{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40881693", "kind": "science-record", "revision": 1, "content_hash": "sha256:977df69d7f0e87d4c92c97d7a13bf3958d23531eb53db8e717128c1709072665", "created_at": "2026-11-01T10:25:52Z", "updated_at": "2026-11-01T10:25:52Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Targeting FCRLA to induce necrosis in lung adenocarcinoma: a novel strategy for prognosis and therapy via MPT-Driven pathways.", "doi": "10.3389/fimmu.2025.1596179", "pmid": "40881693", "authors": null, "journal": "Frontiers in immunology", "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": 82.0, "unit": "candidate genes", "tolerance": null, "source": "chars 1069-1194 of source sha256 1fef0886b20a2ad5c3044325a71b884c423ed91a82dbade59bfd6a342b915052"}, "evidence": [{"asset": "source:pmid:40881693", "locator": "chars 1069-1194 of source sha256 1fef0886b20a2ad5c3044325a71b884c423ed91a82dbade59bfd6a342b915052", "quote": "A total of 82 candidate genes were identified by intersecting 3,231 differentially expressed genes with 566 key module genes."}]}], "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:40881693"], "outputs": ["the published estimate, its unit and its interval"], "instruments": 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"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:40881693' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40881693", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1596179", "sha256": "sha256:1fef0886b20a2ad5c3044325a71b884c423ed91a82dbade59bfd6a342b915052", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1596179", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40881693 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:40881693"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40881693"]}, "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": "19d2f9eb313a7694b2d82919cc6466fc737e7adaf7fa139a768bffa444489105", "source_hash": "1fef0886b20a2ad5c3044325a71b884c423ed91a82dbade59bfd6a342b915052", "raw_response_sha256": "sha256:ec3eac51f2a8e678989c1aa3225272065c3fd20c5103b4fe091a9705cf182ea7", "raw_response_chars": 5965}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "e40961a78616b5d918456c421c2565a9fb5c4b866143ec8fa9f999706252dad0", "source_hash": "1fef0886b20a2ad5c3044325a71b884c423ed91a82dbade59bfd6a342b915052", "raw_response_sha256": "sha256:a70b556e77154b4800a0493c4adaf5e67b4fa6641721766aaf6b95c134e008d6", "raw_response_chars": 71660}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "a2631e9a93f9264347ae7f6f8428f92b79976e0bdb0dc28491b9d1ba0704a6b0", "source_hash": "1fef0886b20a2ad5c3044325a71b884c423ed91a82dbade59bfd6a342b915052", "raw_response": "{\"parent_value\":82,\"unit\":\"candidate genes\",\"evidence\":\"A total of 82 candidate genes were identified by intersecting 3,231 differentially expressed genes with 566 key module genes.\",\"target_result\":\"The paper identifies 82 candidate genes.\",\"number_stated\":true}", "reading": {"parent_value": 82, "unit": "candidate genes", "evidence": "A total of 82 candidate genes were identified by intersecting 3,231 differentially expressed genes with 566 key module genes.", "target_result": "The paper identifies 82 candidate genes.", "number_stated": true, "source_locator": "chars 1069-1194 of source sha256 1fef0886b20a2ad5c3044325a71b884c423ed91a82dbade59bfd6a342b915052"}, "recorded_at": "2026-10-31T15:33:46.790010+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "c7c47059be149652097dc169c9f8c29448f3b894258a8fed6b73c444279b45ca", "source_hash": "1fef0886b20a2ad5c3044325a71b884c423ed91a82dbade59bfd6a342b915052", "raw_response": "<think>We need answer JSON only. Need interpret target: headline numerical result paper states for main finding, single numerical result replication registered target reproduce. Source excerpt abstract/results. Numbers: 82 candidate genes; 3,231 DEGs; 566 module genes; three prognostic genes. What is \"headline numerical result\" for main finding? Need decide. The registered target vague: \"the headline numerical result the paper states for its main finding\". Need extract likely number 82 candidate genes. It says \"A total of 82 candidate genes were identified...\" Main quantitative result. Need report value and unit paper prints. Unit likely \"candidate genes\". Exact contiguous quote containing number, perhaps whole sentence. parent_value 82, unit \"candidate genes\", evidence exact sentence. target_result perhaps \"82 candidate genes\". number_stated true.\n\nBut inspect paper title / abstract. Main finding FCRLA mechanism qualitative. Headline numerical result maybe 82 candidate genes identified by intersecting 3,231 DEGs with 566 key module genes. User asks single numerical result that replication registered target has to reproduce. Could perhaps ask \"headline number\" from abstract, likely 82 candidate genes. Need use exact unit printed—\"candidate genes\". Evidence exact contiguous quote: \"A total of 82 candidate genes were identified by intersecting 3,231 differentially expressed genes with 566 key module genes.\" This contains other numbers, but parent headline 82. They insist exact quote, do not shorten, whole clause attribution. That's fine. Could quote full sentence. target_result maybe \"A total of 82 candidate genes were identified.\" Yet evidence sufficient. They ask headline number only, unit must paper prints. JSON target_result likely perhaps concise \"82 candidate genes\". Need no extra.\n\nCould unit be \"candidate genes\" vs \"genes\"? Exact printed unit. Probably \"candidate genes\". The quote includes 3,231 etc though \"headline number only\" refers output, evidence naturally can include others. Maybe exact quote just \"A total of 82 candidate genes were identified\" is contiguous and contains attribution. It is exact contiguous quotation, not necessarily whole sentence? User says \"When that is how the text links them, quote the whole clause so a reader can check attribution.\" \"A total of 82 candidate genes were identified\" is clause (no explicit target? It states candidate genes). Could quote full sentence to be safe. target_result perhaps \"82 candidate genes\". Let's ensure JSON valid, no markdown.</think>\n\n{\"parent_value\":82,\"unit\":\"candidate genes\",\"evidence\":\"A total of 82 candidate genes were identified by intersecting 3,231 differentially expressed genes with 566 key module genes.\",\"target_result\":\"82 candidate genes\",\"number_stated\":true}", "reading": {"parent_value": 82, "unit": "candidate genes", "evidence": "A total of 82 candidate genes were identified by intersecting 3,231 differentially expressed genes with 566 key module genes.", "target_result": "82 candidate genes", "number_stated": true, "source_locator": "chars 1069-1194 of source sha256 1fef0886b20a2ad5c3044325a71b884c423ed91a82dbade59bfd6a342b915052"}, "recorded_at": "2026-10-31T15:33:49.981481+00:00"}], "agreement": false, "disagreements": {"physical_methods": {"minimax": ["An FCRLA knockdown cell model was constructed in vitro using LUAD cells.", "Cell-related phenotypic experiments, including proliferation and apoptosis, were performed.", "The integrity of the mitochondrial structure was observed using electron microscopy.", "The mitochondrial membrane potential was detected using a JC-1 probe."], "minimax_alt": ["In vitro FCRLA knockdown cell model constructed in LUAD cells", "Cell proliferation and apoptosis phenotypic experiments", "Electron microscopy to assess mitochondrial structural integrity", "JC-1 probe assay of mitochondrial membrane potential"], "decisive": false}, "analysis_methods": {"minimax": ["Differential expression analysis using DESeq2", "Weighted gene co-expression network analysis (WGCNA)", "Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses", "Protein–protein interaction network analysis using STRING", "Univariate and multivariate Cox regression", "Kaplan–Meier survival analysis", "Gene Set Enrichment Analysis (GSEA)", "Gene Set Variation Analysis (GSVA)", "Wilcoxon test", "Kruskal–Wallis test", "Spearman's correlation analysis", "One-way analysis of variance with Tukey's post-hoc significant difference test"], "minimax_alt": ["DESeq2 (version 1.40.2) differential expression analysis", "Weighted gene co-expression network analysis (WGCNA)", "Eulerr (version 7.0.0) intersection of DEGs and key module genes", "Single-sample gene set enrichment analysis (GSVA)", "Wilcoxon test", "Pearson’s correlation analysis", "Kaplan–Meier (KM) survival analysis", "Univariate Cox analysis and multivariate Cox analysis", "Nomogram model with ROC, calibration, and decision curve analysis (DCA)", "Kruskal–Wallis test", "Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses", "Gene Set Enrichment Analysis (GSEA)", "limma differential analysis", "Spearman’s correlation analysis", "One-way analysis of variance with Tukey’s post-hoc significant difference test"], "decisive": false}, "statistical_method": {"minimax": "Differential expression analysis and weighted gene co-expression network analysis (WGCNA)", "minimax_alt": "DESeq2-based differential expression analysis and weighted gene co-expression network analysis (WGCNA), followed by intersection of DEGs and key module genes", "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:cb6507144d79e76fad625eb25abc9548d9bccf0cf0e0ab9090b7db25aa0c16de", "type": "sep_package", "label": "SEP v1 package for pmid:40881693"}], "activities": [{"id": "activity:conversion:pmid:40881693", "type": "conversion", "used": ["package:cb6507144d79e76fad625eb25abc9548d9bccf0cf0e0ab9090b7db25aa0c16de"], "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": "c7c74b74-0ddc-4b4b-b66e-1dae77a98232", "parent_hash": "cb6507144d79e76fad625eb25abc9548d9bccf0cf0e0ab9090b7db25aa0c16de", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40881693 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:40881693' 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":"2026-11-04T01:47:13+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}}}