{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30934933", "kind": "science-record", "revision": 7, "content_hash": "sha256:612fb744752627e2a4d19f5eb680def5f8c1b70ace9a05884a72fab5bbcc667a", "created_at": "2026-11-01T15:40:43Z", "updated_at": "2026-11-01T22:00:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq.", "doi": "10.3390/vetsci6020036", "pmid": "30934933", "authors": ["Chandra Shekhar Pareek", "Mateusz Sachajko", "Jedrzej M Jaskowski", "Magdalena Herudzinska", "Mariusz Skowronski", "Krzysztof Domagalski", "Joanna Szczepanek", "Urszula Czarnik", "Przymeslaw Sobiech", "Dominika Wysocka", "Mariusz Pierzchala", "Ewa Polawska", "Kamila Stepanow", "Magdalena Ogłuszka", "Edyta Juszczuk-Kubiak", "Yaping Feng", "Dibyendu Kumar"], "journal": "Veterinary sciences", "year": 2019, "abstract": "Global gene expression in liver transcriptome varies among cattle breeds. The present investigation was aimed to identify the differentially expressed genes (DEGs), metabolic gene networks and metabolic pathways in bovine liver transcriptome of young bulls. In this study, we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n = 6), beef (Hereford; n = 6), and dual purpose (Polish-Red; n = 6) cattle breeds. This study identified 895, 338, and 571 significant (p < 0.01) differentially expressed (DE) gene-transcripts represented as 745, 265, and 498 hepatic DE genes through the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-HF versus Polish-Red breeds comparisons, respectively. By combining all breeds comparisons, 75 hepatic DE genes (p < 0.01) were identified as commonly shared among all the three breed comparisons; 70, 160, and 38 hepatic DE genes were commonly shared between the following comparisons: (i) Polish-Red versus Hereford and Polish-HF versus Hereford; (ii) Polish-Red versus Hereford and Polish-HF versus Polish-Red; and (iii) Polish-HF versus Hereford and Polish-HF versus Polish-Red, respectively. A total of 440, 82, and 225 hepatic DE genes were uniquely observed for the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-Red versus Polish-HF comparisons, respectively. Gene ontology (GO) analysis identified top-ranked enriched GO terms (p < 0.01) including 17, 16, and 31 functional groups and 151, 61, and 140 gene functions that were DE in all three breed liver transcriptome comparisons. Gene network analysis identified several potential metabolic pathways involved in glutamine family amino-acid, triglyceride synthesis, gluconeogenesis, p38MAPK cascade regulation, cholesterol biosynthesis (Polish-Red versus Hereford); IGF-receptor signaling, catecholamine transport, lipoprotein lipase, tyrosine kinase binding receptor (Polish-HF versus Hereford), and PGF-receptor binding, (Polish-HF versus Polish-Red). Validation results showed that the relative expression values were consistent to those obtained by RNA-seq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90). Our results provide new insights on bovine liver gene expressions among dairy versus dual versus beef breeds by identifying the large numbers of DEGs markers submitted to NCBI gene expression omnibus (GEO) accession number GSE114233, which can serve as useful genetic tools to develop the gene assays for trait-associated studies as well as, to effectively implement in genomics selection (GS) cattle breeding programs in Poland.", "claims": [{"id": "claim-data-access", "statement": "The FASTQ sequencing data of this present study were deposited in the NCBI database under submission number: SRS1296732 (http://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=312148) [31] and the gene expression data of investigated animals (n = 18) were deposited in the NCBI database under submission number: GSE 114233 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114233) and summarized in Table 2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30934933", "locator": "sections[5] \"2.3. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE114233"], "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:GSE114233"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30934933", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/vetsci6020036", "sha256": "sha256:930a0cff3946f91d2ef2208a508fa878b2df7ad7ed4e358826e647d570167e84", "bytes": 65221, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/vetsci6020036", "version": null, "note": "Full article fetched from PMC; 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Animals and Biological Sample Collection", "row_count": 4, "column_count": 9}, "table": {"label": "Table 1", "caption": "Mean phenotypic values of carcass traits in young growing bulls (n = 18) from three cattle breeds.", "rows": [["Breeds", "n", "Cold Carcass Weight (kg)", "Carcass Yield (kg)", "Right Half Carcass (kg)", "Valuable Cut Meat (kg)", "Meat (kg)", "Bones (kg)", "Fat (kg)"], ["Polish-HF", "6", "188.9 ± 5.3", "53 ± 2.4", "94.9 ± 1.6", "59.4 ± 1.9", "42.3 ± 2.6", "15.4 ± 3.6", "9.9 ± 3.8"], ["Polish-Red", "6", "166.6 ± 6.4", "56.5 ± 3.6", "86 ± 2.6", "54.5 ± 3.4", "40.7 ± 4.1", "15.4 ± 5.7", "10.9 ± 6.0"], ["Hereford", "6", "193.9 ± 8.9", "59.6 ± 4.6", "100.2 ± 2.9", "62.9 ± 3.1", "45.4 ± 3.9", "17.1 ± 5.6", "13.0 ± 5.8"]], "row_count": 4, "column_count": 9, "numeric_cells": 24, "header_rows": 1, "locator": "section[3]/table-wrap[1]#vetsci-06-00036-t001"}}, {"id": "asset:table:pmid:30934933:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:633fde0dc7755b66470ab19ab5cedb89ea4645ebe3b48885b04b37c918bd2d7e", "bytes": 2088, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#vetsci-06-00036-t002", "version": null, "note": "Hepatic gene expression NCBI database of Polish-Red, Polish-HF and Hereford cattle breeds.", "structure": {"pmcid": "PMC6631511", "section_index": 5, "section_title": "2.3. 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Validation of DE Gene-Transcripts Using RT-PCR/qPCR", "row_count": 15, "column_count": 9}, "table": {"label": "Table 3", "caption": "List of selected DE gene-transcripts for the validation of RNA-seq experiment by qRT-PCR.", "rows": [["Gene Full Name", "Calpain 11", "Calpain 2", "Insulin Like Growth Factor Binding Protein 1", "Insulin Like Growth Factor Binding Protein 2", "Insulin Like Growth Factor I", "Insulin Like Growth Factor Binding Protein, Acid Labile Subunit (IGFALS)", "Somatotropin", "Family with Sequence Similarity 13 Member A"], ["Gene symbol", "CAPN11", "CAPN2", "IGFBP1", "IGFBP2", "IGF-I", "IGFALS", "GH", "FAM13A"], ["Forward primer", "GAACCTTCAA", "CCAACATTGA", "TAGCGTAAAT", "GTGCAAGAT", "GAGTGCAGG", "CAGGTAACA", "AGCCATCTG", "CCTTTCTATTT"], ["CTGTCAAGCG", "CGAGATTGACA", "TGGCAGGGAA", "GTCTCTGAACG", "AAACAAGAACT", "AGCTGGCCTA", "TTGTTTGCCC", "GAGCAGTGCC"], ["Reverse primer", "TTGAGTCGGT", "ATTGTCTGCA", "ACACTGTGTT", "TGCTCGTTGT", "TTGGTAGGT", "GTGGTCCAG", "TATTAGGAAA", "CTGAGTCCTCT"], ["TCTGGCTTAT", "ACTCAAAGGC", "CCCATGTTTG", "AGAAGAGATGA", "CTTCTGGTGTT", "GTAGAGTTTCT", "GGACAGTGGGAG", "GAACTTTGG"], ["Ensembl Gene ID", "ENSBTAG000", "ENSBTAG000", "ENSBTAG00", "ENSBTAG00", "ENSBTAG00", "ENSBTAG000", "ENSBTAG00", "ENSBTAG000"], ["21066", "12778", "46768", "5596", "11082", "33299", "17220", "11187"], ["Ensembl Transcript ID", "ENSBTAT00", "ENSBTAT00", "ENSBTAT00", "ENSBTAT000", "ENSBTAT00", "ENSBTAT000", "ENSBTAT00", "ENSBTAT00"], ["4690", "47532", "64194", "7349", "14713", "47326", "22885", "14855"], ["BTA chromosome", "23", "16", "4", "2", "5", "25", "19", "6"], ["Gene Start (bp)", "17,807,298", "27,781,671", "76,720,883", "1.05E + 08", "66,532,877", "1,366,647", "48,768,618", "37,355,568"], ["Gene End (bp)", "17,820,479", "27,840,009", "76,725,301", "1.05E + 08", "66,604,734", "1,368,479", "48,772,014", "37,457,493"], ["Transcript Start (bp)", "17,807,298", "27,781,671", "76,720,883", "1.05E + 08", "66,532,877", "1,366,647", "48,768,618", "37,355,568"], ["Transcript length", "2675", "3179", "917", "1141", "862", "1833", "817", "5125"]], "row_count": 15, "column_count": 9, "numeric_cells": 79, "header_rows": 1, "locator": "section[8]/table-wrap[1]#vetsci-06-00036-t003"}}], "gaps": ["asset:data:geo:GSE114233 not downloaded", "asset:data:geo:GSE114233 licence not read", "asset:data:geo:SRS1296732 not downloaded", "asset:data:geo:SRS1296732 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "DEseq"}}, {"id": "method-2", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "EdgeR"}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: deseq2."}, "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": ["SRS1296732", "GSE114233"], "resolved_accessions": ["GSE114233"], "statements": ["The FASTQ sequencing data of this present study were deposited in the NCBI database under submission number: SRS1296732 (http://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=312148) [31] and the gene expression data of investigated animals (n = 18) were deposited in the NCBI database under submission number: GSE 114233 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114233) and summarized in Table 2."], "basis": "The paper names GSE114233 in NCBI Sequence Read Archive (SRA) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:30934933", "data:geo:GSE114233", "asset:table:pmid:30934933:1", "asset:table:pmid:30934933:2", "asset:table:pmid:30934933:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE114233"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:43:22Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 51086, "completion_tokens": 2398, "cached_tokens": 17160}}, "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:30934933", "type": "paper", "label": "pmid:30934933"}, {"id": "source:pmid:30934933", "type": "manuscript", "label": "PMID 30934933 full text"}, {"id": "data:geo:GSE114233", "type": "dataset", "label": "GEO GSE114233"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30934933", "type": "paper", "label": "pmid:30934933"}, {"id": "source:pmid:30934933", "type": "manuscript", "label": "PMID 30934933 full text"}, {"id": "data:geo:GSE114233", "type": "dataset", "label": "GEO GSE114233"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30934933", "type": "extraction", "used": ["source:pmid:30934933"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE114233", "type": "accession_resolution", "used": ["data:geo:GSE114233"], "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:30934933", "parent_hash": "sha256:af7adc181fdd5da9caeea9ddfd14c54cc82c53de564a667761eff31cd1e029f6", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE114233 licence not read", "asset:data:geo:GSE114233 not downloaded", "asset:data:geo:SRS1296732 licence not read", "asset:data:geo:SRS1296732 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["iver Transcriptome among Cattle Breeds Using RNA-seq.", "values were consistent to those obtained by RNA-seq, and significantly correlated between the qu", "tive reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90). Our results provide ne", ", we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n ="], "order_basis": "paper_text_order:29", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90). Our resul", "e quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90). Our resul", "eq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90).", "was made by quantitation of libraries using qPCR according to the Illumina sequencing library"], "order_basis": "paper_text_order:2212", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["DEseq"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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":"2026-11-04T03:34:21+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}}}