{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41399382", "kind": "science-record", "revision": 1, "content_hash": "sha256:18cdd6a8ff5b901d3c3d5c93589527fa1fe8a979abbd6b1635d86718abb4d78a", "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": "Integration of Single-cell and Bulk Transcriptome Analyses Unravels a Macrophage-based Gene Signature for Prognostication and Treatment in Triple-negative Breast Cancer.", "doi": "10.7150/ijms.120593", "pmid": "41399382", "authors": null, "journal": "International journal of medical sciences", "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": 0.9, "unit": "auc", "tolerance": null, "source": "chars 1690-1810 of source sha256 906d70ca5b5d3d2c56b4a6ccca31a3ddcdfc738b6d918cdb2a0d7ad60ac2bdee"}, "evidence": [{"asset": "source:pmid:41399382", "locator": "chars 1690-1810 of source sha256 906d70ca5b5d3d2c56b4a6ccca31a3ddcdfc738b6d918cdb2a0d7ad60ac2bdee", "quote": "This signature demonstrated reliable performance in external validation, particularly for one-year survival (AUC > 0.9)."}]}], "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:41399382"], "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:41399382", "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:41399382' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41399382", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/ijms.120593", "sha256": "sha256:906d70ca5b5d3d2c56b4a6ccca31a3ddcdfc738b6d918cdb2a0d7ad60ac2bdee", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/ijms.120593", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:41399382 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:41399382"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41399382"]}, "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": "b7f1f77f45630936f45b92761c8d79b93e365fa8676e9469cbcb0451e17d658f", "source_hash": "906d70ca5b5d3d2c56b4a6ccca31a3ddcdfc738b6d918cdb2a0d7ad60ac2bdee", "raw_response_sha256": "sha256:14b820d01f97312fe9e46c14a5ca444b1f41cb8d40ff6b5ac8eabf7f1d888b80", "raw_response_chars": 5471}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "4d3dcbef678866f94ca39499e2299e524e1ecc66e9e72b710170f5003763e9f0", "source_hash": "906d70ca5b5d3d2c56b4a6ccca31a3ddcdfc738b6d918cdb2a0d7ad60ac2bdee", "raw_response_sha256": "sha256:786720707fe81293c81fd29453b33d7dcb0c9ff089d294468efd2964de7d880c", "raw_response_chars": 45542}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "071ed8fc2fabfb910ebf947f2a5da6386f8268a46a31b30c754346820f5df3c9", "source_hash": "906d70ca5b5d3d2c56b4a6ccca31a3ddcdfc738b6d918cdb2a0d7ad60ac2bdee", "raw_response": "{\"parent_value\":0.9,\"unit\":\"AUC\",\"evidence\":\"This signature demonstrated reliable performance in external validation, particularly for one-year survival (AUC > 0.9).\",\"target_result\":\"AUC > 0.9 for one-year survival in external validation\",\"number_stated\":true}", "reading": {"parent_value": 0.9, "unit": "AUC", "evidence": "This signature demonstrated reliable performance in external validation, particularly for one-year survival (AUC > 0.9).", "target_result": "AUC > 0.9 for one-year survival in external validation", "number_stated": true, "source_locator": "chars 1690-1810 of source sha256 906d70ca5b5d3d2c56b4a6ccca31a3ddcdfc738b6d918cdb2a0d7ad60ac2bdee"}, "recorded_at": "2026-10-31T15:15:34.056930+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "41fe4c1260199015eb121933a6e71eda66320c98d129b39da69e670625d24ce6", "source_hash": "906d70ca5b5d3d2c56b4a6ccca31a3ddcdfc738b6d918cdb2a0d7ad60ac2bdee", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline main finding. Source abstract. Likely AUC > 0.9 particularly one-year survival. Need report headline number only, value paper states, unit printed. \"AUC > 0.9\". Parent_value numeric 0.9, unit perhaps \"AUC\". Evidence exact contiguous quote containing number, and attribution whole clause. Could quote: \"This signature demonstrated reliable performance in external validation, particularly for one-year survival (AUC > 0.9).\" Number represented 0.9. Unit must paper prints: AUC likely unit \"AUC\" perhaps parent_value 0.9 and unit \"AUC\". Evidence exact contiguous quote containing number, and attribution whole clause. Could quote: \"This signature demonstrated reliable performance in external validation, particularly for one-year survival (AUC > 0.9).\" Number represented 0.9. Unit must paper prints: AUC likely unit \"AUC\" perhaps parent_value 0.9 and unit \"AUC\". target_result perhaps \"one-year survival AUC > 0.9 in external validation\". Need exact evidence. Is headline numerical result maybe AUC > 0.9. It asks single numerical result replication target. Yes.\n\nNeed make JSON valid. No markdown. \"unit\": \"AUC\" (unit printed? AUC is metric, not unit, but schema string). Could perhaps unit \"\". Yet requirement says unit must be unit paper prints. AUC is dimensionless and paper prints it as label. They probably expect \"AUC\". target_result should state. Evidence must exact contiguous quotation from source and do not shorten. Quote full sentence. Exact text: \"This signature demonstrated reliable performance in external validation, particularly for one-year survival (AUC > 0.9).\" Good.\n\nPotential issue > relation omitted in parent numeric. Could target_result include \"AUC > 0.9\". Fine. parent_value 0.9. JSON number cannot encode inequality. Unit \"AUC\". Need no extra.</think>\n\n{\"parent_value\":0.9,\"unit\":\"AUC\",\"evidence\":\"This signature demonstrated reliable performance in external validation, particularly for one-year survival (AUC > 0.9).\",\"target_result\":\"One-year survival AUC > 0.9 in external validation.\",\"number_stated\":true}", "reading": {"parent_value": 0.9, "unit": "AUC", "evidence": "This signature demonstrated reliable performance in external validation, particularly for one-year survival (AUC > 0.9).", "target_result": "One-year survival AUC > 0.9 in external validation.", "number_stated": true, "source_locator": "chars 1690-1810 of source sha256 906d70ca5b5d3d2c56b4a6ccca31a3ddcdfc738b6d918cdb2a0d7ad60ac2bdee"}, "recorded_at": "2026-10-31T15:15:37.587435+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "One-year survival prediction by the macrophage-based gene signature achieved an AUC > 0.9 in external validation.", "minimax_alt": "The macrophage-based gene signature achieved an AUC > 0.9 for one-year survival in external validation.", "decisive": false}, "analysis_methods": {"minimax": ["Single-cell transcriptomic analysis", "Bulk transcriptome analysis", "Principal component analysis", "Cell clustering and annotation", "Uniform manifold approximation and projection", "CIBERSORTX immune infiltration analysis", "Gene Ontology enrichment analysis", "KEGG pathway enrichment analysis", "Gene set enrichment analysis", "SCENIC transcription-factor analysis", "limma differential expression analysis", "Univariate Cox regression", "Least absolute shrinkage and selection operator (LASSO) analysis", "Kaplan-Meier survival analysis", "Log-rank test", "Receiver operator characteristic curve analysis", "Bootstrap resampling", "Calibration curve analysis", "Decision Curve Analysis (DCA)"], "minimax_alt": ["Single-cell transcriptome analysis", "Bulk transcriptome analysis", "Principal component analysis (PCA)", "Uniform manifold approximation and projection (UMAP)", "CIBERSORTX immune infiltration analysis", "Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis", "Gene set enrichment analysis (GSEA)", "SCENIC transcription-factor analysis", "limma differential-expression analysis", "Univariate Cox regression", "Least absolute shrinkage and selection operator (LASSO) regression using glmnet", "1000-iteration Bootstrap resampling for optimism-corrected performance metrics", "Calibration curve analysis using the rms package", "Decision Curve Analysis (DCA)", "Receiver operator characteristic (ROC) analysis using the pROC package", "Kaplan-Meier survival analysis with log-rank test", "Student's t test", "One-way analysis of variance", "Pearson correlation test", "Spearman correlation test"], "decisive": false}, "statistical_method": {"minimax": "Receiver operator characteristic (ROC) analysis", "minimax_alt": "Receiver operator characteristic (ROC) curve analysis using the pROC package", "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:c0502057a3ae71b4b4c7b5e019ef7a990fce95feb2ac36c2826b3d4dd4353dc8", "type": "sep_package", "label": "SEP v1 package for pmid:41399382"}], "activities": [{"id": "activity:conversion:pmid:41399382", "type": "conversion", "used": ["package:c0502057a3ae71b4b4c7b5e019ef7a990fce95feb2ac36c2826b3d4dd4353dc8"], "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": "5f9c8707-7f52-44dc-845e-f2bb0f447711", "parent_hash": "c0502057a3ae71b4b4c7b5e019ef7a990fce95feb2ac36c2826b3d4dd4353dc8", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:41399382 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:41399382' 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":"2026-11-04T01:21:05+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}}}