{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41369518", "kind": "science-record", "revision": 3, "content_hash": "sha256:7de74f9439f7dd4b36021ecba82d8ff161845f3ddf9be404d21bca9cb5f91517", "created_at": "2026-11-01T20:31:23Z", "updated_at": "2026-11-01T22:15:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genomic and proteomic characterization of a newly isolated Paenarthrobacter ilicis strain and its plasmid-mediated xanthan degradation.", "doi": "10.1128/spectrum.01690-25", "pmid": "41369518", "authors": ["Michael Thomas", "Andreas Schlüter", "Jenny Fjodorova", "Christian Rückert", "Tobias Busche", "Karsten Niehaus"], "journal": "Microbiology spectrum", "year": 2026, "abstract": "Environmental soil samples enriched with xanthan gum led to the discovery and isolation of a novel strain of motile Paenarthrobacter ilicis in Bielefeld, Germany, which possesses a previously uncharacterized xanthan utilization gene region on its sole plasmid. This bacterium is the first member of the Paenarthrobacter genus to feature the ability to degrade xanthan. Growth experiments elucidated the optimal growth conditions with regard to pH (7.0) and temperature (28°C-30°C). The genome of Paenarthrobacter ilicis strain 6C consists of two replicons, namely a chromosome with 4,049,144 nucleotides (62.8% GC content) and a plasmid of 147,742 base pairs (61.8% GC content). This novel Paenarthrobacter ilicis strain carries 3,806 predicted coding regions, approximately half (51%) of which were verified with proteome analysis. Cultures grown with either glucose or xanthan as a carbon source were compared in relation to protein abundances at four growth stages and time points with regard to both intracellular and extracellular protein fractions. The proteome analysis (data are available via ProteomeXchange with identifier PXD063987) was undertaken using an LC-ESI-MS-MS shotgun proteomics approach, and the proteins were identified and quantified via label-free quantification using MaxQuant 2.6.6. This proteomics investigation exposed significant differences in protein abundances with regard to time and condition. Among the most highly enriched proteins seen when feeding exclusively on xanthan as a carbon source were enzymes encoded on a xanthan degradation plasmid (pPANIL_6C) with a xanthan utilization region coding for the PL8 xanthan lyase, GH38-, GH3-, GH9-family proteins, and several sugar transporters. These proteins constitute key components of a prospective xanthan degradation pathway.IMPORTANCEA novel Paenarthrobacter isolate was sequenced and characterized by proteome analysis to provide the first clear look at a novel genus in the realm of xanthan-degrading microorganisms. This research provides additional groundwork for the ongoing characterization of Paenarthrobacter, as well as widening the understanding of xanthan-degrading microorganisms. For the first time, a xanthan degradation region was identified on a plasmid 1 kb directly downstream from a mobilization gene (mobF), posing the question of whether this metabolic capacity can be shared through horizontal gene transfer. Overall, this research expands the current knowledge base regarding Paenarthrobacter biology, as well as microbial xanthan degradation and utilization.", "claims": [{"id": "claim-method", "statement": "The proteins in the ROI and “Rest of Genome” groups were compared and used in statistical tests (t-test and K-S test) to determine if the fold change behavior of the ROI group is significantly different from that of all other proteins.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41369518", "locator": "sections[33] \"Statistical evaluation\" paragraph 5", "quote": "The proteins in the ROI and “Rest of Genome” groups were compared and used in statistical tests (t-test and K-S test) to determine if the fold change behavior of the ROI group is significantly different from that of all other proteins."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The trimmed genomic data are available from SRA via BioProject PRJNA1182270. The annotated chromosome and plasmid are available under the GenBank accession numbers CP173685 and CP173686. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD063987 and https://dx.doi.org/10.6019/PXD063987 (53).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41369518", "locator": "sections[36] \"DATA AVAILABILITY\" paragraph 2", "quote": "The trimmed genomic data are available from SRA via BioProject PRJNA1182270. The annotated chromosome and plasmid are available under the GenBank accession numbers CP173685 and CP173686. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD063987 and https://dx.doi.org/10.6019/PXD063987 (53)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "At an OD600 of 1.0, 12 proteins were measured, and all of them were significantly overabundant in the xanthan condition (100%).", "kind": "quantitative", "target": {"value": 100.0, "unit": "per cent", "tolerance": null, "source": "At an OD600 of 1.0, 12 proteins were measured, and all of them were significantly overabundant in the xanthan condition (100%)."}, "evidence": [{"asset": "source:pmid:41369518", "locator": "sections[7] \"Differences in the Paenarthrobacter ilicis 6C proteome grown in medium with xanthan relative to glucose\" paragraph 8", "quote": "At an OD600 of 1.0, 12 proteins were measured, and all of them were significantly overabundant in the xanthan condition (100%)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "At an OD600 of 1.0, 12 proteins were measured, and all of them were significantly overabundant in the xanthan condition (100%).", "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:41369518"], "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:PXD063987"], "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:PXD063987"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41369518", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1128/spectrum.01690-25", "sha256": "sha256:623b5c61583282ee7526a4a9c9492d15899f29ccd6124bb6149ab1440cdac662", "bytes": 89416, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1128/spectrum.01690-25", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12772297", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD063987", "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=PXD063987", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD063987", "version": null, "note": "The trimmed genomic data are available from SRA via BioProject PRJNA1182270. The annotated chromosome and plasmid are available under the GenBank accession numbers CP173685 and CP173686. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD063987 and https://dx.doi.org/10.6019/PXD063987 (53).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The trimmed genomic data are available from SRA via BioProject PRJNA1182270. The annotated chromosome and plasmid are available under the GenBank accession numbers CP173685 and CP173686. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD063987 and https://dx.doi.org/10.6019/PXD063987 (53).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Paenarthrobacter ilicis 6C glucose vs xanthan proteome", "resolution_checked_at": "2026-11-01T20:16:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA1182270", "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=PRJNA1182270", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA1182270", "version": null, "note": "The trimmed genomic data are available from SRA via BioProject PRJNA1182270. The annotated chromosome and plasmid are available under the GenBank accession numbers CP173685 and CP173686. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD063987 and https://dx.doi.org/10.6019/PXD063987 (53).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The trimmed genomic data are available from SRA via BioProject PRJNA1182270. The annotated chromosome and plasmid are available under the GenBank accession numbers CP173685 and CP173686. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD063987 and https://dx.doi.org/10.6019/PXD063987 (53).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:20Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD063987 not downloaded", "asset:data:geo:PXD063987 licence not read", "asset:data:geo:PRJNA1182270 not downloaded", "asset:data:geo:PRJNA1182270 licence not read"]}, "analysis": {"state": "partial", "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": "The proteins in the ROI and “Rest of Genome” groups were compared and used in statistical tests (t-test and K-S test) to determine if the fold change behavior of the ROI group is significantly different from that of all other proteins."}}, {"id": "method-2", "family": "image_quantification", "specific": "densitometry", "label": "Image analysis / quantification", "dsl_operations": ["segment_objects", "quantify_intensity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["image_stack"], "evidence": {"score": 0.8, "band": "high", "quote": "optical density"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "quantify_intensity", "expected_value": 100.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["PRJNA1182270", "PXD063987"], "resolved_accessions": ["PXD063987"], "statements": ["The trimmed genomic data are available from SRA via BioProject PRJNA1182270. The annotated chromosome and plasmid are available under the GenBank accession numbers CP173685 and CP173686. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD063987 and https://dx.doi.org/10.6019/PXD063987 (53)."], "basis": "The paper names PXD063987 in SRA 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:41369518", "data:geo:PXD063987"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD063987"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:07:47Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 24362, "completion_tokens": 2074, "cached_tokens": 264}}, "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:41369518", "type": "paper", "label": "pmid:41369518"}, {"id": "source:pmid:41369518", "type": "manuscript", "label": "PMID 41369518 full text"}, {"id": "data:geo:PXD063987", "type": "dataset", "label": "GEO PXD063987"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41369518", "type": "paper", "label": "pmid:41369518"}, {"id": "source:pmid:41369518", "type": "manuscript", "label": "PMID 41369518 full text"}, {"id": "data:geo:PXD063987", "type": "dataset", "label": "GEO PXD063987"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41369518", "type": "extraction", "used": ["source:pmid:41369518"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD063987", "type": "accession_resolution", "used": ["data:geo:PXD063987"], "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:41369518", "parent_hash": "sha256:871475f5c776dad8bfdbb8ede71ce78969e101e4a1bd9b49d1692491e794dfe1", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PRJNA1182270 licence not read", "asset:data:geo:PRJNA1182270 not downloaded", "asset:data:geo:PXD063987 licence not read", "asset:data:geo:PXD063987 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["The proteins in the ROI and “Rest of Genome” groups were compared and used in statistical tests (t-test and K-S test) to determine if the fold change behavior of the ROI group is significantly different from that of all other proteins."], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T03:13:23+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}}}