{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40435311", "kind": "science-record", "revision": 2, "content_hash": "sha256:d721119de94a311d30624fcf7846ce5212d68857375bb1a74f5a85e3ff8f6fcd", "created_at": "2026-11-01T20:30:34Z", "updated_at": "2026-11-01T21:35:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characteristic genes and immune landscape of interstitial cystitis.", "doi": "10.1371/journal.pone.0320249", "pmid": "40435311", "authors": ["Junhao Wang", "Yan Zhou", "Jie Hu", "Jianpeng Han", "Jianyong Feng", "Kuo Guo", "Wenbin Chen", "Yanrui Yun", "Yongzhang Li"], "journal": "PloS one", "year": 2025, "abstract": "BACKGROUND: Interstitial cystitis (IC) was still a disease with the exclusive diagnosis and lacked an effective gold standard. It was of great significance to find diagnostic markers for IC. Our study was aimed to screen characteristic genes via machine learning algorithms, characterize the immune landscape of IC, and show correlations between characteristic genes and immune cell subtypes.\nMETHODS: RNA sequencing data sets on IC were downloaded from Gene Expression Omnibus (GEO) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. Three machine learning algorithms were applied for identification of characteristic gene for IC. Single sample Gene Set Enrichment Analysis (ssGSEA) was applied to figure out the immune cell infiltration (ICI) of IC and normal tissue samples. Correlation analysis was performed via Spearman test. Receiver operator characteristic curve (ROC) was used to evaluate diagnostic efficacy of key genes.\nRESULTS: CCL18, MMP10 and WIF1 were identified as characteristic gene via machine learning algorithms. MMP10 and CCL18 were with higher expression in IC tissues compared with normal bladder tissues, while WIF1 had lower expressionin IC tissues (P < 0.05). These three genes had good diagnostic efficacy for IC. Compared with normal bladder tissues, 18 immune cell subtypes were up-regulated in interstitial cystitis tissues (P < 0.05). MMP10 and CCL18 were positively correlated to immune scores in IC, while WIF1 was negatively correlated to immune scores (P > 0.05).\nCONCLUSION: We screened the feature genes, CCL18, MMP10 and WIF1, among the differentially expressed genes (DEGs) by three different machine learning algorithms. They showed good diagnostic performance in both training and testing cohorts and were potential diagnostic markers for IC. We paint the immune landscape of IC. In IC tissue, immune cell subtypes infiltrated extensively. Most immune cell subtypes were up-regulated in IC tissue, including mast cells, activated CD4 T cells, and regulatory T cells that suppress immune responses. MMP10 and CCL18 had positive correlation to ICI, while WIF was negatively correlated with ICI. MMP10 and CCL18 may be the driving factors of immune response or their expression levels may be increased by immune response. The effect of characteristic genes of IC on immune cell subtypes still needed to be further explored.", "claims": [{"id": "claim-method", "statement": "Receiver operator characteristic curve (ROC) was conducted to evaluate diagnostic efficacy of key genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40435311", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Receiver operator characteristic curve (ROC) was conducted to evaluate diagnostic efficacy of key genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. GSE57560 include 13 IC tissues and 3 normal baldder tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40435311", "locator": "sections[3] \"Data sets download\" paragraph 2", "quote": "RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. GSE57560 include 13 IC tissues and 3 normal baldder tissues."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In the training cohort, MMP10 (AUC = 0.938, 95 CI%(0.796, 1.000), p < 0.05), CCL18 (AUC = 0.944, 95 CI%(0.840, 1.000), p < 0.05), WIF1 (AUC = 0.883, 95 CI%(0.728, 0.981), p < 0.05) had good diagnostic efficacy for IC (Fig 4G-4I).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "In the training cohort, MMP10 (AUC = 0.938, 95 CI%(0.796, 1.000), p < 0.05), CCL18 (AUC = 0.944, 95 CI%(0.840, 1.000), p < 0.05), WIF1 (AUC = 0.883, 95 CI%(0.728, 0.981), p < 0.05) had good diagnostic efficacy for IC (Fig 4G-4I)."}, "evidence": [{"asset": "source:pmid:40435311", "locator": "sections[11] \"Expression level and diagnostic efficacy of key genes in training cohort and test cohort\" paragraph 2", "quote": "In the training cohort, MMP10 (AUC = 0.938, 95 CI%(0.796, 1.000), p < 0.05), CCL18 (AUC = 0.944, 95 CI%(0.840, 1.000), p < 0.05), WIF1 (AUC = 0.883, 95 CI%(0.728, 0.981), p < 0.05) had good diagnostic efficacy for IC (Fig 4G-4I)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In the training cohort, MMP10 (AUC = 0.938, 95 CI%(0.796, 1.000), p < 0.05), CCL18 (AUC = 0.944, 95 CI%(0.840, 1.000), p < 0.05), WIF1 (AUC = 0.883, 95 CI%(0.728, 0.981), p < 0.05) had good diagnostic efficacy for IC (Fig 4G-4I).", "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:40435311"], "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:GSE11783"], "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:GSE11783"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40435311", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0320249", "sha256": "sha256:2e8c7109c035b572e98e6f69d844dfd943ba71e80962efa44162661ed3d728cc", "bytes": 33031, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0320249", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12119006", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE11783", "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=GSE11783", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE11783", "version": null, "note": "RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. GSE57560 include 13 IC tissues and 3 normal baldder tissues.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. GSE57560 include 13 IC tissues and 3 normal baldder tissues.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM298203", "GSM298204", "GSM298205", "GSM298206", "GSM298207", "GSM298208", "GSM298209", "GSM298210", "GSM298211", "GSM298212", "GSM298213", "GSM298214", "GSM298215", "GSM298216", "GSM298217", "GSM402541"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profile of bladder tissue of patients with ulcerative interstitial cystitis", "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:GSE57560", "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=GSE57560", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57560", "version": null, "note": "RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. GSE57560 include 13 IC tissues and 3 normal baldder tissues.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. GSE57560 include 13 IC tissues and 3 normal baldder tissues.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1384758", "GSM1384759", "GSM1384760", "GSM1384761", "GSM1384762", "GSM1384763", "GSM1384764", "GSM1384765", "GSM1384766", "GSM1384767", "GSM1384768", "GSM1384769", "GSM1384770", "GSM1384771", "GSM1384772", "GSM1384773"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "16699", "taxon": "Homo sapiens", "title": "Correlation of gene expression with bladder capacity in interstitial cystitis/bladder pain syndrome", "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:GSE621", "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=GSE621", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE621", "version": null, "note": "RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. 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GSE57560 include 13 IC tissues and 3 normal baldder tissues.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4688", "GSM4689", "GSM4866", "GSM4867", "GSM4868", "GSM4869", "GSM4870", "GSM4872", "GSM4877", "GSM4878", "GSM4879", "GSM4880", "GSM4881", "GSM4882", "GSM4883", "GSM4884", "GSM4885", "GSM4886", "GSM4887", "GSM4888", "GSM4889", "GSM4890", "GSM4891", "GSM4892", "GSM4893", "GSM4894", "GSM4895", "GSM4896"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "262", "taxon": "Homo sapiens", "title": "Interstitial cystitis and antiproliferative factor treatment", "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:GSE11783 not downloaded", "asset:data:geo:GSE11783 licence not read", "asset:data:geo:GSE57560 not downloaded", "asset:data:geo:GSE57560 licence not read", "asset:data:geo:GSE621 not downloaded", "asset:data:geo:GSE621 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Receiver operator characteristic curve (ROC)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Receiver operator characteristic curve (ROC) was conducted to evaluate diagnostic efficacy of key genes."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Receiver operator characteristic curve (ROC)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE57560", "GSE11783", "GSE621"], "resolved_accessions": ["GSE57560", "GSE11783", "GSE621"], "statements": ["RNA sequencing data sets of IC were downloaded from Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) database, including GSE57560, GSE11783 and GSE621, whose corresponding platforms were GPL16699, GPL570 and GPL262 respectively. GSE57560 include 13 IC tissues and 3 normal baldder tissues."], "basis": "The paper names GSE57560, GSE11783, GSE621 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": [], "assets": ["source:pmid:40435311", "data:geo:GSE11783"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE11783"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:53:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 8856, "completion_tokens": 1611, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:40435311", "type": "paper", "label": "pmid:40435311"}, {"id": "source:pmid:40435311", "type": "manuscript", "label": "PMID 40435311 full text"}, {"id": "data:geo:GSE11783", "type": "dataset", "label": "GEO GSE11783"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40435311", "type": "paper", "label": "pmid:40435311"}, {"id": "source:pmid:40435311", "type": "manuscript", "label": "PMID 40435311 full text"}, {"id": "data:geo:GSE11783", "type": "dataset", "label": "GEO GSE11783"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40435311", "type": "extraction", "used": ["source:pmid:40435311"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE11783", "type": "accession_resolution", "used": ["data:geo:GSE11783"], "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:40435311", "parent_hash": "sha256:e4ecab04344fb66b911b4db90c3b3c319ae3ea678b6cfdf522f75f1a5d291957", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE11783 licence not read", "asset:data:geo:GSE11783 not downloaded", "asset:data:geo:GSE57560 licence not read", "asset:data:geo:GSE57560 not downloaded", "asset:data:geo:GSE621 licence not read", "asset:data:geo:GSE621 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["tic genes and immune cell subtypes. METHODS: RNA sequencing data sets on IC were downloaded from Gene Ex"], "order_basis": "paper_text_order:425", "id": "assay:1"}]},"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":"2026-11-04T00:32:54+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}}}