{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41354850", "kind": "science-record", "revision": 4, "content_hash": "sha256:0135f8c755fb80e58c14cbaf09f2063f83c5c2fe9c338347bcb1e697fbb84d7a", "created_at": "2026-11-01T20:31:22Z", "updated_at": "2026-11-01T22:57:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and identification of differentially expressed miRNA and mRNA for intervertebral disc degeneration on bioinformatics.", "doi": "10.1186/s40001-025-03630-z", "pmid": "41354850", "authors": ["Jing Yan", "Yi Gao", "Rui Chen", "Shuo Miao", "Yuting Gong", "Yuning Zhu", "Quan Zhou"], "journal": "European journal of medical research", "year": 2025, "abstract": "BACKGROUND: Intervertebral disc degeneration (IDD), characterized by multifaceted pathological mechanisms, presents substantial therapeutic challenges. Globally, over 50% of individuals experience IDD-related low back pain (LBP), a debilitating condition associated with high recurrence rates and profound socioeconomic burdens. Current clinical strategies demonstrate limited efficacy in halting IDD progression, underscoring the critical need for targeted therapies.\nMETHODS: We analyzed the gene expression data of IDD mRNA and miRNA in the GEO database. Subsequently, the mRNA was screened for differentially expressed genes (DEGs) using R language. Immediately after that, we conducted a screening analysis of DEGs on miRNAs, and then used Venn diagrams to obtain hub genes by taking the intersection of DEGs. Then, the function of the hub genes is enriched through miRDB. Then, the downstream target genes of miRNA hub genes are predicted through miRDB to construct the possible miRNA-mRNA regulatory network. Finally, we collected clinical nucleus pulposus (NP) tissues and constructed the degeneration models of nucleus pulposus cells (NPCs) and IDD in rats to verify the expression of mRNA DEGs and miRNA hub genes.\nRESULTS: We obtained a total of 29 differentially expressed genes from the GSE34095 and GSE70362 mRNA gene data sets, such as ERBB2 and POSTN. Five hub genes (hsa-miR-4741, hsa-miR-5100, hsa-miR-4306, hsa-miR-3158-5p, and hsa-miR-508-5p) were obtained from GSE63492 and GSE116726. It is functionally related to cell death, differentiation, transmembrane transport and tumorigenesis. Finally, we identified the following miRNA-mRNA regulatory networks: hsa-miR-508-5p-DRP2, hsa-miR-3158-ERBB2, hsa-miR-4306-POSTN and hsa-miR-5100-CAPRIN1. Subsequently, we verified our above findings using clinical IDD samples, senescent nucleus pulposus cell models, and IDD rat models.\nCONCLUSIONS: These findings offer new insights into the occurrence and development of IDD and provide certain reference value for the subsequent diagnosis and treatment of IDD.", "claims": [{"id": "claim-method", "statement": "We used the “limma” package to screen the DEGs of mRNA and miRNA gene data sets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41354850", "locator": "sections[4] \"Microarray data analysis\" paragraph 2", "quote": "We used the “limma” package to screen the DEGs of mRNA and miRNA gene data sets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41354850", "locator": "sections[31] \"notes\" paragraph 1", "quote": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author."}], "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:41354850"], "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:GSE116726"], "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:GSE116726"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41354850", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40001-025-03630-z", "sha256": "sha256:2a5dcfb87ba3ca674ec30f32e688574ee9c6735555695b5e017e7b9db36564b4", "bytes": 26885, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40001-025-03630-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12764095", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116726", "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=GSE116726", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116726", "version": null, "note": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3259525", "GSM3259526", "GSM3259527", "GSM3259528", "GSM3259529", "GSM3259530"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "20712", "taxon": "Homo sapiens", "title": "Therapeutic potential of targeting miR-141 in intervertebral disc degeneration: first steps toward the clinic", "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:GSE34095", "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=GSE34095", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE34095", "version": null, "note": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM841717", "GSM841718", "GSM841719", "GSM841720", "GSM841721", "GSM841722"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data between human degenerative and non-degenerative intervertebral discs", "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:GSE63492", "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=GSE63492", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63492", "version": null, "note": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1551024", "GSM1551025", "GSM1551026", "GSM1551027", "GSM1551028", "GSM1551029", "GSM1551030", "GSM1551031", "GSM1551032", "GSM1551033"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "19449", "taxon": "Homo sapiens", "title": "Revisiting the microRNA expression profiling of human intervertebral disc degeneration (IDD)", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE70362", "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=GSE70362", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70362", "version": null, "note": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1725780", "GSM1725781", "GSM1725782", "GSM1725783", "GSM1725784", "GSM1725785", "GSM1725786", "GSM1725787", "GSM1725788", "GSM1725789", "GSM1725790", "GSM1725791", "GSM1725792", "GSM1725793", "GSM1725794", "GSM1725795", "GSM1725796", "GSM1725797", "GSM1725798", "GSM1725799", "GSM1725800", "GSM1725801", "GSM1725802", "GSM1725803", "GSM1725804", "GSM1725805", "GSM1725806", "GSM1725807", "GSM1725808", "GSM1725809", "GSM1725810", "GSM1725811", "GSM1725812", "GSM1725813", "GSM1725814", "GSM1725815", "GSM1725816", "GSM1725817", "GSM1725818", "GSM1725819", "GSM1725820", "GSM1725821", "GSM1725822", "GSM1725823", "GSM1725824", "GSM1725825", "GSM1725826", "GSM1725827"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "17810", "taxon": "Homo sapiens", "title": "Gene Expression Profiling Identifies Interferon Signalling Molecules and IGFBP3 in Human Degenerative Annulus Fibrosus", "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:GSE116726 not downloaded", "asset:data:geo:GSE116726 licence not read", "asset:data:geo:GSE34095 not downloaded", "asset:data:geo:GSE34095 licence not read", "asset:data:geo:GSE63492 not downloaded", "asset:data:geo:GSE63492 licence not read", "asset:data:geo:GSE70362 not downloaded", "asset:data:geo:GSE70362 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "We used the “limma” package to screen the DEGs of mRNA and miRNA gene data sets."}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE34095", "GSE70362", "GSE63492", "GSE116726"], "resolved_accessions": ["GSE34095", "GSE70362", "GSE63492", "GSE116726"], "statements": ["The data supporting the results of this study are all in the supplementary documents and can also be reasonably obtained from the corresponding author."], "basis": "The paper names GSE34095, GSE70362, GSE63492, GSE116726 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:41354850", "data:geo:GSE116726"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116726"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:07:21Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8625, "completion_tokens": 1513, "cached_tokens": 0}}, "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:41354850", "type": "paper", "label": "pmid:41354850"}, {"id": "source:pmid:41354850", "type": "manuscript", "label": "PMID 41354850 full text"}, {"id": "data:geo:GSE116726", "type": "dataset", "label": "GEO GSE116726"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41354850", "type": "paper", "label": "pmid:41354850"}, {"id": "source:pmid:41354850", "type": "manuscript", "label": "PMID 41354850 full text"}, {"id": "data:geo:GSE116726", "type": "dataset", "label": "GEO GSE116726"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41354850", "type": "extraction", "used": ["source:pmid:41354850"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116726", "type": "accession_resolution", "used": ["data:geo:GSE116726"], "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:41354850", "parent_hash": "sha256:75c03e2faa980e091f7ba2f6eecb2ce7ffcb31bbbd14c5563d9557a551ea2caa", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE116726 licence not read", "asset:data:geo:GSE116726 not downloaded", "asset:data:geo:GSE34095 licence not read", "asset:data:geo:GSE34095 not downloaded", "asset:data:geo:GSE63492 licence not read", "asset:data:geo:GSE63492 not downloaded", "asset:data:geo:GSE70362 licence not read", "asset:data:geo:GSE70362 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": ["els of nucleus pulposus cells (NPCs) and IDD in rats to verify the expression of mRNA DEGs and mi", "of nucleus pulposus cells (NPCs) and IDD in rats to verify the expression of mRNA DEGs and mi", "escent nucleus pulposus cell models, and IDD rat models. CONCLUSIONS: These findings offer ne"], "order_basis": "paper_text_order:1241", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We used the “limma” package to screen the DEGs of mRNA and miRNA gene data sets."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:35:20+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}}}