO:0005694 ~ chromosome", "7", "13.7", "3.38E-02"], ["GOTERM_MF_FAT", "GO:0042826 ~ histone deacetylase binding", "3", "5.9", "3.03E-02"], ["KEGG_PATHWAY", "hsa04512:ECM-receptor interaction", "3", "5.9", "1.68E-02"], ["Down-regulated"], ["GOTERM_BP_FAT", "GO:0006956 ~ complement activation", "6", "10.0", "1.83E-05"], ["GOTERM_BP_FAT", "GO:0072376 ~ protein activation cascade", "6", "10.0", "6.43E-05"], ["GOTERM_BP_FAT", "GO:0019752 ~ carboxylic acid metabolic process", "12", "20.0", "8.21E-05"], ["GOTERM_BP_FAT", "GO:0043436 ~ oxoacid metabolic process", "12", "20.0", "8.66E-05"], ["GOTERM_BP_FAT", "GO:0006955 ~ immune response", "16", "26.7", "1.23E-04"], ["GOTERM_CC_FAT", "GO:0005581 ~ collagen trimer", "4", "6.7", "7.15E-03"], ["GOTERM_CC_FAT", "GO:0072562 ~ blood microparticle", "4", "6.7", "1.91E-02"], ["GOTERM_CC_FAT", "GO:0005579 ~ membrane attack complex", "2", "3.3", "2.67E-02"], ["GOTERM_CC_FAT", "GO:0031988 ~ membrane-bounded vesicle", "21", "35.0", "4.60E-02"], ["GOTERM_CC_FAT", "GO:0044421 ~ extracellular region part", "22", "36.7", "5.00E-02"], ["GOTERM_MF_FAT", "GO:0005496 ~ steroid binding", "4", "6.7", "3.47E-03"], ["GOTERM_MF_FAT", "GO:0070330 ~ aromatase activity", "3", "5.0", "3.57E-03"], ["GOTERM_MF_FAT", "GO:0016712 ~ oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen", "3", "5.0", "4.11E-03"], ["GOTERM_MF_FAT", "GO:0004497 ~ monooxygenase activity", "4", "6.7", "4.77E-03"], ["GOTERM_MF_FAT", "GO:0004252 ~ 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"table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a63f49009273bcd5628c31be2ab5c5b293fb770e11bb11e4562ca06a51589199", "bytes": 1381, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#Tab3", "version": null, "note": "Functional and pathway enrichment analysis of the genes in the module", "structure": {"pmcid": "PMC5356276", "section_index": 12, "section_title": "PPI network construction and analysis of modules", "row_count": 15, "column_count": 5}, "table": {"label": "Table 3", "caption": "Functional and pathway enrichment analysis of the genes in the module", "rows": [["Category", "Term", "Count", "%", "P Value"], ["GOTERM_BP_FAT", "GO:0000302 ~ response to reactive oxygen species", "4", "26.7", "8.25E-04"], ["GOTERM_BP_FAT", "GO:1901700 ~ response to oxygen-containing compound", "7", "46.7", "1.06E-03"], ["GOTERM_BP_FAT", "GO:0006979 ~ response to oxidative stress", "4", "26.7", "4.59E-03"], ["GOTERM_BP_FAT", "GO:0048545 ~ response to steroid hormone", "4", "26.7", "4.78E-03"], ["GOTERM_BP_FAT", "GO:1903047 ~ mitotic cell cycle process", "5", "33.3", "5.21E-03"], ["GOTERM_CC_FAT", "GO:0005654 ~ nucleoplasm", "9", "60.0", "1.54E-03"], ["GOTERM_CC_FAT", "GO:0005829 ~ cytosol", "8", "53.3", "1.94E-02"], ["GOTERM_CC_FAT", "GO:0005694 ~ chromosome", "4", "26.7", "4.75E-02"], ["GOTERM_MF_FAT", "GO:0044877 ~ macromolecular complex binding", "9", "60.0", "4.65E-06"], ["GOTERM_MF_FAT", "GO:0003682 ~ chromatin binding", "6", "40.0", "5.72E-05"], ["GOTERM_MF_FAT", "GO:0019899 ~ enzyme binding", "6", "40.0", "1.67E-02"], ["GOTERM_MF_FAT", "GO:0000982 ~ transcription factor activity, RNA polymer", "3", "20.0", "3.72E-02"], ["GOTERM_MF_FAT", "GO:0097367 ~ carbohydrate derivative binding", "6", "40.0", "4.13E-02"], ["KEGG_PATHWAY", "hsa04512:ECM-receptor interaction", "3", "20.0", "9.53E-03"]], "row_count": 15, "column_count": 5, "numeric_cells": 56, "header_rows": 1, "locator": "section[12]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:28302149:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c116d6514322d45ec9b4bcbfc0d6a087257714b60f0b133ff6a2730b0b81abff", "bytes": 1348, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab4", "version": null, "note": "DEMs in HCC tissue and their potential target genes", "structure": {"pmcid": "PMC5356276", "section_index": 13, "section_title": "miRNA-DEG pairs", "row_count": 11, "column_count": 4}, "table": {"label": "Table 4", "caption": "DEMs in HCC tissue and their potential target genes", "rows": [["miRNA", "Adj. P", "logFC", "Target genes"], ["hsa-mir-106b", "1.94E-41", "1.49", "ANKRD29, IL1RAP, ADARB1, ARID4B, EPHA4, FBXL5, PDCD1LG2, PKD2, PTPN4, SLC40A1"], ["hsa-mir-148b", "9.59E-22", "1.37", "ESR1, ABCB7, B4GALT6, CDK19, LDLR, MXD1, NPTN, RPS6KA5, SOS2, SZRD1"], ["hsa-mir-151", "2.61E-21", "1.14", "AGO2, ZFAND5, CLK1, AQP4, CASD1, RPS6KA5, FAM104A, NAA15, YTHDF3, HIF1A"], ["hsa-mir-221", "7.37E-21", "1.66", "ESR1, FOS, CXCL12, CDKN1B, GABRA1, PANK3, TCF12, HECTD2, RFX7, TMCC1"], ["hsa-mir-18a", "2.16E-20", "2.48", "ESR1, NEDD9, BBX, INADL, MAP7D1, PHF19, RORA, ZBTB47, CDK19, DICER1"], ["hsa-mir-200b", "4.50E-17", "−3.15", "MAGEC2, ESM1, TCEB1, TRIM33, LHFP, PTPN21, ARHGAP6, VASH2, HIPK3, NR5A2"], ["hsa-mir-224", "4.85E-15", "−71.38", "NRCAM, CPNE8, ZNF207, ACSL4, RNF144B, SH3KBP1, RNF38, SLC4A4, GPR158, GGNBP2"], ["hsa-mir-200a", "5.03E-14", "−2.29", "COL15A1, MYBL1, ZEB2, ATP8A1, DCP2, TMEM170B, ZBTB34, DUSP3, TRHDE, RSAD2"], ["hsa-mir-182", "1.41E-06", "−2.69", "NRCAM, ABHD13, MFAP3, PCNX, NADK2, CAMSAP2, SLC39A9, NCALD, ANK3, HOXA9"], ["hsa-mir-142-5p", "6.59E-06", "−1.49", "ANKRD29, IGF2BP3, IGSF3, ZFP36, ZFPM2, BAI3, AFF4, DIAPH2, AHR, ARID4B"]], "row_count": 11, "column_count": 4, "numeric_cells": 40, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab4"}}], "gaps": ["asset:data:geo:GSE22058 not downloaded", "asset:data:geo:GSE22058 licence not read", "asset:data:geo:GSE25097 not downloaded", "asset:data:geo:GSE25097 licence not read", "asset:data:geo:GSE57958 not downloaded", "asset:data:geo:GSE57958 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": "Benjamini–Hochberg false discovery rate (FDR) adjustment using GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The adjusted P values (adj. P) using Benjamini and Hochberg (BH) false discovery rate (FDR) method by default were applied to correct for the occurrence of false positive results. An adj. P < 0.05 and a |logFC| ≥ 1 were set as the cut-off criteria."}}], "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": ["GSE22058", "GSE25097", "GSE57958"], "resolved_accessions": ["GSE22058", "GSE25097", "GSE57958"], "statements": ["The datasets supporting the conclusions of this article are included within the article."], "basis": "The paper names GSE22058, GSE25097, GSE57958 in GEO database 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:28302149", "data:geo:GSE22058", "asset:table:pmid:28302149:1", "asset:table:pmid:28302149:2", "asset:table:pmid:28302149:3", "asset:table:pmid:28302149:4", "asset:table:pmid:28302149:5", "asset:table:pmid:28302149:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE22058"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:40Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 63755, "completion_tokens": 4094, "cached_tokens": 1824}}, "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:28302149", "type": "paper", "label": "pmid:28302149"}, {"id": "source:pmid:28302149", "type": "manuscript", "label": "PMID 28302149 full text"}, {"id": "data:geo:GSE22058", "type": "dataset", "label": "GEO GSE22058"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28302149", "type": "paper", "label": "pmid:28302149"}, {"id": "source:pmid:28302149", "type": "manuscript", "label": "PMID 28302149 full text"}, {"id": "data:geo:GSE22058", "type": "dataset", "label": "GEO GSE22058"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28302149", "type": "extraction", "used": ["source:pmid:28302149"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE22058", "type": "accession_resolution", "used": ["data:geo:GSE22058"], "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:28302149", "parent_hash": "sha256:8c36fe0ab80c6c37369c58831340a064767db53aa5f5214b2d5fdfcf9fc6df78", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE22058 licence not read", "asset:data:geo:GSE22058 not downloaded", "asset:data:geo:GSE25097 licence not read", "asset:data:geo:GSE25097 not downloaded", "asset:data:geo:GSE57958 licence not read", "asset:data:geo:GSE57958 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": ["their potential molecular mechanisms in HCC, microarray data GSE22058, GSE25097, and GSE57958 were a", "97, and GSE57958 were analyzed. METHODS: The microarray datasets GSE22058, GSE25097, and GSE57958, i"], "order_basis": "paper_text_order:410", "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":"2026-11-04T03:12:13+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}}}