{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36226177", "kind": "science-record", "revision": 4, "content_hash": "sha256:8e978619d7789b17c81edac3723475ff0d0a20c48ec314be925af914d96c731c", "created_at": "2026-11-01T18:15:35Z", "updated_at": "2026-11-01T22:07:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A nine-consensus-prognostic -gene-based prognostic signature, recognizing the dichotomized subgroups of gastric cancer patients with different clinical outcomes and therapeutic strategies.", "doi": "10.3389/fgene.2022.909175", "pmid": "36226177", "authors": ["Dan Ji", "Yang Yang", "Fei Zhou", "Chao Li"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Background: The increasing prevalence and mortality of gastric cancer (GC) has promoted the urgent need for prognostic signatures to predict the long-term risk and search for therapeutic biomarkers. Methods and materials: A total of 921 GC patients from three GEO cohorts were enrolled in the current study. The GSE15459 and GSE62254 cohorts were used to select the top prognostic gene via the evaluation of the area under the receiver operating characteristic (ROC) curve (AUC) values. The GSE84437 cohort was used as the external validation cohort. Least absolute shrinkage and selector operation (LASSO) regression analysis was applied to reduce the feature dimension and construct the prognostic signature. Furthermore, a nomogram was constructed by integrating the independent prognostic analysis and validated by calibration plot, decision curve analysis and clinical impact curve. The molecular features and response to chemo-/immunotherapy among risk subgroups were evaluated by the \"MOVICS\" and \"ESTAMATE\" R packages and the SubMap algorithm. Lauren classification and ACRG molecular subtype were obtained to compare with the risk model. Results: Forty-four prognosis-associated genes were identified with a preset cutoff AUC value of 0.65 in both the GSE62254 and GSE15459 cohorts. With the 10-fold cross validation analysis of LASSO, nine genes were selected to construct the nine-consensus-prognostic-gene signature. The signature showed good prognostic value in the GSE62254 (p < 0.001, HR: 3.81, 95% CI: 2.44-5.956) and GSE15459 (p < 0.001, HR: 2.65, 95% CI: 1.892-3.709) cohorts and the external validation GSE84437 cohort (p < 0.001, HR: 2.06, 95% CI: 1.554-2.735). The nomogram constructed based on two independent predictive factors, tumor stage and the signature, predicted events tightly consistent with the actual (Hosmer-Lemeshow p value: 1-year, 0.624; 3-years, 0.795; 5-years, 0.824). For the molecular features, we observed the activation of apical junction, epithelial mesenchymal transition, and immune pathways in the high-risk group, while in the low-risk group, cell cycle associated G2M, E2F and MYC target pathways were activated. Based on the results we obtained, we indicated that gastric patients in the low-risk group are more suitable for 5-fluorouracil therapy, while high-risk group patients are more suitable for anti-CTLA4 immunotherapy, these results need more support in the further studies. After compare with proposed molecular subtypes, we realized that the nine-consensus prognostic gene signature is a powerful addition to identify the gastric patients with poor prognosis. Conclusion: In summary, we constructed a robust nine-consensus-prognostic-gene signature for the prediction of GC prognosis, which can also predict the personalized treatment of GC patients.", "claims": [{"id": "claim-method", "statement": "Least absolute shrinkage and selector operation (LASSO) regression analysis was applied to reduce the feature dimension and construct the prognostic signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36226177", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Least absolute shrinkage and selector operation (LASSO) regression analysis was applied to reduce the feature dimension and construct the prognostic signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36226177", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The signature showed good prognostic value in the GSE62254 (p < 0.001, HR: 3.81, 95% CI: 2.44–5.956) and GSE15459 (p < 0.001, HR: 2.65, 95% CI: 1.892–3.709) cohorts and the external validation GSE84437 cohort (p < 0.001, HR: 2.06, 95% CI: 1.554–2.735).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "The signature showed good prognostic value in the GSE62254 (p < 0.001, HR: 3.81, 95% CI: 2.44–5.956) and GSE15459 (p < 0.001, HR: 2.65, 95% CI: 1.892–3.709) cohorts and the external validation GSE84437 cohort (p < 0.001, HR: 2.06, 95% CI: 1.554–2.735)."}, "evidence": [{"asset": "source:pmid:36226177", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The signature showed good prognostic value in the GSE62254 (p < 0.001, HR: 3.81, 95% CI: 2.44–5.956) and GSE15459 (p < 0.001, HR: 2.65, 95% CI: 1.892–3.709) cohorts and the external validation GSE84437 cohort (p < 0.001, HR: 2.06, 95% CI: 1.554–2.735)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The signature showed good prognostic value in the GSE62254 (p < 0.001, HR: 3.81, 95% CI: 2.44–5.956) and GSE15459 (p < 0.001, HR: 2.65, 95% CI: 1.892–3.709) cohorts and the external validation GSE84437 cohort (p < 0.001, HR: 2.06, 95% CI: 1.554–2.735).", "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:36226177"], "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. 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"GSM2235747", "GSM2235748", "GSM2235749", "GSM2235750", "GSM2235751", "GSM2235752", "GSM2235753", "GSM2235754", "GSM2235755", "GSM2235756", "GSM2235757", "GSM2235758", "GSM2235759", "GSM2235760", "GSM2235761", "GSM2235762", "GSM2235763", "GSM2235764", "GSM2235765", "GSM2235766", "GSM2235767", "GSM2235768", "GSM2235769", "GSM2235770", "GSM2235771", "GSM2235772", "GSM2235773", "GSM2235774", "GSM2235775", "GSM2235776", "GSM2235777", "GSM2235778", "GSM2235779", "GSM2235780", "GSM2235781", "GSM2235782", "GSM2235783", "GSM2235784", "GSM2235785", "GSM2235786", "GSM2235787", "GSM2235788", "GSM2235789", "GSM2235790", "GSM2235791", "GSM2235792", "GSM2235793", "GSM2235794", "GSM2235795", "GSM2235796", "GSM2235797", "GSM2235798", "GSM2235799", "GSM2235800", "GSM2235801", "GSM2235802", "GSM2235803", "GSM2235804", "GSM2235805", "GSM2235806", "GSM2235807", "GSM2235808", "GSM2235809", "GSM2235810", "GSM2235811", "GSM2235812", "GSM2235813", "GSM2235814", "GSM2235815", "GSM2235816", "GSM2235817", "GSM2235818", "GSM2235819", "GSM2235820", "GSM2235821", "GSM2235822", "GSM2235823", "GSM2235824", "GSM2235825", "GSM2235826", "GSM2235827", "GSM2235828", "GSM2235829", "GSM2235830", "GSM2235831", "GSM2235837", "GSM2235838", "GSM2235839", "GSM2235840", "GSM2235841", "GSM2235842", "GSM2235843", "GSM2235844", "GSM2235845", "GSM2235846", "GSM2235847", "GSM2235848", "GSM2235849", "GSM2235850", "GSM2235851", "GSM2235852", "GSM2235853", "GSM2235854", "GSM2235855", "GSM2235862", "GSM2235863", "GSM2235864", "GSM2235865", "GSM2235866", "GSM2235867", "GSM2235878", "GSM2235879", "GSM2235880", "GSM2235881", "GSM2235882", "GSM2235883", "GSM2235884", "GSM2235885", "GSM2235886", "GSM2235887", "GSM2235888", "GSM2235889", "GSM2235899", "GSM2235900", "GSM2235901", "GSM2235902", "GSM2235903", "GSM2235904", "GSM2235905", "GSM2235906", "GSM2235907", "GSM2235908", "GSM2235909", "GSM2235910", "GSM2235921", "GSM2235922", "GSM2235923", "GSM2235924", "GSM2235925", "GSM2235926", "GSM2235927", "GSM2235928", "GSM2235929", "GSM2235930", "GSM2235931", "GSM2235932", "GSM2235933", "GSM2235934", "GSM2235935", "GSM2235936", "GSM2235937", "GSM2235938", "GSM2235939", "GSM2235940", "GSM2235941", "GSM2235942", "GSM2235943", "GSM2235944", "GSM2235945", "GSM2235946", "GSM2235947", "GSM2235948", "GSM2235949", "GSM2235950", "GSM2235951", "GSM2235952", "GSM2235953", "GSM2235954", "GSM2235955", "GSM2235956", "GSM2235957", "GSM2235958", "GSM2235959", "GSM2235960", "GSM2235961", "GSM2235962", "GSM2235963", "GSM2235964", "GSM2235965", "GSM2235966", "GSM2235967", "GSM2235968", "GSM2235969", "GSM2235970", "GSM2235971", "GSM2235972", "GSM2235973", "GSM2235974", "GSM2235975", "GSM2235976", "GSM2235977", "GSM2235978", "GSM2235979", "GSM2235980", "GSM2235981", "GSM2235982", "GSM2235983", "GSM2235984", "GSM2235985", "GSM2235986", "GSM2235987", "GSM2235988", "GSM2235991", "GSM2235992", "GSM2235993", "GSM2235994", "GSM2235995", "GSM2235996", "GSM2235997", "GSM2235998", "GSM2235999", "GSM2236000", "GSM2236001", "GSM2236002", "GSM2236003", "GSM2236004", "GSM2236005", "GSM2236006", "GSM2236007", "GSM2236008", "GSM2236009", "GSM2236010", "GSM2236011", "GSM2236012", "GSM2236013", "GSM2236014", "GSM2236015", "GSM2236016", "GSM2236017", "GSM2236018", "GSM2236019", "GSM2236020", "GSM2236021", "GSM2236022", "GSM2236023", "GSM2236024", "GSM2236025", "GSM2236026", "GSM2236027", "GSM2236028", "GSM2236029", "GSM2236030", "GSM2236031", "GSM2236032", "GSM2236033", "GSM2236034", "GSM2236036", "GSM2236037", "GSM2236038", "GSM2236039", "GSM2236040", "GSM2236041", "GSM2236042", "GSM2236043", "GSM2236044", "GSM2236045", "GSM2236046", "GSM2236047", "GSM2236048", "GSM2236049", "GSM2236050", "GSM2236051", "GSM2236052", "GSM2236053", "GSM2236054", "GSM2236055", "GSM2236056", "GSM2236057", "GSM2236058", "GSM2236059", "GSM2236060", "GSM2236061", "GSM2236062", "GSM2236063", "GSM2236064", "GSM2236065", "GSM2236066", "GSM2236067", "GSM2236068", "GSM2236069", "GSM2236070", "GSM2236071", "GSM2236072", "GSM2236073", "GSM2236074", "GSM2236075", "GSM2236076", "GSM2236077", "GSM2236078", "GSM2236079", "GSM2236080", "GSM2236082", "GSM2236083", "GSM2236084", "GSM2236085", "GSM2236086", "GSM2236087", "GSM2236088", "GSM2236089", "GSM2236090", "GSM2236091", "GSM2236092", "GSM2236093", "GSM2236094", "GSM2236095", "GSM4419484", "GSM4419485", "GSM4419486", "GSM4419487", "GSM4419488", "GSM4419489", "GSM4419490", "GSM4419491", "GSM4419492", "GSM4419493", "GSM4419494", "GSM4419495", "GSM4419496", "GSM4419497", "GSM4419498", "GSM4419499", "GSM4419500", "GSM4419501", "GSM4419502", "GSM4419503", "GSM4419504", "GSM4419505", "GSM4419506", "GSM4419507", "GSM4419508", "GSM4419509", "GSM4419510", "GSM4419511", "GSM4419512", "GSM4419513", "GSM4419514", "GSM4419515", "GSM4419516", "GSM4419517", "GSM4419518", "GSM4419519", "GSM4419520", "GSM4419521", "GSM4419522", "GSM4419523", "GSM4419524", "GSM4419525", "GSM4419526", "GSM4419527", "GSM4419528", "GSM4419529", "GSM4419530", "GSM4419531", "GSM4419532", "GSM4419533"], "sample_count": 483, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular subtypes in gastric cancer.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE84437 not downloaded", "asset:data:geo:GSE84437 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "and log-rank test, and hazard ratio (HR) and 95% confidence", "confidence_interval": "zard ratio (HR) and 95% confidence interval (CI) values of candidat"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "and log-rank test, and hazard ratio (HR) and 95% confidence", "confidence_interval": "zard ratio (HR) and 95% confidence interval (CI) values of candidat"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}, {"id": "method-4", "family": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.7, "band": "medium", "quote": "decision curve analysis"}}, {"id": "method-5", "family": null, "specific": null, "label": "Least absolute shrinkage and selector operation (LASSO) regression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Least absolute shrinkage and selector operation (LASSO) regression analysis was applied to reduce the feature dimension and construct the prognostic signature."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "calibration_bins", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "calibration_bins", "expected_value": 0.001, "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.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE62254", "GSE15459", "GSE84437"], "resolved_accessions": ["GSE62254", "GSE15459", "GSE84437"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE62254, GSE15459, GSE84437 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:36226177", "data:geo:GSE15459"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15459"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:10:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16610, "completion_tokens": 1949, "cached_tokens": 256}}, "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:36226177", "type": "paper", "label": "pmid:36226177"}, {"id": "source:pmid:36226177", "type": "manuscript", "label": "PMID 36226177 full text"}, {"id": "data:geo:GSE15459", "type": "dataset", "label": "GEO GSE15459"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36226177", "type": "paper", "label": "pmid:36226177"}, {"id": "source:pmid:36226177", "type": "manuscript", "label": "PMID 36226177 full text"}, {"id": "data:geo:GSE15459", "type": "dataset", "label": "GEO GSE15459"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36226177", "type": "extraction", "used": ["source:pmid:36226177"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15459", "type": "accession_resolution", "used": ["data:geo:GSE15459"], "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:36226177", "parent_hash": "sha256:5972fc019408147bca0ae3b69523582801fce86cee0cdf9670663c29a0db7cad", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE62254 licence not read", "asset:data:geo:GSE62254 not downloaded", "asset:data:geo:GSE84437 licence not read", "asset:data:geo:GSE84437 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Cox regression"], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T02:52:06+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}}}