{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31666027", "kind": "science-record", "revision": 7, "content_hash": "sha256:54f537287807250714082a27dcdf3aa3f105e2bdc6b1a62a3d7df1ea023345ba", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T22:00:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The olfactory secretome varies according to season in female sheep and goat.", "doi": "10.1186/s12864-019-6194-z", "pmid": "31666027", "authors": ["Paul Cann", "Malika Chabi", "Aliénor Delsart", "Chrystelle Le Danvic", "Jean-Michel Saliou", "Manon Chasles", "Matthieu Keller", "Patricia Nagnan-Le Meillour"], "journal": "BMC genomics", "year": 2019, "abstract": "BACKGROUND: Small ungulates (sheep and goat) display a seasonal breeding, characterised by two successive periods, sexual activity (SA) and sexual rest (SR). Odours emitted by a sexually active male can reactivate the ovulatory cycle of anoestrus females. The plasticity of the olfactory system under these hormonal changes has never been explored at the peripheral level of odours reception. As it was shown in pig that the olfactory secretome (proteins secreted in the nasal mucus) could be modified under hormonal control, we monitored its composition in females of both species through several reproductive seasons, thanks to a non-invasive sampling of olfactory mucus. For this purpose, two-dimensional gel electrophoresis (2D-E), western-blot with specific antibodies, MALDI-TOF and high-resolution (nano-LC-MS/MS) mass spectrometry, RACE-PCR and molecular modelling were used.\nRESULTS: In both species the olfactory secretome is composed of isoforms of OBP-like proteins, generated by post-translational modifications, as phosphorylation, N-glycosylation and O-GlcNAcylation. Important changes were observed in the olfactory secretome between the sexual rest and the sexual activity periods, characterised in ewe by the specific expression of SAL-like proteins and the emergence of OBPs O-GlcNAcylation. In goat, the differences between SA and SR did not come from new proteins expression, but from different post-translational modifications, the main difference between the SA and SR secretome being the number of isoforms of each protein. Proteomics data are available via ProteomeXchange with identifier PXD014833.\nCONCLUSION: Despite common behaviour, seasonal breeding, and genetic resources, the two species seem to adapt their olfactory equipment in SA by different modalities: the variation of olfactory secretome in ewe could correspond to a specialization to detect male odours only in SA, whereas in goat the stability of the olfactory secretome could indicate a constant capacity of odours detection suggesting that the hallmark of SA in goat might be the emission of specific odours by the sexually active male. In both species, the olfactory secretome is a phenotype reflecting the physiological status of females, and could be used by breeders to monitor their receptivity to the male effect.", "claims": [{"id": "claim-method", "statement": "The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [49].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31666027", "locator": "sections[32] \"Molecular phylogenetic analysis by maximum likelihood method\" paragraph 2", "quote": "The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [49]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The full-length sequences of Chir-OBP2, Chir-OBP4, Oari-OBP2, and Oari-OBP4 were deposited in GenBank database with accession numbers: MK908982, MK908983, MK908984 and MK908985, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31666027", "locator": "sections[41] \"notes\" paragraph 1", "quote": "The full-length sequences of Chir-OBP2, Chir-OBP4, Oari-OBP2, and Oari-OBP4 were deposited in GenBank database with accession numbers: MK908982, MK908983, MK908984 and MK908985, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:31666027"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31666027", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12864-019-6194-z", "sha256": 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"structure": {"pmcid": "PMC6822404", "section_index": 5, "section_title": "Olfactory secretome of ewes", "row_count": 9, "column_count": 7}, "table": {"label": "Table 1", "caption": "Proteins identified in spots from SR and SA 2D-E gels of ewes", "rows": [["Protein name Accession number UniProt KB", "Ewe 30,118 (Fig. 1a, b)", "Ewe 30,094 (Additional file 1: Figure S2a, S2b)", "Ewe 30,056 (Additional file 1: Figure S2c, S2d)"], ["SRa", "SAa", "SRa", "SAa", "SR¤", "SA¤"], ["Protein found in spot n°"], ["Oari-OBP1 W5PHM2", "Not found", "25", "45", "Not found", "Not found", "88 to 90, 92 & 93"], ["Oari-OBP2 W5PGN0", "1 to 4, 8 to 10", "11, 15, 17, 18 & 24 to 29", "35 to 38 & 45 to 48", "49 to 51, 53 to 56, 58 to 68, 70 & 71", "72, 73 & 76 to 83", "84 to 86, 89 & 93 to 103"], ["Oari-OBP3 W5PGW3", "Not found", "18 to 21", "Not found", "60", "72, 78 & 81 to 83", "87, 88, 95, 98, 99 & 101"], ["Oari-OBP4 W5PHS2", "1, 8 & 9", "11, 12, 15, 17, 18 & 24 to 28", "35, 45 & 46", "51, 55, 56, 58, 61 to 68 & 71", "72 to 83", "93, 98 to 100"], ["Oari-SAL1/2 W5P8W4 / W5P8Y1", "Not found", "11 to 15", "Not found", "49 to 53, 55, 56, 58 & 60", "75 & 81", "84 to 89, 91 & 99"], ["Oari-VEG1 W5NUS5", "Not found", "Not found", "Not found", "69 & 70", "Not found", "Not found"]], "row_count": 9, "column_count": 7, "numeric_cells": 28, "header_rows": 2, "locator": "section[5]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31666027:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:21b4d222423b76db9186e74f0f24dd5b5b532f1fc1783e18a247990c11cc7e49", "bytes": 1816, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#Tab2", "version": null, "note": "Proteins identified in spots from SR and SA 2D-E gels of goats", "structure": {"pmcid": "PMC6822404", "section_index": 5, "section_title": "Olfactory secretome of ewes", "row_count": 13, "column_count": 7}, "table": {"label": "Table 2", "caption": "Proteins identified in spots from SR and SA 2D-E gels of goats", "rows": [["Protein name Accession number GenPept", "Goat 30,363 (Fig. 1c, d)", "Goat 30,422 (Additional file 1: Figure S3a, S3b)", "Goat 30,432 (Additional file 1: Figure S3c, S3d)"], ["SRa", "SA¤", "SR¤", "SA¤", "SRa", "SAa"], ["Protein found in spot n°"], ["Chir-OBP1 XP_017899536.1", "Not found", "Not found", "Not found", "Not found", "85", "124, 129 & 144"], ["Chir-OBP2 XP_017899208.1", "1, 2, 5 to 15, 17, 20, 22, 24 & 25", "27 to 29, 31 to 43 & 45", "46 to 64, 66 to 70 & 73", "74 to 82", "83 to 105", "108, 109, 121, 122, 124, 126 to 134, 136, 137, 139, 140 & 142 to 145"], ["Chir-OBP3 XP_005701296.1", "Not found", "30 to 32", "47 to 49, 51 to 54, 57, 59, 62, 66 & 67", "75, 76 & 80", "Not found", "127"], ["Chir-OBP4 XP_017899515.1", "1 to 3, 5 to 15 & 17 to 19", "31 to 35, 38, 40, 41 & 45", "46 to 48, 51 to 63, 65 & 73", "76 & 78", "83 to 95 & 97 to 104", "108 to 114, 117 to 119, 122 to 124, 127 to 134, 136 to 138, 140, 142, 144 & 145"], ["Chir-OBP5 XP_017899538.1", "Not found", "28, 30 & 32", "46, 47, 50, 52 to 56, 59, 60, 64, 68, 70 & 71", "76, 78 & 79", "86", "121 & 122"], ["Chir-OBP6 XP_017900101.1", "1", "28 to 31, 36, 37 & 45", "47, 49 & 72", "74 & 76 to 78", "86", "Not found"], ["Chir-SAL1/2 XP_017908099/8.1", "2", "31, 32, 35, 41, 43 & 44", "46 to 48, 50 to 57, 59 to 67, 69, 71 & 72", "74, 77, 78 & 80 to 82", "87 & 90", "Not found"], ["Chir-VEG1 XP_005687416.1", "10", "30 & 34", "54, 55 & 63", "Not found", "Not found", "Not found"], ["Chir-VEG2 XP_017911671.1", "11", "32, 35 & 39 to 43", "46 to 67, 69, 71 & 73", "78 & 80 to 82", "97 to 100", "134"], ["Chir-VEG3 XP_017910286.1", "Not found", "32 & 38", "Not found", "74 & 77", "Not found", "Not found"]], "row_count": 13, "column_count": 7, "numeric_cells": 57, "header_rows": 2, "locator": "section[5]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:31666027:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c91f4ecb767315133bf0647b4abbcd6a94d6bb41add6dc85b97fd2e3ee4d9203", "bytes": 567, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[26]/table-wrap[1]#Tab3", "version": null, "note": "Olfactory-binding protein sequences used in Blast searches for predicted ovine and caprine sequences", "structure": {"pmcid": "PMC6822404", "section_index": 26, "section_title": "In silico search for O. aries and C. hircus OBP sequences", "row_count": 7, "column_count": 3}, "table": {"label": "Table 3", "caption": "Olfactory-binding protein sequences used in Blast searches for predicted ovine and caprine sequences", "rows": [["", "Uniprot accession #for sheep OBP search", "GenBank accession #for goat OBP search"], ["Porcine OBP", "P81245", "NM_213796.1"], ["Bovine OBP", "P07435", "XM_002700469.6"], ["Porcine VEG", "P53715", "NM_213856.2"], ["Rat VEG", "P20289", "NM_022945"], ["Human VEG", "P31025", "NM_001252617"], ["Porcine SAL", "P81608", "NM_213814.2"]], "row_count": 7, "column_count": 3, "numeric_cells": 12, "header_rows": 1, "locator": "section[26]/table-wrap[1]#Tab3"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "Blast"}}, {"id": "method-2", "family": null, "specific": null, "label": "Maximum Likelihood method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [49]."}}], "targets": 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"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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The full-length sequences of Chir-OBP2, Chir-OBP4, Oari-OBP2, and Oari-OBP4 were deposited in GenBank database with accession numbers: MK908982, MK908983, MK908984 and MK908985, respectively."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:31666027", "asset:table:pmid:31666027:1", "asset:table:pmid:31666027:2", "asset:table:pmid:31666027:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:51:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 57064, "completion_tokens": 3367, "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:31666027", "type": "paper", "label": "pmid:31666027"}, {"id": "source:pmid:31666027", "type": "manuscript", "label": "PMID 31666027 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31666027", "type": "paper", "label": "pmid:31666027"}, {"id": "source:pmid:31666027", "type": "manuscript", "label": "PMID 31666027 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31666027", "type": "extraction", "used": ["source:pmid:31666027"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:31666027", "parent_hash": "sha256:5177e3d7034f02b193b81e2aabe7e2e3acd57f8e7f449c48c418630011670055", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": ["ALDI-TOF and high-resolution (nano-LC-MS/MS) mass spectrometry, RACE-PCR and molecular modelling were used.", "ibodies, MALDI-TOF and high-resolution (nano-LC-MS/MS) mass spectrometry, RACE-PCR and molecular m", "eing the number of isoforms of each protein. Proteomics data are available via ProteomeXchange with"], "order_basis": "paper_text_order:843", "id": "assay:1"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Blast"], "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":"2026-11-04T03:06:59+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}}}