{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35847584", "kind": "science-record", "revision": 4, "content_hash": "sha256:40a71ef78292c52b4aad7596a0fa7085dd014add759927a9bffff04291193d9d", "created_at": "2026-11-01T18:14:55Z", "updated_at": "2026-11-01T22:07:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a Prognostic Transcriptome Signature for Hepatocellular Carcinoma with Lymph Node Metastasis.", "doi": "10.1155/2022/7291406", "pmid": "35847584", "authors": ["Jie Ma", "Xue-Qin Chen", "Zuo-Lin Xiang"], "journal": "Oxidative medicine and cellular longevity", "year": 2022, "abstract": "Hepatocellular carcinoma (HCC) is one of the most aggressive malignant tumors, and the prognosis of HCC patients with lymph node metastasis (LNM) is poor. However, robust biomarkers for predicting the prognosis of HCC LNM are still lacking. This study used weighted gene coexpression network analysis of GSE28248 (N = 80) microarray data to identify gene modules associated with HCC LNM and validated in GSE40367 dataset (N = 18). The prognosis-related genes in the HCC LNM module were further screened based on the prognostic curves of 371 HCC samples from TCGA. We finally developed a prognostic signature, PSG-30, as a prognostic-related biomarker in HCC LNM. The HCC subtypes identified by PSG-30-based consensus clustering analysis showed significant differences in prognosis, clinicopathological stage, m6A modification, ferroptosis activation, and immune characteristics. In addition, RAD54B was selected by regression model as an independent risk factor affecting the prognosis of HCC patients with LNM, and its expression was significantly positively correlated with tumor mutational burden and microsatellite instability in high-risk subtypes. Patients with high RAD54B expression had a better prognosis in the immune checkpoint inhibitor-treated cohorts but had a poor prognosis in the HCC sorafenib-treated group. The association of high RAD54B expression with LNM in breast cancer (BRCA) and cholangiocarcinoma and its prognostic effect in BRCA LNM cases suggest the value of RAD54B at the pancancer level. In conclusion, PSG-30 can effectively identify HCC LNM population with poor prognosis, and high-risk patients with high RAD54B expression may be more suitable for immunotherapy.", "claims": [{"id": "claim-method", "statement": "Specifically, the Pearson correlation matrix and average linkage method were first used for paired genes, and the power function a|mn = |C|mn^β (c | mn = Pearson correlation between gene m and gene n; a | mn = adjacency between gene m and gene n) was then used for weighted adjacency matrix construction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35847584", "locator": "sections[5] \"2.3. WGCNA Analysis\" paragraph 2", "quote": "Specifically, the Pearson correlation matrix and average linkage method were first used for paired genes, and the power function a|mn = |C|mn^β (c | mn = Pearson correlation between gene m and gene n; a | mn = adjacency between gene m and gene n) was then used for weighted adjacency matrix construction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35847584", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Weighted gene coexpression network analysis of GSE28248 (N = 80) identified HCC LNM-associated gene modules and was validated with GSE40367 (N = 18), ultimately yielding PSG-30.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35847584", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This study used weighted gene coexpression network analysis of GSE28248 (N = 80) microarray data to identify gene modules associated with HCC LNM and validated in GSE40367 dataset (N = 18)."}, {"asset": "source:pmid:35847584", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We finally developed a prognostic signature, PSG-30, as a prognostic-related biomarker in HCC LNM."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Weighted gene coexpression network analysis of GSE28248 (N = 80) identified HCC LNM-associated gene modules and was validated with GSE40367 (N = 18), ultimately yielding PSG-30.", "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:35847584"], "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:GSE28248"], "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": {"median_survival": "ean time represents the median survival time in years"}, "inputs": ["data:geo:GSE28248"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35847584", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/7291406", "sha256": "sha256:df748ea4b711833ff6b16f454742865943a66bfccfa4d693a43ca1d4b544e083", "bytes": 82923, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/7291406", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9279092", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28248", "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=GSE28248", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28248", "version": null, "note": "Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM699172", "GSM699173", "GSM699174", "GSM699175", "GSM699176", "GSM699177", "GSM699178", "GSM699179", "GSM699180", "GSM699181", "GSM699182", "GSM699183", "GSM699184", "GSM699185", "GSM699186", "GSM699187", "GSM699188", "GSM699189", "GSM699190", "GSM699191", "GSM699192", "GSM699193", "GSM699194", "GSM699195", "GSM699196", "GSM699197", "GSM699198", "GSM699199", "GSM699200", "GSM699201", "GSM699202", "GSM699203", "GSM699204", "GSM699205", "GSM699206", "GSM699207", "GSM699208", "GSM699209", "GSM699210", "GSM699211", "GSM699212", "GSM699213", "GSM699214", "GSM699215", "GSM699216", "GSM699217", "GSM699218", "GSM699219", "GSM699220", "GSM699221", "GSM699222", "GSM699223", "GSM699224", "GSM699225", "GSM699226", "GSM699227", "GSM699228", "GSM699229", "GSM699230", "GSM699231", "GSM699232", "GSM699233", "GSM699234", "GSM699235", "GSM699236", "GSM699237", "GSM699238", "GSM699239", "GSM699240", "GSM699241", "GSM699242", "GSM699243", "GSM699244", "GSM699245", "GSM699246", "GSM699247", "GSM699248", "GSM699249", "GSM699250", "GSM699251"], "sample_count": 80, "group_sizes": null, "group_sizes_basis": null, "platform": "5858", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Fixed Tissues of Lymph Node Metastasis in Hepatocellular Carcinoma", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE40367", "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=GSE40367", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40367", "version": null, "note": "Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM992272", "GSM992273", "GSM992274", "GSM992275", "GSM992276", "GSM992277", "GSM992278", "GSM992279", "GSM992280", "GSM992281", "GSM992282", "GSM992283", "GSM992284", "GSM992285", "GSM992286", "GSM992287", "GSM992288", "GSM992289", "GSM992290", "GSM992291", "GSM992292", "GSM992293", "GSM992294", "GSM992295", "GSM992296", "GSM992297", "GSM992298", "GSM992299", "GSM992300", "GSM992301", "GSM992302", "GSM992303", "GSM992304", "GSM992305", "GSM992306", "GSM992307", "GSM992308", "GSM992309", "GSM992310", "GSM992311", "GSM992312", "GSM992313", "GSM992314", "GSM992315", "GSM992316", "GSM992317", "GSM992318", "GSM992319", "GSM992320", "GSM992321", "GSM992322", "GSM992323", "GSM992324", "GSM992325", "GSM992326", "GSM992327", "GSM992328", "GSM992329", "GSM992330", "GSM992331", "GSM992332"], "sample_count": 61, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression analysis of liver and colon cancer primary tumors and metastasis", "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:GSE5975", "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=GSE5975", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE5975", "version": null, "note": "Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM138758", "GSM138759", "GSM138760", "GSM138761", "GSM138762", "GSM138763", "GSM138764", "GSM138765", "GSM138766", "GSM138767", "GSM138768", "GSM138769", "GSM138770", "GSM138771", "GSM138772", "GSM138773", "GSM138774", "GSM138775", "GSM138776", "GSM138777", "GSM138778", "GSM138779", "GSM138780", "GSM138781", "GSM138782", "GSM138783", "GSM138784", "GSM138785", "GSM138786", "GSM138787", "GSM138788", "GSM138789", "GSM138790", "GSM138791", "GSM138792", "GSM138793", "GSM138794", "GSM138795", "GSM138796", "GSM138797", "GSM138798", "GSM138799", "GSM138800", "GSM138801", "GSM138802", "GSM138803", "GSM138804", "GSM138805", "GSM138806", "GSM138807", "GSM138808", "GSM138809", "GSM138810", "GSM138811", "GSM138812", "GSM138813", "GSM138814", "GSM138815", "GSM138816", "GSM138817", "GSM138818", "GSM138819", "GSM138820", "GSM138821", "GSM138822", "GSM138823", "GSM138824", "GSM138825", "GSM138826", "GSM138827", "GSM138828", "GSM138829", "GSM138830", "GSM138831", "GSM138832", "GSM138833", "GSM138834", "GSM138835", "GSM138836", "GSM138837", "GSM138838", "GSM138839", "GSM138840", "GSM138841", "GSM138842", "GSM138843", "GSM138844", "GSM138845", "GSM138846", "GSM138847", "GSM138848", "GSM138849", "GSM138850", "GSM138851", "GSM138852", "GSM138853", "GSM138854", "GSM138855", "GSM138856", "GSM138857", "GSM138858", "GSM138859", "GSM138860", "GSM138861", "GSM138862", "GSM138863", "GSM138864", "GSM138865", "GSM138866", "GSM138867", "GSM138868", "GSM138869", "GSM138870", "GSM138871", "GSM138872", "GSM138873", "GSM138874", "GSM138875", "GSM138876", "GSM138877", "GSM138878", "GSM138879", "GSM138880", "GSM138881", "GSM138882", "GSM138883", "GSM138884", "GSM138885", "GSM138886", "GSM138887", "GSM138888", "GSM138889", "GSM138890", "GSM138891", "GSM138892", "GSM138893", "GSM138894", "GSM138895", "GSM138896", "GSM138897", "GSM138898", "GSM138899", "GSM138900", "GSM138901", "GSM138902", "GSM138903", "GSM138904", "GSM138905", "GSM138906", "GSM138907", "GSM138908", "GSM138909", "GSM138910", "GSM138911", "GSM138912", "GSM138913", "GSM138914", "GSM138915", "GSM138916", "GSM138917", "GSM138918", "GSM138919", "GSM138920", "GSM138921", "GSM138922", "GSM138923", "GSM138924", "GSM138925", "GSM138926", "GSM138927", "GSM138928", "GSM138929", "GSM138930", "GSM138931", "GSM138932", "GSM138933", "GSM138934", "GSM138935", "GSM138936", "GSM138937", "GSM138938", "GSM138939", "GSM138940", "GSM138941", "GSM138942", "GSM138943", "GSM138944", "GSM138945", "GSM138946", "GSM138947", "GSM138948", "GSM138949", "GSM138950", "GSM138951", "GSM138952", "GSM138953", "GSM138954", "GSM138955", "GSM138956", "GSM138957", "GSM138958", "GSM138959", "GSM138960", "GSM138961", "GSM138962", "GSM138963", "GSM138964", "GSM138965", "GSM138966", "GSM138967", "GSM138968", "GSM138969", "GSM138970", "GSM138971", "GSM138972", "GSM138973", "GSM138974", "GSM138975", "GSM138976", "GSM138977", "GSM138978", "GSM138979", "GSM138980", "GSM138981", "GSM138982", "GSM138983", "GSM138984", "GSM138985", "GSM138986", "GSM138987", "GSM138988", "GSM138989", "GSM138990", "GSM138991", "GSM138992", "GSM138993", "GSM138994", "GSM138995"], "sample_count": 238, "group_sizes": null, "group_sizes_basis": null, "platform": "1528", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Hepatocellular Carcinoma", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE28248 not downloaded", "asset:data:geo:GSE28248 licence not read", "asset:data:geo:GSE40367 not downloaded", "asset:data:geo:GSE40367 licence not read", "asset:data:geo:GSE5975 not downloaded", "asset:data:geo:GSE5975 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {"median_survival": "ean time represents the median survival time in years"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "KM"}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"median_survival": "ean time represents the median survival time in years"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}, {"id": "method-5", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "logistic regression"}}, {"id": "method-6", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-7", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}, {"id": "method-8", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "dendrogram"}}, {"id": "method-9", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}, {"id": "method-10", "family": null, "specific": null, "label": "Weighted gene coexpression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Specifically, the Pearson correlation matrix and average linkage method were first used for paired genes, and the power function a|mn = |C|mn^β (c | mn = Pearson correlation between gene m and gene n; a | mn = adjacency between gene m and gene n) was then used for weighted adjacency matrix construction."}}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE28248", "GSE40367", "GSE5975"], "resolved_accessions": ["GSE28248", "GSE40367", "GSE5975"], "statements": ["Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information."], "basis": "The paper names GSE28248, GSE40367, GSE5975 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:35847584", "data:geo:GSE28248"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE28248"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:55:51Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 21991, "completion_tokens": 2510, "cached_tokens": 128}}, "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:35847584", "type": "paper", "label": "pmid:35847584"}, {"id": "source:pmid:35847584", "type": "manuscript", "label": "PMID 35847584 full text"}, {"id": "data:geo:GSE28248", "type": "dataset", "label": "GEO GSE28248"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35847584", "type": "paper", "label": "pmid:35847584"}, {"id": "source:pmid:35847584", "type": "manuscript", "label": "PMID 35847584 full text"}, {"id": "data:geo:GSE28248", "type": "dataset", "label": "GEO GSE28248"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35847584", "type": "extraction", "used": ["source:pmid:35847584"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE28248", "type": "accession_resolution", "used": ["data:geo:GSE28248"], "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:35847584", "parent_hash": "sha256:6f94b966a0170c0ea792bd3267a4f4b8f0acd8f63f9b3b07b20909b1f184ccc2", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE28248 licence not read", "asset:data:geo:GSE28248 not downloaded", "asset:data:geo:GSE40367 licence not read", "asset:data:geo:GSE40367 not downloaded", "asset:data:geo:GSE5975 licence not read", "asset:data:geo:GSE5975 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Identification of a Prognostic Transcriptome Signature for Hepatocellular Carcinoma with", "ds 2.2. Data Processing For the unnormalized RNA-seq dataset, the original expression of each gen"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["protein expression level in HCC and CHOL via immunohistochemistry (IHC) staining, and the typical IHC images w", "to develop LNM earlier and more frequently. Immunohistochemical results showed that the expression intensity", "el in HCC and CHOL via immunohistochemistry (IHC) staining, and the typical IHC images were o", "stochemistry (IHC) staining, and the typical IHC images were obtained from the HPA database."], "order_basis": "paper_text_order:9530", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["KM"], "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":"2026-11-04T02:46:32+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}}}