{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39921793", "kind": "science-record", "revision": 1, "content_hash": "sha256:0de973ab5a328db9caec5b5990fd3906283c858c9907ed31b709355b40ed3a08", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T10:25:49Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Multivariate Cox regression analysis of prognostic genes and therapeutic mechanisms of gastric cancer.", "doi": "10.1007/s12672-025-01907-7", "pmid": "39921793", "authors": null, "journal": "Discover oncology", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 74.0, "unit": "prognostic related genes", "tolerance": null, "source": "chars 460-587 of 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[], "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:39921793"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39921793"]}, "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": "8c5c36bb05c4012841d10df4723bd3f9655eaddf20713ad5c6c1e8adf50ce464", "source_hash": "ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d", "raw_response_sha256": "sha256:694654f3107ae3f3f8c45e04f72b73a376713554ae87b18e019dc22ae1f8b3e4", "raw_response_chars": 4437}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "c02a59b0ba89429c7b6f85823264828425d22a8bc9eec2bdbbf010777675aa59", "source_hash": "ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d", "raw_response_sha256": "sha256:5dd37deb9435427f9147f3b62b1f013033b78e18c8e040e9b4064bda73c74ce5", "raw_response_chars": 53883}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "016a0913d1b5cd701b23a5775e8b76ee17189b7f8c0108ff85a46c40866a056c", "source_hash": "ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d", "raw_response": "{\"parent_value\":74,\"unit\":\"prognostic related genes\",\"evidence\":\"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.\",\"target_result\":\"The paper states that 74 prognostic related genes (PRG) were screened out.\",\"number_stated\":true}", "reading": {"parent_value": 74, "unit": "prognostic related genes", "evidence": "Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.", "target_result": "The paper states that 74 prognostic related genes (PRG) were screened out.", "number_stated": true, "source_locator": "chars 460-587 of source sha256 ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d"}, "recorded_at": "2026-10-31T15:23:14.847239+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "784d0ed322f920717d28c05b4387c82ed9601e39898a496de001606f8e3b2d08", "source_hash": "ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d", "raw_response": "<think>We need answer JSON only. Need interpret registered target: headline numerical result paper states for main finding. Source says 74 prognostic related genes screened, identify four key genes. \"headline numerical result\" likely 74? Registered target main finding maybe headline numerical result perhaps number of PRGs. Need determine singular numerical result replication target. They ask value paper itself states for registered target. Target defined \"the headline numerical result the paper states for its main finding\". Main finding likely 74 prognostic related genes, perhaps abstract: \"Through ... 74 prognostic related genes (PRG) were screened out.\" Is headline numerical result 74 genes. Need report headline number only and unit paper prints. Exact contiguous quote contains number, whole clause attribution. Unit should be printed unit? \"74 prognostic related genes (PRG)\" unit perhaps \"prognostic related genes\". Evidence exact quote whole clause: \"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.\" parent_value 74, unit \"prognostic related genes\". target_result maybe \"74 prognostic related genes (PRG) were screened out.\" number_stated true.\n\nBut ambiguity: Main finding is four key genes? Yet those are named, numerical count four. User singular target says headline numerical result. Could be 74 in abstract is central sample/result. Let's inspect wording. Title. Abstract has findings. \"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out. A PPI network was established for PRG to identify four key genes...\" Headline numerical result could be 74 prognostic genes. The prompt likely benchmark asks extract target result. Need perhaps infer \"headline numerical result the paper states for its main finding\" perhaps exact abstract key quantitative statement. There is no explicit registry elsewhere. Need return strongest numeric. 74 likely. Unit as paper prints: \"prognostic related genes\" perhaps \"genes\". User says unit must be unit paper prints. Could set \"prognostic related genes\" exact phrase. Evidence quote entire clause. target_result maybe state result. Ensure valid JSON.</think>\n\n{\"parent_value\":74,\"unit\":\"prognostic related genes\",\"evidence\":\"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.\",\"target_result\":\"74 prognostic related genes (PRG) were screened out.\",\"number_stated\":true}", "reading": {"parent_value": 74, "unit": "prognostic related genes", "evidence": "Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.", "target_result": "74 prognostic related genes (PRG) were screened out.", "number_stated": true, "source_locator": "chars 460-587 of source sha256 ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d"}, "recorded_at": "2026-10-31T15:23:16.182526+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "74 prognostic related genes (PRG) were identified, with four key genes (LMOD1, CRYAB, VCL and MYL9); high expression of the key genes was associated with poor prognosis, and multivariate Cox regression analysis showed that the key genes were an independent prognostic factor.", "minimax_alt": "Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out. A PPI network was established for PRG to identify four key genes (KG), namely LMOD1, CRYAB, VCL and MYL9.", "decisive": false}, "analysis_methods": {"minimax": ["Kaplan–meier analysis", "univariate Cox regression analysis", "multivariate Cox regression analysis", "Wilcoxon rank sum test", "Kruskal–Wallis H test", "Gene Ontology functional enrichment analysis", "KEGG pathway enrichment analysis"], "minimax_alt": ["Kaplan–meier analysis", "univariate Cox regression analysis", "multivariate Cox multiple regression analysis", "Wilcoxon rank sum test", "Kruskal–Wallis H test", "PPI network analysis", "Gene Ontology functional enrichment analysis", "KEGG pathway enrichment analysis"], "decisive": false}, "statistical_method": {"minimax": "multivariate Cox regression analysis", "minimax_alt": "Kaplan–meier analysis, univariate Cox regression analysis and multivariate Cox multiple regression analysis for prognosis-related gene assessment; Wilcoxon rank sum test and Kruskal–Wallis H test for clinical-correlation comparisons", "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:f536f4aca50204d8eb6cafa86720bfacbdb913849bd06fd9d9046be63c4b4f46", "type": "sep_package", "label": "SEP v1 package for pmid:39921793"}], "activities": [{"id": "activity:conversion:pmid:39921793", "type": "conversion", "used": ["package:f536f4aca50204d8eb6cafa86720bfacbdb913849bd06fd9d9046be63c4b4f46"], "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": "973629b8-47e9-4046-86bf-6ef022603cae", "parent_hash": "f536f4aca50204d8eb6cafa86720bfacbdb913849bd06fd9d9046be63c4b4f46", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:39921793 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:39921793' 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":"2026-11-04T02:48:21+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}}}