{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39457549", "kind": "science-record", "revision": 3, "content_hash": "sha256:b28bc1b7e5534b78094d1a5c614079420e86d084a13a25a41ced1a4e449fb03f", "created_at": "2026-11-01T20:29:43Z", "updated_at": "2026-11-01T22:13:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Bioinformatics Analysis Reveals the Potential Role of the hsa_circ_0001081/miR-26b-5p Axis in Regulating COL15A1 and TRIB3 within Hypoxia-Induced miRNA/mRNA Networks in Glioblastoma Cells.", "doi": "10.3390/biomedicines12102236", "pmid": "39457549", "authors": ["Bartosz Lenda", "Marta Żebrowska-Nawrocka", "Ewa Balcerczak"], "journal": "Biomedicines", "year": 2024, "abstract": "Background/Objectives: The intrinsic molecular heterogeneity of glioblastoma (GBM) is one of the main reasons for its resistance to conventional treatment. Mesenchymal GBM niches are associated with hypoxic signatures and a negative influence on patients' prognosis. To date, competing endogenous RNA (ceRNA) networks have been shown to have a broad impact on the progression of various cancers. In this study, we decided to construct hypoxia-specific microRNA/ messengerRNA (miRNA/mRNA) networks with a putative circular RNA (circRNA) regulatory component using available bioinformatics tools. Methods: For ceRNA network construction, we combined publicly available data deposited in the Gene Expression Omnibus (GEO) and interaction pairs obtained from miRTarBase and circBank; a differential expression analysis of GBM cells was performed with limma and deseq2. For the gene ontology (GO) enrichment analysis, we utilized clusterProfiler; GBM molecular subtype analysis was performed in the Glioma Bio Discovery Portal (Glioma-BioDP). Results: We observed that miR-26b-5p, generally considered a tumor suppressor, was upregulated under hypoxic conditions in U-87 MG cells. Moreover, miR-26b-5p could potentially inhibit TRIB3, a gene associated with tumor proliferation. Protein-protein interaction (PPI) network and GO enrichment analyses identified a hypoxia-specific subcluster enriched in collagen-associated terms, with six genes highly expressed in the mesenchymal glioma group. This subcluster included hsa_circ_0001081/miR-26b-5p-affected COL15A1, a gene downregulated in hypoxic U-87 MG cells yet highly expressed in the mesenchymal GBM subtype. Conclusions: The interplay between miR-26b-5p, COL15A1, and TRIB3 suggests a complex regulatory mechanism that may influence the extracellular matrix composition and the mesenchymal transformation in GBM. However, the precise impact of the hsa_circ_0001081/miR-26b-5p axis on collagen-associated processes in hypoxia-induced GBM cells remains unclear and warrants further investigation.", "claims": [{"id": "claim-method", "statement": "Differences in expression levels of the examined genes between pairs of each subtype were compared by t-test; we assumed that a p < 0.05 means that the difference is statistically significant. For survival analysis, we obtained data from the TCGA-GBM cohort deposited in the GDC Data Portal (https://portal.gdc.cancer.gov/, accessed on 19 June 2024) using the TCGAbiolinks package. A Kaplan–Meier analysis and log-rank test were conducted using the survminer and survival packages. We assumed that a log-rank p < 0.05 was statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39457549", "locator": "sections[6] \"2.4. Glioma Bio Discovery Portal Molecular Subtype and Survival Analyses\" paragraphs 1-3", "quote": "Differences in expression levels of the examined genes between pairs of each subtype were compared by t-test; we assumed that a p < 0.05 means that the difference is statistically significant. For survival analysis, we obtained data from the TCGA-GBM cohort deposited in the GDC Data Portal (https://portal.gdc.cancer.gov/, accessed on 19 June 2024) using the TCGAbiolinks package. A Kaplan–Meier analysis and log-rank test were conducted using the survminer and survival packages. We assumed that a log-rank p < 0.05 was statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39457549", "locator": "sections[18] \"notes\" paragraph 1", "quote": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:39457549"], "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:GSE142719"], "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:GSE142719"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39457549", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/biomedicines12102236", "sha256": "sha256:f16aff17158a950277fb1227141675f67eed23ea03691fa2a3493408f6921720", "bytes": 32383, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/biomedicines12102236", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11504030", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE142719", "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=GSE142719", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE142719", "version": null, "note": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4238207", "GSM4238208", "GSM4238209", "GSM4238210", "GSM4238211", "GSM4238212", "GSM4238213", "GSM4238214", "GSM4238215", "GSM4238216", "GSM4238217", "GSM4238218", "GSM4238219", "GSM4238220", "GSM4238221"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "HIF1α/HIF2α-miR210-3p network promotes glioblastoma proliferation and tumorigenesis through EGFR-PI3K/AKT signaling pathway with a positive feedback", "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:GSE146463", "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=GSE146463", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE146463", "version": null, "note": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4386266", "GSM4386267", "GSM4386268", "GSM4386269", "GSM4386270", "GSM4386271", "GSM4386272", "GSM4386273", "GSM4386274", "GSM4386275", "GSM4386276"], "sample_count": 11, "group_sizes": null, "group_sizes_basis": null, "platform": "21825", "taxon": "Homo sapiens", "title": "Development of circRNA expression signatures for glioblastoma cells.", "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:GSE245800", "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=GSE245800", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE245800", "version": null, "note": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. These data were derived from the following resources available in the public domain: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245800 [accessed on 16 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142719 [accessed on 8 June 2024]; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146463 [accessed on 23 June 2024]; The original data presented in the study are openly available in Zenodo at DOI 10.5281/zenodo.13770443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM7849243", "GSM7849244", "GSM7849245", "GSM7849246", "GSM7849247", "GSM7849248"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Proteotranscriptomic decoding of the surface-endocytome in primary glioblastoma cells identifies potential target antigens in the hypoxic tumor niche [U87_mRNA_Norm_Hyp]", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE142719 not downloaded", "asset:data:geo:GSE142719 licence not read", "asset:data:geo:GSE146463 not downloaded", "asset:data:geo:GSE146463 licence not read", "asset:data:geo:GSE245800 not downloaded", "asset:data:geo:GSE245800 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differences in expression levels of the examined genes between pairs of each subtype were compared by t-test; we assumed that a p < 0.05 means that the difference is statistically significant. For survival analysis, we obtained data from the TCGA-GBM cohort deposited in the GDC Data Portal (https://portal.gdc.cancer.gov/, accessed on 19 June 2024) using the TCGAbiolinks package. A Kaplan–Meier analysis and log-rank test were conducted using the survminer and survival packages. We assumed that a log-rank p < 0.05 was statistically significant."}}, {"id": "method-2", "family": "differential_expression", "specific": "deseq2", "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": "deseq2"}}, {"id": "method-3", "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-4", "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-5", "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": "GO enrichment"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE245800", "GSE142719", "GSE146463"], "resolved_accessions": ["GSE245800", "GSE142719", "GSE146463"], "statements": ["The data presented in this study are available in the Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/, [accessed on 13 August 2024], reference numbers GSE245800, GSE142719, and GSE146463. 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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":"2026-11-04T00:35:40+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}}}