{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39915534", "kind": "science-record", "revision": 1, "content_hash": "sha256:614a2f9952a4a055e0f7c51608f82273c945c0169ff8e52d20bb6dfe2c85d865", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T10:25:49Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma.", "doi": "10.1038/s41598-025-88120-2", "pmid": "39915534", "authors": null, "journal": "Scientific reports", "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": 18.0, "unit": "microbial genera", "tolerance": null, "source": "chars 779-867 of source sha256 3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458"}, "evidence": [{"asset": "source:pmid:39915534", "locator": "chars 779-867 of source sha256 3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "quote": "18 microbial genera were found to be significantly associated with RFS in LUSC patients."}]}], "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:39915534"], "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:39915534", "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:39915534' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39915534", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-88120-2", "sha256": "sha256:3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-88120-2", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:39915534 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:39915534"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39915534"]}, "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": "76a98ad9cf962515f83afc39a4070116bc6294bcbbe34c073a46b753f974087f", "source_hash": "3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "raw_response_sha256": "sha256:ecd05a945bde0aecc73a7f77373f58f0c75687138f640f03ab52d8271baf963c", "raw_response_chars": 4647}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "794f7960016dea602082eadfac06bec410d4211c864bf81c89453f643991a0e0", "source_hash": "3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "raw_response_sha256": "sha256:36aefab4b8208eaf32a1cb022883b893aadb335adfe1ae265286824c0e4b43b8", "raw_response_chars": 44171}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "8719c88a18edad84f5bcb5e7eec78055daef7fee8e35a74ad94359792d70c484", "source_hash": "3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "raw_response": "{\"parent_value\":18,\"unit\":\"microbial genera\",\"evidence\":\"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\",\"target_result\":\"The paper states that 18 microbial genera were significantly associated with recurrence-free survival (RFS) in LUSC patients.\",\"number_stated\":true}", "reading": {"parent_value": 18, "unit": "microbial genera", "evidence": "18 microbial genera were found to be significantly associated with RFS in LUSC patients.", "target_result": "The paper states that 18 microbial genera were significantly associated with recurrence-free survival (RFS) in LUSC patients.", "number_stated": true, "source_locator": "chars 779-867 of source sha256 3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458"}, "recorded_at": "2026-10-31T15:29:26.675986+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "e73fb191414a2d3476f6aefde418bddbe714bd915ec1219a60c1d36f7d436b52", "source_hash": "3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "raw_response": "<think>We need answer JSON only. Need inspect supplied text. Asked single numerical result headline for main finding. Source only abstract + methods, no results section except abstract: \"18 microbial genera were found significantly associated...\" \"four mRNA...\" Is headline numerical result perhaps 18 microbial genera? Registered target vague \"headline numerical result the paper states for its main finding\". Need identify number stated for main finding. Likely 18 microbial genera? Could be four mRNA. Need determine perhaps paper title, main finding is microbial and genetic markers; abstract highlights \"18 microbial genera were found to be significantly associated with RFS...\" and \"finally identifying four mRNA...\" Which single numerical result replication target? They ask headline number only, value paper itself states for registered target. The source text likely omitted Results due truncated? We can only extract. Registered target defined generically. Need perhaps answer 18 microbial genera because first/headline count, main finding. Need quote exact contiguous clause containing number and attribution. Evidence exact quote. Unit \"microbial genera\" perhaps unit. parent_value 18. target_result could say \"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\" number_stated true. Evidence same exact quote. But perhaps headline numerical result is four mRNA? Let's carefully parse.\n\nPrompt probably benchmark asks identify \"single numerical result that a replication of the registered target has to reproduce.\" Registered target is \"the headline numerical result the paper states for its main finding\". In source, abstract likely has key numbers, and methods. The paper's title exploring prognostic role. Main finding could involve risk score model with 18 microbial genera and 4 mRNAs. Which is headline? Maybe the benchmark expects article's key finding metric (e.g., AUC) but supplied source lacks result values. Yet abstract says counts. They want single numerical result, likely \"18 microbial genera\". Let's reason wording: \"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.\" This task generated with target maybe specific claim hidden in source. Registered target description generic, and source may contain exact number. Need output.\n\nCould select 18 microbial genera as headline because sentence \"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\" This is main finding and a count. Unit perhaps \"microbial genera\" (not a physical unit). JSON unit must string. Evidence exact contiguous quote. target_result perhaps concise. Ensure exact punctuation. Source has:\n\"18 microbial genera were found to be significantly associated with RFS in LUSC patients. The microbial signature built with these microbial genera, exhibited robust predictive accuracy in both the training and validation datasets. Furthermore, hub mRNA between high- and low-risk groups were selected by XGBOOST and intersect with mRNAs screened by univariate Cox regression analysis, finally identifying four mRNA significantly associated with LUSC prognosis.\"\n\nCould evidence quote whole clause/sentence. They request headline number only perhaps target_result could be \"18 microbial genera\". Need no extra prose outside JSON.\n\nBut maybe main headline is four mRNA because final main finding. Which one would replication need reproduce? Let's inspect title and abstract ordering. Main finding: microbiome risk score based on 18 genera. Abstract says 18 microbial genera associated; microbial signature predictive. Then four mRNA. If asked \"single numerical result\" perhaps likely number in paper's title? No title no number. They may expect first/most headline number = 18. \"the headline numerical result the paper states for its main finding\" and evidence must attribution. The abstract's central finding is risk score model from 18 genera, likely count.\n\nCould unit be \"microbial genera\" exactly. The number is count. parent_value 18. target_result perhaps \"18 microbial genera were significantly associated with recurrence-free survival (RFS) in LUSC patients.\" But exact source calls RFS; don't expand unless target result no evidence constraint? Better mirror.\n\nNeed valid JSON, escaped perhaps no issue.</think>\n\n{\"parent_value\":18,\"unit\":\"microbial genera\",\"evidence\":\"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\",\"target_result\":\"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\",\"number_stated\":true}", "reading": {"parent_value": 18, "unit": "microbial genera", "evidence": "18 microbial genera were found to be significantly associated with RFS in LUSC patients.", "target_result": "18 microbial genera were found to be significantly associated with RFS in LUSC patients.", "number_stated": true, "source_locator": "chars 779-867 of source sha256 3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458"}, "recorded_at": "2026-10-31T15:29:30.240024+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "18 microbial genera were significantly associated with recurrence-free survival (RFS) in LUSC patients.", "minimax_alt": "18 microbial genera were found to be significantly associated with RFS in LUSC patients.", "decisive": false}, "analysis_methods": {"minimax": ["univariate Cox proportional hazards analysis", "least absolute shrinkage and selection operator (LASSO) regression", "10-fold cross-validation", "multivariate Cox regression analysis"], "minimax_alt": ["univariate Cox proportional hazards analysis", "LASSO regression", "10-fold cross-validation", "multivariate Cox regression analysis"], "decisive": false}, "statistical_method": {"minimax": "univariate Cox regression analysis combined with the least absolute contraction and selection operator (LASSO) regression", "minimax_alt": "Univariate Cox proportional hazards analysis combined with LASSO regression, with the LASSO regularization parameter selected by 10-fold cross-validation", "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:151e519206a3fff4f44a32f5e10f09db321b5bd8832ab8ef095bd0faa01b0de8", "type": "sep_package", "label": "SEP v1 package for pmid:39915534"}], "activities": [{"id": "activity:conversion:pmid:39915534", "type": "conversion", "used": ["package:151e519206a3fff4f44a32f5e10f09db321b5bd8832ab8ef095bd0faa01b0de8"], "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": "e9423780-c4b4-4514-8965-efa167158bd1", "parent_hash": "151e519206a3fff4f44a32f5e10f09db321b5bd8832ab8ef095bd0faa01b0de8", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:39915534 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:39915534' 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":"2026-11-04T02:39:08+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}}}