{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27471570", "kind": "science-record", "revision": 9, "content_hash": "sha256:46c4df662515959f5461d6431a51c5132f1149882b78ed2347b60ac0a8470c14", "created_at": "2026-11-01T15:40:19Z", "updated_at": "2026-11-01T22:42:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic Impact of Thrombospodin-2 (THBS2) Overexpression on Patients with Urothelial Carcinomas of Upper Urinary Tracts and Bladders.", "doi": "10.7150/jca.15696", "pmid": "27471570", "authors": ["I-Wei Chang", "Chien-Feng Li", "Victor Chia-Hsiang Lin", "Hong-Lin He", "Per-In Liang", "Wen-Jeng Wu", "Ching-Chia Li", "Chun-Nung Huang"], "journal": "Journal of Cancer", "year": 2016, "abstract": "PURPOSE: Urothelial carcinoma (UC) is a type of tumor, especially of the urinary bladder, that affects people worldwide. Clarification of its detailed tumor biology and discovery of potential targets for developing treatment strategies are imperative because of frequent recurrences and poor prognosis of advanced UCs. By data mining a published dataset of UC of bladder (UCB) transcriptome (GSE31684) from Gene Expression Omnibus, National Center of Biotechnology Information (GEO, NCBI), we identified that THBS2 was the most significantly upregulated gene among those related to structural molecule activity (GO:0005198). Therefore, we evaluated the clinical significance and prognostic impact of thrombospondin-2 (THBS2) protein, A.K.A. TSP2, which encoded by THBS2 gene.\nMATERIALS AND METHODS: THBS2 immunostaining was performed in 340 UCs of upper urinary tract (UC-UUTs) and 295 UCBs; subsequently, both groups were dichotomized into high- and low-expression subgroups. Moreover, statistical analyses were performed to correlate the association between THBS2 expression and clinicopathological parameters with two survival indexes: disease-specific survival (DSS) and metastasis-free survival (MeFS).\nRESULTS: High THBS2 immunoexpression was significantly associated with advanced primary tumor status, nodal metastasis, and vascular invasion in both UC-UUT and UCB groups (all P ≤ .001). In addition, THBS2 overexpression was linked to adverse DSS and MeFS in univariate analyses and served as an independent prognosticator indicating poor outcomes in both groups in multivariate analyses.\nCONCLUSION: THBS2 may play a crucial role in UC progression and may be a novel prognostic marker. Additional investigations to elucidate the molecular pathway are necessary for developing potential THBS2-targeted therapies for UCs.", "claims": [{"id": "claim-method", "statement": "We applied Pearson's chi-squared test to compare the association between THBS2 expression and miscellaneous critical categorical clinical and pathological parameters and Mann-Whitney U test for numerical parameters. For univariate survival analyses, Kaplan-Meier survival curves, with comparison by using log-rank test, were utilized. Parameters demonstrating P < .05 in univariate analyses were included in multivariate tests by using Cox proportional hazards regression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27471570", "locator": "sections[6] \"Statistical Analyses\" paragraph 2", "quote": "We applied Pearson's chi-squared test to compare the association between THBS2 expression and miscellaneous critical categorical clinical and pathological parameters and Mann-Whitney U test for numerical parameters."}, {"asset": "source:pmid:27471570", "locator": "sections[6] \"Statistical Analyses\" paragraph 2", "quote": "For univariate survival analyses, Kaplan-Meier survival curves, with comparison by using log-rank test, were utilized."}, {"asset": "source:pmid:27471570", "locator": "sections[6] \"Statistical Analyses\" paragraph 2", "quote": "Parameters demonstrating P < .05 in univariate analyses were included in multivariate tests by using Cox proportional hazards regression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "A transcriptomic dataset (GSE31684), comprising 93 radically resected UCB cases from GEO, NCBI, was selected for research; of these, 78 belonged to muscle-invasive tumors (pT2 to pT4) and 15 to non-muscle-invasive (pTa and pT1); 28 exhibited distant metastasis whereas 49 did not 29. In this data set, GeneChip® Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA, USA) was used for analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27471570", "locator": "sections[3] \"Data Mining of Transcriptomic Database from GEO to Identify the Most Altered Gene\" paragraph 2", "quote": "A transcriptomic dataset (GSE31684), comprising 93 radically resected UCB cases from GEO, NCBI, was selected for research; of these, 78 belonged to muscle-invasive tumors (pT2 to pT4) and 15 to non-muscle-invasive (pTa and pT1); 28 exhibited distant metastasis whereas 49 did not 29. In this data set, GeneChip® Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA, USA) was used for analysis."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High THBS2 immunoexpression was associated with aggressive clinicopathological features and independently predicted worse disease-specific and metastasis-free survival in both UC-UUT and UCB groups.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "In multivariate analysis, THBS2 overexpression was an independent negative prognosticator that predicted unfavorable outcomes in both UC groups (all P < 0.05)."}, "evidence": [{"asset": "source:pmid:27471570", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "High THBS2 immunoexpression was significantly associated with advanced primary tumor status, nodal metastasis, and vascular invasion in both UC-UUT and UCB groups (all P ≤ .001)."}, {"asset": "source:pmid:27471570", "locator": "sections[12] \"Prognostic Impact of THBS2 Expression on UC-UUTs and UCBs\" paragraph 2", "quote": "In multivariate analysis, THBS2 overexpression was an independent negative prognosticator that predicted unfavorable outcomes in both UC groups (all P < 0.05)."}, {"asset": "source:pmid:27471570", "locator": "sections[6] \"Statistical Analyses\" paragraph 2", "quote": "We used SPSS Version 14.0 (SPSS Inc., Chicago, IL, USA) for statistical analysis."}, {"asset": "source:pmid:27471570", "locator": "sections[6] \"Statistical Analyses\" paragraph 2", "quote": "For univariate survival analyses, Kaplan-Meier survival curves, with comparison by using log-rank test, were utilized."}, {"asset": "source:pmid:27471570", "locator": "sections[6] \"Statistical Analyses\" paragraph 2", "quote": "Parameters demonstrating P < .05 in univariate analyses were included in multivariate tests by using Cox proportional hazards regression."}, {"asset": "source:pmid:27471570", "locator": "sections[3] \"Data Mining of Transcriptomic Database from GEO to Identify the Most Altered Gene\" paragraph 2", "quote": "After downloading the raw data, Nexus Expression 3 statistical software (BioDiscovery, El Segundo, CA, USA) was used to analyze all probe sets without filtering or preselection."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "High THBS2 immunoexpression was associated with aggressive clinicopathological features and independently predicted worse disease-specific and metastasis-free survival in both UC-UUT and UCB groups.", "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:27471570"], "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:GSE31684"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_mann_whitney", "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:GSE31684"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_mann_whitney"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27471570", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.15696", "sha256": "sha256:591b5bddeb1076ac1f164b43212d2a2813b307c3e90934de1276dcb75919aae1", "bytes": 17907, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/jca.15696", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4964138", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE31684", "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=GSE31684", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31684", "version": null, "note": "A transcriptomic dataset (GSE31684), comprising 93 radically resected UCB cases from GEO, NCBI, was selected for research; of these, 78 belonged to muscle-invasive tumors (pT2 to pT4) and 15 to non-muscle-invasive (pTa and pT1); 28 exhibited distant metastasis whereas 49 did not 29. In this data set, GeneChip® Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA, USA) was used for analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "A transcriptomic dataset (GSE31684), comprising 93 radically resected UCB cases from GEO, NCBI, was selected for research; of these, 78 belonged to muscle-invasive tumors (pT2 to pT4) and 15 to non-muscle-invasive (pTa and pT1); 28 exhibited distant metastasis whereas 49 did not 29. In this data set, GeneChip® Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA, USA) was used for analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM786491", "GSM786492", "GSM786493", "GSM786494", "GSM786495", "GSM786496", "GSM786497", "GSM786498", "GSM786499", "GSM786500", "GSM786501", "GSM786502", "GSM786503", "GSM786504", "GSM786505", "GSM786506", "GSM786507", "GSM786508", "GSM786509", "GSM786510", "GSM786511", "GSM786512", "GSM786513", "GSM786514", "GSM786515", "GSM786516", "GSM786517", "GSM786518", "GSM786519", "GSM786520", "GSM786521", "GSM786522", "GSM786523", "GSM786524", "GSM786525", "GSM786526", "GSM786527", "GSM786528", "GSM786529", "GSM786530", "GSM786531", "GSM786532", "GSM786533", "GSM786534", "GSM786535", "GSM786536", "GSM786537", "GSM786538", "GSM786539", "GSM786540", "GSM786541", "GSM786542", "GSM786543", "GSM786544", "GSM786545", "GSM786546", "GSM786547", "GSM786548", "GSM786549", "GSM786550", "GSM786551", "GSM786552", "GSM786553", "GSM786554", "GSM786555", "GSM786556", "GSM786557", "GSM786558", "GSM786559", "GSM786560", "GSM786561", "GSM786562", "GSM786563", "GSM786564", "GSM786565", "GSM786566", "GSM786567", "GSM786568", "GSM786569", "GSM786570", "GSM786571", "GSM786572", "GSM786573", "GSM786574", "GSM786575", "GSM786576", "GSM786577", "GSM786578", "GSM786579", "GSM786580", "GSM786581", "GSM786582", "GSM786583"], "sample_count": 93, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer  ", "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:GSE31684 not downloaded", "asset:data:geo:GSE31684 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "We applied Pearson's chi-squared test to compare the association between THBS2 expression and miscellaneous critical categorical clinical and pathological parameters and Mann-Whitney U test for numerical parameters. For univariate survival analyses, Kaplan-Meier survival curves, with comparison by using log-rank test, were utilized. Parameters demonstrating P < .05 in univariate analyses were included in multivariate tests by using Cox proportional hazards regression."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox proportional hazards"}}, {"id": "method-4", "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"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cox_ph", "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.group_comparison_mann_whitney"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney."}, "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": ["GSE31684"], "resolved_accessions": ["GSE31684"], "statements": ["A transcriptomic dataset (GSE31684), comprising 93 radically resected UCB cases from GEO, NCBI, was selected for research; of these, 78 belonged to muscle-invasive tumors (pT2 to pT4) and 15 to non-muscle-invasive (pTa and pT1); 28 exhibited distant metastasis whereas 49 did not 29. In this data set, GeneChip® Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA, USA) was used for analysis."], "basis": "The paper names GSE31684 in Gene Expression Omnibus, National Center of Biotechnology Information and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:27471570", "data:geo:GSE31684"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_mann_whitney", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE31684"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:00Z", "independence": "same_provider"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 39082, "completion_tokens": 4559, "cached_tokens": 1840}}, "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:27471570", "type": "paper", "label": "pmid:27471570"}, {"id": "source:pmid:27471570", "type": "manuscript", "label": "PMID 27471570 full text"}, {"id": "data:geo:GSE31684", "type": "dataset", "label": "GEO GSE31684"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27471570", "type": "paper", "label": "pmid:27471570"}, {"id": "source:pmid:27471570", "type": "manuscript", "label": "PMID 27471570 full text"}, {"id": "data:geo:GSE31684", "type": "dataset", "label": "GEO GSE31684"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27471570", "type": "extraction", "used": ["source:pmid:27471570"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE31684", "type": "accession_resolution", "used": ["data:geo:GSE31684"], "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:27471570", "parent_hash": "sha256:da10b6f6a91a8f147bf8bd756067adea923a99f7a1424d7fd336483f1fbfc0d6", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE31684 licence not read", "asset:data:geo:GSE31684 not downloaded", "execution.not_run", "method.group_comparison_mann_whitney", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_mann_whitney"], "assays": [{"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": ["by THBS2 gene. MATERIALS AND METHODS: THBS2 immunostaining was performed in 340 UCs of upper urinary tr"], "order_basis": "paper_text_order:898", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We applied Pearson's chi-squared test to compare the association between THBS2 expression and miscellaneous critical categorical clinical and pathological parameters and Mann-Whitney U test for numerical parameters. For univariate survival analyses, Kaplan-Meier survival curves, with comparison by using log-rank test, were utilized. Parameters demonstrating P < .05 in univariate analyses were included in multivariate tests by using Cox proportional hazards regression."], "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":"2026-11-04T00:47:21+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}}}