{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38871957", "kind": "science-record", "revision": 3, "content_hash": "sha256:023ebaeb3ddd2acc87288d494ff76886c09737718bf4d83a1f67ba913a1d15d1", "created_at": "2026-11-01T20:28:55Z", "updated_at": "2026-11-01T22:12:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction and Bioinformatics Analysis of ceRNA Regulatory Networks in Idiopathic Pulmonary Fibrosis.", "doi": "10.1007/s10528-024-10853-y", "pmid": "38871957", "authors": ["Menglin Zhang", "Xiao Wu", "Honglan Zhu", "Chenkun Fu", "Wenting Yang", "Xiaoting Jing", "Wenqu Liu", "Yiju Cheng"], "journal": "Biochemical genetics", "year": 2025, "abstract": "Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive form of pulmonary fibrosis of unknown etiology. Despite ongoing research, there is currently no cure for this disease. Recent studies have highlighted the significance of competitive endogenous RNA (ceRNA) regulatory networks in IPF development. Therefore, this study investigated the ceRNA network associated with IPF pathogenesis. We obtained gene expression datasets (GSE32538, GSE32537, GSE47460, and GSE24206) from the Gene Expression Omnibus (GEO) database and analyzed them using bioinformatics tools to identify differentially expressed messenger RNAs (DEmRNAs), microRNAs (DEmiRNAs), and long non-coding RNAs (DElncRNA). For DEmRNAs, we conducted an enrichment analysis, constructed protein-protein interaction networks, and identified hub genes. Additionally, we predicted the target genes of differentially expressed mRNAs and their interacting long non-coding RNAs using various databases. Subsequently, we screened RNA molecules with ceRNA regulatory relations in the lncACTdb database based on the screening results. Furthermore, we performed disease and functional enrichment analyses and pathway prediction for miRNAs in the ceRNA network. We also validated the expression levels of candidate DEmRNAs through quantitative real-time reverse transcriptase polymerase chain reaction and analyzed the correlation between the expression of these candidate DEmRNAs and the percent predicted pre-bronchodilator forced vital capacity [%predicted FVC (pre-bd)]. We found that three ceRNA regulatory axes, specifically KCNQ1OT1/XIST/NEAT1-miR-20a-5p-ITGB8, XIST-miR-146b-5p/miR-31-5p- MMP16, and NEAT1-miR-31-5p-MMP16, have the potential to significantly affect IPF progression. Further examination of the underlying regulatory mechanisms within this network enhances our understanding of IPF pathogenesis and may aid in the identification of diagnostic biomarkers and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "The GEO2R tool, available at http://www.ncbi.nlm.nih.gov/geo/geo2r, was used to identify DEGs between patients with IPF and healthy control tissues. |log fold change|> 1 and adjusted P-value < 0.05 were considered statistically significant. The 2−ΔΔCt method was employed to determine the relative expression levels of the relevant genes. The obtained data are presented as mean ± standard error of the mean and analyzed using GraphPad PRISM 9.5.0 software (USA). Differences between the two groups were determined using a t-test. p < 0.05 was regarded as statistically significant. Correlation among the candidate DEmRNAs was evaluated using Pearson's correlation analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38871957", "locator": "sections[4] \"Differentially Expressed Genes (DEG) Identification\" paragraph 2", "quote": "The GEO2R tool, available at http://www.ncbi.nlm.nih.gov/geo/geo2r, was used to identify DEGs between patients with IPF and healthy control tissues. |log fold change|> 1 and adjusted P-value < 0.05 were considered statistically significant."}, {"asset": "source:pmid:38871957", "locator": "sections[11] \"Statistical Analysis\" paragraph 2", "quote": "The 2−ΔΔCt method was employed to determine the relative expression levels of the relevant genes."}, {"asset": "source:pmid:38871957", "locator": "sections[11] \"Statistical Analysis\" paragraph 2", "quote": "The obtained data are presented as mean ± standard error of the mean and analyzed using GraphPad PRISM 9.5.0 software (USA)."}, {"asset": "source:pmid:38871957", "locator": "sections[11] \"Statistical Analysis\" paragraph 2", "quote": "Differences between the two groups were determined using a t-test. p < 0.05 was regarded as statistically significant."}, {"asset": "source:pmid:38871957", "locator": "sections[11] \"Statistical Analysis\" paragraph 2", "quote": "Correlation among the candidate DEmRNAs was evaluated using Pearson's correlation analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The row data included in this study are available in GEO [https://www.ncbi.nlm.nih.gov/geo/, (accessed on 25 May 2022)].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38871957", "locator": "sections[27] \"notes\" paragraph 1", "quote": "The row data included in this study are available in GEO [https://www.ncbi.nlm.nih.gov/geo/, (accessed on 25 May 2022)]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study found three ceRNA regulatory axes that may significantly affect IPF progression: KCNQ1OT1/XIST/NEAT1-miR-20a-5p-ITGB8, XIST-miR-146b-5p/miR-31-5p-MMP16, and NEAT1-miR-31-5p-MMP16.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38871957", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found that three ceRNA regulatory axes, specifically KCNQ1OT1/XIST/NEAT1-miR-20a-5p-ITGB8, XIST-miR-146b-5p/miR-31-5p- MMP16, and NEAT1-miR-31-5p-MMP16, have the potential to significantly affect IPF progression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study found three ceRNA regulatory axes that may significantly affect IPF progression: KCNQ1OT1/XIST/NEAT1-miR-20a-5p-ITGB8, XIST-miR-146b-5p/miR-31-5p-MMP16, and NEAT1-miR-31-5p-MMP16.", "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:38871957"], "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:GSE24206"], "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": {"p_value": "old change and adjusted P-value thresholds, followed by"}, "inputs": ["data:geo:GSE24206"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38871957", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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"GSM1150354", "GSM1150355", "GSM1150356", "GSM1150357", "GSM1150358", "GSM1150359", "GSM1150360", "GSM1150361", "GSM1150362", "GSM1150363", "GSM1150364", "GSM1150365", "GSM1150366", "GSM1150367", "GSM1150368", "GSM1150369", "GSM1150370", "GSM1150371", "GSM1150372", "GSM1150373", "GSM1150374", "GSM1150375", "GSM1150376", "GSM1150377", "GSM1150378", "GSM1150379", "GSM1150380", "GSM1150381", "GSM1150382", "GSM1150383", "GSM1150384", "GSM1150385", "GSM1150386", "GSM1150387", "GSM1150388", "GSM1150389", "GSM1150390", "GSM1150391", "GSM1150392", "GSM1150393", "GSM1150394", "GSM1150395", "GSM1150396", "GSM1150397", "GSM1150398", "GSM1150399", "GSM1150400", "GSM1150401", "GSM1150402", "GSM1150403", "GSM1150404", "GSM1150405", "GSM1150406", "GSM1150407", "GSM1150408", "GSM1150409", "GSM1150410", "GSM1150411", "GSM1150412", "GSM1150413", "GSM1150414", "GSM1150415", "GSM1150416", "GSM1150417", "GSM1150418", "GSM1150419", "GSM1150420", "GSM1150421", "GSM1150422", "GSM1150423", "GSM1150424", 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"GSM1150496", "GSM1150497", "GSM1150498", "GSM1150499", "GSM1150500", "GSM1150501", "GSM1150502", "GSM1150503", "GSM1150504", "GSM1150505", "GSM1150506", "GSM1150507", "GSM1150508", "GSM1150509", "GSM1150510", "GSM1150511", "GSM1150512", "GSM1150513", "GSM1150514", "GSM1150515", "GSM1150516", "GSM1150517", "GSM1150518", "GSM1150519", "GSM1150520", "GSM1150521", "GSM1150522", "GSM1150523", "GSM1150524", "GSM1150525", "GSM1150526", "GSM1150527", "GSM1150528", "GSM1150529", "GSM1150530", "GSM1150531", "GSM1150532", "GSM1150533", "GSM1150534", "GSM1150535", "GSM1150536", "GSM1150537", "GSM1150538", "GSM1150539", "GSM1150540", "GSM1150541", "GSM1150542", "GSM1150543", "GSM1150544", "GSM1150545", "GSM1150546", "GSM1150547"], "sample_count": 582, "group_sizes": null, "group_sizes_basis": null, "platform": "6480;14550", "taxon": "Homo sapiens", "title": "Gene expression profiling of chronic lung disease for the Lung Genomics Research Consortium", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE24206 not downloaded", "asset:data:geo:GSE24206 licence not read", "asset:data:geo:GSE32537 not downloaded", "asset:data:geo:GSE32537 licence not read", "asset:data:geo:GSE32538 not downloaded", "asset:data:geo:GSE32538 licence not read", "asset:data:geo:GSE47460 not downloaded", "asset:data:geo:GSE47460 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {"p_value": "old change and adjusted P-value thresholds, followed by"}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The GEO2R tool, available at http://www.ncbi.nlm.nih.gov/geo/geo2r, was used to identify DEGs between patients with IPF and healthy control tissues. |log fold change|> 1 and adjusted P-value < 0.05 were considered statistically significant. The 2−ΔΔCt method was employed to determine the relative expression levels of the relevant genes. The obtained data are presented as mean ± standard error of the mean and analyzed using GraphPad PRISM 9.5.0 software (USA). Differences between the two groups were determined using a t-test. p < 0.05 was regarded as statistically significant. Correlation among the candidate DEmRNAs was evaluated using Pearson's correlation analysis."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway 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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "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": ["GSE32537", "GSE47460", "GSE32538", "GSE24206"], "resolved_accessions": ["GSE32537", "GSE47460", "GSE32538", "GSE24206"], "statements": ["The row data included in this study are available in GEO [https://www.ncbi.nlm.nih.gov/geo/, (accessed on 25 May 2022)]."], "basis": "The paper names GSE32537, GSE47460, GSE32538, GSE24206 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": ["pearson_r"], "assets": ["source:pmid:38871957", "data:geo:GSE24206"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE24206"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:20:56Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11065, "completion_tokens": 1716, "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:38871957", "type": "paper", "label": "pmid:38871957"}, {"id": "source:pmid:38871957", "type": "manuscript", "label": "PMID 38871957 full text"}, {"id": "data:geo:GSE24206", "type": "dataset", "label": "GEO GSE24206"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38871957", "type": "paper", "label": "pmid:38871957"}, {"id": "source:pmid:38871957", "type": "manuscript", "label": "PMID 38871957 full text"}, {"id": "data:geo:GSE24206", "type": "dataset", "label": "GEO GSE24206"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38871957", "type": "extraction", "used": ["source:pmid:38871957"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE24206", "type": "accession_resolution", "used": ["data:geo:GSE24206"], "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:38871957", "parent_hash": "sha256:290dbf771faa6df450683c0d71c9263dfd1d997ca8c49e8ca3d0cf85468d1cb5", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE24206 licence not read", "asset:data:geo:GSE24206 not downloaded", "asset:data:geo:GSE32537 licence not read", "asset:data:geo:GSE32537 not downloaded", "asset:data:geo:GSE32538 licence not read", "asset:data:geo:GSE32538 not downloaded", "asset:data:geo:GSE47460 licence not read", "asset:data:geo:GSE47460 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["was set at 0.01. Animal Model Male C57BL/6J mice were procured from SiPeiFu Biotechnology (http://", "lowing a one-week acclimatization period, 12 mice were randomly assigned to two groups using a rand", "in (BLM) groups. On the day of modeling, all mice were intraperitoneally injected with pentobarbita", "human type II alveolar epithelial (A549) and mouse embryonic fibroblast (3T3) cell lines were o"], "order_basis": "paper_text_order:2785", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["manufacturer’s instructions. A549 cells were cultured in Ham’s F-12 K medium (Gibco, Thermo Fisher Sc", "her Scientific, USA), whereas 3T3 cells were cultured in Dulbecco’s Modified Eagle’s medium (Gibco, T", "lture The human type II alveolar epithelial (A549) and mouse embryonic fibroblast (3T3) cell l", "ccording to the manufacturer’s instructions. A549 cells were cultured in Ham’s F-12 K medium ("], "order_basis": "paper_text_order:3850", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["nriched in 10 MF, including inflammation and apoptosis (Fig. 7b). KEGG pathway analysis further rev"], "order_basis": "paper_text_order:5508", "id": "assay:3"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The GEO2R tool, available at http://www.ncbi.nlm.nih.gov/geo/geo2r, was used to identify DEGs between patients with IPF and healthy control tissues. |log fold change|> 1 and adjusted P-value < 0.05 were considered statistically significant. The 2−ΔΔCt method was employed to determine the relative expression levels of the relevant genes. The obtained data are presented as mean ± standard error of the mean and analyzed using GraphPad PRISM 9.5.0 software (USA). Differences between the two groups were determined using a t-test. p < 0.05 was regarded as statistically significant. Correlation among the candidate DEmRNAs was evaluated using Pearson's correlation 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. 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":"2026-11-04T02:48:41+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}}}