{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39341197", "kind": "science-record", "revision": 1, "content_hash": "sha256:dde4caa799b1567884daa18365021e5699202ac4801486ce77aa5c676dd2a3be", "created_at": "2026-11-01T10:25:48Z", "updated_at": "2026-11-01T10:25:48Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Development of the TP53 mutation associated hypopharyngeal squamous cell carcinoma prognostic model through bulk multi-omics sequencing and single-cell sequencing.", "doi": "10.1016/j.bjorl.2024.101499", "pmid": "39341197", "authors": null, "journal": "Brazilian journal of otorhinolaryngology", "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", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39341197"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "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:39341197", "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:39341197' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39341197", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.bjorl.2024.101499", "sha256": "sha256:60c5f57c19c7a54bc9929ee4e6e2aa3a75a13a8007b047a7c29ef41b486a9566", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.bjorl.2024.101499", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:39341197 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:39341197"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39341197"]}, "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": "8aa8f464b8f6fb3c0f588b5e36feee73d8b8948e29fb8262ddb89b6d48140b42", "source_hash": "60c5f57c19c7a54bc9929ee4e6e2aa3a75a13a8007b047a7c29ef41b486a9566", "raw_response_sha256": "sha256:480af8b215a1a308c0b83ddb20ac1db95593a8a69d18796a7b19fe9fb4a9bf47", "raw_response_chars": 5405}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "a914a48fd907c6b10e347f8c89bdf373ca23d3baacbd3cf336f80d8994eddce1", "source_hash": "60c5f57c19c7a54bc9929ee4e6e2aa3a75a13a8007b047a7c29ef41b486a9566", "raw_response_sha256": "sha256:3adc276f76735d32227e23f42cf879c0dae1a9cb85621d1788a92e585925ca7d", "raw_response_chars": 68248}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "4fc1107f53a146827b4ffed7bdb5895f248f103e25bb6592903aa5b77d4f6519", "source_hash": "60c5f57c19c7a54bc9929ee4e6e2aa3a75a13a8007b047a7c29ef41b486a9566", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that the TP53 mutation-associated HPSCC prognostic model was constructed via POLD2 and POLR2G, with high-risk group samples exhibiting poorer prognosis, but it does not state a headline numerical result for the registered target.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that the TP53 mutation-associated HPSCC prognostic model was constructed via POLD2 and POLR2G, with high-risk group samples exhibiting poorer prognosis, but it does not state a headline numerical result for the registered target.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:18:34.363212+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "1b2385b8a478be917944b22f2f9cdffd899739f55d33a1d36f8debb50af26115", "source_hash": "60c5f57c19c7a54bc9929ee4e6e2aa3a75a13a8007b047a7c29ef41b486a9566", "raw_response": "<think>We need solve extraction task. We have source text abstract etc no headline numerical result for main finding. Need JSON object with false parent 0 unit empty evidence empty target_result describing text states instead. Need ensure no numerical result attached to main model. We should carefully examine source for perhaps \"29 immune-related gene sets\" but not main finding. Registered target headline numerical result paper states for main finding. Paper text no numerical model performance, no C-index/AUC etc. It gives \"29 immune-related gene sets\", \"KNN 0.3 resolution\", etc irrelevant. Need not choose those. Need report no number. target_result likely text states prognostic model of TP53 mutation constructed via POLD2 and POLR2G; high-risk group poorer prognosis; correlations with lymphatic metastasis and immune scores; single-cell higher expressions in epithelial cells and macrophages. We need concise describe no headline numerical result; text states qualitative findings.\n\nNeed output strict JSON no markdown. Fields exact. Could use evidence empty \"\". target_result \"No headline numerical result is stated for the main finding. The text instead reports that the TP53 mutation-associated HPSCC prognostic model was constructed via POLD2 and POLR2G, that high-risk group samples had poorer prognosis, and that risk scores correlated with lymphatic metastasis and immune scores.\" Should not perhaps quote as no evidence requirement if number_stated false evidence empty. Unit empty.\n\nWe should consider user asks \"find the single numerical result that a replication of the registered target has to reproduce\". No number. We should accurately say no headline numerical result. parent_value zero as instructed. no invention.\n\nNeed ensure target_result not introduce numeric values not related? It can state numbers 29? Not needed. Maybe \"The paper reports qualitative findings only: ...\" Good.\n\nPotential interpretation headline numerical result may be 2 key genes? But user says \"the value the paper itself states for the registered target, not a value you calculated...\" Main finding model via POLD2 and POLR2G, two key genes. \"two key genes\" is numeric but not headline numerical result the paper itself states for main finding? We should examine what benchmark likely wants. Often these tasks are extract numerical results from papers with target registered. If no headline numerical result in source text e.g abstract lacks metrics, answer false. We must not infer \"two key genes\" headline result because main finding is prognostic model and no performance outcome. Need no number.\n\nCould there be result metric hidden in exact wording \"a total of 29 immune-related gene sets\"? That's a numerical result for immune score analysis, but not main finding. No.\n\nMaybe \"TP53 mutation associated hypopharyngeal...\" no actual numbers. Fine.\n\nWe can finish JSON concise.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"No headline numerical result is stated for the main finding. The paper instead reports that the TP53 mutation-associated HPSCC prognostic model was constructed via POLD2 and POLR2G, that high-risk group samples exhibited poorer prognosis, and that risk scores correlated with lymphatic metastasis and immune scores.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "No headline numerical result is stated for the main finding. The paper instead reports that the TP53 mutation-associated HPSCC prognostic model was constructed via POLD2 and POLR2G, that high-risk group samples exhibited poorer prognosis, and that risk scores correlated with lymphatic metastasis and immune scores.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:18:43.015261+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "unclear", "minimax_alt": "Initially, two key genes, POLD2 and POLR2G, were identified and utilized to construct the prognostic model.", "decisive": false}, "analysis_methods": {"minimax": ["Gene Set Enrichment Analysis (GSEA)", "univariate Cox analysis", "multivariate Cox analysis", "LASSO analysis", "ROC curve analysis", "Gene Ontology analysis", "GSVA", "single-cell RNA sequencing analysis using Seurat", "Harmony integration", "unbiased K-Nearest Neighbor (KNN) clustering", "SingleR cell annotation", "AddModuleScore"], "minimax_alt": ["GSEA", "univariate Cox analysis", "multivariate Cox analysis", "LASSO analysis", "ROC curve validation of OS and RFS results", "risk-score-based stratification into high-risk and low-risk groups"], "decisive": false}, "statistical_method": {"minimax": "", "minimax_alt": "GSEA, univariate and multivariate Cox analyses, and LASSO analysis", "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:dd8a3aef1358a8cc03f70433c7da7c34ff14ea972cf3ea439d5ab6d12cccc243", "type": "sep_package", "label": "SEP v1 package for pmid:39341197"}], "activities": [{"id": "activity:conversion:pmid:39341197", "type": "conversion", "used": ["package:dd8a3aef1358a8cc03f70433c7da7c34ff14ea972cf3ea439d5ab6d12cccc243"], "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": "3a866b12-43a2-43bd-97bc-09db969ee245", "parent_hash": "dd8a3aef1358a8cc03f70433c7da7c34ff14ea972cf3ea439d5ab6d12cccc243", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:39341197 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:39341197' 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":"2026-11-04T02:48:25+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}}}