{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31547269", "kind": "science-record", "revision": 6, "content_hash": "sha256:2e8aa0400c3ff791295e99f4cea82e2b38e2133591ea46a012b0ece950443771", "created_at": "2026-11-01T15:40:49Z", "updated_at": "2026-11-01T21:22:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteome Profiling of the Exhaled Breath Condensate after Long-Term Spaceflights.", "doi": "10.3390/ijms20184518", "pmid": "31547269", "authors": ["Alexey S Kononikhin", "Alexander G Brzhozovskiy", "Anna M Ryabokon", "Kristina Fedorchenko", "Natalia V Zakharova", "Alexander I Spasskii", "Igor A Popov", "Vyacheslav K Ilyin", "Zoya O Solovyova", "Lyudmila Kh Pastushkova", "Alexey V Polyakov", "Sergey D Varfolomeev", "Irina M Larina", "Evgeny N Nikolaev"], "journal": "International journal of molecular sciences", "year": 2019, "abstract": "Comprehensive studies of the effects of prolonged exposure to space conditions and the overload experienced during landing on physiological and biochemical changes in the human body are extremely important in the context of planning long-distance space flights, which can be associated with constant overloads and various risk factors for significant physiological changes. Exhaled breath condensate (EBC) can be considered as a valuable subject for monitoring physiological changes and is more suitable for long-term storage than traditional monitoring subjects such as blood and urine. Herein, the EBC proteome changes due to the effects of spaceflight factors are analyzed. Thirteen EBC samples were collected from five Russian cosmonauts (i) one month before flight (background), (ii) immediately upon landing modules in the field (R0) after 169-199 days spaceflights, and (iii) on the seventh day after landing (R+7). Semi-quantitative label-free EBC proteomic analysis resulted in 164 proteins, the highest number of which was detected in EBC after landing (R0). Pathways enrichment analysis using the GO database reveals a large group of proteins which take part in keratinization processes (CASP14, DSG1, DSP, JUP, and so on). Nine proteins (including KRT2, KRT9, KRT1, KRT10, KRT14, DCD, KRT6C, KRT6A, and KRT5) were detected in all three groups. A two-sample Welch's t-test identified a significant change in KRT2 and KRT9 levels after landing. Enrichment analysis using the KEGG database revealed the significant participation of detected proteins in pathogenic E. coli infection (ACTG1, TUBA1C, TUBA4A, TUBB, TUBB8, and YWHAZ), which may indicate microbiota changes associated with being in space. This assumption is confirmed by microbial composition analysis. In general, the results suggest that EBC can be used for noninvasive monitoring of health status and respiratory tract pathologies during spaceflights, and that the obtained data are important for the development of medicine for use in extreme situations. Data are available from ProteomeXchange using the identifier PXD014191.", "claims": [{"id": "claim-method", "statement": "A two-sample Welch’s t-test was applied to identify the significantly changed proteins between the study groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31547269", "locator": "sections[2] \"2. Results and Discussion\" paragraph 10", "quote": "A two-sample Welch’s t-test was applied to identify the significantly changed proteins between the study groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All LC-MS/MS and proteomic data are available via ProteomeXchange with identifier PXD014191.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31547269", "locator": "sections[9] \"Supplementary Materials\" paragraph 2", "quote": "All LC-MS/MS and proteomic data are available via ProteomeXchange with identifier PXD014191."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31547269"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD014191"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD014191"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31547269", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms20184518", "sha256": "sha256:7a344f9a064395d2bdba532225d3b0985d03225976a96af0cb8868208f45b7e0", "bytes": 32855, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms20184518", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6770753", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD014191", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD014191", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD014191", "version": null, "note": "All LC-MS/MS and proteomic data are available via ProteomeXchange with identifier PXD014191.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All LC-MS/MS and proteomic data are available via ProteomeXchange with identifier PXD014191.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteome profiling of the exhaled breath condensate after long-term spaceflights", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31547269:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e023528bbb776697e96538f227a05975ca300626efce3fa321508c6adc0ee5a0", "bytes": 1100, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[1]#ijms-20-04518-t001", "version": null, "note": "List of proteins belongs to keratins family presented in three study groups: background (month before flight), R0, and R+7 groups.", "structure": {"pmcid": "PMC6770753", "section_index": 2, "section_title": "2. Results and Discussion", "row_count": 8, "column_count": 7}, "table": {"label": "Table 1", "caption": "List of proteins belongs to keratins family presented in three study groups: background (month before flight), R0, and R+7 groups.", "rows": [["Protein IDs", "Protein Names", "Gene Names", "Background", "1 Day After Landing", "7 Day After Landing", "Peptides"], ["P04264", "Keratin, type II cytoskeletal 1", "KRT1", "17.6 ± 1.5", "18.4 ± 0.3", "17.8 ± 0.6", "34"], ["P13645", "Keratin, type I cytoskeletal 10", "KRT10", "16.2 ± 1.4", "18.2 ± 0.4", "16.1 ± 1.3", "30"], ["P02533", "Keratin, type I cytoskeletal 14", "KRT14", "15.4 ± 0.1", "15.1 ± 1.4", "14.5 ± 0.1", "23"], ["P35908", "Keratin, type II cytoskeletal 2 epidermal", "KRT2", "16 ± 0.2", "17 ± 0.4", "15.4 ± 0.9", "29"], ["P13647", "Keratin, type II cytoskeletal 5", "KRT5", "14.1 ± 0.2", "13.8 ± 1.1", "13.6 ± 0.3", "24"], ["P02538", "Keratin, type II cytoskeletal 6", "KRT6", "14.1 ± 0.1", "14.5 ± 1.5", "13.1 ± 0", "25"], ["P35527", "Keratin, type I cytoskeletal 9", "KRT9", "17 ± 0", "15.6 ± 1.2", "16.5 ± 0.2", "16"]], "row_count": 8, "column_count": 7, "numeric_cells": 46, "header_rows": 1, "locator": "section[2]/table-wrap[1]#ijms-20-04518-t001"}}, {"id": "asset:table:pmid:31547269:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:73fe275d9e86f08b65929731fcbb6427d6a95759766119fbd3d35c5cf701c8aa", "bytes": 1610, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[2]#ijms-20-04518-t002", "version": null, "note": "List of Micro-organisms of selected biotopes (mouth, dental plaque, tongue, and cheek) collected from cosmonauts. Colony-forming units (CFU) are presented.", "structure": {"pmcid": "PMC6770753", "section_index": 2, "section_title": "2. Results and Discussion", "row_count": 37, "column_count": 3}, "table": {"label": "Table 2", "caption": "List of Micro-organisms of selected biotopes (mouth, dental plaque, tongue, and cheek) collected from cosmonauts. Colony-forming units (CFU) are presented.", "rows": [["Biotopes", "Micro-Organisms", "CFU"], ["45 days before spaceflight"], ["Mouth", "Enterobacterium sp.", "107"], ["Enterococcus sp.", "104"], ["Dental plaque", "Streptococcus sp.", "102"], ["Enterobacterium sp.", "105"], ["Tongue", "Enterobacterium sp", "103"], ["Streptococcus sp.", "102"], ["Enterococcus sp.", "104"], ["Cheek", "Staphylococcus sp.", "104–105"], ["1 day before spaceflight"], ["Dental plaque", "Staphylococcus sp.", "102"], ["Tongue", "Enterococcus sp.", "106"], ["Cheek", "Staphylococcus sp.", "104"], ["During the spaceflight"], ["Mouth", "Staphylococcus sp.", "102"], ["Dental plaque", "Staphylococcus sp.", "103–107"], ["Tongue", "Staphylococcus sp.", "102"], ["E.coli", "107"], ["Cheek", "Staphylococcus sp.", "~101"], ["Immediately after landing (R0)"], ["Mouth", "Enterococcus sp.", "101–106"], ["Staphylococcus sp.", "101"], ["Dental plaque", "Enterococcus sp.", "103–106"], ["Staphylococcus sp.", "103"], ["Tongue", "Staphylococcus sp.", "103"], ["Enterococcus sp.", "103"], ["Cheek", "Staphylococcus sp.", "~103"], ["7 day after landing (R+7)"], ["Mouth", "Enterococcus sp.", "103–105"], ["S. Aureus", "104 Met S"], ["Dental plaque", "Staphylococcus sp.", "101"], ["Enterococcus sp.", "105"], ["Tongue", "Enterococcus sp.", "105–108"], ["S. Aureus", "107 Met S."], ["Cheek", "Staphylococcus sp.", "101–106"], ["S. Aureus", "104 Met S"]], "row_count": 37, "column_count": 3, "numeric_cells": 34, "header_rows": 1, "locator": "section[2]/table-wrap[2]#ijms-20-04518-t002"}}], "gaps": ["asset:data:geo:PXD014191 not downloaded", "asset:data:geo:PXD014191 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "welch_t_test", "label": "Group comparison", "dsl_operations": ["welch_t"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A two-sample Welch’s t-test was applied to identify the significantly changed proteins between the study groups."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["welch_t"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: welch_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD014191"], "resolved_accessions": ["PXD014191"], "statements": ["All LC-MS/MS and proteomic data are available via ProteomeXchange with identifier PXD014191."], "basis": "The paper names PXD014191 in ProteomeXchange Consortium through the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["welch_t"], "assets": ["source:pmid:31547269", "data:geo:PXD014191", "asset:table:pmid:31547269:1", "asset:table:pmid:31547269:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD014191"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:16:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28400, "completion_tokens": 830, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:31547269", "type": "paper", "label": "pmid:31547269"}, {"id": "source:pmid:31547269", "type": "manuscript", "label": "PMID 31547269 full text"}, {"id": "data:geo:PXD014191", "type": "dataset", "label": "GEO PXD014191"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31547269", "type": "paper", "label": "pmid:31547269"}, {"id": "source:pmid:31547269", "type": "manuscript", "label": "PMID 31547269 full text"}, {"id": "data:geo:PXD014191", "type": "dataset", "label": "GEO PXD014191"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31547269", "type": "extraction", "used": ["source:pmid:31547269"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD014191", "type": "accession_resolution", "used": ["data:geo:PXD014191"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:31547269", "parent_hash": "sha256:2a32815ce6ce5cbdb8b221ed54ed7479e8a34ed208e1f99841a306c72ad7fef3", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD014191 licence not read", "asset:data:geo:PXD014191 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ding (R+7). Semi-quantitative label-free EBC proteomic analysis resulted in 164 proteins, the highe", "om/1422-0067/20/18/4518/s1. All LC-MS/MS and proteomic data are available via ProteomeXchange with", "://www.mdpi.com/1422-0067/20/18/4518/s1. All LC-MS/MS and proteomic data are available via Proteom"], "order_basis": "paper_text_order:993", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["welch_t"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["A two-sample Welch’s t-test was applied to identify the significantly changed proteins between the study groups."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T00:47:24+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}}}