{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30045750", "kind": "science-record", "revision": 6, "content_hash": "sha256:35fa22946c06c2910e4c0203c9365005624bc88a34a6d8b10fa688d2f57366ac", "created_at": "2026-11-01T15:40:36Z", "updated_at": "2026-11-01T21:21:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "SWATH-MS based quantitative proteomics analysis reveals that curcumin alters the metabolic enzyme profile of CML cells by affecting the activity of miR-22/IPO7/HIF-1α axis.", "doi": "10.1186/s13046-018-0843-y", "pmid": "30045750", "authors": ["Francesca Monteleone", "Simona Taverna", "Riccardo Alessandro", "Simona Fontana"], "journal": "Journal of experimental & clinical cancer research : CR", "year": 2018, "abstract": "BACKGROUND: Chronic myelogenous leukemia (CML) is a myeloproliferative disorder caused by expression of the chimeric BCR-ABL tyrosine kinase oncogene, resulting from the t(9;22) chromosomal translocation. Imatinib (gleevec, STI-571) is a selective inhibitor of BCR-ABL activity highly effective in the treatment of CML. However, even though almost all CML patients respond to treatment with imatinib or third generation inhibitors, these drugs are not curative and need to be taken indefinitely or until patients become resistant. Therefore, to get a definitive eradication of leukemic cells, it is necessary to find novel therapeutic combinations, for achieving greater efficacy and fewer side effects. Curcumin is an Indian spice with several therapeutic properties: anti-oxidant, analgesic, anti-inflammatory, antiseptic and anti-cancer. In cancer disease, it acts by blocking cell transformation, proliferation, and invasion and by inducing cell apoptosis.\nMETHODS: In the present study, the effect of a sub-toxic dose of curcumin on K562 cells was evaluated by using the technique of Sequential Window Activation of All Theoretical Mass Spectra (SWATH-MS). Bioinformatic analysis of proteomic data was performed to highlight the pathways mostly affected by the treatment. The involvement of Hypoxia inducible factor 1 α (HIF-1α) was assayed by evaluating its activation status and the modulation of importin 7 (IPO7) and miR-22 was assessed by quantitative PCR and western blot analysis. Finally, K562 cells transfected with miR-22 inhibitor were used to confirm the ability of curcumin to elicit miR-22 expression.\nRESULTS: Our findings revealed that the most relevant effect induced by curcumin was a consistent decrease of several proteins involved in glucose metabolism, most of which were HIF-1α targets, concomitant with the up-regulation of functional and structural mitochondrial proteins. The mechanism by which curcumin affects metabolic enzyme profile was associated with the reduction of HIF-1α activity, due to the miR-22-mediated down-regulation of IPO7 expression. Finally, the ability of curcumin to enhance in vitro the efficiency of imatinib was reported.\nCONCLUSIONS: In summary, our data indicates that the miR-22/IPO7/HIF-1α axis may be considered as a novel molecular target of curcumin adding new insights to better define therapeutic activity and anticancer properties of this natural compound. The MS proteomic data have been deposited to the ProteomeXchange with identifier <PXD007771>.", "claims": [{"id": "claim-method", "statement": "The protein list with FDR lower than 5% generated by analyzing SWATH data with PeakView 2.2, was exported to MarkerView 1.2.1 (AB SCIEX; Framingham, US) for normalization of protein intensity (peak area) using the total area sums algorithm and t-test analysis [13, 16]. Mean of all biological and technical replicates was used to compare proteins of Ctrl-K562 and Curcu-K562. Fold Change (FC) Curcu-K562 vs Ctrl-K562 thresholds at ±1.5 with a corrected p-value inferior to 0.05 were used to consider a protein up or down-regulated. GraphPad Prism 7.00 for Windows was used for (i) performing the p-value Benjamini-Yekutieli (BY-Pvalue) correction (13); (ii) to make a volcano plot scaling in which the FC was transformed using the log2 function, so that the data is centered on zero, while the BY corrected p-value was −log10 transformed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30045750", "locator": "sections[8] \"Statistical analysis, gene ontology analysis, functional networks and pathway mapping\" paragraph 2", "quote": "The protein list with FDR lower than 5% generated by analyzing SWATH data with PeakView 2.2, was exported to MarkerView 1.2.1 (AB SCIEX; Framingham, US) for normalization of protein intensity (peak area) using the total area sums algorithm and t-test analysis [13, 16]. Mean of all biological and technical replicates was used to compare proteins of Ctrl-K562 and Curcu-K562. Fold Change (FC) Curcu-K562 vs Ctrl-K562 thresholds at ±1.5 with a corrected p-value inferior to 0.05 were used to consider a protein up or down-regulated. GraphPad Prism 7.00 for Windows was used for (i) performing the p-value Benjamini-Yekutieli (BY-Pvalue) correction (13); (ii) to make a volcano plot scaling in which the FC was transformed using the log2 function, so that the data is centered on zero, while the BY corrected p-value was −log10 transformed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) [14] via the PRIDE partner repository [15] with the dataset identifier <PXD007771>.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30045750", "locator": "sections[7] \"SWATH-MS analysis and targeted data extraction\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) [14] via the PRIDE partner repository [15] with the dataset identifier <PXD007771>."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:30045750"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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(http://proteomecentral.proteomexchange.org) [14] via the PRIDE partner repository [15] with the dataset identifier <PXD007771>.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) [14] via the PRIDE partner repository [15] with the dataset identifier <PXD007771>.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "SWATH-MS based quantitative proteomics analysis reveals that curcumin alters the metabolic enzyme profile of CML cells by affecting the activity of miR-22/IPO7/HIF-1α axis.", "resolution_checked_at": "2026-10-31T18:28:56Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, 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protein library", "13616"], ["Numbers of proteins quantified in SWATH analysis", "1801"], ["Numbers (and percentage) of quantified protein with CV ≤ 25% among technical and biological replicates", "1629 (90.7%)", "1632 (90.8%)"]], "row_count": 7, "column_count": 8, "numeric_cells": 20, "header_rows": 3, "locator": "section[15]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:30045750:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:394d33ee49e306bab9a4f4722938fc9971ced8c493a9fe30dd9f1d1fc5bf97aa", "bytes": 2557, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#Tab2", "version": null, "note": "Most significantly enriched GO categories (adjP ≤10−5) within the differentially Curcu-regulated proteins datasets", "structure": {"pmcid": "PMC6060558", "section_index": 16, "section_title": "Bioinformatic analysis for enriched terms", 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activity", "17", "126", "7.30", "11.14", "4.68E-11"], ["Translation regulator activity", "11", "101", "4.72", "9", "2.97E-06"], ["Isomerase activity", "7", "45", "3", "12.85", "6.02E-05"], ["Enriched in Curcu-Up Regulated protein dataset"], ["Oxidoreductase activity", "12", "161", "8.45", "10.1", "5.99E-07"], ["Biological Process (BP)"], ["Enriched in Curcu-Down Regulated protein dataset"], ["Protein metabolism", "59", "1323", "25.32", "3.68", "1.24E-16"], ["Metabolism", "58", "1683", "24.89", "2.84", "9.15E-12"], ["Enriched in Curcu-Up Regulated protein dataset"], ["Metabolism", "38", "1683", "26.76", "3.06", "2.22E-08"], ["Transport", "30", "1215", "21.13", "3.34", "2.32E-07"]], "row_count": 39, "column_count": 6, "numeric_cells": 145, "header_rows": 1, "locator": "section[16]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:30045750:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3606e938f3cbc2d38a97675fd703046c48bb1a99bc0875155fcc38b8f0084094", "bytes": 1979, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#Tab3", "version": null, "note": "Biological Pathway enrichment analysis of “metabolic” proteins down-regulated and up-regulated by curcumin", "structure": {"pmcid": "PMC6060558", "section_index": 16, "section_title": "Bioinformatic analysis for enriched terms", "row_count": 16, "column_count": 4}, "table": {"label": "Table 3", "caption": "Biological Pathway enrichment analysis of “metabolic” proteins down-regulated and up-regulated by curcumin", "rows": [["Biological pathway", "% of proteins", "AdjP-Value (BH method)", "Proteins"], ["Curcu-Down-Regulated “metabolic” proteins"], ["Metabolism", "29.82", "2.04E-07", "TALDO1; ARG2; GSTP1; AHCY; TXN; FASN; TKT; COX6B1; GMPS; PAICS; HPRT1; CAD; ATIC; GSTO1; ACLY; GOT1; TK1;"], ["Metabolism of carbohydrates", "14.04", 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synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.", "40.5", "1.9E-23", "UQCRC1; CYC1; COX5B; NDUFS1; NDUFA5; NDUFB4; NDUFV1; UQCRH; NDUFA9; UQCRB; MT-ND5; NDUFB6; NDUFB5; NDUFB3; NDUFB9;"], ["Metabolism", "45.9", "1.4E-11", "UQCRC1; CYC1; COX5B; NDUFS1; NDUFA5; NDUFB4; NDUFV1; CYP51A1; UQCRH; NDUFA9; UQCRB; MT-ND5; NNT; NDUFB6; NDUFB5; NDUFB3; NDUFB9;"], ["Cholesterol biosynthesis", "8.1", "1.5E-03", "FDFT1; CYP51A1; DHCR24;"]], "row_count": 16, "column_count": 4, "numeric_cells": 29, "header_rows": 1, "locator": "section[16]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:30045750:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9407f92f71bad2d00278d1ab5bf2e9f0da602be4466aeedefcf3021644fe05e9", "bytes": 1508, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab4", "version": null, "note": "Proteins implicated in nuclear import/export identified by MS in K562cells", "structure": {"pmcid": "PMC6060558", "section_index": 17, "section_title": "Effects of curcumin on HIF-1α activity and IPO7 expression", "row_count": 15, "column_count": 7}, "table": {"label": "Table 4", "caption": "Proteins implicated in nuclear import/export identified by MS in K562cells", "rows": [["UniProt Accession Number", "UniProt Entry Name", "Gene Name", "Protein Name", "Fold Change (Curcu-K562 vs Ctrl K562)", "p-Value", "BY-Pvalue"], ["O00410", "IPO5_HUMAN", "IPO5", "Importin-5", "-1.530", "0.002162", "0.0383"], ["O95373", "IPO7_HUMAN", "IPO7", "Importin-7", "-2.332", "0.000107", "0.0030"], ["Q96P70", "IPO9_HUMAN", "IPO9", "Importin-9", "−2.241", "0.121934", "> 0.999"], ["P52292", "IMA1_HUMAN", "KPNA2", "Importin subunit alpha-1", "−1.040", "0.040815", "0.5065"], ["O00629", "IMA3_HUMAN", "KPNA4", "Importin subunit alpha-3", "−1.279", "0.002692", "0.0465"], ["O00505", "IMA4_HUMAN", "KPNA3", "Importin subunit alpha-4", "−1.667", "0.086100", "0.9772"], ["Q14974", "IMB1_HUMAN", "KPNB1", "Importin subunit beta-1", "−1.114", "0.000088", "0.0026"], ["Q92973", "TNPO1_HUMAN", "TNPO1", "Transportin-1", "−1.801", "0.00045", "0.0099"], ["E9PFH4", "E9PFH4_HUMAN", "TNPO3", "Transportin-3", "−1.875", "0.221323", "> 0.999"], ["O14980", "XPO1_HUMAN", "XPO1", "Exportin-1", "−1.804", "0.000086", "0.0026"], ["P55060", "XPO2_HUMAN", "CSE1L", "Exportin-2", "−1.530", "0.011327", "0.1659"], ["Q9HAV4", "XPO5_HUMAN", "XPO5", "Exportin-5", "−1.698", "0.000021", "0.0008"], ["P12270", "TPR_HUMAN", "TPR", "Nucleoprotein TPR", "−1.121", "0.001823", "0.0330"], ["Q9UKX7", "NUP50_HUMAN", "NUP50", "Nuclear pore complex protein Nup50", "1.334", "0.246", "> 0.999"]], "row_count": 15, "column_count": 7, "numeric_cells": 69, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab4"}}], "gaps": ["asset:data:geo:PXD007771 not downloaded", "asset:data:geo:PXD007771 licence not read"]}, "analysis": {"state": "partial", 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Mean of all biological and technical replicates was used to compare proteins of Ctrl-K562 and Curcu-K562. Fold Change (FC) Curcu-K562 vs Ctrl-K562 thresholds at ±1.5 with a corrected p-value inferior to 0.05 were used to consider a protein up or down-regulated. GraphPad Prism 7.00 for Windows was used for (i) performing the p-value Benjamini-Yekutieli (BY-Pvalue) correction (13); (ii) to make a volcano plot scaling in which the FC was transformed using the log2 function, so that the data is centered on zero, while the BY corrected p-value was −log10 transformed."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["ols_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ols."}, "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": ["PXD007771"], "resolved_accessions": ["PXD007771"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) [14] via the PRIDE partner repository [15] with the dataset identifier <PXD007771>."], "basis": "The paper names PXD007771 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["ols_fit"], "assets": ["source:pmid:30045750", "data:geo:PXD007771", "asset:table:pmid:30045750:1", "asset:table:pmid:30045750:2", "asset:table:pmid:30045750:3", "asset:table:pmid:30045750:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD007771"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:30045750", "type": "paper", "label": "pmid:30045750"}, {"id": "source:pmid:30045750", "type": "manuscript", "label": "PMID 30045750 full text"}, {"id": "data:geo:PXD007771", "type": "dataset", "label": "GEO PXD007771"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30045750", "type": "paper", "label": "pmid:30045750"}, {"id": "source:pmid:30045750", "type": "manuscript", "label": "PMID 30045750 full text"}, {"id": "data:geo:PXD007771", "type": "dataset", "label": "GEO PXD007771"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30045750", "type": "extraction", "used": ["source:pmid:30045750"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD007771", "type": "accession_resolution", "used": ["data:geo:PXD007771"], "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:30045750", "parent_hash": "sha256:f603f55c835b3ac8dc3430fb9324b3af67c5e3df3649d73902a7769ce2c6251c", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD007771 licence not read", "asset:data:geo:PXD007771 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["iferation, and invasion and by inducing cell apoptosis. METHODS: In the present study, the effect o"], "order_basis": "paper_text_order:1078", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["he effect of a sub-toxic dose of curcumin on K562 cells was evaluated by using the technique o", "tive PCR and western blot analysis. Finally, K562 cells transfected with miR-22 inhibitor were", "nd LAMA84 (DSMZ, Braunschweig, Germany) were cultured in RPMI 1640 medium (Euroclone, UK), supplement", "ents and treatments The human CML cell lines K562 and LAMA84 (DSMZ, Braunschweig, Germany) wer"], "order_basis": "paper_text_order:1166", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["miR-22 was assessed by quantitative PCR and western blot analysis. Finally, K562 cells transfected wi"], "order_basis": "paper_text_order:1599", "id": "assay:3"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["d western blot analysis. Finally, K562 cells transfected with miR-22 inhibitor were used to confirm t"], "order_basis": "paper_text_order:1641", "id": "assay:4"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["ols_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["linear regression"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"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":"2026-11-04T00:39:22+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}}}