{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34233668", "kind": "science-record", "revision": 5, "content_hash": "sha256:e2d7159cddc75c66fe374ff04f722b7a5758af82b8db12d954f667465b6203f8", "created_at": "2026-11-01T15:41:42Z", "updated_at": "2026-11-01T22:04:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer.", "doi": "10.1186/s12920-021-01029-3", "pmid": "34233668", "authors": ["Soheila Delgir", "Khandan Ilkhani", "Asma Safi", "Yazdan Rahmati", "Vahid Montazari", "Zahra Zaynali-Khasraghi", "Farhad Seif", "Milad Bastami", "Mohammad Reza Alivand"], "journal": "BMC medical genomics", "year": 2021, "abstract": "BACKGROUND: Breast cancer (BC) is the most invasive cancer with different subtypes that its metabolism is unique compared with normal cells. Glutamine is considered critical nutrition that many cancer cells, particularly BC cells, are dependent on it for growth and proliferation. Therefore, targeting glutamine metabolism, especially enzymes that are related to this pathway, can be beneficial to design anti-cancer agents. Recent evidence has shown that microRNAs (miRNAs), with a short length and single-strand properties, play a prominent role in regulating the genes related to glutamine metabolism, which may control the development of cancer.\nMETHODS: In silico analysis confirmed that miR-513c and miR-3163 might be involved in glutamine metabolism. The expression level of these two miRNAs was evaluated in eighty BC tissues and normal adjacent tissues. Furthermore, GSE38167, GSE38867, GSE42128, GSE45666, and GSE53179 were employed from gene expression omnibus (GEO). The Limma package was utilized to identify differentially expressed miRNAs (DEMs) of mentioned datasets to evaluate miR-513c and miR-3163 expression. Further, in silico analysis was utilized to predict the potential biological processes and molecular pathways of miR-513c and miR-3163, based on their target genes.\nRESULTS: In silico studies revealed top categories of biological processes and cellular pathways that might play a critical role in metabolism reprogramming and cancer development and were target genes for miR-513c and miR-3163. The current study showed that miR-513c (p value = 0.02062 and FC = - 2.3801) and miR-3163 (p value = 0.02034 and FC = - 2.3792) were downregulated in tumor tissues compared to normal adjacent tissues. The analysis of GEO microarray datasets showed that miR-513c was downregulated in GSE38167, GSE38867, GSE42128, GSE45666 and GSE53179, whereas there was a significant downregulation of miR-3163 in only two studies, including GSE38867 and GSE42128 that they were in accordance with our experimental results. Furthermore, the subgroup analysis did not show any substantial relationship between expression levels of these two miRNAs and factors such as age, family history of cancer, and abortion history.\nCONCLUSION: MiR-513c and miR-3163 were downregulated in BC tissues, which might serve as tumor suppressors. They are suggested as potential therapeutic targets for patients with BC.", "claims": [{"id": "claim-method", "statement": "Paired T-test and delta-CTs were used for comparison of the gene expressions between tumor and normal adjacent tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34233668", "locator": "sections[8] \"Statistical analysis\" paragraph 2", "quote": "Paired T-test and delta-CTs were used for comparison of the gene expressions between tumor and normal adjacent tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions e.g. containing information that could compromise the privacy of research participants.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34233668", "locator": "sections[25] \"notes\" paragraph 1", "quote": "The data that support the findings of this study are available on request from the corresponding author. 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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:34233668", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-021-01029-3", "sha256": 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["Mir-513c-5pNIMAT 0022728", "Mir-513c (F)", "5′-GGGTTCTCAAGGAGGTGTCG-3′"], ["MiR-3163 and Mir-513c", "Common (R)", "5′-GTGCAGGGTCCGAGGT-3′"], ["RNU6NR_003027.2", "U6 (F)", "5′-GCTTCGGCAGCACATATACTAAAAT-3′"], ["U6 (R)", "5′-CGCTTCACGAATTTGCGTGTCAT-3′"]], "row_count": 9, "column_count": 4, "numeric_cells": 19, "header_rows": 1, "locator": "section[6]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:34233668:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7803da2816c7d4c06eb6f4be12a5681f89dcf1cb4aa8672b29ea9ebfe61f4e5d", "bytes": 570, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab3", "version": null, "note": "Pathways that are enriched among target genes of mir-513c", "structure": {"pmcid": "PMC8265124", "section_index": 7, "section_title": "In silico analysis", "row_count": 5, "column_count": 7}, "table": {"label": "Table 3", "caption": "Pathways that are enriched among target genes of mir-513c", "rows": [["No", "ID", "Pathway name", "O", "FDR", "E", "p valuea"], ["1", "hsa05222", "Small cell lung cancer", "92", "1", "0.34163", "0.0046026"], ["2", "hsa00130", "Ubiquinone and other terpenoid-quinone biosynthesis", "11", "1", "0.040847", "0.040124"], ["3", "hsa05200", "Pathways in cancer", "524", "1", "1.9458", "0.041062"], ["4", "hsa05032", "Morphine addiction", "91", "1", "0.33792", "0.044411"]], "row_count": 5, "column_count": 7, "numeric_cells": 24, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:34233668:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ea4fb9b34ef042294ae52e6b4f9af0370219a68ff3a5abe9346093caa343b845", "bytes": 1177, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#Tab4", "version": null, "note": "Pathways that are enriched among target genes of miRNA-3163", "structure": {"pmcid": "PMC8265124", "section_index": 7, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 4", "caption": "Pathways that are enriched among target genes of miRNA-3163", "rows": [["Nos", "Gene set", "Pathway name", "C", "E", "R", "FDR", "p valuea"], ["1", "hsa05170", "Human immunodeficiency virus 1 infection", "212", "3.6155", "3.3191", "0.081094", "2.5E−04"], ["2", "hsa04110", "Cell cycle", "124", "2.1147", "3.783", "0.09676", "1E−03"], ["3", "hsa04114", "Oocyte meiosis", "124", "2.1147", "3.783", "0.09676", "1E−03"], ["4", "hsa05202", "Transcriptional misregulation in cancer", "186", "3.1721", "3.1525", "0.09676", "1E−03"], ["5", "hsa04010", "MAPK signaling pathway", "295", "5.0309", "2.584", "0.09676", "1.5E−03"], ["6", "hsa05167", "Kaposi sarcoma-associated herpesvirus infection", "186", "3.1721", "2.8373", "0.2378", "4.4E−03"], ["7", 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"PMC8265124", "section_index": 7, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 5", "caption": "Top ten enriched biological processes among target genes of miR-513c", "rows": [["No", "GO ID", "Biological process", "O", "FDR", "E", "R", "p valuea"], ["1", "GO: 0042148", "Strand invasion", "5", "1", "0.024004", "83.32", "2.2E−04"], ["2", "GO: 0006612", "Protein targeting to membrane", "187", "1", "0.89774", "6.6834", "2.7E−04"], ["3", "GO: 0045047", "Protein targeting to ER", "107", "1", "0.51368", "7.7869", "1.7E−03"], ["4", "GO: 0072599", "Establishment of protein localization to endoplasmic reticulum", "111", "1", "0.53289", "7.5063", "1.9E−03"], ["5", "GO: 0008340", "Determination of adult lifespan", "17", "1", "0.081613", "24.506", "2.9−E3"], ["6", "GO: 0006605", "Protein targeting", "412", "1", "1.9779", "3.5391", "3.6E−03"], ["7", "GO: 0090150", "Establishment of protein localization to membrane", "313", "1", "1.5026", "3.993", "3.9–03"], ["8", "GO: 0070972", "Protein localization to endoplasmic reticulum", "137", "1", "0.65771", "6.0818", "4.2E−03"], ["9", "GO: 0031297", "Replication fork processing", "95", "1", "0.15362", "13.019", "1E−02"], ["10", "GO: 0006614", "SRP-dependent co-translational protein targeting to membrane", "95", "1", "0.45607", "6.5779", "1E−02"]], "row_count": 11, "column_count": 8, "numeric_cells": 70, "header_rows": 1, "locator": "section[17]/table-wrap[3]#Tab5"}}, {"id": "asset:table:pmid:34233668:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:93da04f037c7bd1c8dea0314251456fbed3b5da00dcdbc4b1b1615613e258364", "bytes": 1385, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[4]#Tab6", "version": null, "note": "Top ten enriched biological processes among target genes of miR-3163", "structure": {"pmcid": "PMC8265124", 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"0.09676", "1E−03"], ["5", "hsa04010", "MAPK signaling pathway", "295", "5.0309", "2.584", "0.09676", "1.5E−03"], ["6", "hsa05167", "Kaposi sarcoma-associated herpesvirus infection", "186", "3.1721", "2.8373", "0.2378", "4.4E−03"], ["7", "hsa04340", "Hedgehog signaling pathway", "47", "0.80154", "4.9904", "0.3802", "8.2E−03"], ["8", "hsa04310", "Wnt signaling pathway", "146", "2.4899", "2.8114", "0.49589", "1E−02"], ["9", "hsa05206", "MicroRNAs in cancer", "150", "2.5581", "2.7364", "0.50585", "1.4E−02"], ["10", "hsa04218", "Cellular senescence", "160", "2.7286", "2.5654", "0.58131", "2E−02"]], "row_count": 11, "column_count": 8, "numeric_cells": 71, "header_rows": 1, "locator": "section[17]/table-wrap[2]#Tab4"}}, {"id": "asset:table:pmid:34233668:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0c5034a5a6d0829118fb937f7fd18a23a0845eeb3ed94b0cefbec2c34205600f", "bytes": 1270, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[3]#Tab5", "version": null, "note": "Top ten enriched biological processes among target genes of miR-513c", "structure": {"pmcid": "PMC8265124", "section_index": 17, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 5", "caption": "Top ten enriched biological processes among target genes of miR-513c", "rows": [["No", "GO ID", "Biological process", "O", "FDR", "E", "R", "p valuea"], ["1", "GO: 0042148", "Strand invasion", "5", "1", "0.024004", "83.32", "2.2E−04"], ["2", "GO: 0006612", "Protein targeting to membrane", "187", "1", "0.89774", "6.6834", "2.7E−04"], ["3", "GO: 0045047", "Protein targeting to ER", "107", "1", "0.51368", "7.7869", "1.7E−03"], ["4", "GO: 0072599", "Establishment of protein localization to endoplasmic reticulum", "111", "1", "0.53289", "7.5063", "1.9E−03"], ["5", "GO: 0008340", "Determination of adult 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"reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[4]#Tab6", "version": null, "note": "Top ten enriched biological processes among target genes of miR-3163", "structure": {"pmcid": "PMC8265124", "section_index": 17, "section_title": "In silico analysis", "row_count": 11, "column_count": 8}, "table": {"label": "Table 6", "caption": "Top ten enriched biological processes among target genes of miR-3163", "rows": [["No", "Gene set", "Biological pathways", "C", "E", "R", "FDR", "p value"], ["1", "GO: 0045934", "Negative regulation of nucleobase-containing compound metabolic process", "1418", "22.805", "1.9732", "0.04352", "8E−06"], ["2", "GO: 0033554", "Cellular response to stress", "1867", "30.026", "1.7984", "0.04352", "1E−05"], ["3", "GO: 0010629", "Negative regulation of gene expression", "1733", "27.871", "1.8299", "0.04352", "1E−05"], ["4", "GO: 1903311", "Regulation of mRNA metabolic process", "266", "4.278", "3.5063", "0.06326", "3E−05"], ["5", "GO: 0045935", "Positive regulation of nucleobase-containing compound metabolic process", "1847", "29.705", "1.7169", "0.12664", "8E−05"], ["6", "GO: 0000278", "Mitotic cell cycle", "927", "14.909", "2.0793", "0.12664", "9E−05"], ["7", "GO: 0051253", "Negative regulation of RNA metabolic process", "1295", "20.827", "1.8726", "0.12664", "1E−04"], ["8", "GO: 0000902", "Cell morphogenesis", "982", "15.793", "2.0262", "0.12664", "1E−04"], ["9", "GO: 0032989", "Cellular component morphogenesis", "1082", "17.401", "1.9539", "0.12664", "1E−04"], ["10", "GO: 2000113", "Negative regulation of cellular macromolecule biosynthetic process", "1359", "21.856", "1.8301", "0.12664", "1E−04"]], "row_count": 11, "column_count": 8, "numeric_cells": 70, "header_rows": 1, "locator": "section[17]/table-wrap[4]#Tab6"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", 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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 data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions e.g. containing information that could compromise the privacy of research participants."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34233668", "asset:table:pmid:34233668:1", "asset:table:pmid:34233668:2", "asset:table:pmid:34233668:3", "asset:table:pmid:34233668:4", "asset:table:pmid:34233668:5", "asset:table:pmid:34233668:6", "asset:table:pmid:34233668:7", "asset:table:pmid:34233668:8", "asset:table:pmid:34233668:9", "asset:table:pmid:34233668:10"], "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": "2026-10-31T18:31:58Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28027, "completion_tokens": 898, "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:34233668", "type": "paper", "label": "pmid:34233668"}, {"id": "source:pmid:34233668", "type": "manuscript", "label": "PMID 34233668 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34233668", "type": "paper", "label": "pmid:34233668"}, {"id": "source:pmid:34233668", "type": "manuscript", "label": "PMID 34233668 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34233668", "type": "extraction", "used": ["source:pmid:34233668"], "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:34233668", "parent_hash": "sha256:2790dcf09fd5213a8c2b14a2e6b6096702652107781478583d86b857919124b5", "fork_of": null, "generation": 4}, "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": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["normal adjacent tissues. 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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":"2026-11-04T01:45:38+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}}}