{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39696012", "kind": "science-record", "revision": 3, "content_hash": "sha256:7a5b474d79dc2f571874b76430c908d7ded96509712501d08c2f7c4b061f6f5b", "created_at": "2026-11-01T20:29:59Z", "updated_at": "2026-11-01T22:13:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key necroptosis-related genes and immune landscape in patients with immunoglobulin A nephropathy.", "doi": "10.1186/s12882-024-03885-4", "pmid": "39696012", "authors": ["Ruikun Hu", "Ziyu Liu", "Huihui Hou", "Jingyu Li", "Ming Yang", "Panfeng Feng", "Xiaorong Wang", "Dechao Xu"], "journal": "BMC nephrology", "year": 2024, "abstract": "BACKGROUND: Immunoglobulin A nephropathy (IgAN) is a major cause of chronic kidney disease (CKD) and kidney failure. Necroptosis is a novel type of programmed cell death that has been proved to be associated with the pathogenesis of infectious disease, cardiovascular disease, neurological disorders and so on. However, the role of necroptosis in IgAN remains unclear.\nMETHODS: In this study, we explored the role of necroptosis-related genes in the pathogenesis of IgAN using a comprehensive bioinformatics method. Microarray datasets GSE93798 and GSE115857 were downloaded from Gene Expression Omnibus (GEO). \"limma\" package of R software was employed to identify necroptosis-related differentially expressed genes (NRDEGs) between IgAN and healthy controls. GO and KEGG functional enrichment analysis was performed by Clusterprofiler. Least absolute shrinkage and selection operator (LASSO) regression analysis identified hub NRDEGs. We further established a diagnostic model consisting of 7 diagnostic hub NRDEGs and validated the efficacy by an external dataset. The expression of hub genes was confirmed in sc-RNA dataset GSE171314. Immune infiltration, gene set enrichment analysis and transcription factor binding motifs enrichment analysis were conducted to further uncover their roles.\nRESULTS: 1076 differentially expressed genes were identified between healthy individuals and IgAN patients from RNA-seq dataset GSE9379. Then we cross-linked them with necroptosis-related genes to obtain 9 NRDEGs. LASSO regression analysis screened out 7 hub genes (JUN, CD274, SERTAD1, NFKBIA, H19, UCHL1 and EZH2) of IgAN. We further conducted functional enrichment analysis and constructed the diagnostic model based on dataset GSE93798. GSE115857 was used as the independent validation cohort and indicated a great predictive efficacy. Immune infiltration, gene set enrichment analysis and transcription factor binding motifs enrichment analysis revealed their potential function. Finally, we screened out four drugs that were predicted to have therapeutic value of IgAN.\nCONCLUSIONS: In summary, we identified 7 hub necroptosis-associated genes, which can be used as potential genetic biomarkers for IgAN prediction and treatment. Four drugs were predicted as the potential therapeutic solutions. Collectively, we provided insights into the necroptosis-related mechanisms and treatment of IgAN at the transcriptome level.", "claims": [{"id": "claim-method", "statement": "LASSO regression analysis was applied based on the 9 overlapping genes (Fig. 4a, b).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39696012", "locator": "sections[16] \"Construction and validation of a diagnosis-associated risk model\" paragraph 2", "quote": "LASSO regression analysis was applied based on the 9 overlapping genes (Fig. 4a, b)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). GSE93798: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798. GSE115857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115857. GSE171314 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171314.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39696012", "locator": "sections[30] \"notes\" paragraph 1", "quote": "The datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). GSE93798: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798. GSE115857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115857. GSE171314 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171314."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The area under the curve (AUC) was 0.966 (Fig. 4e), demonstrating the great predictive performance of the diagnosis-associated risk model.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39696012", "locator": "sections[16] \"Construction and validation of a diagnosis-associated risk model\" paragraph 2", "quote": "The area under the curve (AUC) was 0.966 (Fig. 4e), demonstrating the great predictive performance of the diagnosis-associated risk model."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The area under the curve (AUC) was 0.966 (Fig. 4e), demonstrating the great predictive performance of the diagnosis-associated risk model.", "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:39696012"], "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:GSE115857"], "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:GSE115857"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39696012", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12882-024-03885-4", "sha256": "sha256:2c25ea0c85e15d7248af732bd628119c6c9818332ee14975760ef096e0cef0a7", "bytes": 29244, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12882-024-03885-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11653910", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE115857", "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=GSE115857", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE115857", "version": null, "note": "The datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). GSE93798: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798. GSE115857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115857. GSE171314 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171314.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). GSE93798: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798. GSE115857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115857. GSE171314 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171314.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3191893", "GSM3191894", "GSM3191895", "GSM3191896", "GSM3191897", "GSM3191898", "GSM3191899", "GSM3191900", "GSM3191901", "GSM3191902", "GSM3191903", "GSM3191904", "GSM3191905", "GSM3191906", "GSM3191907", "GSM3191908", "GSM3191909", "GSM3191910", "GSM3191911", "GSM3191912", "GSM3191913", "GSM3191914", "GSM3191915", "GSM3191916", "GSM3191917", "GSM3191918", "GSM3191919", "GSM3191920", "GSM3191921", "GSM3191922", "GSM3191923", "GSM3191924", "GSM3191925", "GSM3191926", "GSM3191927", "GSM3191928", "GSM3191929", "GSM3191930", "GSM3191931", "GSM3191932", "GSM3191933", "GSM3191934", "GSM3191935", "GSM3191936", "GSM3191937", "GSM3191938", "GSM3191939", "GSM3191940", "GSM3191941", "GSM3191942", "GSM3191943", "GSM3191944", "GSM3191945", "GSM3191946", "GSM3191947", "GSM3191948", "GSM3191949", "GSM3191950", "GSM3191951", "GSM3191952", "GSM3191953", "GSM3191954", "GSM3191955", "GSM3191956", "GSM3191957", "GSM3191958", "GSM3191959", "GSM3191960", "GSM3191961", "GSM3191962", "GSM3191963", "GSM3191964", "GSM3191965", "GSM3191966", "GSM3191967", "GSM3191968", "GSM3191969", "GSM3191970", "GSM3191971", "GSM3191972", "GSM3191973", "GSM3191974", "GSM3191975", "GSM3191976", "GSM3191977", "GSM3191978"], "sample_count": 86, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "SPECIFIC BIOMARKERS ASSOCIATED WITH CHRONIC RENAL LESIONS IN IGA NEPHROPATHY PATIENTS. A MULTICENTER STUDY", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE171314", "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=GSE171314", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE171314", "version": null, "note": "The datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). GSE93798: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798. GSE115857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115857. GSE171314 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171314.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). GSE93798: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798. GSE115857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115857. GSE171314 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171314.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5222730", "GSM5222731", "GSM5222732", "GSM5222733", "GSM5222734"], "sample_count": 5, "group_sizes": null, "group_sizes_basis": null, "platform": "20795", "taxon": "Homo sapiens", "title": "A partial picture of the single-cell transcriptomics of human IgA nephropathy", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE93798", "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=GSE93798", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE93798", "version": null, "note": "The datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). GSE93798: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798. GSE115857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115857. GSE171314 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171314.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). GSE93798: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798. GSE115857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115857. GSE171314 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171314.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2462533", "GSM2462534", "GSM2462535", "GSM2462536", "GSM2462537", "GSM2462538", "GSM2462539", "GSM2462540", "GSM2462541", "GSM2462542", "GSM2462543", "GSM2462544", "GSM2462545", "GSM2462546", "GSM2462547", "GSM2462548", "GSM2462549", "GSM2462550", "GSM2462551", "GSM2462552", "GSM2462553", "GSM2462554", "GSM2462555", "GSM2462556", "GSM2462557", "GSM2462558", "GSM2462559", "GSM2462560", "GSM2462561", "GSM2462562", "GSM2462563", "GSM2462564", "GSM2462565", "GSM2462566", "GSM2462567", "GSM2462568", "GSM2462569", "GSM2462570", "GSM2462571", "GSM2462572", "GSM2462573", "GSM2462574"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "22945", "taxon": "Homo sapiens", "title": "Transcriptomic and proteomic profiling reveal insights of mesangial cell function in patients with IgA Nephropathy", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE115857 not downloaded", "asset:data:geo:GSE115857 licence not read", "asset:data:geo:GSE171314 not downloaded", "asset:data:geo:GSE171314 licence not read", "asset:data:geo:GSE93798 not downloaded", "asset:data:geo:GSE93798 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": "principal component analysis"}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-3", "family": null, "specific": null, "label": "LASSO regression", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "LASSO regression analysis was applied based on the 9 overlapping genes (Fig. 4a, b)."}}], "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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "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": ["GSE93798", "GSE115857", "GSE171314"], "resolved_accessions": ["GSE93798", "GSE115857", "GSE171314"], "statements": ["The datasets were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus (GEO). GSE93798: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93798. GSE115857: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115857. GSE171314 : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171314."], "basis": "The paper names GSE93798, GSE115857, GSE171314 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": ["pca_fit"], "assets": ["source:pmid:39696012", "data:geo:GSE115857"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE115857"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:42:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8716, "completion_tokens": 1561, "cached_tokens": 256}}, "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:39696012", "type": "paper", "label": "pmid:39696012"}, {"id": "source:pmid:39696012", "type": "manuscript", "label": "PMID 39696012 full text"}, {"id": "data:geo:GSE115857", "type": "dataset", "label": "GEO GSE115857"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39696012", "type": "paper", "label": "pmid:39696012"}, {"id": "source:pmid:39696012", "type": "manuscript", "label": "PMID 39696012 full text"}, {"id": "data:geo:GSE115857", "type": "dataset", "label": "GEO GSE115857"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39696012", "type": "extraction", "used": ["source:pmid:39696012"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE115857", "type": "accession_resolution", "used": ["data:geo:GSE115857"], "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:39696012", "parent_hash": "sha256:2174f2f1e654ca4241ca187593b42981ffb25ccfde2db850f61b72dbcfa89d39", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE115857 licence not read", "asset:data:geo:GSE115857 not downloaded", "asset:data:geo:GSE171314 licence not read", "asset:data:geo:GSE171314 not downloaded", "asset:data:geo:GSE93798 licence not read", "asset:data:geo:GSE93798 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": 0.93, "evidence": ["using a comprehensive bioinformatics method. Microarray datasets GSE93798 and GSE115857 were downloa"], "order_basis": "paper_text_order:587", "id": "assay:1"}, {"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": ["n healthy individuals and IgAN patients from RNA-seq dataset GSE9379. Then we cross-linked them w", "ated mechanisms and treatment of IgAN at the transcriptome level."], "order_basis": "paper_text_order:1479", "id": "assay:2"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["egistration.Fig. 1The workflow of this study scRNA-seq data processing Seurat R package [18] was us"], "order_basis": "paper_text_order:2679", "id": "assay:3"}, {"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["principal component analysis"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]},"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. 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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}}}