{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26334995", "kind": "science-record", "revision": 8, "content_hash": "sha256:c8cc1dcb720e059c98da7f5895d1842376b2b6b3769eeb100101c91dfc1db01e", "created_at": "2026-11-01T15:40:10Z", "updated_at": "2026-11-01T21:58:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genes related to inflammation and bone loss process in periodontitis suggested by bioinformatics methods.", "doi": "10.1186/s12903-015-0086-7", "pmid": "26334995", "authors": ["Liang Song", "Jueqi Yao", "Zhijing He", "Bin Xu"], "journal": "BMC oral health", "year": 2015, "abstract": "BACKGROUND: Despite of numerous studies on periodontitis, the mechanism underlying the progression of periodontitis still remains largely unknown. This study aimed to have an expression profiling comparison between periodontitis and normal control and to identify more candidate genes involved in periodontitis and to gain more insights into the molecular mechanisms of periodontitis progression.\nMETHODS: The gene expression profile of GSE16134, comprising 241 gingival tissue specimens and 69 healthy samples as control which were obtained from 120 systemically healthy patients with periodontitis (65 with chronic and 55 with aggressive periodontitis), was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in periodontitis samples were screened using the limma package in R compared with control samples. Gene Ontology (GO) and pathway enrichment analysis upon the DEGs were carried out using Hypergeometric Distribution test. Protein-protein interaction (PPI) network of the DEGs was constructed using Cytoscape, followed by module selection from the PPI network using MCODE plugin. Moreover, transcription factors (TFs) of these DEGs were identified based on TRANSFAC database and then a regulatory network was constructed.\nRESULTS: Totally, 762 DEGs (507 up- and 255 down-regulated) in periodontitis samples were identified. DEGs were enriched in different GO terms and pathways, such as immune system process, cell activation biological processes, cytokine-cytokine receptor interaction, and metabolic pathways. Cathepsin S (CTSS) and pleckstrin (PLEK) were the hub proteins in the PPI network and 3 significant modules were selected. Moreover, 19 TFs were identified including interferon regulatory factor 8 (IRF8), and FBJ murine osteosarcoma viral oncogene homolog B (FOSB).\nCONCLUSION: This study identified genes (CTSS, PLEK, IRF-8, PTGS2, and FOSB) that may be involved in the development and progression of periodontitis.", "claims": [{"id": "claim-method", "statement": "GO categories such as biological process (BP), molecular function (MF), and cellular component (CC) upon the identified DEGs were enriched from GO databases using the Hypergeometric Distribution test [18]. Also, the pathways that the DEGs involved in were enriched using the Hypergeometric Distribution test from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database [19], which had not been used by Kebschull et al. [12].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26334995", "locator": "sections[5] \"Function and pathway enrichment analysis of DEGs\" paragraph 2", "quote": "GO categories such as biological process (BP), molecular function (MF), and cellular component (CC) upon the identified DEGs were enriched from GO databases using the Hypergeometric Distribution test [18]. Also, the pathways that the DEGs involved in were enriched using the Hypergeometric Distribution test from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database [19], which had not been used by Kebschull et al. [12]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profile data of GSE16134 [11] was downloaded from the Gene Expression Omnibus (GEO) in NCBI (http://www.ncbi.nlm.nih.gov/geo/) based on the platform of GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. This dataset included 241 ‘diseased’ gingival tissue specimens (bleeding on probing, probing depth ≥ 4 mm, and clinical attachment loss ≥ 3 mm) and 69 ‘healthy’ gingival tissue samples (no bleeding on probing, probing depth ≤ 4 mm, and clinical attachment loss ≤ 4 mm), obtained from 120 systemically healthy, non-smoking individuals with moderate/severe periodontitis (65 with chronic and 55 with aggressive periodontitis), as previously described [11, 12].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26334995", "locator": "sections[3] \"Microarray data and data preprocessing\" paragraph 2", "quote": "The gene expression profile data of GSE16134 [11] was downloaded from the Gene Expression Omnibus (GEO) in NCBI (http://www.ncbi.nlm.nih.gov/geo/) based on the platform of GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. This dataset included 241 ‘diseased’ gingival tissue specimens (bleeding on probing, probing depth ≥ 4 mm, and clinical attachment loss ≥ 3 mm) and 69 ‘healthy’ gingival tissue samples (no bleeding on probing, probing depth ≤ 4 mm, and clinical attachment loss ≤ 4 mm), obtained from 120 systemically healthy, non-smoking individuals with moderate/severe periodontitis (65 with chronic and 55 with aggressive periodontitis), as previously described [11, 12]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using limma-based differential expression analysis of GSE16134 downloaded from GEO, the study identified 762 periodontitis-associated DEGs relative to healthy controls.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26334995", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The gene expression profile of GSE16134, comprising 241 gingival tissue specimens and 69 healthy samples as control which were obtained from 120 systemically healthy patients with periodontitis (65 with chronic and 55 with aggressive periodontitis), was downloaded from the Gene Expression Omnibus (GEO) database."}, {"asset": "source:pmid:26334995", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed genes (DEGs) in periodontitis samples were screened using the limma package in R compared with control samples."}, {"asset": "source:pmid:26334995", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Totally, 762 DEGs (507 up- and 255 down-regulated) in periodontitis samples were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using limma-based differential expression analysis of GSE16134 downloaded from GEO, the study identified 762 periodontitis-associated DEGs relative to healthy controls.", "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:26334995"], "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:GSE16134"], "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:GSE16134"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26334995", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12903-015-0086-7", "sha256": "sha256:3fa9ef5202031c4776cde41658eed3b4ae2807b3649748b36b553b5029291b5c", "bytes": 33305, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12903-015-0086-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4559289", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16134", "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=GSE16134", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16134", "version": null, "note": "The gene expression profile data of GSE16134 [11] was downloaded from the Gene Expression Omnibus (GEO) in NCBI (http://www.ncbi.nlm.nih.gov/geo/) based on the platform of GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. This dataset included 241 ‘diseased’ gingival tissue specimens (bleeding on probing, probing depth ≥ 4 mm, and clinical attachment loss ≥ 3 mm) and 69 ‘healthy’ gingival tissue samples (no bleeding on probing, probing depth ≤ 4 mm, and clinical attachment loss ≤ 4 mm), obtained from 120 systemically healthy, non-smoking individuals with moderate/severe periodontitis (65 with chronic and 55 with aggressive periodontitis), as previously described [11, 12].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profile data of GSE16134 [11] was downloaded from the Gene Expression Omnibus (GEO) in NCBI (http://www.ncbi.nlm.nih.gov/geo/) based on the platform of GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. This dataset included 241 ‘diseased’ gingival tissue specimens (bleeding on probing, probing depth ≥ 4 mm, and clinical attachment loss ≥ 3 mm) and 69 ‘healthy’ gingival tissue samples (no bleeding on probing, probing depth ≤ 4 mm, and clinical attachment loss ≤ 4 mm), obtained from 120 systemically healthy, non-smoking individuals with moderate/severe periodontitis (65 with chronic and 55 with aggressive periodontitis), as previously described [11, 12].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM404005", "GSM404006", "GSM404007", "GSM404008", "GSM404009", "GSM404010", "GSM404011", "GSM404012", "GSM404013", "GSM404014", "GSM404015", "GSM404016", "GSM404017", "GSM404018", "GSM404019", "GSM404020", "GSM404021", "GSM404022", "GSM404023", "GSM404024", "GSM404025", "GSM404026", "GSM404027", "GSM404028", "GSM404029", "GSM404030", "GSM404031", "GSM404032", "GSM404033", "GSM404034", "GSM404035", "GSM404036", "GSM404037", "GSM404038", "GSM404039", 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"pathway enrichment"}}, {"id": "method-4", "family": null, "specific": null, "label": "Hypergeometric Distribution test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "GO categories such as biological process (BP), molecular function (MF), and cellular component (CC) upon the identified DEGs were enriched from GO databases using the Hypergeometric Distribution test [18]. Also, the pathways that the DEGs involved in were enriched using the Hypergeometric Distribution test from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database [19], which had not been used by Kebschull et al. [12]."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["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": ["GSE16134"], "resolved_accessions": ["GSE16134"], "statements": ["The gene expression profile data of GSE16134 [11] was downloaded from the Gene Expression Omnibus (GEO) in NCBI (http://www.ncbi.nlm.nih.gov/geo/) based on the platform of GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. This dataset included 241 ‘diseased’ gingival tissue specimens (bleeding on probing, probing depth ≥ 4 mm, and clinical attachment loss ≥ 3 mm) and 69 ‘healthy’ gingival tissue samples (no bleeding on probing, probing depth ≤ 4 mm, and clinical attachment loss ≤ 4 mm), obtained from 120 systemically healthy, non-smoking individuals with moderate/severe periodontitis (65 with chronic and 55 with aggressive periodontitis), as previously described [11, 12]."], "basis": "The paper names GSE16134 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:26334995", "data:geo:GSE16134", "asset:table:pmid:26334995:1", "asset:table:pmid:26334995:2", "asset:table:pmid:26334995:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16134"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:41Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 71745, "completion_tokens": 3650, "cached_tokens": 2104}}, "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:26334995", "type": "paper", "label": "pmid:26334995"}, {"id": "source:pmid:26334995", "type": "manuscript", "label": "PMID 26334995 full text"}, {"id": "data:geo:GSE16134", "type": "dataset", "label": "GEO GSE16134"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26334995", "type": "paper", "label": "pmid:26334995"}, {"id": "source:pmid:26334995", "type": "manuscript", "label": "PMID 26334995 full text"}, {"id": "data:geo:GSE16134", "type": "dataset", "label": "GEO GSE16134"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26334995", "type": "extraction", "used": ["source:pmid:26334995"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16134", "type": "accession_resolution", "used": ["data:geo:GSE16134"], "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:26334995", "parent_hash": "sha256:9681c505fd84c5b2450bc7d5274783ba2af60813d854ed8411836fd2b9a45db2", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE16134 licence not read", "asset:data:geo:GSE16134 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.77, "evidence": ["terferon regulatory factor 8 (IRF8), and FBJ murine osteosarcoma viral oncogene homolog B (FOSB)"], "order_basis": "paper_text_order:1842", "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": 0.7, "evidence": ["limma"], "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":"2026-11-04T03:16:30+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}}}