{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39147662", "kind": "science-record", "revision": 2, "content_hash": "sha256:130df95b6631e194f65e1a68be57f3e016c1835af6de7ea75cdfb38833f3ee6e", "created_at": "2026-11-01T10:25:48Z", "updated_at": "2026-11-01T14:01:32Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "The Predictive Value of BUB1 in the Prognosis of Oral Squamous Cell Carcinoma.", "doi": "10.1016/j.identj.2024.07.012", "pmid": "39147662", "authors": null, "journal": "International dental journal", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", 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"reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:39147662", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39147662' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39147662", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.identj.2024.07.012", "sha256": "sha256:3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.identj.2024.07.012", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:39147662:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bdcd6d48ad0f3a88eae710f28f6bb4bcb81135a65cda9b627fe8146caa4d8eaa", "bytes": 673, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl0001", "version": null, "note": "Clinicopathologic characteristics of patients with oral squamous cell carcinoma from The Cancer Genome Atlas database.", "structure": {"pmcid": "PMC11976542", "section_index": 3, "section_title": "Data preparation", "row_count": 13, "column_count": 4}, "table": {"label": "Table", "caption": "Clinicopathologic characteristics of patients with oral squamous cell carcinoma from The Cancer Genome Atlas database.", "rows": [["Characteristics", "", "Patients (N = 355)"], ["No.", "%"], ["Age, y", "≤60 (median)", "180", "50.70"], [">60 (median)", "175", "49.30"], ["Pathologic stage", "I", "15", "4.23"], ["II", "82", "23.10"], ["III", "71", "20.00"], ["IV", "177", "49.86"], ["Unknown", "10", "2.82"], ["Survival time", "Long (>5 y)", "33", "9.30"], ["Short (<5 y)", "322", "90.70"], ["Overall survival status", "Deceased", "155", "43.66"], ["Alive", "200", "56.34"]], "row_count": 13, "column_count": 4, "numeric_cells": 27, "header_rows": 2, "locator": "section[3]/table-wrap[1]#tbl0001"}}], "gaps": ["asset:source:pmid:39147662 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:39147662", "asset:table:pmid:39147662:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39147662"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "f8929209aa6f72b11a7a9ecc932a3e5252c646e9e131c492e74199bf4a9738f2", "source_hash": "3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "raw_response_sha256": "sha256:31802050787780d7f063a903dcb13ecede847602e3e245848dcaffe04218daa6", "raw_response_chars": 4808}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "66619eab0f0c54da87aad21a6cf72ff6fa10a3460b641d821ecab51a72ea6335", "source_hash": "3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "raw_response_sha256": "sha256:8e208a0bed070a4f96154545984b5d3c984e95c055235ecd892aa9bf1a628ca2", "raw_response_chars": 36350}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "90e1ebfcfae12671e43ad46a48b137bacf408ad6e7a73a76fadd48f771fddaa7", "source_hash": "3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that high BUB1 levels may be related to poor prognosis in patients with OSCC and that BUB1 may serve as an independent predictor of prognosis, but it gives no numerical result for this registered target.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states that high BUB1 levels may be related to poor prognosis in patients with OSCC and that BUB1 may serve as an independent predictor of prognosis, but it gives no numerical result for this registered target.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:17:39.533364+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "9c4c9b1aa4b33172f6f9703fff2d2fbc37c05c5a43ee3e912c741ad6b22e85e8", "source_hash": "3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "raw_response": "<think>We need answer JSON only. Need identify single numerical result replication registered target headline numerical result paper states for main finding. Source supplied perhaps truncated, no survival numerical result. Need decide perhaps headline is elevated BUB1 but no number stated. Registered target \"the headline numerical result the paper states for its main finding\". Need find exact number attached to main finding. Text abstract/results conclusions qualitative. Other numbers are methods and secondary. No headline numeric value for BUB1 expression or prognosis. Thus number_stated false, parent_value 0, unit \"\", evidence \"\", target_result say text states high BUB1 mRNA significantly upregulated in OSCC vs healthy controls and high BUB1 associated poor prognosis, but no numerical value. Need JSON valid, no markdown.\n\nBut carefully: Could target headline numerical result be one of source's numbers, perhaps 62%, 21%, etc? Main finding likely poor prognosis but no KM HR/p value. \"single numerical result that a replication ... has to reproduce.\" The supplied paper text might omit figures with exact survival data, but instruction says source only. We should false.\n\nNeed ensure target_result describes what text does state instead. Exact no evidence required if false. Could mention \"The text states...\" no numbers. JSON:\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that BUB1 mRNA levels were significantly upregulated in OSCC tissues compared with healthy controls and that high BUB1 expression was associated with poor prognosis, but it does not state a numerical result for this headline finding.\",\"number_stated\":false}\nShould evidence maybe exact quotation despite false? User explicitly says leave evidence empty if no number. Yes.\n\nNeed no invented source.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that BUB1 mRNA levels were significantly upregulated in OSCC tissues compared with healthy controls and that high BUB1 expression may be an independent indicator of poor prognosis, but it does not state a numerical value for this headline finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that BUB1 mRNA levels were significantly upregulated in OSCC tissues compared with healthy controls and that high BUB1 expression may be an independent indicator of poor prognosis, but it does not state a numerical value for this headline finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:17:41.950814+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "High BUB1 mRNA levels were associated with poor prognosis in oral squamous cell carcinoma, but the source text does not report a numerical effect estimate for this headline result.", "minimax_alt": "No headline numerical result is stated; the paper's main prognostic finding is that high expression of BUB1 may serve as an independent indicator of poor prognosis in OSCC.", "decisive": false}, "analysis_methods": {"minimax": ["Differential expression analysis using the limma R package", "Kaplan–Meier survival analysis", "Log-rank test", "Gene set enrichment analysis (GSEA)", "Pearson correlation analysis"], "minimax_alt": ["Median-based dichotomisation of BUB1 mRNA expression into high- and low-expression groups", "Differential expression analysis using the limma R package", "Kaplan–Meier survival analysis", "Log-rank test", "Gene set enrichment analysis using MSigDB c2.cp.kegg.v7.0 and GSEA software version 4.0", "Pearson correlation analysis of BUB1 or transcription-factor mRNA levels with drug IC50 values", "Copy-number variation, somatic mutation, and tumour mutation burden analysis", "Disease Ontology functional analysis"], "decisive": false}, "statistical_method": {"minimax": "Kaplan–Meier survival curve with survival differences evaluated by log-rank test", "minimax_alt": "Kaplan–Meier survival analysis with log-rank test", "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:c89937ea59905721c019b71f1e44bdab6759c9365d597de2c4d009d821dc3085", "type": "sep_package", "label": "SEP v1 package for pmid:39147662"}], "activities": [{"id": "activity:conversion:pmid:39147662", "type": "conversion", "used": ["package:c89937ea59905721c019b71f1e44bdab6759c9365d597de2c4d009d821dc3085"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:39147662", "parent_hash": "sha256:5f855a47781a08a6f78143c0a60711e6f7341e3ae27f771e524bfc88eacc93de", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39147662 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39147662' does not resolve to a declared asset", "targets"]},"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":"2026-11-04T02:21:32+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}}}