{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41469955", "kind": "science-record", "revision": 4, "content_hash": "sha256:2b0baf9255c95305af2a763e3e01a8203957a0506e14c0381071ea9a00662a19", "created_at": "2026-11-01T20:31:26Z", "updated_at": "2026-11-01T22:57:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Silencing TMEM105 suppresses gastric cancer cell growth and migration via proliferation-associated pathways.", "doi": "10.1186/s12885-025-15522-w", "pmid": "41469955", "authors": ["Behnoosh Nikonezhad", "Mobina Shahriarizade", "Atefeh Zamani", "Mohammad Mahdevar"], "journal": "BMC cancer", "year": 2025, "abstract": "BACKGROUND: Numerous studies in the field of cancer indicate that long non-coding RNAs (lncRNAs) play a significant role in the development and malignancy of various cancers. In this study, the expression changes of TMEM105 in gastric cancer (GC) and its association with malignancy were examined.\nMETHODS: In the in silico section, TMEM105 expression in GC and its correlation with patient prognosis were analyzed using publicly available datasets. Using WGCNA analysis on TCGA data, modules and potential pathways associated with TMEM105 were identified. Expression changes of TMEM105 in GC tissues compared with adjacent healthy tissues were analyzed by RT-qPCR. The expression level of TMEM105 in GC cell lines, including AGS and MKN-45, was modulated using siRNA. The relationship between TMEM105 expression and malignant characteristics, including cell proliferation, migration, and colony formation, was examined in these cell lines.\nRESULTS: TMEM105 was significantly upregulated in public datasets, including TCGA, GSE19826, and GSE54129. TMEM105 expression was associated with advanced disease stage and poor prognosis. WGCNA analysis revealed that TMEM105 expression clustered with genes related to cell proliferation, such as E2F target genes, within the same module. Silencing TMEM105 reduced the viability of GC cell lines and decreased mRNA expression of proliferation-related genes, including E2F1, Cyclin D1, and Ki-67. Silencing TMEM105 markedly reduced migration rates in GC cells. Moreover, TMEM105 expression affected the colony-forming ability of these cell lines.\nCONCLUSION: High TMEM105 expression in GC is associated with poorer patient outcomes. It appears to influence cellular proliferation and contribute to the development and malignancy of gastric carcinoma. Consequently, TMEM105 could be a valuable therapeutic and prognostic target.", "claims": [{"id": "claim-method", "statement": "A Cox regression analysis was conducted to examine the association between TMEM105 expression and clinical outcomes. Further evaluation was carried out using Kaplan–Meier survival curves. For the Kaplan–Meier analysis, TCGA tumor samples were divided into high- and low-expression groups based on the median TMEM105 expression level. The log-rank test was employed to determine statistical significance in all survival analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41469955", "locator": "sections[5] \"Survival analysis\" paragraph 2", "quote": "A Cox regression analysis was conducted to examine the association between TMEM105 expression and clinical outcomes. Further evaluation was carried out using Kaplan–Meier survival curves. For the Kaplan–Meier analysis, TCGA tumor samples were divided into high- and low-expression groups based on the median TMEM105 expression level. The log-rank test was employed to determine statistical significance in all survival analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "No datasets were generated or analyzed during the current study. The present investigation examined information from publicly accessible databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41469955", "locator": "sections[25] \"notes\" paragraph 1", "quote": "No datasets were generated or analyzed during the current study. The present investigation examined information from publicly accessible databases."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Analysis of public TCGA and GEO datasets found that TMEM105 was significantly upregulated in gastric cancer, and high expression was associated with advanced stage and poor prognosis.", "kind": "quantitative", "target": {"value": 1.29, "unit": "hazard ratio", "tolerance": null, "source": "Cox regression analysis revealed that high TMEM105 expression was associated with poor prognosis (hazard ratio = 1.29; P = 0.01). Moreover, Kaplan-Meier analysis indicated that samples with higher TMEM105 expression had a significantly lower survival rate (Fig. 1H; P = 0.02)."}, "evidence": [{"asset": "source:pmid:41469955", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "TMEM105 was significantly upregulated in public datasets, including TCGA, GSE19826, and GSE54129. TMEM105 expression was associated with advanced disease stage and poor prognosis."}, {"asset": "source:pmid:41469955", "locator": "sections[15] \"Increased expression ofTMEM105in GC and its association with advanced stage and poor patient survival\" paragraph 2", "quote": "Cox regression analysis revealed that high TMEM105 expression was associated with poor prognosis (hazard ratio = 1.29; P = 0.01). Moreover, Kaplan-Meier analysis indicated that samples with higher TMEM105 expression had a significantly lower survival rate (Fig. 1H; P = 0.02)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Analysis of public TCGA and GEO datasets found that TMEM105 was significantly upregulated in gastric cancer, and high expression was associated with advanced stage and poor prognosis.", "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:41469955"], "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:GSE19826"], "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:GSE19826"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41469955", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-025-15522-w", "sha256": "sha256:e01df82f8ed334adba8286b611e80b638266bc66936e9ef26d29827ba6a8574e", "bytes": 32962, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-025-15522-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12866457", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19826", "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=GSE19826", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19826", "version": null, "note": "No datasets were generated or analyzed during the current study. The present investigation examined information from publicly accessible databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "No datasets were generated or analyzed during the current study. The present investigation examined information from publicly accessible databases.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM495051", "GSM495052", "GSM495053", "GSM495054", "GSM495055", "GSM495056", "GSM495057", "GSM495058", "GSM495059", "GSM495060", "GSM495061", "GSM495062", "GSM495063", "GSM495064", "GSM495065", "GSM495066", "GSM495067", "GSM495068", "GSM495069", "GSM495070", "GSM495071", "GSM495072", "GSM495073", "GSM495074", "GSM495075", "GSM495076", "GSM495077"], "sample_count": 27, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from gastric cancer", "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:GSE54129", "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=GSE54129", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54129", "version": null, "note": "No datasets were generated or analyzed during the current study. The present investigation examined information from publicly accessible databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "No datasets were generated or analyzed during the current study. The present investigation examined information from publicly accessible databases.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1308392", "GSM1308393", "GSM1308394", "GSM1308395", "GSM1308396", "GSM1308397", "GSM1308398", "GSM1308399", "GSM1308400", "GSM1308401", "GSM1308402", "GSM1308403", "GSM1308404", "GSM1308405", "GSM1308406", "GSM1308407", "GSM1308408", "GSM1308409", "GSM1308410", "GSM1308411", "GSM1308412", "GSM1308413", "GSM1308414", "GSM1308415", "GSM1308416", "GSM1308417", "GSM1308418", "GSM1308419", "GSM1308420", "GSM1308421", "GSM1308422", "GSM1308423", "GSM1308424", "GSM1308425", "GSM1308426", "GSM1308427", "GSM1308428", "GSM1308429", "GSM1308430", "GSM1308431", "GSM1308432", "GSM1308433", "GSM1308434", "GSM1308435", "GSM1308436", "GSM1308437", "GSM1308438", "GSM1308439", "GSM1308440", "GSM1308441", "GSM1308442", "GSM1308443", "GSM1308444", "GSM1308445", "GSM1308446", "GSM1308447", "GSM1308448", "GSM1308449", "GSM1308450", "GSM1308451", "GSM1308452", "GSM1308453", "GSM1308454", "GSM1308455", "GSM1308456", "GSM1308457", "GSM1308458", "GSM1308459", "GSM1308460", "GSM1308461", "GSM1308462", "GSM1308463", "GSM1308464", "GSM1308465", "GSM1308466", "GSM1308467", "GSM1308468", "GSM1308469", "GSM1308470", "GSM1308471", "GSM1308472", "GSM1308473", "GSM1308474", "GSM1308475", "GSM1308476", "GSM1308477", "GSM1308478", "GSM1308479", "GSM1308480", "GSM1308481", "GSM1308482", "GSM1308483", "GSM1308484", "GSM1308485", "GSM1308486", "GSM1308487", "GSM1308488", "GSM1308489", "GSM1308490", "GSM1308491", "GSM1308492", "GSM1308493", "GSM1308494", "GSM1308495", "GSM1308496", "GSM1308497", "GSM1308498", "GSM1308499", "GSM1308500", "GSM1308501", "GSM1308502", "GSM1308503", "GSM1308504", "GSM1308505", "GSM1308506", "GSM1308507", "GSM1308508", "GSM1308509", "GSM1308510", "GSM1308511", "GSM1308512", "GSM1308513", "GSM1308514", "GSM1308515", "GSM1308516", "GSM1308517", "GSM1308518", "GSM1308519", "GSM1308520", "GSM1308521", "GSM1308522", "GSM1308523"], "sample_count": 132, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Global gene expression analysis of gastric cancer by oligonucleotide microarrays", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE19826 not downloaded", "asset:data:geo:GSE19826 licence not read", "asset:data:geo:GSE54129 not downloaded", "asset:data:geo:GSE54129 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A Cox regression analysis was conducted to examine the association between TMEM105 expression and clinical outcomes. Further evaluation was carried out using Kaplan–Meier survival curves. For the Kaplan–Meier analysis, TCGA tumor samples were divided into high- and low-expression groups based on the median TMEM105 expression level. The log-rank test was employed to determine statistical significance in all survival analyses."}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "ed with poor prognosis (hazard ratio = 1"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "edgeR"}}, {"id": "method-5", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 1.29, "unit": "hazard ratio", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:41469955", "data:geo:GSE19826"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19826"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:09:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9250, "completion_tokens": 1480, "cached_tokens": 264}}, "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:41469955", "type": "paper", "label": "pmid:41469955"}, {"id": "source:pmid:41469955", "type": "manuscript", "label": "PMID 41469955 full text"}, {"id": "data:geo:GSE19826", "type": "dataset", "label": "GEO GSE19826"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41469955", "type": "paper", "label": "pmid:41469955"}, {"id": "source:pmid:41469955", "type": "manuscript", "label": "PMID 41469955 full text"}, {"id": "data:geo:GSE19826", "type": "dataset", "label": "GEO GSE19826"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41469955", "type": "extraction", "used": ["source:pmid:41469955"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19826", "type": "accession_resolution", "used": ["data:geo:GSE19826"], "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:41469955", "parent_hash": "sha256:3815cc6b37e157562b031cde2556c8a3aba74f0ac6d08367cf420838860127b3", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE19826 licence not read", "asset:data:geo:GSE19826 not downloaded", "asset:data:geo:GSE54129 licence not read", "asset:data:geo:GSE54129 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["th adjacent healthy tissues were analyzed by RT-qPCR. The expression level of TMEM105 in GC cell", "adjacent healthy tissues were analyzed by RT-qPCR. The expression level of TMEM105 in GC cell", "d with that in adjacent normal tissues using RT-qPCR. The ex vivo results demonstrated a signific", "adjacent healthy samples are presented using RT-qPCR. TMEM105 expression was significantly higher"], "order_basis": "paper_text_order:721", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ncluding AGS and MKN-45, was modulated using siRNA. The relationship between TMEM105 expression"], "order_basis": "paper_text_order:826", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["elated genes, including E2F1, Cyclin D1, and Ki-67. Silencing TMEM105 markedly reduced migratio"], "order_basis": "paper_text_order:1494", "id": "assay:3"}, {"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": ["ture Human GC cell lines AGS and MKN-45 were cultured in DMEM (Genex, Iran) medium supplemented with", "e cells reached 70–80% confluency, they were passaged using 0.25% trypsin-EDTA (DENAzist, Iran) an"], "order_basis": "paper_text_order:4173", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["A Cox regression analysis was conducted to examine the association between TMEM105 expression and clinical outcomes. Further evaluation was carried out using Kaplan–Meier survival curves. For the Kaplan–Meier analysis, TCGA tumor samples were divided into high- and low-expression groups based on the median TMEM105 expression level. The log-rank test was employed to determine statistical significance in all survival analyses."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"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. 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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}}}