{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40779729", "kind": "science-record", "revision": 2, "content_hash": "sha256:63eed595ec9f2b965efa5d135900e60159c135c6590162c280c371d85620f666", "created_at": "2026-11-01T10:25:52Z", "updated_at": "2026-11-01T14:01:45Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Risk Score Model of Aging-Related Genes for Bladder Cancer and Its Application in Clinical Prognosis.", "doi": "10.1200/cci-25-00019", "pmid": "40779729", "authors": null, "journal": "JCO clinical cancer informatics", "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": 12.0, "unit": "genes", "tolerance": null, "source": "chars 857-1060 of source 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"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:40779729' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40779729", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1200/cci-25-00019", "sha256": "sha256:5ae08633552aaf9a3ef14a62439b4d46fce1c3fe9f70746280990d6d22fc042b", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1200/cci-25-00019", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40779729:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b9dacbf345bbb6723aaa1ee6423389ce4bc2e2883fe6f2bafb9bb5b2638025b8", "bytes": 2127, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#tbl1", "version": null, "note": "Demographic and Clinical Data of the Training Group and the Internal Test Group", "structure": {"pmcid": "PMC12360192", "section_index": 11, "section_title": "Prognostic Modeling", "row_count": 41, "column_count": 5}, "table": {"label": "TABLE 1.", "caption": "Demographic and Clinical Data of the Training Group and the Internal Test Group", "rows": [["Characteristic", "TCGA LUAD", "Chi-Square P"], ["Training (n = 246), No. (%)", "Internal Testing (n = 161), No. (%)", "All (n = 407), No. (%)"], ["Clinical_T", "", "", "", ""], ["T1/2", "73 (29.67)", "54 (33.54)", "127 (31.20)", ".712709"], ["T3/4", "173 (70.33)", "107 (66.46)", "280 (68.80)"], ["Lymphovascular_invasion", "", "", "", ""], ["No", "85 (49.13)", "44 (41.12)", "129 (46.07)", ".425746"], ["Yes", "88 (50.87)", "63 (58.88)", "151 (53.93)"], ["Neoplasm_grade", "", "", "", ""], ["Low", "11 (4.53)", "10 (6.21)", "21 (5.20)", ".756701"], ["High", "232 (95.47)", "151 (93.79)", "383 (94.80)"], ["Pathologic_M", "", "", "", ""], ["m0", "119 (94.44)", "77 (95.06)", "196 (94.69)", ".981504"], ["m1", "7 (5.56)", "4 (4.94)", "11 (5.31)"], ["Pathologic_N", "", "", "", ""], ["N0", "139 (56.50)", "98 (60.87)", "237 (58.23)", ".683015"], ["N1/2/3", "107 (43.50)", "63 (39.13)", "170 (41.77)"], ["Pathologic_T", "", "", "", ""], ["T1/2", "76 (30.89)", "46 (28.57)", "122 (29.98)", ".88243"], ["T3/4", "170 (69.11)", "115 (71.43)", "285 (70.02)"], ["Sex", "", "", "", ""], ["Female", "66 (26.83)", "40 (24.84)", "106 (26.04)", ".9053"], ["Male", "180 (73.17)", "121 (75.16)", "301 (73.96)"], ["Stage", "", "", "", ""], ["Stage I/II", "77 (31.30)", "55 (34.16)", "132 (32.43)", ".833851"], ["Stage III/IV", "169 (68.70)", "106 (65.84)", "275 (67.57)"], ["BMI", "", "", "", ""], ["≤24", "71 (33.65)", "48 (32.88)", "119 (33.33)", ".988478"], [">24", "140 (66.35)", "98 (67.12)", "238 (66.67)"], ["Cigarettes_per_day", "", "", "", ""], ["≤2", "79 (61.24)", "47 (51.09)", "126 (57.01)", ".323213"], [">2", "50 (38.76)", "45 (48.91)", "95 (42.99)"], ["Time", "", "", "", ""], ["≤2", "165 (67.07)", "102 (63.35)", "267 (65.60)", ".742121"], [">2", "81 (32.93)", "59 (36.65)", "140 (34.40)"], ["Status", "", "", "", ""], ["0", "134 (54.47)", "95 (59.01)", "229 (56.27)", ".665915"], ["1", "112 (45.53)", "66 (40.99)", "178 (43.73)"], ["Risk", "", "", "", ""], ["Low", "120 (48.78)", "89 (55.28)", "209 (51.35)", ".439271"], ["High", "126 (51.22)", "72 (44.72)", "198 (48.65)"]], "row_count": 41, "column_count": 5, "numeric_cells": 107, "header_rows": 2, "locator": "section[11]/table-wrap[1]#tbl1"}}], "gaps": ["asset:source:pmid:40779729 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:40779729", "asset:table:pmid:40779729:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40779729"]}, "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": "3c7022374e763dfe265899197771ea10613c04e1d78b1fef7d806c49f5b33778", "source_hash": "5ae08633552aaf9a3ef14a62439b4d46fce1c3fe9f70746280990d6d22fc042b", "raw_response_sha256": "sha256:eca1870c5a223e46f634611d86e5d6a8664b8983dc17237486f94f8299096185", "raw_response_chars": 3419}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "a345623563780caa135be9f2b41e99db1068a8a885a97e96748f5d68c159cd09", "source_hash": "5ae08633552aaf9a3ef14a62439b4d46fce1c3fe9f70746280990d6d22fc042b", "raw_response_sha256": "sha256:d0363f5056b0f9a3cf9a2fb450d92d9ef0d24e574f6058595bd4da2723e37745", "raw_response_chars": 71249}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "8a89481e5252da25b2be60c21f22f5d3579d6af04017f7faf13731c7c6882f79", "source_hash": "5ae08633552aaf9a3ef14a62439b4d46fce1c3fe9f70746280990d6d22fc042b", "raw_response": "{\"parent_value\":12,\"unit\":\"genes\",\"evidence\":\"Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus were used to construct a 12-gene ARG-based prognostic signature through LASSO and Cox regression analyses.\",\"target_result\":\"The paper's headline result was a 12-gene aging-related-gene prognostic signature for bladder cancer.\",\"number_stated\":true}", "reading": {"parent_value": 12, "unit": "genes", "evidence": "Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus were used to construct a 12-gene ARG-based prognostic signature through LASSO and Cox regression analyses.", "target_result": "The paper's headline result was a 12-gene aging-related-gene prognostic signature for bladder cancer.", "number_stated": true, "source_locator": "chars 857-1060 of source sha256 5ae08633552aaf9a3ef14a62439b4d46fce1c3fe9f70746280990d6d22fc042b"}, "recorded_at": "2026-10-31T15:29:08.479888+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "817f7eb64512b9a4a89d77b5c2c1d9e5dc2c60c2ba28290e8729a3c43b1770f6", "source_hash": "5ae08633552aaf9a3ef14a62439b4d46fce1c3fe9f70746280990d6d22fc042b", "raw_response": "<think>We need answer JSON only. Need interpret target headline numerical result main finding. Source states 12-gene signature, P<.0001, AUC range .772-.794. Asked single numerical result replication registered target has reproduce. Headline number only value paper states for registered target. Registered target \"the headline numerical result the paper states for its main finding\". Likely AUC values? Need determine expected parent value perhaps 0.794? Headline numerical result perhaps range impossible parent_value number singular. Main finding model yielded AUC values ranging from 0.772 to 0.794 across 1-5 years. They demand single numerical result and parent_value number, unit string. Could choose 0.772? Let's parse wording carefully.\n\n\"Read supplied paper text and find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed. The unit must be the unit the paper prints. The evidence must be an exact, contiguous quotation from SOURCE TEXT that contains the number; do not shorten it, do not add an ellipsis and do not paraphrase it. Attribution may be carried by the text's own wording: a number may be attached to the target by a parenthetical list, by the word 'respectively', or by words that name the target directly. When that is how the text links them, quote the whole clause so a reader can check the attribution for themselves. If the text states no number for the registered target, set number_stated to false, leave parent_value at 0, leave unit and evidence empty, and say in target_result what the text does state instead.\"\n\nREGISTERED TARGET: the headline numerical result the paper states for its main finding\n\nCould be 12-gene ARG-based prognostic signature, as main finding and headline numerical result. \"12-gene\" explicitly. Replication target likely number of genes in model. They ask numerical result rather than unit perhaps \"12\" and unit \"genes\". Evidence whole clause: \"Transcriptomic and clinical data ... were used to construct a 12-gene ARG-based prognostic signature through LASSO and Cox regression analyses.\" That sounds a replication must reproduce 12 genes. The abstract/results headline: \"Twelve ARGs were identified.\" That's exactly headline numerical result of main finding. Parent value 12, unit maybe \"genes\" or \"ARGs\". Which unit paper prints? It says \"Twelve ARGs\" word, not numeric 12 in results. But exact evidence containing \"number\": \"Twelve ARGs were identified.\" They require evidence exact contiguous quote contains the number. Written number counts? Parent number 12. Unit \"ARGs\" perhaps paper prints acronym. Or \"genes\" from 12-gene. \"headline number only\". Likely 12 genes.\n\nCould target instead P &lt; .0001 (better OS) because main headline finding is significantly better OS, single numerical result. Replication would reproduce P-value? Parent_value .0001 unit maybe \"P value\". But wording \"main finding\" likely abstract's key result includes 12 genes, OS P, AUC range. Need infer benchmark intent. Registered target generic \"the headline numerical result the paper states for its main finding\" likely asks identify headline value from text. There may be a task framework where parent_value is numeric answer, target_result prose. Need report exact source number. Which is \"headline numerical result\"? In abstract, \"In the TCGA cohort, the model yielded AUC values ranging from 0.772 to 0.794 across 1-5 years.\" That is a range, not single. Could headline number be 12-gene signature? This is likely because they specifically phrase \"single numerical result\". The study's main finding is 12 ARG signature. A replication has to reproduce \"12\" genes. Let's inspect title and abstract. \"This study aimed to develop a prognostic model on basis...\" Then results: \"Transcriptomic ... used to construct a 12-gene ARG-based prognostic signature...\" Then findings. Headline numerical result perhaps AUC? Yet range means two values, contrary to single number. Registered target says headline numerical result paper states for main finding, perhaps 12 genes is singular.\n\nCould be AUC at specific horizon hidden? No.\n\nNeed output JSON fields:\nparent_value: 12\nunit: \"genes\" perhaps paper prints \"12-gene\", and later \"Twelve ARGs\". They say unit must be unit paper prints. Unit perhaps \"ARGs\" because target is number of aging-related genes. The evidence exact quote should include number and attribution. Could use \"Twelve ARGs were identified.\" This is exact contiguous. Unit \"ARGs\" is paper's own. But parent_value numeric 12 is conversion from \"Twelve\" to digits. Instruction says not a value you calculated, converted, averaged or reconstructed. Is converting spelled Twelve to numeric 12 considered conversion? Yet schema parent_value number forces digits. Usually numerical extraction accepts words. They might want 12 from \"12-gene\". Better evidence exact contains Arabic numeral: \"Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus were used to construct a 12-gene ARG-based prognostic signature through LASSO and Cox regression analyses.\" This exact sentence appears twice. Unit \"gene\" from 12-gene. They say headline number only value paper itself states—not converted. Use Arabic 12. Evidence full sentence. target_result describe \"The paper reports a 12-gene ARG-based prognostic signature.\" This repeats perhaps acceptable.\n\nCould unit be empty? Unit must unit paper prints. \"gene\" clear.\n\nNeed ensure quote exact contiguous. Yes.\n\n\"headline number only\" likely don't include range or P. JSON only.\n\nLet's think if perhaps target result expected \"AUC = 0.794\" because headline performance number and unit AUC. Replication of registered target \"the headline numerical result the paper states for its main finding\" often these prompts derive from a \"claim\" where target may be numeric finding. The source includes multiple numeric findings intentionally. Need determine which is headline. The abstract's main result likely survival difference P&lt;.0001 and AUC range. But if target is singular headline numerical result, perhaps they expect 12 genes because that's named in aim/model. Let's analyze semantics deeply.\n\nPrompt likely generated in a benchmark where \"REGISTERED TARGET\" is a natural language description. They ask \"find the single numerical result that a replication of the registered target has to reproduce.\" Here registered target says \"the headline numerical result the paper states for its main finding.\" This is ambiguous because source has many numerical values. Maybe expected to classify false if no single headline number? Yet source states several. They explicitly say \"single numerical result.\" The target could refer to a target entity (e.g., risk score model) and ask the number. Main finding: \"12-gene ARG-based prognostic signature\" is headline numerical descriptor. Yes.\n\nCould \"headline numerical result\" refer to \"Twelve ARGs were identified.\" That's the first sentence in Results and repeated abstract. Number of identified genes is the headline numerical result. \"Patients ... P &lt; .0001\" is statistical significance, not headline number perhaps. AUC is range and thus not single. So 12.\n\nUnit \"genes\" or \"ARGs\". Exact sentence with 12-gene lets unit be \"gene.\" target_result perhaps \"12 aging-related genes were identified.\" They demand \"headline number only\" maybe target_result should say \"The model is based on 12 aging-related genes.\" It isn't evidence field, can summarize.\n\nNeed only JSON no markdown. Ensure number_stated true.\n\nPotential concern: Unit field expects a unit in paper prints. It prints \"12-gene\", singular adjective. Use \"gene\". Maybe \"ARGs\" isn't a unit but category. They may expect unit \"genes\". Typical answer style from these tasks: parent_value 12, unit \"genes\", evidence quote, target_result \"12 aging-related genes\". Use \"genes\" although exact printed elsewhere says \"ARGs\" and \"12-gene\". Unit \"genes\" printed in title (\"Aging-Related Genes\"), and sentence \"Twelve ARGs\". Grammatically unit can pluralize. But \"unit must be the unit the paper prints\" maybe likely unit \"genes\". Could be \"ARG-based prognostic signature\" count.\n\nLet's inspect prompt mention \"parent_value\" oddly. Maybe this task involves \"parent numerical value\" in chart/table, and \"target_result\". They require one number. Parent_value maybe numeric result. No issue.\n\nCould there be a specific headline result from title? Risk Score Model... The main model has 12 genes. Exactly.\n\nLet's formulate evidence one complete sentence. Must not paraphrase and exact contiguous. Source:\n\"Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus were used to construct a 12-gene ARG-based prognostic signature through LASSO and Cox regression analyses.\"\nQuote exact. Includes attribution and number.\n\nUnit \"genes\". target_result \"The paper's main model is a 12-gene aging-related-gene prognostic signature.\" Maybe they said headline number only, perhaps target_result can state this. Fine.\n\nCould use \"Twelve ARGs were identified.\" More direct headline result, but numerical representation written. The instruction exact evidence contains the number; Twelve is a number. Yet \"parent_value\" 12 is straightforward. The full sentence \"Transcriptomic...\" clearly model. I'd use 12 numeric evidence.\n\nAny possibility they want 0.794 because AUC is headline numerical performance? Let's examine abstract ordering:\n- aim\n- methods construct 12-gene signature\n- \"Twelve ARGs were identified. Patients in low-risk group exhibited significantly better overall survival (P&lt;.0001). In TCGA cohort, model yielded AUC values ranging 0.772 to 0.794 across 1-5 years.\"\nMain finding might be risk stratification significantly better survival with P&lt;.0001. If someone asks \"headline numerical result paper states for its main finding,\" perhaps P &lt; .0001 is headline. But replication target of \"main finding\" could be P value. Yet \"single numerical result\" likely they designed target based on paper's \"headline number.\" What qualifies headline? Usually article abstracts have a key numerical result; \"12-gene signature\" is methodological output, while AUC range is model performance. The paper title highlights model, not number.\n\nMaybe the benchmark asks agents to find \"a single numerical result that a replication of registered target has to reproduce\" with registered target intentionally vague but perhaps source itself uniquely supports one headline number. They may regard \"12 genes\" as count because other values aren't a \"result for target\" and range is not single. The wording \"the value the paper itself states for the registered target\" and attribution via parenthetical lists/respectively suggests task originally about matching values to entities in prose. Here target main finding. They expect one numeric value linked directly.\n\nCould target_result say \"The paper reports a 12-gene ARG-based prognostic signature.\" Unit \"genes\". Good.\n\nLet's ensure no extraneous prose.</think>\n\n{\"parent_value\":12,\"unit\":\"genes\",\"evidence\":\"Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus were used to construct a 12-gene ARG-based prognostic signature through LASSO and Cox regression analyses.\",\"target_result\":\"The paper reports a 12-gene aging-related-gene prognostic signature.\",\"number_stated\":true}", "reading": {"parent_value": 12, "unit": "genes", "evidence": "Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus were used to construct a 12-gene ARG-based prognostic signature through LASSO and Cox regression analyses.", "target_result": "The paper reports a 12-gene aging-related-gene prognostic signature.", "number_stated": true, "source_locator": "chars 857-1060 of source sha256 5ae08633552aaf9a3ef14a62439b4d46fce1c3fe9f70746280990d6d22fc042b"}, "recorded_at": "2026-10-31T15:29:26.456123+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "In the TCGA cohort, the model yielded AUC values ranging from 0.772 to 0.794 across 1–5 years.", "minimax_alt": "Patients in the low-risk group exhibited significantly better overall survival (P < .0001).", "decisive": false}, "analysis_methods": {"minimax": ["LASSO regression", "Cox regression", "Kaplan-Meier survival analysis", "receiver operating characteristic analysis", "nomogram analysis", "univariate and multivariate Cox regression", "Spearman's method for correlation analysis", "CIBERSORT algorithm", "TIMER algorithm", "gene set enrichment analysis"], "minimax_alt": ["LASSO regression", "Univariate Cox regression", "Multivariate Cox regression", "Kaplan-Meier survival analysis", "Receiver operating characteristic analysis", "Nomogram"], "decisive": false}, "statistical_method": {"minimax": "The ROC curve was plotted via the “TimeROC” R package, and the AUC was calculated via the “survivalROC” R package.", "minimax_alt": "Kaplan-Meier survival 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:6ab8323d813a9f7a71b32a6ea6c37de8498b8262c235d62eb981f79ae38c6eb0", "type": "sep_package", "label": "SEP v1 package for pmid:40779729"}], "activities": [{"id": "activity:conversion:pmid:40779729", "type": "conversion", "used": ["package:6ab8323d813a9f7a71b32a6ea6c37de8498b8262c235d62eb981f79ae38c6eb0"], "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:40779729", "parent_hash": "sha256:2d24643392ba19de597806d405579c90058e7e2880a8b941da8ac0623bd8cfc1", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40779729 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:40779729' 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":"2026-11-04T01:30:34+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}}}