{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41496405", "kind": "science-record", "revision": 1, "content_hash": "sha256:c4104e1c6f1533d4dc8d396f892569bffd5f2e553f4551cabfc6e36dadeb2835", "created_at": "2026-11-01T10:25:54Z", "updated_at": "2026-11-01T10:25:54Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Integrated spatial and single-cell transcriptomics reveals RPL8 as a prognostic biomarker and therapeutic target in hepatocellular carcinoma.", "doi": "10.1016/j.tranon.2025.102663", "pmid": "41496405", "authors": null, "journal": "Translational oncology", "year": 2026, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 0.95, "unit": "auc", "tolerance": null, "source": "chars 142-253 of source sha256 1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365"}, "evidence": [{"asset": "source:pmid:41496405", "locator": "chars 142-253 of source sha256 1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "quote": "Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC."}]}], "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:41496405"], "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:41496405", "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:41496405' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41496405", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.tranon.2025.102663", "sha256": "sha256:1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.tranon.2025.102663", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:41496405 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:41496405"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41496405"]}, "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": "e916feecee9bfca06840bdea8d9d11581e8b96ddcb7cf92c893fa07f849a55eb", "source_hash": "1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "raw_response_sha256": "sha256:5328c8018013a28a5d817f6c49ee54030b2f8fec497e6cbe46182a29241e0d9b", "raw_response_chars": 2933}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "f372affa765397d57a6d94c1b28107a613798a7cd1ca1c0bc9cf64bcc0acd061", "source_hash": "1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "raw_response_sha256": "sha256:edff96497d4f11d05e8d51845935b7419efb242c1bd06ac35a5140bf76667560", "raw_response_chars": 68999}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "fc37cf343621b7911fcf143bb5101ab1f049c160957c2fe842c4ba65ba5a8e83", "source_hash": "1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "raw_response": "{\"parent_value\":0.95,\"unit\":\"AUC\",\"evidence\":\"Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.\",\"target_result\":\"RPL8 was identified as a highly specific diagnostic biomarker for hepatocellular carcinoma.\",\"number_stated\":true}", "reading": {"parent_value": 0.95, "unit": "AUC", "evidence": "Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.", "target_result": "RPL8 was identified as a highly specific diagnostic biomarker for hepatocellular carcinoma.", "number_stated": true, "source_locator": "chars 142-253 of source sha256 1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365"}, "recorded_at": "2026-10-31T15:27:41.752946+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "e18e8e7c70fef8547ab68a76a981dcf7e8ec1db1c99cbda90f01b09592c86ccf", "source_hash": "1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline main finding. Paper title/main finding RPL8 biomarker/target HCC. Headline result likely AUC=0.95 diagnostic performance. Need report headline number only, value paper states for registered target, unit paper prints. Need exact contiguous quote containing number, attribution via wording, quote whole clause. Need determine target_result perhaps \"AUC = 0.95\" and unit likely \"AUC\" perhaps no unit. Parent_value 0.95. Evidence exact quote e.g. \"Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.\" Unit maybe \"AUC\" (dimensionless). User says headline number only, unit must be unit paper prints. Could use unit \"AUC\" because printed metric. Or empty unit? They expect number and unit. \"AUC=0.95\" no physical unit; unit could be \"AUC\". Usually extraction task unit as \"AUC\". Need target_result describe. Exact contiguous quotation. Ensure no spaces altered? Source: \"Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.\" We can quote exact. target_result maybe \"Diagnostic AUC for RPL8 in HCC: 0.95\" but \"headline number only\" perhaps target_result should state number and unit? Schema includes target_result. number_stated true. Parent_value 0.95. unit \"AUC\". Evidence exact full clause. Could target_result be \"AUC = 0.95\" only. They ask \"Report headline number only\". likely output target_result concise. Let's understand perhaps benchmark expects parent_value, unit, evidence. Main finding could instead be IC50 decrease from 75.1 to 52.16 µM, but that's later functional result, not headline. Abstract highlights AUC 0.95 prominently. \"single numerical result that a replication of the registered target has to reproduce\" likely they registered target as headline numerical result. Need infer extraction from paper. Main finding headline numerical result likely AUC 0.95 in bullet \"highly specific diagnostic (AUC=0.95).\" Prognostic HRs 1.42 and 1.35 also numerical, but headline bullet singular AUC. The registered target wording generic. Use AUC.\n\nCould unit be \"\" because AUC is unitless, but requirement says unit must be unit paper prints. Paper prints \"AUC=0.95\", so \"AUC\" as unit/metric. JSON valid.</think>\n\n{\"parent_value\":0.95,\"unit\":\"AUC\",\"evidence\":\"Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.\",\"target_result\":\"AUC = 0.95\",\"number_stated\":true}", "reading": {"parent_value": 0.95, "unit": "AUC", "evidence": "Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.", "target_result": "AUC = 0.95", "number_stated": true, "source_locator": "chars 142-253 of source sha256 1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365"}, "recorded_at": "2026-10-31T15:27:44.365097+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "RPL8 mRNA/protein were markedly elevated (p < 0.001) with AUC 0.95 for diagnosis.", "minimax_alt": "AUC=0.95 for diagnosis of HCC using RPL8.", "decisive": false}, "work_type": {"minimax": "analysis_only_for_target", "minimax_alt": "analysis_plus_physical_validation", "decisive": true}, "physical_methods": {"minimax": [], "minimax_alt": ["RPL8 knockdown in HUH7 cells", "Proliferation and migration assays", "Drug-sensitivity screens and sirolimus dose-response assays", "Quantitative real-time PCR", "Western blotting", "Flow-cytometric cell-cycle analysis"], "decisive": false}, "analysis_methods": {"minimax": ["Differential gene expression analysis using the limma package with empirical Bayes moderation"], "minimax_alt": ["Multistage survival analysis with survminer-determined optimal cutoffs", "Kaplan-Meier survival analysis with log-rank test", "Univariate Cox proportional hazards regression", "Multivariable Cox regression adjusted for age, gender, and TNM stage", "Random-effects meta-analysis with I² heterogeneity assessment", "limma differential expression analysis with empirical Bayes moderation", "Gene set enrichment analysis with Benjamini-Hochberg FDR correction", "GSVA with z-score transformation", "CancerSEA functional-state assessment using Lee et al.'s algorithm", "Pearson correlation analysis", "Spearman correlation analysis", "Wilcoxon rank-sum test", "UMAP dimensionality reduction", "One-way analysis of variance and t-tests"], "decisive": false}}, "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:4f383d8f2b2e262d31d349d65792f091b3c803e59c55765aa75f9ed9a846f6b4", "type": "sep_package", "label": "SEP v1 package for pmid:41496405"}], "activities": [{"id": "activity:conversion:pmid:41496405", "type": "conversion", "used": ["package:4f383d8f2b2e262d31d349d65792f091b3c803e59c55765aa75f9ed9a846f6b4"], "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": "e8c5452e-07db-4e48-a87b-5e8c70083264", "parent_hash": "4f383d8f2b2e262d31d349d65792f091b3c803e59c55765aa75f9ed9a846f6b4", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:41496405 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:41496405' 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":"2026-11-04T03:34:19+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}}}