{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25852701", "kind": "science-record", "revision": 8, "content_hash": "sha256:5acabe354b51a2cac23671c8b3dbfa360f4217e879c41daa2f6d6b6d69d4f5d4", "created_at": "2026-11-01T15:40:08Z", "updated_at": "2026-11-01T22:42:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteome readjustments in the apoplastic space of Arabidopsis thaliana ggt1 mutant leaves exposed to UV-B radiation.", "doi": "10.3389/fpls.2015.00128", "pmid": "25852701", "authors": ["Anna Rita Trentin", "Micaela Pivato", "Syed M M Mehdi", "Leonard Ebinezer Barnabas", "Sabrina Giaretta", "Marta Fabrega-Prats", "Dinesh Prasad", "Giorgio Arrigoni", "Antonio Masi"], "journal": "Frontiers in plant science", "year": 2015, "abstract": "Ultraviolet-B radiation acts as an environmental stimulus, but in high doses it has detrimental effects on plant metabolism. Plasma membranes represent a major target for Reactive Oxygen Species (ROS) generated by this harmful radiation. Oxidative reactions occurring in the apoplastic space are counteracted by antioxidative systems mainly involving ascorbate and, to some extent, glutathione. The occurrence of the latter and its exact role in the extracellular space are not well documented, however. In Arabidopsis thaliana, the gamma-glutamyl transferase isoform (GGT1) bound to the cell wall takes part in the so-called gamma-glutamyl cycle for extracellular glutathione degradation and recovery, and may be implicated in redox sensing and balance. In this work, oxidative conditions were imposed with Ultraviolet-B radiation (UV-B) and studied in redox altered ggt1 mutants. The response of ggt1 knockout Arabidopsis leaves to UV-B radiation was assessed by investigating changes in extracellular glutathione and ascorbate content and their redox state, and in apoplastic protein composition. Our results show that, on UV-B exposure, soluble antioxidants respond to the oxidative conditions in both genotypes. Rearrangements occur in their apoplastic protein composition, suggesting an involvement of Hydrogen Peroxide (H2O2), which may ultimately act as a signal. Other important changes relating to hormonal effects, cell wall remodeling, and redox activities are discussed. We argue that oxidative stress conditions imposed by UV-B and disruption of the gamma-glutamyl cycle result in similar stress-induced responses, to some degree at least. Data are available via ProteomeXchange with identifier PXD001807.", "claims": [{"id": "claim-method", "statement": "After checking for a normal distribution, data were tested with One-Way ANOVA using the General linear models (GLM) procedure in SAS (SAS 9.2, 2008). Data with a non-normal distribution were submitted to a non-parametric test (Kruskal-Wallis) using XLSTAT (2014 version). In both cases, Bonferroni's test was used to ascertain differences between means. Significance was established at P = 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25852701", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "After checking for a normal distribution, data were tested with One-Way ANOVA using the General linear models (GLM) procedure in SAS (SAS 9.2, 2008). Data with a non-normal distribution were submitted to a non-parametric test (Kruskal-Wallis) using XLSTAT (2014 version). In both cases, Bonferroni's test was used to ascertain differences between means. Significance was established at P = 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001807.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25852701", "locator": "sections[28] \"Supplementary material\" paragraph 3", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001807."}], "state": "complete"}, {"id": "claim-target-result", "statement": "UV-B exposure and disruption of the gamma-glutamyl cycle produced similar stress-induced responses in Arabidopsis leaves, with rearrangements in the apoplastic proteome and changes in soluble-antioxidant responses.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "After checking for a normal distribution, data were tested with One-Way ANOVA using the General linear models (GLM) procedure in SAS (SAS 9.2, 2008). Data with a non-normal distribution were submitted to a non-parametric test (Kruskal-Wallis) using XLSTAT (2014 version). In both cases, Bonferroni's test was used to ascertain differences between means. Significance was established at P = 0.05."}, "evidence": [{"asset": "source:pmid:25852701", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our results show that, on UV-B exposure, soluble antioxidants respond to the oxidative conditions in both genotypes. Rearrangements occur in their apoplastic protein composition, suggesting an involvement of Hydrogen Peroxide (H2O2), which may ultimately act as a signal."}, {"asset": "source:pmid:25852701", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We argue that oxidative stress conditions imposed by UV-B and disruption of the gamma-glutamyl cycle result in similar stress-induced responses, to some degree at least."}, {"asset": "source:pmid:25852701", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "After checking for a normal distribution, data were tested with One-Way ANOVA using the General linear models (GLM) procedure in SAS (SAS 9.2, 2008). Data with a non-normal distribution were submitted to a non-parametric test (Kruskal-Wallis) using XLSTAT (2014 version). In both cases, Bonferroni's test was used to ascertain differences between means. Significance was established at P = 0.05."}, {"asset": "source:pmid:25852701", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD001807."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "UV-B exposure and disruption of the gamma-glutamyl cycle produced similar stress-induced responses in Arabidopsis leaves, with rearrangements in the apoplastic proteome and changes in soluble-antioxidant responses.", "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:25852701"], "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. 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We investigate the effects of UV-B radiation as an oxidizing stress condition affecting the apoplastic environment in wild type Arabidopsis and a previously-characterized ggt1 knockout mutant line.", "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:25852701:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0ff524552865bd3d80c06a33ce7460339aaaf1de1fb4c69d68f1e4a0262515c9", "bytes": 5082, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#T2", "version": null, "note": "Brief overview of expression changes in apoplastic and unlocalized proteins in the four conditions analyzed: wt (UV-B/ctrl), ggt1 (UV-B/ctrl), ctrl (ggt1/wt), and UV-B (ggt1/wt).", "structure": {"pmcid": "PMC4371699", 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["Q9FW48", "At1g33600", "Leucine-rich repeat-containing protein", "1", "", "", "0.58", ""], ["Q9LXU5", "At5g12940", "Leucine-rich repeat-containing protein", "1", "", "", "0.51", ""], ["Q9LYE7", "At5g11420", "Putative uncharacterized protein At5g11420", "1", "", "", "0.55", ""], ["Q9M2U7", "At3g54400", "AT3g54400/T12E18_90", "1", "", "", "0.64", "2.0"], ["Q9LT39", "At3g20820", "Leucine-rich repeat-containing protein", "1", "", "", "0.68", ""], ["O24603", "At2g43570", "Chitinase class 4-like protein", "1", "", "", "0.34", "0.17"], ["P33154", "At2g14610", "Pathogenesis-related protein 1", "1", "", "", "0.34", ""], ["Q8W112", "At5g20950", "Beta-D-glucan exohydrolase-like protein", "1", "", "", "0.65", ""], ["P28493", "At1g75040", "Pathogenesis-related protein 5", "1", "", "", "0.30", ""], ["Q94K76", "At5g18470", "Curculin-like (Mannose-binding) lectin family protein", "1", "", "", "0.53", ""], ["Q9LEW3", "At5g10760", "Aspartyl protease family protein", "1", "", "", "0.44", ""], ["Q9LRJ9", "At3g22060", "Cysteine-rich repeat secretory protein 38", "1", "", "", "0.49", ""], ["Q9LV60", "At5g48540", "Cysteine-rich repeat secretory protein 55", "1", "", "", "0.5", ""], ["Q9C5M8", "At4g24780", "Probable pectate lyase 18", "1", "", "", "0.68", ""], ["O23255", "At4g13940", "Adenosylhomocysteinase 1", "1", "", "", "1.5", ""], ["O50008", "At5g17920", "5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase", "1", "", "", "2.4", ""], ["Q9SVG4-2", "At4g20830", "Isoform 2 of Reticuline oxidase-like protein", "1", "", "", "", "0.43"], ["Q940G5", "At4g25900", "Aldose 1-epimerase family protein", "1", "", "", "", "0.61"], ["Q9LFA6", "At3g52840", "Beta-galactosidase 2", "1", "", "", "", "0.59"], ["Q9LU14", "At3g16370", "GDSL esterase/lipase APG", "1", "", "", "", "1.6"], ["Q39099", "At2g06850", "Xyloglucan endotransglucosylase/hydrolase prot 4", "1", "", "", "", "1.8"], ["Q9LFR3", "At5g14920", "Gibberellin-regulated protein 14", "1", "", "", "", "1.8"], ["O04496", "At1g09750", "Aspartyl protease-like protein", "1", "", "", "", "1.9"], ["Q9FH82", "At5g45280", "AT5g45280/K9E15_6", "1", "", "", "", "2.0"]], "row_count": 60, "column_count": 8, "numeric_cells": 270, "header_rows": 1, "locator": "section[17]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:PXD001807 not downloaded", "asset:data:geo:PXD001807 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "After checking for a normal distribution, data were tested with One-Way ANOVA using the General linear models (GLM) procedure in SAS (SAS 9.2, 2008). Data with a non-normal distribution were submitted to a non-parametric test (Kruskal-Wallis) using XLSTAT (2014 version). In both cases, Bonferroni's test was used to ascertain differences between means. Significance was established at P = 0.05."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD001807"], "resolved_accessions": ["PXD001807"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001807."], "basis": "The paper names PXD001807 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:25852701", "data:geo:PXD001807", "asset:table:pmid:25852701:1", "asset:table:pmid:25852701:2", "asset:table:pmid:25852701:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001807"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:23:48Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 125794, "completion_tokens": 4508, "cached_tokens": 1544}}, "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:25852701", "type": "paper", "label": "pmid:25852701"}, {"id": "source:pmid:25852701", "type": "manuscript", "label": "PMID 25852701 full text"}, {"id": "data:geo:PXD001807", "type": "dataset", "label": "GEO PXD001807"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25852701", "type": "paper", "label": "pmid:25852701"}, {"id": "source:pmid:25852701", "type": "manuscript", "label": "PMID 25852701 full text"}, {"id": "data:geo:PXD001807", "type": "dataset", "label": "GEO PXD001807"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25852701", "type": "extraction", "used": ["source:pmid:25852701"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001807", "type": "accession_resolution", "used": ["data:geo:PXD001807"], "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:25852701", "parent_hash": "sha256:36468a20fa53e6a9e3f81c2926231c386c42ca2ffb9eb1df7a185df27453b0d1", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD001807 licence not read", "asset:data:geo:PXD001807 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": ["ournal/10.3389/fpls.2015.00128/abstract. The mass spectrometry proteomics data have been deposited to the P", "s.2015.00128/abstract. The mass spectrometry proteomics data have been deposited to the ProteomeXcha"], "order_basis": "paper_text_order:3852", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["After checking for a normal distribution, data were tested with One-Way ANOVA using the General linear models (GLM) procedure in SAS (SAS 9.2, 2008). Data with a non-normal distribution were submitted to a non-parametric test (Kruskal-Wallis) using XLSTAT (2014 version). In both cases, Bonferroni's test was used to ascertain differences between means. Significance was established at P = 0.05."], "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":"2026-11-04T01:42:44+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}}}